Gut Virome Analysis of Cameroonians Reveals High Diversity ... · Caliciviridae, and Reoviridae), the phylogenies of the identiﬁed orthoreovirus, pico- birnavirus, and smacovirus

Gut Virome Analysis of Cameroonians Reveals High Diversityof Enteric Viruses, Including Potential Interspecies TransmittedViruses

Claude Kwe Yinda,a,b Emiel Vanhulle,a Nádia Conceição-Neto,a,b Leen Beller,a Ward Deboutte,a Chenyan Shi,a

Stephen Mbigha Ghogomu,c Piet Maes,b Marc Van Ranst,b Jelle Matthijnssensa

aDepartment of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, KU Leuven-University of Leuven, Leuven,Belgium

bDepartment of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, KU Leuven-University ofLeuven, Leuven, Belgium

cDepartment of Biochemistry and Molecular Biology, Biotechnology Unit, Molecular and Cell Biology Laboratory, University of Buea, Buea, Cameroon

ABSTRACT Diarrhea remains one of the most common causes of deaths in chil-dren. A limited number of studies have investigated the prevalence of enteric patho-gens in Cameroon, and as in many other African countries, the cause of many diar-rheal episodes remains unexplained. A proportion of these unknown cases ofdiarrhea are likely caused by yet-unidentified viral agents, some of which could bethe result of (recent) interspecies transmission from animal reservoirs, like bats. Us-ing viral metagenomics, we screened fecal samples of 221 humans (almost all withgastroenteritis symptoms) between 0 and 89 years of age with different degrees ofbat contact. We identified viruses belonging to families that are known to causegastroenteritis such as Adenoviridae, Astroviridae, Caliciviridae, Picornaviridae, andReoviridae. Interestingly, a mammalian orthoreovirus, picobirnaviruses, a smacovirus,and a pecovirus were also found. Although there was no evidence of interspeciestransmission of the most common human gastroenteritis-related viruses (Astroviridae,Caliciviridae, and Reoviridae), the phylogenies of the identified orthoreovirus, pico-birnavirus, and smacovirus indicate a genetic relatedness of these viruses identifiedin stools of humans and those of bats and/or other animals. These findings pointsout the possibility of interspecies transmission or simply a shared host of these vi-ruses (bacterial, fungal, parasitic, . . .) present in both animals (bats) and humans. Fur-ther screening of bat viruses in humans or vice versa will elucidate the epidemiolog-ical potential threats of animal viruses to human health. Furthermore, this studyshowed a huge diversity of highly divergent novel phages, thereby expanding theexisting phageome considerably.

IMPORTANCE Despite the availability of diagnostic tools for different enteric viralpathogens, a large fraction of human cases of gastroenteritis remains unexplained.This could be due to pathogens not tested for or novel divergent viruses of poten-tial animal origin. Fecal virome analyses of Cameroonians showed a very diversegroup of viruses, some of which are genetically related to those identified in ani-mals. This is the first attempt to describe the gut virome of humans from Cameroon.Therefore, the data represent a baseline for future studies on enteric viral pathogensin this area and contribute to our knowledge of the world’s virome. The studies alsohighlight the fact that more viruses may be associated with diarrhea than the typicalknown ones. Hence, it provides meaningful epidemiological information on diarrhea-related viruses in this area.

KEYWORDS Cameroon, gut, human, virome

Citation Yinda CK, Vanhulle E, Conceição-NetoN, Beller L, Deboutte W, Shi C, Ghogomu SM,Maes P, Van Ranst M, Matthijnssens J. 2019. Gutvirome analysis of Cameroonians reveals highdiversity of enteric viruses, including potentialinterspecies transmitted viruses. mSphere4:e00585-18. https://doi.org/10.1128/mSphere.00585-18.

Editor Marilyn J. Roossinck, Pennsylvania StateUniversity

Copyright © 2019 Yinda et al. This is an open-access article distributed under the terms ofthe Creative Commons Attribution 4.0International license.

Address correspondence to Jelle Matthijnssens,[email protected].

First study on virome of Cameroonians.@JMatthijnssens

Received 24 October 2018Accepted 17 December 2018Published 23 January 2019

RESEARCH ARTICLEClinical Science and Epidemiology

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Diarrhea is the second most common cause of death worldwide and accounts forabout 8 to 9% of the 5.9 million yearly deaths in children under the age of 5 (1, 2).

Most of these deaths occur in Southeast Asia and sub-Saharan Africa (3, 4). The chancesof infection with enteric viruses are higher in developing countries than developedcountries, probably due to suboptimal sanitation and hygienic conditions and lowquality of drinking water, especially in rural areas (5). In Cameroon, a limited number ofstudies have investigated the prevalence of enteric pathogens as the cause of gastro-enteritis in humans. These studies mainly focused on the epidemiology of a limitednumber of pathogens such as rotavirus, norovirus, and enteroviruses, revealing signif-icant differences in the prevalence of these viruses in different settings and timeperiods (4, 6, 7). In parts of Cameroon, a high prevalence of several enteric viruses suchas enterovirus, norovirus, rotavirus, and adenovirus was found in children and adults (8).Generally in Africa, many episodes of gastroenteritis remain unexplained as no etio-logical agent is determined (9, 10). A proportion of the unexplained gastroenteritiscases are likely due to other known viruses, for which no tests were performed.However, a part of these gastroenteritis cases could also be caused by novel viralagents.

Transmission of these enteric viruses is predominantly fecal-oral, and humans areconstantly exposed to these viruses through various routes (11). One of these routes iszoonosis from reservoirs in wild or domestic animals, either by insect vectors or byexposure to animal droppings or tissues. One rich but, until recently, underappreciatedreservoir of emergent viruses is bats. Of the �5,500 known terrestrial species ofmammals, about 20% are bats (12). Several viruses pathogenic to humans are believedto have originated in bats over the last several years, including severe acute respiratorysyndrome (SARS)- and Middle East respiratory syndrome (MERS)-related coronaviruses,as well as filoviruses, such as Ebola and Marburg viruses, or henipaviruses, such asNipah and Hendra viruses (13–18).

In the Southwest region of Cameroon, bats are hunted and eaten. Such closeinteractions provide ample opportunity for zoonotic events to occur (19).

Previously, we identified a plethora of known and novel eukaryotic viruses inCameroonian fruit bats using a viral metagenomics approach, including viruses knownto cause gastroenteritis in humans (sapovirus, sapelovirus, and rotaviruses A and H) andthose not yet associated with gastroenteritis (bastrovirus and picobirna-like viruses)(20–23). In the current study, we metagenomically screened 221 human fecal samplescollected in the same region (where bats are hunted and eaten), to assess (i) if anyviruses of animal origin could be identified and (ii) which known human gastrointes-tinal viruses were present. These fecal samples were collected from children less thana year old to adults of more than 60 years who had gastroenteritis and/or were incontact with bats. Additionally, since the gut virome typically contains both eukaryoticand prokaryotic viruses (phages), of which the latter usually represents the largestfraction of the gut virome, we also analyzed the phageome of these samples.

RESULTSSample characterization. A total of 221 human fecal samples (131 from Kumba and

90 from Lysoka) were collected from two hospitals in the Southwest region of Camer-oon, for viral metagenomics screening. From these fecal samples, a total of 63 poolswere constituted in categories based on age, bat contact status, and location (seeTable S1 in the supplemental material). Illumina sequencing of all the 63 human poolsgenerated in total approximately 708 million raw paired-end (PE) reads (between 4.3and 53.4 million reads per pool). After trimming, 67% of the reads (471 million) wereretained and 86% of these retained trimmed reads (405 million) were annotated usingDiamond. Of these, 18% (74 million) could be attributed as viral.

NGS viral read distribution/abundances. In each of the categories of pools,phages make up at least 84% of the total number of viral reads while the maximumproportion of eukaryotic viral reads is 16%. A similar annotation profile was observed

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for pools of patients in different age groups, different locations, and different batcontact statuses (Fig. S1).

Further analysis of eukaryotic viral reads revealed that at least 70% of the readsmapped to viruses of the families Astroviridae, Reoviridae, and Anelloviridae (Fig. 1A).Other viruses were also present, particularly those that are known to cause gastroen-teritis belonging to the families Adenoviridae, Caliciviridae (Sapovirus and Norovirus),and Picornaviridae (of which about 60% were enteroviruses [Fig. 1B and Fig. S2]). Also,reads from viruses known to cause other human diseases (Parvoviridae) or other animaldiseases (Circoviridae) or not associated with any diseases at all (Picobirnaviridae) werepresent in variable numbers in the different groups (Fig. 1B to E). The rest of the viralfamilies were either plant- or insect-associated viruses. Notably, in age groups A to D,the percentage of pools in which Picobirnaviridae viruses were present increased withage with low percentages in age groups A and B (Fig. 1C). Also, the percentages ofpools positive for anelloviruses differed with respect to age, with higher percentages inyoung children and the elderly. Further, there were no observable trends in thepercentage of eukaryotic viral presence with respect to bat contact status or location(Fig. 1D and E).

Figure 1F shows a heat map of the percentage of pools in which eukaryotic viralfamilies were present in human and bat pools, while Fig. S3 compares the viral

All P

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viruses

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NodaviridaeMycodnaviridae

LuteoviridaeIridoviridae

IflaviridaeHerpesviridae

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PicobirnaviridaePhycodnaviridae

ParvoviridaePartitiviridae

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NodaviridaeMycodnaviridae

MimiviridaeMarseilleviridae

LuteoviridaeIridoviridae

HepadnaviridaeDicistroviridae

CircoviridaeCaliciviridae

BetaflexiviridaeAstroviridaeAsfarviridae

AnelloviridaeAlphaflexiviridae

Adenoviridae

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FIG 1 (A) Overview of the most abundant viral families and genera identified in humans in this study based on assigned reads. Low-abundance mammalianviruses not present in this figure belong to the Caliciviridae, Circoviridae, Geminiviridae, Hepadnaviridae, Nodaviridae, Parvoviridae, and unclassified Picornavirales.Other low-abundance plant/insect viruses not in this figure are Alphatetraviridae, Betatetraviridae, Luteoviridae, Maiseilleviridae, Partitiviridae, Peribunyaviridae,Phycodnaviridae, Pithoviridae, Totiviridae, and Tymoviridae. The viruses of families that could not be assigned to any known genus are referred to as unclassifiedviruses. Families represented by fewer than 100 reads were excluded. (B to E) Heat map of the presence of eukaryotic viral families in feces from all 63 poolsin relation to different parameters (B, individual pools; C, age; D, bat contact status; E, location). Color code for panel B: blue square, presence of viral familyin pool (more than 0.001% of total reads of that pool); white square, absence of viral family in pool (less than 0.001% of total reads of that pool). (F) Heat mapof viral family presence in human and bat pools.

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presence in human and bats at the genus level (23). Astroviridae (Mamastrovirus),Calciviridae (Sapovirus), Picornaviridae (Parechovirus), and Reoviridae (Rotavirus), viralfamilies known to cause gastroenteritis in humans, were identified in both bat andhuman pools from the same region. Also, mammalian viruses not yet established tocause gastroenteritis (Picobirnaviridae, Circoviridae, and Parvoviridae [Bocaparvovirus])were also common in both bats and humans from the same regions (Fig. 1F andFig. S3).

Phylogeny of eukaryotic viruses. In this study, we focused on viruses from whichnear- complete genomes were obtained, particularly those that are known to causeviral gastroenteritis (belonging to the Astroviridae, Caliciviridae [norovirus and sapovi-rus], Picornaviridae [enterovirus, parechovirus, cosavirus], Parvoviridae, Reoviridae, andAdenoviridae [human mastadenovirus]). Furthermore, we also looked at other virusesnot fully proven to cause gastroenteritis in humans but which have only sporadicallybeen associated with gastroenteritis, like Picobirnaviridae and small circular single-stranded DNA viruses.

Phylogenetic analysis was done for each of the selected viruses using the protein ornucleotide sequences of suitable conserved regions and representative members oftheir viral family, genus, or species.

Reoviridae. Reoviridae is a large viral family of segmented dsRNA viruses with awide host range. They are further divided into two subfamilies and 15 genera. Genomesof viruses belonging to the Reoviridae contain 9 to 12 segments (24). In total, Reoviridaereads were found in 6 pools, and (nearly) complete genomes of 2 viruses of the familyReoviridae were obtained from pool HP55. Samples in this pool were from two diarrheicchildren (less than 5 years), originating from Kumba and without contact with bats.

Mammalian orthoreovirus. Mammalian orthoreoviruses (MORVs) contain 10 seg-ments, L1 to L3, M1 to M3, and S1 to S4, coding for 12 to 13 proteins (24, 25). A MORVstrain was identified represented by 16,913 reads (0.4% of all viral reads of the pool).Phylogenetic analysis based on the nucleotide sequences of each of the 10 segmentsof this MORV (Fig. 2 and Fig. S4) showed topological incongruence with four distinctivepatterns. Based on segments L2 and S1, this strain clustered with bat strains WIV3 andWIV5 from China with 86% and 70% nucleotide (nt) identity, respectively (Fig. 2A andB). For the L1 and S2 segments, the human strain clustered with the Ndelle murinestrain, also from Cameroon, with 95% and 92% nt identity, respectively (Fig. 2C and D).On the other hand, segment S3 of the Cameroonian MORV strain clustered with ahuman strain and a civet MORV strain from China (88% and 89% nt identity, respec-tively [Fig. 2E]). The rest of the segments (L3, M1 to M3, and S4) did not cluster togetherclearly with any of the abovementioned strains (Fig. S4).

Rotavirus A. Rotavirus A (RVA) contains 11 segments coding for 11 or 12 proteins:VP1 to VP4, VP6, VP7, and NSP1 to NSP6 (26, 27). We identified a near-complete RVAsequence which made up 99% (4.3 million) of the eukaryotic viral reads of that pool.The NSP3 segment was not identified in the sample. The VP7 gene of this strain wasgenetically most related to RVA/Human-tc/USA/Wa/1974/G1P1A[8] and RVA/Human-TC/USA/Rotarix/2009/G1P[8] (nt identity of 92 and 97%, respectively) while the VP4gene was 90% identical to the same strains. The phylogenetic trees of the remainingsegments shared the same clustering pattern (Fig. 3A and B and Fig. S5). According tothe rotavirus classification scheme, this strain is a typical Wa-like G1P[8] named RVA/Human-wt/CMR/CMRHP55/2014/G1P[8]. CMRHP55 was distantly related to bat RVAstrains identified from the same regions (only 69 to 71% nt identity).

Picornaviridae. The Picornaviridae represent a large family of small, cytoplasmic,nonenveloped icosahedral ssRNA viruses consisting of 80 species, grouped into 35genera. They have a genome of 7.1 to 8.9 kb in size and are most often composed ofa single ORF encoding a polyprotein flanked by a 5= and 3= UTR (28). The members ofthe family Picornaviridae can cause gastroenteritis, meningitis, encephalitis, paralysis(nonpolio and polio-type), myocarditis, hepatitis, upper respiratory tract infections, anddiabetes (29, 30). Out of the 63 pools, 41 contained Picornaviridae reads, making the

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0.1

GQ468267_T2/CHN/Civet/MPC/04/2004

JQ412756_T3/DEU/Bat/342/08/2008

KJ676380_T1/USA/Bovine/MRV00304/2014

JX415467_T1/CHN/Porcine/SHR-A/2011

JX204739_T2/DEU/Vole/TRALAU2004/2004

KT900696_T1/ITA/Bat/BatMVR1-IT2011/2011

KM087106_T2/CHN/Bat/RpMVR-YN2012/2012

KT444573_T2/CHN/Bat/WIV3/2011

AF378007_T3/FRA/Murine/T3C9-61/1961

KX384847_T2/HUN/Vole/47Ma/06/2006

AF378005_T2/USA/Jones

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Tx/CMR/Human/CMR-HP55/2014

KF154725_T3/SVN/Human/SI-MVR01

HM159614_T3/USA/Human/T3D/2002

DQ664185_T2/CHN/Human/BYD1/2006

KM820755_T3/USA/Porcine/FS-03/2014

JN799427_T2/AUT/Porcine/729/1998

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FIG 2 Maximum likelihood phylogenetic trees based on the nucleotide sequences of the L2, S1, L1, S2,and S3 coding segments of the novel MORV (indicated in red) and representative strains from GenBankshowing 3 patterns of clustering with respect to the novel strain: A and B, clustering of novel strain with

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Picornaviridae the eukaryotic viral family of which reads could be identified in thehighest number of pools.

Enterovirus. The genus Enterovirus (EV) consists of 15 species: Enterovirus A to L andRhinovirus A to C. EV A, B, C, and D are found in humans; E and F in cattle; G in pigs;H, J, and L in monkeys; K in rodents; and species I in dromedary camels (http://www.picornaviridae.com). In this study, eighteen (nearly) complete genomes of EVs wereobtained. The strains were named EV/Human/CMRHPxx/CMR/2014, here referred to asEV-CMRHPxx. All eighteen genomes were found in pools of age groups A and B (�3and 3 to 20 years, respectively). Eight of these were identified in age group A, three(EV-CMRHP1, 5A, and 5B) of which were pools consisting of samples of infants who hadindirect contact with bats while the rest (EV-CMRHP14, 45, 52A, 52B, and 55) were thosethat had no contact with bats. The ten other strains were identified in pools belongingto age group B, three of which had direct contact with bats (EV-CMRHP8A, 8B, and 9),5 indirect contact (EV-CMRHP3, 4, 35A, 35B, and 39) and two with no contact (EV-CMRHP18 and 58). Based on the phylogenetic analysis of the VP1 nucleotide sequences,the EVs found in this study were quite divergent from each other, belonging to threedifferent species of Enterovirus, A, B, and C (Fig. 4A). Most of the strains belonged to theEnterovirus C clade (EV-CMRHP1, 3, 4, 8A, 8B, 9, 14, 18, 35A, 52A, and 55), whileEV-CMRHP35B, 39, and 45 clustered within the Enterovirus B genotype, andEVCMRHP5A, 5B, 52B, and 58 in the genogroup Enterovirus A. Some pools had multiplestrains of EV present, and some of these clustered together (CMRHP8A and 8B: vaccinetype PV-3), whereas other pools contained distinct EV species (EV-CMRHP35A and 35B;52A and 52B). The presence of vaccine strains (PV-3) in pool HP8 probably indicatesrecent vaccination events of the infants in this pool. Apart from EV-CMRHP39 (whichclustered with 11C52_CMR), all the EV strains identified here were distantly related tothose previously identified in the Far North region of Cameroon (31). Furthermore,none of the human strains from Cameroon were related to any of the animal EV strains(from chimp or gorilla). A summary of the detailed classification of these EVs using anonline typing tool (32) is shown in Table 1.

Parechovirus. The genus Parechovirus is comprised of two species, Parechovirus A(human parechovirus [HPeV]) and Parechovirus B (Ljungan virus, isolated from bankvoles) (33). HPeV is subdivided into 19 types (HPeV1 to -19). HPeV is associated withmild gastrointestinal or respiratory illness; however, severe disease conditions, such asmeningitis/encephalitis, acute flaccid paralysis, and neonatal sepsis, may occur (34–36).Here, three (nearly) complete HPeVs were identified in pools HP2, HP46, and HP48 withsequence lengths of 7,142 bp, 7,202 bp, and 7,219 bp, respectively, collected fromchildren less than 3 years old (age group A). In terms of bat contact status, they werein pools of those either in indirect contact with bats (HP2 and HP48) or without contact(HP46). They were all distantly related to each other, with HPeV-CMRHP46 and HPeV-CMRHP48 having the highest identity (76% and 86% nt and aa identity, respectively).Phylogenetically, HPeVs in HP46 and in HP48 fell into a clade of type 1 HPeVs (Fig. 4B).The HPeV in HP46 clustered together with HPeV1/Harris strain with 76% nt identity,while CMRHP48 clustered closely with Japanese and Norwegian strains A1086-99 andNO-3694 (84 to 90% nt identity). Furthermore, HPeV-CMRHP2 clustered distantly withtype 16 HPeVs from China and Bangladesh with only 70 to 71% nt identity. Consideringthe 75% identity demarcation for HPeV types (37, 38), this strain potentially representsa novel type.

Cosavirus. The genus Cosavirus consists of five species (Cosavirus A, B, and D to F),which have been associated with gastroenteritis in children (39). Six near-complete

FIG 2 Legend (Continued)bat strains from China; C and D, clustering of novel strain with murine strain from Cameroon; and E,clustering of novel strain with human and civet strains from China. Trees were constructed using theGTR�G�I nucleotide substitution model using RAxML, with the autoMRE flag, which enables a posterioribootstrapping analysis. Only bootstrap values greater than 70% are shown. Bars indicate nucleotidesubstitutions per site.

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P[6]_RVA/Human-tc/GBR/ST3/1975/G4P2A[6]

P[5]_RVA/Cow-tc/GBR/UK/1973/G6P[5]P[3]_RVA/Dog-tc/AUS/K9/1981/G3P[3]

P[37]_RVA/Pheasant-tc/GER/10V0112H5/2010/G23P[37]

P[43]_RVA/Bat-wt/CMR/BatLy03/2014/G25P[43]

P[31]_RVA/Chicken-tc/DEU/06V0661/2006/G19P[31]

P[35]_RVA/Turkey-tc/DEU/03V0002E10/2003/G22P[35]

P[3]_RVA/Bat-tc/CHN/MSLH14/2012/G3P[3]

P[32]_RVA/Pig-wt/IRL/61-07-ire/2007/G2P[32]

P[23]_RVA/Pig_wt/China/NMTL/2008/G9P[23]

P[16]_RVA/Mouse-tc/USA/EW/XXXX/G16P[16]

P[24]_RVA/Rhesus-tc/USA/TUCH/2002/G3P[24]

P[38]_RVA/Turkey-tc/IRL/Ty-1/1979/G17P[38]

P[2]_RVA/LabStr/USA/SA11g4O-5N/XXXX/G3P[2]

P[11]_RVA/Human-tc/IND/116E/1985/G9P[11]

P[23]_RVA/Pig-wt/JPN/GUB46/2006/GxP[23]

P[10]_RVA/Human-tc/IND/69M/1980/G8P[10]

P[15]_RVA/Sheep-wt/CHN/Lp14/xxxx/G10P[15]

P[4]_RVA/Human-tc/USA/DS-1/1976/G2P1B[4]

P[18]_RVA/Horse-tc/GBR/L338/1991/G13P[18]

P[36]_RVA/SugarGlider-tc/JPN/SG385/2012/G27P[36]

P[19]_RVA/Human-tc/THA/Mc323/1989/G9P[19]

P[26]_RVA/Pig-wt/ITA/134-04-15/2003/G5P[26]

P[9]_RVA/Human-tc/JPN/AU-1/1982/G3P[9]

P[6]_RVA_Bat-wt/Kenya/KE4852/2007/G25P[6]

P[8]_RVA/Human-tc/USA/Wa/1974/G1P1A[8]

P[10]_RVA/Bat-wt/CHN/MYAS33/2013/G3P[10]

P[7]_RVA/Pig-tc/USA/OSU/1977/G5P[7]

P[25]_RVA/Human-wt/BGD/Dhaka6/2001/G11P[25[

P[17]_RVA/Pigeon-tc/JPN/PO-13/1983/G18P[17]

P42_RVA/Bat-wt/CMR/BatLi10/2014/G30P42

P[28]_RVA/Human-wt/ECU/Ecu534/2006/G20P[28]

P[8]_RVA/Human-wt/CMR/CMRHP55/2014/G1P[8]

P[12]_RVA/Horse-tc/GBR/H-2/1976/G3P[12]

P[8]_RVA/Human-TC/USA/Rotarix/2009/G1P[8]

P[20]_RVA/Mouse-tc/XXX/EHP/1981/G16P[20]

P[30]_RVA/Chicken-tc/DEU/02V0002G3/2002/G19P[30]


P[27]_RVA/Pig-wt/THA/CMP034/2000/G2P[27]

P[21]_RVA/Cow-tc/IND/Hg18/1995/G15P[21]

P[33]_RVA/Cow-tc/JPN/Dai-10/2007/G24P[33]

P[22]_RVA/Rabbit-wt/ITA/160/01/GxP[22]

P[29]_RVA/Cow-wt/JPN/Azuk-1/2006/G21P[29]


P[14]_RVA/Human-tc/GBR/A64/1987/G10P[14]

P[1]_RVA/Cow-wt//FRA/RF/xxxx/GxP[1]_P1

P47_RVA/Bat-wt/CMR/BatLy17/2014/G30P47

P[34]_RVA/Pig-wt/JPN/FGP51/2009/G4P[34]

P[13]_RVA/Pig-wt/xxx/A46/xxxx/GxP[13]

8 2

8 3

8 2

100

7 6

100

100

100

100

100

9 0

8 7

100

100

100

100

100

100

100

100

100

7 4

8 2

9 4

100

9 3

100

100

100

0.2

G17_RVA/Turkey-tc/IRL/Ty-1/1979/G17P[17]

G4_RVA/Human-tc/GBR/ST3/1975/G4P[2]A6

G31_RVA/Bat-wt/CMR/BatLi08/2014/G31P[42]


G3_RVA/Bat-wt/CHN/MYAS33/2013_G3P[10]

G25_RVA/Bat-wt/KEN/KE4852/07/2007/G25P[6]

G21_RVA/Cow-wt/JPN/Azuk-1/2006/G21P[29]

G13_RVA/Horse-tc/GBR/L338/1991/G13P[18]

G3_RVA/Human-tc/JPN/AU-1/1982/G3P[39]

G15_RVA/Cow-tc/IND/Hg18/1995/G15P[21]


G22_RVA/Turkey-tc/DEU/03V0002E10/2003/G22P[35]

G8_RVA/Human-tc/IND/69M/1980/G8P[4]10

G23_RVA/Pheasant-wt/HUN/Phea14246/2008/G23P[x]

G18_RVA/Pigeon-tc/JPN/PO-13/1983/G18P[17]

G20_RVA/Human-wt/ECU/Ecu534/2006/G20P[28]

G26_RVA/Pig-wt/JPN/TJ4-1/2010/G26P[x]

G14_RVA/Horse-tc/USA/FI23/1981/G14P[12]

G1_RVA/Human-wt/CMR/CMRHP55/2014/G1P[8]

G7_RVA/Turkey-tc/IRL/Ty-3/1979/G7P[17]

G3_RVA/Bat-tc/MSLH14/2012/G3P[3]

G6_Cow-tc/USA/NCDV/1971/G6P[1]

G1_RVA/Human-TC/USA/Rotarix/2009/G1P[8]

G12_RVA/Human-tc/PHL/L26/1987/G12P[4]

G2_RVA/Human-tc/USA/DS-1/1976/G2P[1]B4

G5_RVA/Pig-tc/USA/OSU/1977/G5P[9]7

G25_RVA/Bat-wt/CMR/BatLy03/2014/G25P[43]

G19_RVA/Chicken-tc/GBR/Ch-1/197x/G19P[17]

G1_RVA/Human-tc/USA/Wa/1974/G1P[1]A8

G10_RVA/Human-tc/GBR/A64/1987/G10P[14]

G9_RVA/Human-tc/USA/WI61/1983/G9P[1]A8

G30_RVA/Bat-wt/CMR/BatLy17/2014/G30P[47]

G27_RVA/SugarGlider-tc/JPN/SG385/2012/G27P[36]

G24_RVA/Cow-tc/JPN/Dai-10/2007/G24P[33]

G11_RVA/Pig-tc/MEX/YM/1983/G11P[9]7

G16_RVA/Mouse-tc/USA/EW/XXXX/G16P[16]

100

100

100

9 1

8 9100

9 9

100

9 1

100

100

8 5

100

9 9

9 1

8 9

A

B

FIG 3 Phylogenetic trees of full-length ORF nucleotide sequences of RVA VP4 (A) and VP7 (B) genesegments showing close genetic relatedness to typical Wa-like genotype G1P[8] strains. Red, Cameroo-nian human RVA strain identified in this study; blue, Cameroonian bat RVA strains. Trees were constructed





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human cosavirus (HCoSV) genomes were identified: 1 from children less than 3 yearsold (HP49), 3 from those between 3 and �20 years old (HP6A and HP6B, HP57), and 2from pools of individuals between 20 and �60 years old (HP44, HP24). Some of thesepools had direct or indirect contact with bats (HP6, HP24, and HP44), while others hadno contact with bats (HP49 and HP57). Phylogenetic analysis (Fig. 4C) showed thatcosaviruses from HP6B, HP49, and HP57 formed a clade with two other strains fromAustralia and Nigeria (HCoSV/E1/AUS and HCoSV/NG385/NGA) in species HCoSV E.Meanwhile the strains in HP6A, HP24, and HP44 clustered with HCoSV in species A, D,and B, respectively. Therefore, it seems that humans in Cameroon host a diverse rangeof cosaviruses.

Cardiovirus. The genus Cardiovirus consists of three species, Cardiovirus A to C.Species B includes Saffold virus (SafV) infecting humans. It has been found in cases withacute flaccid paralysis, respiratory tract infections, and diarrhea in China (40–42). Here,we found a near-complete genome of a SafV in one pool (HP35) belonging to the agegroup between 3 and �20 years old who had indirect contact with bats. The VP1

FIG 3 Legend (Continued)using the GTR�G�I nucleotide substitution model using RAxML, with the autoMRE flag, which enablesa posteriori bootstrapping analysis. Only bootstrap values greater than 70% are shown. Bars indicatenucleotide substitutions per site.

0.3

EF015019/EV/Human/CVA20b-Cecil/ZAF

EV/Human/CMRHP8B/CMR/2014

AF448783/EV/Human/034/EGY/1993

FJ007373/EV/Monkey/POo-1/USA/1999

KC787147/EV/Human/11C74_CMR/CMR/2011

EV/Human/CMRHP55/CMR/2014

AF326754/EV/Simian/M19s-P2/1956EV/Human/CMRHP58/CMR/2014

KJ641623/EV/Human/CVA10_JB141310010/CHN/2013

KP247597/EV/Human/Saukett-3/GBR/2014

AF201894/EV/Human/A-2_plaque_virus/USA

EF015023/EV/Human/Wa89-10620/USA

EV/Human/CMRHP52A/CMR/2014

FJ751915/EV/Human/FIN05-2/2005


JX274982/EV/Human/11448/NGA/2005

KP289363/EV/Human/CV-A5_P836/CHN/2013

AB575916/EV/Human/16173/NLD/1976

DQ995644/EV/Human//Ca98-10615/USA/2004

M16560/EV/CXA1G




HQ728261/EV/Human/CVA5_SD/CHN/2009

KF040080/EV/Gorilla/MB6201/CMR/2010

EF015009/EV/Human/10582/BAN/2001



AB552988EV/Human/3692/NLD/2007

JF260921/EV/Human/CV-A13_67900/MDG/2002

EF015011/EV/Human/10696/OMN/1999

DQ995640/EV/Human/10419/BAN1999



AF405666/EV/Human/007/HTI/2001

HQ728260/EV/Human/CVA4_SZ/CHN/2009

AF414372.2/EV/Simian/N125/USA/1972

DQ995637/EV/Human/89-10611/AUS

KP793035/EV/Human/IJC04/COG/2011

DQ916376/EV/Human/E210/EGY/

KX430808/EV/Human/CVA10/VNM/2014

EF015010/EV/Human/10697/BAN/2004



HQ415758/EV/Human/05517/CHN/2005

NC_010415/EV/Simian/1631

JX174177/EV/HumanKS-ZPH01F/XJ/CHN/2011


AF029859.2/EV/Farouk-TCC-VR-1038EGY/1951


DQ995634/EV/Human/10589/BAN/2001

AF414373.2/EV/Simian/N203/USA/1972


HQ738287/EV/Human/V2-SAK/MDG/2005

FJ357382/EV/Human/238/TWN/1986

KR018815/EV/Human/12MYKL1607/MYS/2012


AF465513/EV/Human/G-13/AUS

KX433167/EV/Human/D68-U797/USA/2007

EF667344/EV/Human/RJG7


AF326759.2/EV/Simian/1715-UWB/USA/1954

AY421762/EV/2004

KU183495/EV/Human/K282-YN/CHN/2013


KJ541163/EV/Human/701_SH/CHN/2010

KU172420/EV/Bovine/KSU/MEX/2015



JF260926/EV/Human/HEV-99_68229/MDG/2002

JF742576/EV/Human/GD46/CHN/2010

D17612/EV/Human/V1635-81/PAK/1981


AY421760/EV/Human/Fleetwood-CA2

AF499639/EV-G12/Human

KR919804/EV/Human/SZ-GD/CHN/2015


KC787138/EV/Human/11C59-CMR/CMR/2011

AF499642/EV/Human/IH35/USA/1955

EF555644/EV/Human/99/USA

EV/Human/CMRPHP3/CMR/2014

AY302560/EV/Human/Toluca-1/MEX/1959

KF040081/EV/Gorilla/MB6128/CMR/2010

EF015012/EV/Human/Ok85-10627/USA


DQ995646/EV/Human/03-10616/BAN

JF416935/EV/Chimpanzee/KK2640/CMR/2007

8 3

100

100

100

100

100

7 1

9 1

100

100

8 1

9 8

100

100

9 8

9 9

100

9 2

8 2

100

100

9 5

100

9 2

8 7

9 8

100

9 7

100

9 4

8 9

100

9 6

100

8 5

9 8

100

8 4

100

100

100

100

9 9

9 4

100

100

8 1

100

9 9

9 1

9 9

100

7 6

7 5

8 4

100

7 6

100

100

8 59 3

9 5

9 7

9 9

100

100

8 9

9 2

100

8 2

7 5

Enterovirus C

Enterovirus B

Enterovirus J

Enterovirus FEnterovirus EEnterovirus G

Enterovirus D

Enterovirus H

Enterovirus A

Rhinovirus CRhinovirus ARhinovirus B

A

B

0.2

AB112485_HPeV-1/A1086-99/JPN/1999

EF051629_HPeV-1/BNI-788St/DEU/xx

KM407606_HPeV-18/CMH-N166-12/THA/2012HPeV-1/CMRHP48/CMR/2014

HPeV-1/CMRHP46/CMR/2014

HPeV-16/CMRHP2/CMR/2014

KJ743665_HPeV-16/PP083856/NIV/IND/2008KJ743661_HPeV-16/PP0815387/NIV/IND/2008

EU360550_HPeV-1/NO-7695/NOR/2005

EU360536_HPeV-1/NO-6785/NOR/2005

S45208_HPeV-1/EV22/Harris/1956

JX219580_HPeV-16/08-11615/BAN/2008

EU360524_HPeV-1/NO-3694/NOR/2005

EU360523_HPeV-1/NO-3680/NOR/2005

7 49 8

100

7 8

9 1

9 3

HPeV1

HPeV16

C

0.2

FJ438907/HCoSV/B1-2263/PAK

HCoSV/CMRHP24/CMR/2014

JN867756/HCoSV/A20-NG263/NGA/2007

JN867761/HCosV/D4-NP3/NPL

JN867757/HCoSV/E/D-NG385/NGA/2007

KP213322/HCoSV/1213-144/CHN/2012

JN867789/HCoSV/D5-TN07-E126/TUN/2007

JN867759/HCoSV/A19-PK6187/PAK/2006

JQ811826/HCosV/A21-NG295-2/NGA/2007

JN867762/HCoSV/D2-NP4/NPLFJ438908/HCoSV/D1-5004/PAK

JN867764/HCoSV/A13-NP6/NPL

JN867758/HCoSV/F-PK5006/PAK2007


HCoSV/CMRHP6A/CMR/2014

JN867775/HCosV/A18-NG15/NGA/2007

FJ555055/HCoSV/E1/AUS/1981

JN867778/HCosV/D3-NG20/NGA/2007

JN867777/HCosV/D5-NG19/NGA/2007

KX545380/HCoSV/zj-1/CHN/2014

HCoSV/CMRHP49/CMR2014


JQ811832/HCosV/D4-NG366-1/NGA/2007

FJ438902/HCoSV/A1-0553/PAK

HCoSV/CMRHP6B/CMR/2014

KJ194505/HCoSV/Amsterdam/NDL/1994

9 7

9 8

100

9 6

9 8

8 7

100

9 7

100

8 4

100

9 1

100

9 9

9 9

100

100

A

B

D

E

F

D

0.07

AB747181/SAFV6/Afg-1157/AFG/2009

AB747220/SAFV6/Pak-1655/PAK/2009

FJ463615/SAFV5/Pak5003/PAK/2007

AB747227/SAFV6/Pak-2124/PAK/2009

CardioVirusB/CAMHP35/CAM/2014

AB747231/SAFV6/Pak-2396/PAK/2009

AB747223/SAFV6/Pak-2026/PAK/2009

FJ463617/SAFV6/Pak6572/PAK/2007

AB747253/SAFV6/Pak-1570/PAK/2009

AB747192/SAFV6/Pak-1709/PAK/2009

AB747252/SAFV5/Pak-3290/PAK/2009

FJ463616/SAFV5/Pak5152/PAK/2007

9 9

9 8

8 7

100

100

9 9

7 7

100

9 8

SAFV6

SAFV5

E

0.008

AY644676_HAV-IIB/Human/CF53-Berne-FRHK-4/FRAAY644670_HAV/Human/SLF88/SLE/1988

HAV/Human/CMRHP4/CAM/2014

HAV/Human/CMRHP2/CAM/2014KF706411_HAV/GIA/BA/2012

HAV/Human/CMRHP6/CAM/2014

AY574059_HAV_BRAB13/NLD

FJ829494_HAV/G2B1-VP/FRA/2004

8 2

8 2

9 9

7 4

IIA

IIB

FIG 4 Phylogenetic relationships of picornaviruses identified in this study: A, genus Enterovirus; B, genus Parechovirus; C, genus Cosavirus; D, genus Cardiovirus;E, species Hepatovirus A. Phylogenetic trees were based on the nucleotide sequences of the VP1-P2A region for the species Hepatovirus A and the VP1 regionfor the rest of the genera. All the trees were constructed using the GTR�G�I nucleotide substitution model using RAxML, with the autoMRE flag, which enablesa posteriori bootstrapping analysis. Only bootstrap values greater than 70% are shown. Bars indicate nucleotide substitutions per site. Red, novel strains fromthis study; blue, human Cameroonian enterovirus strains from other studies; green, animal enterovirus strains from Cameroon.

Yinda et al.



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segment of the identified SafV was 72 to 74% and 78 to 80% identical (on nt level) toSafV strains in types 5 and 6, respectively. Phylogenetic analysis based on the VP1region confirmed the clustering of the novel strain between types 5 and 6 with morephylogenetic relatedness to type 6 (Fig. 4D). Hence, this novel SafV strain may be adistant member of type 6 or represent a new type.

Hepatovirus A. Hepatitis A virus (HAV), now Hepatovirus A, belongs to the genusHepatovirus, which consists of nine species (Hepatovirus A to I). The Hepatovirus Aspecies is comprised of a single serotype, HAV, subdivided into human and simianviruses (43). It causes acute hepatitis throughout the world (44). There were three(nearly) complete HAV genomes in pools HP2, HP4, and HP6, all of which were poolsfrom those in direct (HP6) or indirect (HP2 and HP4) contact with bats. These strainswere either from infants less than 3 years old (HP2) or from children between 3 and�20 years old (HP4 and HP6). Based on the VP1-P2A region, the nt identity betweenthese strains was 98 to 99%. Strains in HP4 and HP6 were 99% identical to BRAB13,isolated from a patient from the Netherlands in 2001, who was staying in a hippiecommunity with visitors from all over the world and under primitive living conditions(45). On the other hand, the HAV strain in HP2 was closely related to strain G2B1-VPfrom France (98% nt identity). Therefore, all strains identified here are genotype IIA(Fig. 4E), increasing the number of completely sequenced genotype II strains to five (theother two strains are BA/ITA/2012 and CF53/Berne).

Astroviridae. Astroviridae is a family of nonenveloped, spherical viruses with a linearssRNA(�) genome of 6.8 to 7kb, containing three overlapping ORFs. The family isdivided into two genera: genus Mamastrovirus (MAstVs) and genus Avastrovirus(AAstVs). The genera are further divided into 33 and 7 species, respectively (46).Fourteen out of the sixty-three human pools contained Astroviridae reads, and we wereable to obtain eight near-complete genomes of MAstVs (HP2, 3, 6, 34, 35, 43, 45, and46). Additionally, these pools were either from children less than 3 years old (HP2, HP45,and HP46), age group 3 to �20 (HP3, HP6, and HP35), or between 20 and �60 (HP34and HP43). Phylogenetic analysis of the RdRp and capsid regions (Fig. 5A and B)depicted clustering of the novel MAstVs in species 1 (CMRHP2, 3, 34, 35D, 43, and 46),6 (CMRHP45), and 9 (CMRHP6). In the MAstVs1 clade, there seems to be topologicalinconsistency in the different phylogenetic trees. Strain AstV8_Yuc8 (AF260508) clus-tered with the novel strains CMRHP2, 3, and 35D in the capsid tree, while in the RdRptree it clustered with the Chinese strain V4-Guangzhou, suggesting a recombinationevent between these strains in the past. Bat astrovirus identified in Cameroon (23)

TABLE 1 Classification of Cameroonian EVsa

Strain nameb RefSeqEnterovirusspecies

% ntidentity Type

% typesupport

EV-CMRHP1 NC_002058 Enterovirus C 76.9 CV-A13 100.0EV-CMRPHP3 NC_002058 Enterovirus C 80.1 CV-A13 100.0EV-CMRHP5A NC_001612 Enterovirus A 84.7 CV-A4 100.0EV-CMRHP5B NC_001612 Enterovirus A 83.1 CV-A5 100.0EV-CMRHP8A NC_002058 Enterovirus C 99.9 PV-3 100.0EV-CMRHP8B NC_002058 Enterovirus C 99.9 PV-3 100.0EV-CMRHP9 NC_002058 Enterovirus C 76.8 EV-C116 100.0EV-CMRHP14 NC_002058 Enterovirus C 79.6 EV-C99 99.0EV-CMRHP4 NC_002058 Enterovirus C 79.5 EV-C99 100.0EV-CMRHP18 NC_002058 Enterovirus C 83.1 EV-C99 100.0EV-CMRHP35A NC_002058 Enterovirus C 79.8 EV-C99 100.0EV-CMRHP35B NC_001472 Enterovirus B 81.4 E-20 100.0EV-CMRHP45 NC_001472 Enterovirus B 80.9 E-20 100.0EV-CMRHP52A NC_002058 Enterovirus C 81.6 CV-A11 100.0EV-CMRHP52B NC_001612 Enterovirus A 77.3 CV-A3 100.0EV-CMRHP55 NC_002058 Enterovirus C 80.0 EV-C99 100.0EV-CMRHP58 NC_001612 Enterovirus A 76.0 EV-A90 96.0EV-CMRHP39 NC_001472 Enterovirus B 83.5 EV-B88 100.0aThe classification was done with an online typing tool (32).bFull name of enterovirus strain EV/Human/CMRHPxx/CMR/2014.




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https://www.ncbi.nlm.nih.gov/nuccore/AF260508

https://www.ncbi.nlm.nih.gov/nuccore/NC_002058




















A

0.2

Human-AstV_CMRHP2

AF260508_HumanAstV8_Yuc8

Human-AstV_CMRHP34

HQ916313_BovineAstV/B18/HK

JX556692_PorcineAstV4-US-IL135

KF233994_BovineAstV-NeuroS1

DQ344027_HumanAstV4-Guangzhou

GU985458_Mink_AstV-SMS

AY720892_HumanAstV5-Goiania/GO/12/94/Brazil

HM447045_DeerAstV-CcAstV-1/DNK/2010

FJ890351_Sea_lionAstV1

Human-AstV_CMRHP35D

GQ891990_HumanAstV-SG

JF729316_RabbitAstV-TN/2208/2010

JX857868_HumanAstV-VA3/human/Vellore/28054/2005

GQ502193_HumanAstV-VA2/human/Stl/WD0680/2009

EU143847_TurkeyAstV-MN/01


HM045005_DogAstV-Bari/2008Human-AstV_CMRHP45

KC609001_MurineAstV-BSRI1GQ415662_HumanAstV-HMO-C/NE-3010

GQ914773_PorcineAstV2-Shanghai/2008

AF206663_TurkeyAstV-AK/98

GQ415661_HumanAstV-HMO-B/NI-196

JF742759_HumanAstV-MLB2/human/Stl/WD0559/2008

HQ889774_PigeonANV-SH10

Human-AstV_CMRHP6

DQ070852_HumanAstV4-Goiania/GO/12/95/Brazil

EU143843_TurkeyAstV-AK/98

AF141381_HumanAstV3-Berlin

HM450381_RatAstV-RS118/HKG/2007

Z25771_HumanAstV-Newcastle

Human-AstV_CMRHP46

JX857870_HumanAstV-MLB3/human/Vellore/26564/2004

AB033998_ANV1-G-4260

AB829252_HumanAstV-MLB2-GUP187

JX439643_DuckAstV1-WF1201

Human-AstV_CMRHP3

FJ973620_HumanAstV-VA1

JF414802_ChickenAstV-GA2011

AY179509_MinkAstV


JF713710_PorcineAstV2-43/USA



Human-AstV_CMRHP43

JN052023_RabbitAstV-Nausica/2008/ITA

FJ402983_HumanAstV-MLB1-WD0016



JX556690_PorcineAstV2-US-IA122

L23513_HumanAstV1-Oxford

JX857869_HumanAstV-VA4/human/Nepal/s5363

JX556691_PorcineAstV3-US-MO123

FJ571068_BatAstV-Ha/Guangxi/LS11/2007


HQ916317_BovineAstV/B76-2/HK

FJ571066_BatAstV-Tm/Guangxi/LD77/2007

AB823731_HumanAstV-MLB1

HQ916315_BovineAstV-B34/HK

FJ434664_DuckAstV3-C-NGB

HM447046_DeerAstV-CcAstV-2/DNK/2010


FJ222451_HumanAstV-MLB1


HM029238_ANV1_CHN

KF499111_FelineAstV2-1637F

JQ340310_Wild_boarAstV-WBAstV-1/2011/HUN

1

0.99

0.86

1

1

1

1

0.87

1

0.92

0.99

1

1

1

0.98

0.97

0.83

0.99

07

0.82

1

1

1

0.99

0.79

1

0.941

0.99

1

1

1

0.91

1

1

1

0.99

1

1

1

0.97

1

0.94

0.93

0.96

1

0.96

1

1

0.96

1

0.96

0.85

0.94

1

0.97

0.99

1

1

0.94

1

Bat-AstroV_CMR/Bat-AsV/P02

MAstV-28^

MAstV 1

MAstV 2

MAstV 3 MAstV 4 MAstV 5

MAstV 6

MAstV 9

MAstV 8

MAstV 12

MAstV 10

MAstV 17 MAstV 15 MAstV 16MAstV-24^

MAstV-26^

MAstV-23^

MAstV-25^

MAstV-29^MAstV-30^

MAstV-32^

Avastrovirus

MAstV 11

?

?

B

0.3

L23513_HumanAstV1-Oxford

JX857868_HumanAstV-VA3/human/Vellore/28054/2005

HM447045_DeerAstV-CcAstV-1/DNK/2010HM447046_DeerAstV-CcAstV-2/DNK/2010

FJ571066_BatAstV-Tm/Guangxi/LD77/2007

FJ434664_DuckAstV3-C-NGB

FJ973620_HumanAstV-VA1


GU985458_Mink_AstV-SMS


EU143847_TurkeyAstV-MN/01


Z25771_HumanAstV-Newcastle


GQ502193_HumanAstV-VA2/human/Stl/WD0680/2009

Human-AstroV_CMRHP2

KF499111_FelineAstV2-1637F

JX556691_PorcineAstV3-US-MO123


DQ344027_HumanAstV4-Guangzhou

HM045005_DogAstV-Bari/2008

GQ415662_HumanAstV-HMO-NE-3010

AF141381_HumanAstV3-Berlin

Bat-AstroV_CMR/Bat-AsV/P02

AB829252_HumanAstV-MLB2-GUP187

HQ916316_BovineAstV/B76/HKHQ916315_BovineAstV-B34/HK


JF414802_ChickenAstV-GA2011

GQ415661_HumanAstV-HMO-NI-196

FJ402983_HumanAstV-MLB1-WD0016

JN052023_RabbitAstV-Nausica/2008/ITA

KC609001_MurineAstV-BSRI1



FJ571068_BatAstV-Ha/Guangxi/LS11/2007

AF260508_HumanAstV8_Yuc8

KF233994_BovineAstV-NeuroS1

EU143843_TurkeyAstV-AK/98

Human-AstroV_CMRHP6

Human-AstroV_CMRHP45

AB033998_ANV1-G-4260


JQ340310_Wild_boarAstV-WBAstV-1/2011/HUN

FJ222451_HumanAstV-MLB1

JX556692_PorcineAstV4-US-IL135

HQ889774_PigeonANV-SH10

JF729316_RabbitAstV-TN/2208/2010

Human-AstroV_CMRHP3

AY179509_MinkAstV

AF206663_TurkeyAstV-AK/98

HM029238_ANV1_CHN


JX439643_DuckAstV1-WF1201

AB823731_HumanAstV-MLB1


JX857869_HumanAstV-VA4/human/Nepal/s5363




HQ916317_BovineAstV/B76-2/HK

JX857870_HumanAstV-MLB3/human/Vellore/26564/2004

Human-AstroV_CMRHP35D


GQ914773_PorcineAstV2-Shanghai/2008

JF742759_HumanAstV-MLB2/human/Stl/WD0559/2008


GQ891990_HumanAstV-SG

FJ890351_BatAstV-Hp/Guangxi/LC03/2007


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MAstV-23^

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MAstV-32^

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MAstV-26^

MAstV-24^

Avastrovirus

MAstV 6

MAstV-13 MAstV-16 MAstV-15 MAstV-17

MAstV-21^

MAstV 8

MAstV 11

?

FIG 5 Phylogenetic trees based on the nucleotide sequences of the RdRp (A) and capsid (B) genes ofthe AstVs identified in this study and representative strains from GenBank. Trees were constructed usingthe GTR�G�I nucleotide substitution model using RAxML, with the autoMRE flag, which enables a


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formed a clade (in the RdRp tree) with other bat astroviruses from Guangxi but wasdistantly related to the human AstVs from the same region.

Caliciviridae. Caliciviridae are a family of nonenveloped viruses with a linear ss-RNA(�) genome of 7.3 to 8.3 kb, containing two or three ORFs. The family contains fivegenera (47, 48). In total, Caliciviridae reads were found in 16 pools belonging to eitherthe Norovirus or Sapovirus genus.

Norovirus. This genus consists of a single species, Norwalk virus (NV), divided into5 genogroups. Genogroups I, II, and IV infect humans, whereas genogroup III infectsbovine species and genogroup V has been isolated from mice (49). Three near-complete NVs were present in the 16 pools that contained Caliciviridae reads (HP1,HP18, and HP59), from people who had indirect (HP1 and HP59) or no (HP18) contactwith bats, and from age group A (HP1), B (HP18), or C (HP59). The phylogenetic tree(Fig. 6A) showed that the four NVs belonged to two genogroups: I (NV_CMRHP18,genotype I.3) and II (NV_CMRHP1 and NV_CMRHP59, genotypes II.12 and II.13, respec-tively). The novel strain NV_CMRHP18 was more than 98% similar to strain C13/2009CMR_GI.3 (a partial sequence [JF802509]) isolated from the Littoral Region of

FIG 5 Legend (Continued)posteriori bootstrapping analysis. Only bootstrap values greater than 70% are shown. Bars indicatenucleotide substitutions per site. Red, HAstVs identified in this study; blue, bat AstV strain from the sameregion in Cameroon; ^, proposed novel astrovirus species.

0.3

AF195848_CaliciVirus/Human/NLV-Amsterdam98-18-GII.8/NLD/1998

AB445395_NV-GII/Human/Apeldoorn317-GII.4/NLD/2007

AJ277608_CaliciVirus/Human/NLV-Leeds90-GII.7/GBR/1990

AY038599.2_CaliciVirus/Human/NLV-VA97207-GII.9/USA/1997

AY502023_NV-GII/Human/Farmington-Hills-GII.4/USA/2002

X81879_CaliciVirus/Human/MelkshamGII.2/GBR/1994

AJ277618_CaliciVirus/Human/NLV-Wortley90-GII.12/GBR/1990

AJ277607_CaliciVirus/Human/NLV-Hillingdon90-GII.5/GBR/1990

GU445325.2_NV-GII/Human/New-Orleans1805-GII.4/USA/2009

AY502010_NV-GII/Human/NoV-Tiffin-GII.16/USA/1999

AJ277609_CaliciVirus/Human/NLV-Winchester-GI.7/GBR/1994

NV/CMRHP18/CMR/2014

AY113106_NV-GII/Human/NLV-Fayetteville-GII.13/USA/1998

EF126965_NV-GII/Human/DenHaag89-GII.4/NLD/2006

JX459908_NV-GII/Human/Sydney-NSW0514-GII.4/AUS/2012

AB074893_CaliciVirus/Swine/Sw918-GII1/JPN/1997

NV/CMRHP59/CMR/2014

EF126963_NV-GII/Human/Yerseke38-GII.4/NLD/2006

AJ277615_CaliciVirus/Human/NLV-Sindlesham-95-GI.6/GBR/1995

M87661.2/NV-GI/Human/US/GI.1/USA/1968

AY823304_NV-GII/Swine/OH-QW101-GII8/USA/2003

U02030_MinireoVirus/Human/Toronto-TV24GII.3/CAN/1991

AF427118_CaliciVirus/Human/NLV-Erfurt546GII.10/DEU/2000

L07418_NV-GI/Human/SOUCAPPRO-GI.2-Southampton/GBR/1991

AF538679_CaliciVirus/Human/NLV-Boxer-USGI.8/USA/2001

AY675554_NV-GII/Human/NLV-IF1998-GII.21/IRQ/2003

KJ194510_NV-GI.3/Human/NV_Amsterdam_2_1995/NMD/1995

AY130761|_CaliciVirus/Human/NLV-M7-GII.14/USA/1999

AJ277614_CaliciVirus/Human/NLV-Musgrove-89-GI.5/GBR/1989

EU373815_NV-GII/Human/Luckenwalde591-GII.20/DEU/2002

AB083780_NV-GII/Human/Yuri-GII.22/JPN/2002

DQ078814.2_NV-GII/Human/Hunter504D-04O-GII.4/AUS/2004

AY502009_NV-GII/Human/CS-E1-GII.17/USA/2002

AY823306_NV-GII/Swine/OH-QW170-GII9/USA/2003

NV/CMRHP1/CMR/2014

KJ196292_NV-GI/Human/GI.P3-GI.3/Shimizu/KK2866/JPN/2007

U07611.2_CaliciVirus/Human/NLV-HawaiiGII.1/USA/1971

AJ277620_CaliciVirus/Human/NLV-Seacroft90-GII.6/GBR/1990

AB042808_ChibaVirus/Human/Chiba407-GI.4/JPN/1987

HQ637267_NV-GI/Human/Vancouver730-GI.9/CAN/2004

AB541319_NV-GII/Human/Osaka1-GII.4/JPN/2007

AY130762_CaliciVirus/Human/NLV-J23-GII.15/USA/1999

AB187514_NV-GI/Human/Otofuke-GI.3/JPN/1979

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8 1

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100

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GI

GII

0.2

2437829_Human/Manchester/GBR/1995/GI.6

115292231_Human/Chiba671/JPN/1999/GIV

HumanSaV/CMR/Kumba-HP56/2014/xxxx

HumanSaV/CMR/Lysoka-HP4/2014/xxxx

Bat/CMR/Limbe65/2014/GXIX

Bat/CMR/Limbe899b/2014/GXIX

115292207_Human/Chiba/JPN/2000/GI.4

JN899072_Bat/TLC34/HK/HKG/xxxx/GXIV

KJ950880_Rodent/Manhattan1/USA/2013

FJ498786_Pig/F19-10/CAN/2007/GVIII

AY237422_Human/Mc114/JPN/2001/GI.1

KJ641703_Bat/JX2010/CHN/2010/GXVII

AY646856_Human/NongKhai-24/THA/2003/GV

KJ508818.1_Pig/OH-JJ674/USA/2000/GVI

AY144337_Mink/Canada151A/CAN/xxxx/GXII

291088271_Pig/TYMPo31/JPN/2008/GV

KF204570_Pig/Gansu-CH430/CHN/2012/GIII

90991029_Pig/K7-JP/JPN/2002/GVII

JN420370_Sea_lion/CSL-SaV1/2010_GV

AF435814_Human/Hou7-1181/USA/1992/GIV

Bat/CMR/Lysoka36/2014/GXVIII

KJ858687_Chimp/IJC09-Tchimpounga/COD/2011/GI

Bat/CMR/Limbe900/2014/GXVIII

GU230161_Pig/F2-4/CAN/2006/GVII

AF182760_Pig/Cowden/USA/xxxx/GIII

291088274_Pig/TYMPo239/JPN/2008/GV

KC309417_Pig/WG197C/USA/2009/GVIII

56692993_Human/C12/JPN/2001/GII.3

363809331_Human/Kumamoto6/JPN/2003/GII.4

GU230162_Pig/F8-9/CAN/2006/GVII

JN387134_Dog/AN210D/USA/2009/GXIII


51950963_Human/Dresden/DEU/xxxx/GI.1

JN867772.1/HCosV/A10-NG11/NGA/2007

KJ950882_Rodent/Manhattan2/USA/2013/GII

DQ359100_Pig/2053P4/BRA/xxxx/GXI


363809325_Human/20072248/JPN/2008/GII.7

AF435813_HumanMex14917/MEX/2000/GI.3

Bat/CMR/Limbe899a/2014/GXIX

AY974192_Pig/OH-JJ681/USA/2000/GVI

JN387135_Dog/AN196/USA/2009/GXIII

KJ858686_Chimp/IJC04-Tchimpounga/COD/2011/GI

FJ498788_Pig/F16-7/CAN/2007/GIX

Bat/CMR/Limbe25/2014/GXIX

AY289804_Human/CruiseShip/USA/2000/GII.5

118442705_Human/Ehime04-1680/JPN/2004/GI.7

EU221477_Pig/43-06-18p3/ITA/2006/GVIII

149850257_Human/Yokote1/JPN/2006/GI.2

JN899074_Bat/TLC39/HKG/xxxx/GXIV

KC309415_Pig/WG180B/USA/2009/GVIII

737520661_Human/Nagoya1/JPN/2012/GV.2

DQ104357_Human/Sydney3/AUS/2004/GIV

KC309418.2_Swine/WG214C/USA/2009


18073224_Human/Bristol/GRB/1998/GII.1

387935512_Bat/TLC58/HKG/xxxx/GXIV

U65427_Human/Sapporo/JPN/1982/GI.1

AY646855_Human/SaKaeo-15/THA/2003/GII.6

FJ387164_Pig/Sav1/CHN/2008/GIII

Bat/CMR/Limbe894/2014/GXVIII

KJ641701_Bat/GX2012/CHN/2012/GXVI

AB242873_Pig/K8-JP/JPN/xxxx/GX

HumanSaV/CMR/Kumba-HP15/2014xxxx

FJ844411_Human/Kecskemet/HUN/2008/GI.2

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A B

FIG 6 Phylogenetic relationships of representative members of the family Caliciviridae identified in this study: A, genus Norovirus; B, genus Sapovirus. Trees wereconstructed based on the nucleotide sequences of the RdRp (for norovirus) and VP1 region (for sapovirus) using the GTR�G�I substitution model using RAxML,with the autoMRE flag, which enables a posteriori bootstrapping analysis. Only bootstrap values greater than 70% are shown. Bars indicate nucleotidesubstitutions per site. Red, Cameroonian human SV strains; blue, Cameroonian bat SaVs.




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Cameroon in 2009, whereas strains of genogroup II from the same study (II.4, II.8, II.17)were distantly related to those identified here (II.12 and II.13) (7). Strains from thisprevious study were not included in the phylogenetic analysis because only 200 to300 nt of the capsid region was available in databases.

Sapovirus. The genus Sapovirus (SaV) consists of a single species, Sapporo virus. Ithas been detected in humans, pigs, minks, dogs, sea lions, bats, chimpanzees, rodents,and carnivores (50, 51). Three near-complete SaV genomes were present in pools HP4(age group B), HP15 (age group A), and HP22 (age group D) from people who were inindirect contact, were not in contact, and were in direct contact with bats, respectively.Phylogenetic analysis (Fig. 6B) showed that SaV from HP22 could be classified as a GIVgenotype, and the SaVs HP4, HP53, HP46, HP56, and HP15 belonged to genotype GII.The phylogenetic tree showed that the bat SaVs found in Cameroon (in blue) (22)clustered together and formed a clade with other bat SaVs from China and Hong Kongbut divergent from these human SaVs, indicating no evidence of interspecies trans-mission of SaVs in this region.

Picobirnaviridae. Picobirnaviruses (PBVs) belong to the family Picobirnaviridae,genus Picobirnavirus, and are small bisegmented dsRNA viruses with a total genomesize of about 4 kb. Segment one encodes a polyprotein, containing the capsid protein,and segment two encodes the RdRp. Based on the RdRp gene, PBVs are classified intotwo genogroups. Although PBV is genetically highly diverse and has been found instool samples of a broad range of mammals, its true host(s) remain(s) enigmatic. Thedisease association is unclear, but PBV infection has been associated with gastroen-teritis in both animals and humans (52, 53). Up to 28 out of the 63 pools containedreads annotated as Picobirnaviridae with most of the positive pools from individuals inage groups above 20. We could obtain 37 (near-complete) RdRp sequences of PBVsfrom these 28 pools. Phylogenetic analysis based on RdRp (Fig. 7) revealed theclustering of the novel strains in four different clades: in genogroup I (26 strains), ingenogroup II (9 strains), and in 2 clades (3 strains) of uncharacterized picobirna-likeviruses that use an alternative mitochondrial invertebrate genetic code (Lysokapicobirna-like virus CMRHP9 and CMRHP10B and Kumba picobirna-like virusCMRHP21A). Interestingly, a wolf PBV strain from Portugal (ANS53886) from genogroupI clustered together with human strains from Cameroon with an aa identity of 76% withstrains CMRHP26A and CMRHP35. Likewise, in genogroup II, strains CMRHP34A,CMRHP63B, and CMRHP26C clustered closely (75 to 76% aa identity) with a Portuguesefeline strain (AGZ93689). Intriguingly, the Cameroonian human picobirna-like virusesCMRHP9 and CMRHP10B were 99% identical to a Cameroonian bat strain picobirna-likevirus, P11-300, suggesting a possible interspecies transmission. However, their true hosthas not yet been determined. It could be that the true hosts of PBVs are found in bothhumans and bats and that this therefore explains their presence in both.

Small circular, Rep-encoding, ssDNA (CRESS-DNA) genomes. (i) Smacovirus.Smacovirus (SCV) is a relatively recently described virus with a small circular DNAgenome with a size of about 2,529 bp. It belongs to the smacovirus group and is anunclassified eukaryotic virus of unknown origin (54). In this study, we identified two SCVsequences, one complete genome (HuSCV-CMRHP10) and a near-complete genome(HuSCV-CMRHP03). They were identified in pools of patients belonging to age group B,coming from Lysoka and having direct (HP3) or indirect (HP10) contact with bats. Thesestrains shared 99% amino acid identity. Their replicase genes were 94% and 95%identical to chimpanzee (KP233190) and human (HuSCV3, KT600069) strains from theUnited States, respectively. Based on the capsid region, these novel Cameroonianstrains were 98 to 99% identical to the chimp strain and only 85% identical to thehuman strain HuSCV3. The close genetic relatedness of human strains to a strain foundin a chimpanzee sample suggest that these viruses infect a host shared betweenchimps and humans, and if indeed smacovirus infects mammals, this could be a caseof interspecies transmission (55). Phylogenies of the replicase (Fig. 8A) and the capsidgenes (Fig. 8B) indeed showed a cluster of these Cameroonian strains with a human

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https://www.ncbi.nlm.nih.gov/nuccore/KP233190

https://www.ncbi.nlm.nih.gov/nuccore/KT600069



0.6

AIY31285_Dromedary_picobirnavirus

SHWC0209c12590_Shahe_picobirna-like_virus_1

PBV/Human/CMRHP32A/CMR/2014

AAG53584_human_picobirnavirus

BHJJX24179_Beihai_picobirna-like_virus_4

PBV/Human/CMRHP22B/CMR/2014

Limbe_picobirna-like_virus_P1490_GC25



BHTH13093_Beihai_picobirna-like_virus_3

AOW41971_Picobirnavirus/human/1385/2015

BAU79482_Diatom_colony_associated_dsRNA_virus_1


Lysoka_picobirna-like_virus_P16366_GC66

AIB06801_Fox_fecal_picobirnavirus


AAG53583_human_picobirnavirus

BHZY58752_Beihai_picobirna-like_virus_13

BAJ53293_Human_picobirnavirus


GCM11219_Hubei_earwig_virus_2

PBV/Human/CMRHP35/CMR/2014


YP_239361_Human_picobirnavirus

PBV/Human/CMRHP60C/CMR/2014


Kumba_picobirna-like virus_CMRHP21A




ACT64131_Picobirnavirus_bovineRUBVPIND2005


WLJQ144192_Wenling_picobirna-like_virus_1

AOW41972_Picobirnavirus/human/959/2015

BHNXC71065_Beihai_picobirna-like_virus_8_RdRp



AGZ93689_Feline_picobirnavirus

BHZC36972_Beihai_picobirna-like_virus_10



BWBFG40030_Beihai_picobirna-like_virus_11

JMYJCC46554_Jingmen_picobirna-like_virus_1


PBV/Human/CMRHP26D/CMR/2014



AHX00960_Human_picobirnavirus

ANS53886_Picobirnavirus_wolf/PRT/1109/2015

BHNXC57916_Beihai_picobirna-like_virus_7_RdRp

WHBL66087_Hubei_picobirna-like_virus_4

PBV/Human/CMRHP6//CMR/2014

BAN58175_Picobirnavirus_cowtottori7944Jap2013






AHI59999_Porcine_picobirnavirus




AFJ79071_Otarine_picobirnavirus

WGML128211_Hubei_picobirna-like_virus_3



AHZ46150_Picobirnavirus_TKMN2011

AGK45545_Fox_picobirnavirus

Limbe_picobirna-like_virus_P11300_GC902Lysoka_picobirna-like_virus_CMRHP10B

WHSFII41391_Hubei_picobirna-like_virus_1


PBV/Human/CMRHP26B/CMR/2014AOW41973_Picobirnavirus/human/1352/2015




PBV/Human/CMRHP26E/CMR/2014


SHWC01c3537_Shahe_picobirna-like_virus_2


WHSFII2200_Wuhan_pillworm_virus_4

WHBL68697_Hubei_picobirna-like_virus_2




AHX00958_Human_picobirnavirus





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FIG 7 Phylogenetic relationships between PBVs isolated in this study and representative members of the family Picobirnaviridae, based on the amino acidsequence of the RdRp domain. The tree was constructed using the LG�G�I substitution model using RAxML, with the autoMRE flag, which enables a posterioribootstrapping analysis. Only bootstrap values greater than 70% are shown. Bars indicate amino acid substitutions per site. Red, Cameroonian human PBVs; blue,Cameroonian bat PBVs; green, PBVs isolated from a wolf and a feline in Portugal.




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KP233183_HuSCV_USA_D56

KP233176_HuSCV_France_2449

KP264967_HuSCV_France_3454b

KC545229_PoSCV3


KP233184_HuSCV_USA_H19

KM030278_RatSCV

KP233189_Black Howler monkey SCV


GQ351274_ChiSCVGM476

KP233193_HuSCV_USA_D53


KJ577816_PoSCV9



KJ577815_PoSCV7


KC545227_PoSCV3

KP233185_HuSCV_USA_5I17


KJ577810__PoSCV1

KJ577819__PoSCV6

KM030277_RatSCV

KJ577818_PoSCV2

JX274036__PoSCV1


KP233192_GorillaSCVSF4KP233191_GorillaSCVSF3

KC545226_PoSCV2


KP233188_HuSCV_USA_G16

KC545230_PoSCV3

KJ577817_PoSCV8

KC545228_PoSCV3

KP233180_HuSCV_USA_5A1

KJ577811__PoSCV1

JQ023166_PigSCV

KT600069_HuSCV3_USA

HuSCV-CMRHP10_REP

KJ577814_PoSCV7

KJ577812_PoSCV7

KP233190_ChimpanzeeSCV


GQ351272_ChiSCVDP152GQ351278_ChiSCVGT306

KP233187_HuSCV_USA_I22

HuSCV-CMRHP03_Rep

KJ577813_PoSCV7


KF880727_TuSCV



KP233181_HuSCV_USA_B3

KP233182_HuSCV_USA_B45

GQ351275_ChiSCVGM510KP233194_lemursSCV

JN634851_BoSCV

KP233186_HuSCV_USA_VJ23

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KT600069_HuSCV3_USAHuSCV-CMRHP03_cap

KP233190_ChimpanzeeSCV

JX274036_PoSCV1KJ577811_PoSCV1

HuSCV-CMRHP10_cap

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GQ404855_CyclovirusNG14

KT600066_Hu_PeCV_NI

AJD07568_Sewage-associated_circular_DNA_molecule

DQ100076_Duck_circovirus

GQ404846_Cyclovirus_PK5222

KT600067_Hu_PeCV_CH

KJ206566_Hu_PeCV

NC001439_Bean golden yellow mosaic virus

JF938082_Bat_circovirus

HQ738634_Bovine_CyclovirusPK23

GQ404857_CyclovirusTN25

DQ845075_Finch_circovirus

AF071878_Beak feather disease virus

KF246569_Seal_PeCV_as50

DQ845074_Gullcircovirus

HM228874_Bat_cyclovirus

GQ404850_CyclovirusChimp12

NC_00141_Beet curlytop virus

HP38-Sewage-associated-like virus

AF252610_Columbid_circovirus

EU056309_Swan_circovirus


NC_011052_Sweet potato leaf curl Spain virus

NC_002543_Horse radish curlytop virus


GQ404858_CyclovirusTN18

AJ301633_Canary_circovirus

Hu_PeCV_CMRHP60

GQ404849_CyclovirusChimp11

DQ146997_Raven_circovirus

HQ738644_Chicken_Cyclovirus_NG

HQ638064_Dragonfly_cyclovirus

AY394721_Muscovy duck _circovirus

KJ417134_Porcine_PeCV_PoSCV

KM573766_Dromedary_PeCV_c1054

HQ738637_Cyclovirusbat

HQ738636_Goat_Cyclovirus_PKgoat11




GQ404845_CyclovirusPK5034

HQ738642_chicken_Circovirus-NG_38

GQ404851_Chimpanzee_stool avian-like circovirus

DQ172906_Starling_circovirus

KT600065_Hu_PeCV_PE

AY228555_Mulard duck_circovirus

GQ404854_CyclovirusNG12

HP38-Sewage-associated-like virus

100

8 5

9 6

8 0

8 3

9 9

100

8 7

9 9

9 0

7 7

9 6

7 6

8 8

7 7

100

8 3

9 8

9 8

8 4

100

100

9 3

0.5

KT600066_Hu_PeCV_NI

KJ206566_Hu_PeCV

KF246569_Seal_PeCV_as50

KT600065_Hu_PeCV_PE

KJ417134_Porcine_PeCV_PoSCV

KM573766_Dromedary_PeCV_c1054

KT600067_Hu_PeCV_CH9 9

9 49 1

100

Hu_PeCV-CMRHP60

C

D

FIG 8 Phylogenetic tree of amino acid sequences of human and animal smacoviruses (A and B) and pecovirus (C and D) of the replicaseand capsid genes, respectively. The trees were constructed using the LG�G�I substitution model using RAxML, with the autoMRE flag, whichenables a posteriori bootstrapping analysis. Only bootstrap values greater than 70% are shown. Bars indicate amino acid substitutions persite. Red, Cameroonian human strains; blue, previously known human smacoviruses or pecovirus.

Yinda et al.



sphere.asm.org/

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and a chimpanzee strain from the United States. However, the topological inconsis-tency in the replicase and capsid trees may suggest a recombination event betweenthese strains in the (distant) past.

(ii) Pecovirus. Pecoviruses (Peruvian stool-associated circo-like viruses [PeCVs]) areCRESS-DNA genomes that were first identified in the feces of a patient during anoutbreak of acute gastroenteritis in the Netherlands and later in samples of Peruvianchildren (55, 56). Subsequently, they were identified in other humans, pigs, a drome-dary camel, and a seal (55–58). Here we identified a genome sequence (HuPeCV-CMRHP60) of 2,937 bases made up of two ORFs that code for a capsid (372 aa) and areplicase protein (336 aa). Unlike other human PeCVs, the Cameroonian strain sharedthe same canonical nonamer (NANTATTAC) atop the predicted stem-loop structurewith seal, dromedary, and porcine PeCV strains. The Rep showed 31 to 42% aasequence identity to all other Rep genes, and a Rep-based phylogenetic analysis(Fig. 8C) showed that HuPeCV-CMRHP60 clustered together with pecovirus genomesfrom a seal and 3 human strains. Based on the cap protein (Fig. 8D), the Cameroonianstrain was only 22 to 42% identical to all other pecoviruses and clustered only distantlyfrom the seal strain, a porcine strain, and the human strains. This demonstrates theexistence of a high level of genetic diversity within this group of circular DNA genomes,pointing to the possible existence of multiple species in this clade. Furthermore, weidentified 2 incomplete sequences related to sewage-associated circular DNA mole-cules recovered from a sewage treatment oxidation pond in New Zealand (59), withonly 38% aa identity on the Rep protein, further expanding the great diversity ofCRESS-DNA genomes in the Cameroonian population.

Bacteriophages. Bacteriophages are viruses that infect and replicate within bacte-ria. Their presence therefore reflects the gut microbiota of the patients. Because mostof the obtained viral reads were classified as bacteriophages, we further investigatedthe bacteriophage composition of the human samples. With VirSorter (60), a tooldeveloped to identify highly divergent dsDNA phages from metagenomics data, 5,905of the contigs in our data set were identified as phages. From these, the tool Diamond(61) annotated 2,647 as bacterial, 21 as metazoan, and only 606 (�10%) as viral, while1,309 contigs remained unannotated. From the contigs annotated as viral by Diamond,most were phages belonging to the Myoviridae (236 contigs), Podoviridae (95 contigs),Siphoviridae (145 contigs), and Microviridae (36 contigs) families. To get insight into thedifferences in the bacteriophage communities, we compared the VirSorter-identifiedbacteriophage richness between the different age groups (Fig. S6A), locations(Fig. S6B,) and bat contact status (Fig. S6C), all of which showed no significantdifferences. To identify the potential bacterial hosts of these phages, we searched forbacterial CRISPR spacer sequences in the phage contigs, to identify its potential host.The search revealed that the most likely hosts of these phages are bacteria of thefamilies Bacteroidaceae, Bifidobacteriaceae, Enterobacteriaceae, Enterococcaceae, Erysip-elotrichaceae, Eubacteriaceae, Lactobacillaceae, Odoribacteraceae, Streptococcaceae, andVeillonellaceae (Table S2).

Network analysis of human and bat phageomes. In order to visualize the geneticrelatedness between the human and bat gut phageome, a recently developed bioin-formatics tool (vConTACT) was used. It groups phages based on their genome se-quences into viral clusters which correlate rather well with viral genera as defined bythe International Committee of Taxonomy of Viruses (ICTV) (62). A total of 30,875protein clusters were predicted using the prokaryotic and archaeal RefSeq combinedwith the proteins predicted from the phage contigs identified from the human and batspools using VirSorter. Using a network analysis approach (Fig. 9), 792 viral genomeclusters were predicted of which 173 contained reference phages together with bat orhuman phage contigs, whereas the rest contained only bat, only human, or bat-humanclusters. Figure 9 shows that both Cameroonian human and bat phage contigs iden-tified in our studies are spread across the known phage sequence space. However,several of the phage contigs constituted completely new clusters (indicated by filled




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nloaded from



gray ovals), completely unconnected to phages in the reference database. Also, thegenetic diversity of several previously known phage subclusters was significantlyexpanded (as indicated by open ovals) while some clusters (in brown ovals) were madeup of only bat and human phages identified in this study.

DISCUSSION

Recently, we thoroughly investigated the gut virome of fruit bats from Cameroon(20–23, 63) and showed the presence of many novel and divergent eukaryotic viralfamilies, including viruses known to cause gastroenteritis in humans. The aim of thecurrent study was to investigate the gut virome of humans (n � 221) from Cameroonand to further determine if bat viruses are possible causative agents of gastrointestinalinfections in humans.

Twenty-four percent of the 471 million generated trimmed reads were assigned asviral. Most of these reads were bacteriophages, which is in accordance with previousstudies (64). The eukaryotic viral reads include those that belong to viral families thatare commonly associated with gastroenteritis in humans (Adenoviridae, Astroviridae,Caliciviridae, Picornaviridae, and Reoviridae), viruses that are uncommon causes ofgastroenteritis (orthoreovirus), or those that have been identified in humans but notassociated with disease (anellovirus, smacovirus, and picrobirna-like viruses).

Common human gastroenteric viruses: Picornaviridae and rotavirus A. Amongthe viruses known to cause gastroenteric disease, reads belonging to the Picornaviridae

VIRSorter_NODE_31_length_6743_cov_42_0759-cat_1

VIRSorter_NODE_92_length_6299_cov_95_5373-circular-cat_1




VIRSorter_NODE_144_length_6228_cov_26_9059-circular-cat_1 VIRSorter_NODE_241_length_5783_cov_8_16947-cat_1



Escherichia~phage~IME11

Sulfitobacter~phage~EE36phi1

Escherichia~phage~N4

Escherichia~phage~Bp4

Achromobacter~phage~phiAxp-3

Silicibacter~phage~DSS3phi2

Salmonella~phage~FSL~SP-058

Escherichia~phage~Pollock

Escherichia~phage~vB_EcoP_PhAPEC5

Vibrio~phage~VBP32

Pseudomonas~phage~KPP21




Microviridae~IME-16












Pseudomonas~phage~LUZ7

Sulfitobacter~phage~phiCB2047-B

Pseudoalteromonas~phage~pYD6-A

Escherichia~phage~vB_EcoP_PhAPEC7

Escherichia~phage~vB_EcoP_G7C

Escherichia~phage~ECBP1


Achromobacter~phage~JWAlpha

VIRSorter_NODE_170_length_2973_cov_6_72099_GC025894_GC025894-cat_1

Erwinia~phage~vB_EamP_Frozen

Enterobacter~phage~EcP1



Shigella~phage~pSb-1




Alteromonas~phage~vB_AmaP_AD45-P1

Vibrio~phage~JA-1

Pseudomonas~phage~YH30

Erwinia~phage~vB_EamP-S6


Delftia~phage~RG-2014

Pseudomonas~phage~PEV2

Pseudomonas~phage~DL64

Dinoroseobacter~phage~DFL12phi1

Erwinia~phage~Ea9-2

Pseudomonas~phage~LIT1Pseudomonas~phage~YH6

Vibrio~phage~phi~1

Pseudomonas~phage~vB_PaeP_C2-10_Ab09


Vibrio~phage~VBP47

Pseudomonas~phage~vB_PaeP_MAG4

Acinetobacter~phage~Presley

Pseudomonas~phage~Pa2





VIRSorter_NODE_55_length_5904_cov_148_609_ID_1559528-circular-cat_1









Microviridae~phi-CA82









Spiroplasma~phage~4



VIRSorter_NODE_69_length_5849_cov_2781_54-cat_1VIRSorter_NODE_55_length_5767_cov_4704_89-circular-cat_1




VIRSorter_NODE_65_length_5458_cov_54_0402-circular-cat_1VIRSorter_NODE_172_length_4315_cov_10_7522-cat_1



Chimpanzee~faeces~associated~microphage~2





















Clostridium~phage~phi24R




Clostridium~phage~phiCPV4







Lactococcus~phage~asccphi28


Bacillus~phage~MG-B1


Bacillus~virus~phi29

Streptococcus~phage~Cp-1


Bacillus~phage~Claudi


Clostridium~phage~phiCP7R

Clostridium~phage~phiZP2





Actinomyces~virus~Av1



Bacillus~virus~B103

Bacillus~phage~Aurora




Bacillus~phage~VMY22

Bacillus~virus~GA1


Bacillus~phage~Stitch






VIRSorter_NODE_31_length_9121_cov_54_8852_ID_1233948-cat_2





VIRSorter_NODE_49_length_9044_cov_26_3401-cat_2VIRSorter_NODE_36_length_9371_cov_23_0629-cat_2VIRSorter_NODE_31_length_16099_cov_54_8351-cat_2



Chlamydia~phage~1





Chlamydia~phage~4




Chlamydia~phage~2


Chlamydia~pneumoniae~phage~CPAR39



Guinea~pig~Chlamydia~phage








Marine~gokushovirus VIRSorter_NODE_41_length_5831_cov_317_749-circular-cat_1


Gokushovirinae~Bog8989_22

Gokushovirinae~Fen7875_21

Bdellovibrio~phage~phiMH2K

VIRSorter_NODE_14_length_5068_cov_1367_82_GC025899_GC025899-cat_1Gokushovirinae~Bog5712_52

Gokushovirinae~Fen672_31


Gokushovirinae~Bog1183_53










Lactococcus~phage~WRP3

Staphylococcus~phage~SPbeta-like

Lactococcus~phage~949

Lactococcus~phage~phiL47

Geobacillus~virus~E3












VIRSorter_NODE_242_length_2147_cov_7_64155-cat_2VIRSorter_NODE_810_length_1156_cov_3_50232-cat_2


Bacillus~phage~0305phi8-36



Bacteroides~phage~B124-14


Bacteroides~phage~B40-8














Croceibacter~phage~P2559S




Cyanophage~S-TIM5






Bacillus~phage~SPBc2



Prochlorococcus~phage~P-TIM68

Prochlorococcus~phage~P-SSM2







Staphylococcus~phage~6ec















Bacillus~phage~BM5









Lactococcus~phage~bIL310






Cellulophaga~phage~phiSM








Brevibacillus~phage~Sundance

Campylobacter~virus~CP21

Klebsiella~phage~0507-KN2-1

Campylobacter~phage~PC14

Deftia~phage~phiW-14

Erwinia~phage~phiEa2809







Pseudomonas~phage~PaBG



Bacillus~phage~SP-15

Bacillus~virus~G


Vibrio~phage~phi~3


Bacillus~phage~vB_BanS-Tsamsa










VIRSorter_NODE_190_length_2903_cov_9_43277-cat_2 VIRSorter_NODE_194_length_2819_cov_11_4019-cat_2





VIRSorter_NODE_26_length_9385_cov_11_1715-cat_2Campylobacter~virus~CPt10

Sinorhizobium~phage~phiN3

Campylobacter~virus~NCTC12673

Sphingomonas~phage~PAUVIRSorter_NODE_115_length_4126_cov_11_3472-cat_1

Salmonella~phage~PhiSH19

Salmonella~phage~GG32

VIRSorter_NODE_72_length_5570_cov_7_19862-cat_2VIRSorter_NODE_39_length_7044_cov_13_7955-cat_2Escherichia~phage~HX01











Corynebacterium~phage~P1201

Dickeya~virus~Limestone

Citrobacter~phage~IME-CF2

Escherichia~phage~Av-05






















VIRSorter_NODE_448_length_1854_cov_4_30219-cat_2Lactococcus~phage~bIL312

Synechococcus~phage~S-SSM5

Synechococcus~phage~S-SM2

Cyanophage~P-TIM40


Cyanophage~P-RSM1

Prochlorococcus~phage~Syn33


Synechococcus~phage~S-CAM8


Synechococcus~phage~S-IOM18

Dickeya~phage~RC-2014

Synechococcus~phage~ACG-2014b

Vibrio~phage~ValKK3

Synechococcus~phage~Syn19Prochlorococcus~phage~MED4-213

Synechococcus~phage~S-RIM8~A.HR1

Synechococcus~phage~ACG-2014d

Prochlorococcus~phage~P-RSM4

Synechococcus~phage~metaG-MbCM1

Synechococcus~phage~ACG-2014j

Prochlorococcus~phage~P-SSM7Synechococcus~phage~S-ShM2

Cyanophage~S-RIM50

Synechococcus~phage~S-SM1


Salmonella~phage~Det7

Sinorhizobium~phage~phiM12

Prochlorococcus~phage~P-HM2

Salmonella~phage~ViI

Campylobacter~virus~CP220

Pelagibacter~phage~HTVC008M

Campylobacter~phage~CP30A

Synechococcus~phage~ACG-2014h

Serratia~phage~phiMAM1

Synechococcus~phage~S-MbCM100Synechococcus~phage~S-CAM7

Synechococcus~phage~S-WAM1

Escherichia~phage~Cba120Synechococcus~phage~S-CAM22Synechococcus~phage~ACG-2014f

Prochlorococcus~phage~Syn1


Synechococcus~phage~ACG-2014e


Synechococcus~phage~ACG-2014g

Synechococcus~phage~S-RSM4

Synechococcus~phage~ACG-2014i

Synechococcus~phage~S-SKS1

Synechococcus~phage~S-WAM2














Rhodothermus~phage~RM378













































Klebsiella~phage~KP15Aeromonas~virus~31

Vibrio~phage~KVP40

Acinetobacter~virus~133

Acinetobacter~phage~Acj61

Salmonella~phage~vB_SalM_SJ3Vibrio~phage~VH7D

Citrobacter~phage~vB_CfrM_CfP1

Aeromonas~virus~25

Synechococcus~phage~syn9

Enterobacteria~phage~vB_KleM-RaK2

Vibrio~phage~henriette~12B8

Escherichia~phage~121Q

Cronobacter~phage~S13

Aeromonas~phage~phiAS5

Cronobacter~phage~vB_CsaM_GAP161

Aeromonas~virus~65

Klebsiella~phage~KP27Enterobacteria~phage~RB16Citrobacter~phage~MillerRhizobium~phage~vB_RleM_P10VF

Aeromonas~phage~CC2

Aeromonas~virus~Aeh1

Salmonella~phage~38Prochlorococcus~phage~P-HM1

Salmonella~phage~SKML-39Salmonella~phage~vB_SalM_SJ2Klebsiella~phage~K64-1

Cyanophage~P-RSM6

Escherichia~phage~PBECO~4

Escherichia~phage~PhaxI


Stenotrophomonas~phage~IME13Synechococcus~phage~S-CRM01


Vibrio~phage~nt-1

Shigella~phage~Ag3

Caulobacter~phage~Cr30

Cyanophage~S-RIM32

Escherichia~phage~ECML-4

Salmonella~phage~MarshallSynechococcus~phage~S-RIM2~R1_1999

Synechococcus~phage~ACG-2014c

Campylobacter~virus~CPX

Salmonella~phage~MaynardSynechococcus~phage~S-PM2

Cyanophage~Syn30

Salmonella~phage~vB_SalM_PM10

Sinorhizobium~phage~phiM9



Ralstonia~phage~RSP15


Salmonella~phage~vB_SenMS16

Yersinia~phage~vB_YenM_TG1

Enterobacteria~phage~Phi1

Enterobacteria~phage~GEC-3SEnterobacteria~phage~RB49

Escherichia~phage~vB_EcoM_VR20Escherichia~phage~vB_EcoM_VR26

Edwardsiella~phage~PEi20Enterobacteria~phage~Bp7

Shigella~phage~SP18

Escherichia~phage~vB_EcoM_VR25Escherichia~phage~vB_EcoM_VR7Escherichia~phage~WG01

Enterobacteria~phage~vB_EcoM_VR5

Acinetobacter~phage~Acj9

Acinetobacter~phage~ZZ1Aeromonas~phage~Aes508

Salmonella~phage~SFP10

Acinetobacter~phage~Ac42

Aeromonas~phage~PX29


Salmonella~phage~STML-198

Aeromonas~phage~Aes012

Enterobacteria~phage~RB43

Citrobacter~phage~Moon

Salmonella~phage~STP4-a

Enterobacter~phage~CC31

Klebsiella~phage~PKO111

Salmonella~phage~vB_SnwM_CGG4-1

Shigella~phage~pSs-1

Enterobacteria~phage~JSE

Klebsiella~phage~vB_KpnM_KpV477

Pectobacterium~bacteriophage~PM2
































Escherichia~phage~HY01Shigella~phage~SHFML-11

Escherichia~phage~vB_EcoM_ACG-C40

Escherichia~phage~vB_EcoM-UFV13Escherichia~phage~AR1Escherichia~phage~ECML-134

Escherichia~phage~slur07Shigella~phage~SHBML-50-1Enterobacteria~phage~T4

Escherichia~phage~wV7

Enterobacteria~phage~RB14Klebsiella~phage~JD18

Yersinia~phage~PSTYersinia~phage~phiD1


Yersinia~phage~phiR1-RTSerratia~phage~PS2

Morganella~phage~vB_MmoM_MP1

Aeromonas~virus~44RR2

Escherichia~phage~Lw1

Proteus~phage~vB_PmiM_Pm5461

Enterobacteria~phage~JS98

Escherichia~phage~APCEc01

Enterobacteria~phage~IME08

Shigella~phage~Shfl2

Enterobacter~phage~PG7


Escherichia~phage~UFV-AREG1

Escherichia~phage~slur14

Escherichia~phage~vB_EcoM_112

Escherichia~phage~HY03Shigella~phage~SHSML-52-1

Escherichia~phage~ime09

Escherichia~phage~vB_EcoM_JS09

Escherichia~phage~MX01Enterobacteria~phage~QL01Enterobacteria~phage~JS10

Escherichia~phage~vB_EcoM_PhAPEC2

Shigella~phage~Shf125875



Shigella~phage~SHFML-26

Salmonella~phage~SJ46





Flavobacterium~phage~Fpv10




Caulobacter~phage~CcrColossus





Caulobacter~virus~Swift















Caulobacter~virus~Magneto


Escherichia~virus~P1









VIRSorter_NODE_12_length_4696_cov_7_28513_GC022962_GC022962-cat_2VIRSorter_NODE_33_length_2064_cov_8_17011_GC022962_GC022962-cat_2



Caulobacter~virus~Rogue


Caulobacter~virus~phiCbK



Enterobacteria~phage~phi92


Escherichia~phage~vB_EcoM-VpaE1


Vibrio~phage~qdvp001


Vibrio~phage~ICP1

Shewanella~sp.~phage~1/4

Escherichia~phage~SUSP1






Salmonella~phage~SSE121

Salmonella~phage~PVP-SE1

Pseudoalteromonas~phage~H101

Enterobacteriaphage~UAB_Phi87

Escherichia~phage~JH2

Escherichia~phage~vB_EcoM_Alf5

Escherichia~phage~HY02

Escherichia~phage~4MG


Salmonella~phage~BPS15Q2

Acinetobacter~phage~vB_AbaM_phiAbaA1

Escherichia~phage~SUSP2


Salmonella~phage~FelixO1VIRSorter_NODE_18_length_18290_cov_34_638-cat_2

Nitrincola~phage~1M3-16


Pseudomonas~phage~vB_PaeM_C2-10_Ab1

Pseudomonas~phage~PAK_P1

Pseudomonas~phage~phiPsa374

Pseudomonas~phage~PaP1

Pseudomonas~phage~K5


Pseudomonas~phage~JG004


Pseudomonas~phage~vB_PsyM_KIL1



Pseudomonas~phage~phiPto-bp6g






Pseudomonas~phage~vB_PaeM_MAG1








VIRSorter_NODE_1_length_140222_cov_490_737_GC021846_GC021846-circular-cat_2

Escherichia~phage~wV8

Escherichia~phage~EC6

Escherichia~phage~phAPEC8










Acinetobacter~phage~YMC13/03/R2096






Shewanella~phage~Spp001










Mycobacterium~phage~PLot

Gordonia~phage~GRU1




Escherichia~phage~FV3

Cronobacter~phage~CR9



Salmonella~phage~21

Cronobacter~phage~PBES~02


Escherichia~phage~V5


Mycobacterium~phage~HawkeyeMycobacterium~phage~Oaker

Flavobacterium~phage~Fpv11Mycobacterium~phage~Gumball






Pectobacterium~phage~phiTE

Vibrio~phage~11895-B1

Vibrio~phage~PWH3a-P1

Salmonella~phage~19


Mycobacterium~phage~Predator

VIRSorter_NODE_145_length_3260_cov_7_32202-cat_2Mycobacterium~phage~PBI1

Gordonia~phage~Terapin











Mycobacterium~phage~Damien

VIRSorter_NODE_234_length_2510_cov_10_2104-cat_2Mycobacterium~phage~Konstantine

Gordonia~phage~GTE8

Gordonia~phage~GTE5



VIRSorter_NODE_222_length_1531_cov_4_3652_ID_443_GC022959_GC022959-cat_2

Flavobacterium~phage~FCL-2


Mycobacterium~phage~PatienceVIRSorter_NODE_665_length_1903_cov_9_25849-cat_1



Mycobacterium~phage~Papyrus

Mycobacterium~phage~Barnyard


Mycobacterium~phage~Troll4





Clostridium~phage~vB_CpeS-CP51


Acinetobacter~phage~vB_AbaM_Acibel004



Vibrio~phage~eugene~12A10










Pseudomonas~phage~K8

Pseudomonas~phage~vB_PaeM_PS24

Pseudomonas~phage~PaoP5

Pseudomonas~phage~VCMPseudomonas~phage~PAK_P4

Pseudomonas~phage~phiMK

Pseudomonas~phage~C11

Pseudomonas~phage~CHA_P1






Cronobacter~phage~vB_CsaP_GAP52







Salmonella~phage~7-11


Pseudomonas~phage~vB_PaeM_PAO1_Ab03


VIRSorter_NODE_10_length_30533_cov_27_9641-cat_2Pseudomonas~phage~PAK_P5









Staphylococcus~phage~SA1

Clostridium~phage~c-st


















































Clostridium~phage~phiCD211


Pelagibacter~phage~HTVC010P











































VIRSorter_NODE_112_length_6833_cov_14_6159-cat_2 VIRSorter_NODE_221_length_4703_cov_8_57631-cat_2VIRSorter_NODE_512_length_1567_cov_32_2356-cat_2




















































VIRSorter_NODE_41_length_6364_cov_4_82249-cat_1VIRSorter_NODE_100_length_3091_cov_6_31287_GC021842_GC021842-cat_2






Caulobacter~virus~Karma

Escherichia~phage~FFH2


Salmonella~phage~HB-2014

Escherichia~phage~JES2013

Escherichia~phage~vB_EcoM_AYO145A

Vibrio~phage~helene~12B3VIRSorter_NODE_362_length_2560_cov_5_33548-cat_2

Klebsiella~phage~vB_KpnM_KB57





Erwinia~phage~phiEa21-4













































Vibrio~phage~QH






Vibrio~phage~J2

Vibrio~phage~VP2




Clostridium~phage~phiCP34O













































































Pectobacterium~phage~My1


Staphylococcus~phage~phiSA12


Bacillus~phage~SageFayge

Listeria~phage~LMSP-25

Bacillus~phage~Shanette















Staphylococcus~phage~S25-4

Staphylococcus~phage~Sb-1

Brevibacillus~phage~Jenst


Staphylococcus~phage~Stau2

Bacillus~phage~Megatron

Bacillus~phage~KidaBacillus~phage~Riley

Staphylococcus~phage~GH15

Lactobacillus~phage~LfeInf

Staphylococcus~virus~KStaphylococcus~phage~Team1


Staphylococcus~phage~P108Listeria~phage~LMTA-148

Staphylococcus~phage~phiIPLA-RODI

Bacillus~phage~CP-51

Bacillus~virus~SPO1

Listeria~phage~WIL-1




Enterococcus~phage~EFDG1

Bacillus~phage~BigBertha


Salmonella~phage~Shivani


Staphylococcus~phage~JD007

Escherichia~virus~T5

Escherichia~phage~vB_EcoS_FFH1Escherichia~virus~DT57C


VIRSorter_NODE_89_length_4129_cov_7_75074-cat_2Erwinia~phage~phiEaH2Ralstonia~phage~RSF1

Erwinia~phage~vB_EamM_HuxleyErwinia~phage~vB_EamM_Asesino

Erwinia~phage~vB_EamM_EarlPhillipIV


Ralstonia~phage~RSL2








Halocynthia~phage~JM-2012

Erwinia~phage~vB_EamM_Caitlin

Erwinia~phage~vB_EamM_ChrisDB

Erwinia~phage~Ea35-70

Erwinia~phage~vB_EamM_Kwan


Pseudomonas~phage~OBPVIRSorter_NODE_271_length_2100_cov_4_39298-cat_2





Bacillus~phage~Zuko


Bacillus~phage~Hakuna

Bacillus~phage~Bp8p-C

Enterococcus~phage~phiEF24C

Bacillus~phage~Phrodo

Bacillus~phage~Troll

Bacillus~phage~BPS10C

Bacillus~phage~SPG24


Bacillus~phage~Bcp1

Bacillus~phage~phiNIT1


Bacillus~phage~SalinJah

Bacillus~phage~vB_BceM-Bc431v3

Brochothrix~phage~A9


Bacillus~phage~Hoody~T

Listeria~virus~A511

Bacillus~phage~B4

Listeria~phage~vB_LmoM_AG20

Listeria~phage~List-36

VIRSorter_NODE_88_length_3448_cov_6_61673_GC022960_GC022960-cat_2VIRSorter_NODE_352_length_1647_cov_4_25032-cat_2





Erwinia~phage~PhiEaH1





Bacillus~phage~Staley





Bacillus~phage~AR9


Salmonella~phage~SPN3US


Erwinia~phage~vB_EamM_Phobos

Pseudomonas~phage~phiKZ


Pseudomonas~phage~201phi2-1







Bacillus~phage~Bastille

Bacillus~phage~Nigalana

Bacillus~phage~DIGNKC

Bacillus~phage~BPS13

Bacillus~phage~Slash


Bacillus~phage~JL


Enterococcus~phage~ECP3


Bacillus~phage~NotTheCreek

Bacillus~phage~BelindaListeria~phage~LP-083-2


Bacillus~phage~W.Ph.

Enterococcus~phage~EFLK1




Pseudomonas~phage~EL


Pseudomonas~phage~PhiPA3



Yersinia~phage~phiR1-37


















Lactococcus~phage~P118































Streptomyces~phage~YDN12



Streptomyces~phage~TP1604

Streptomyces~phage~phiSAJS1







Mycobacterium~phage~Akoma
























Shigella~phage~SHSML-45

Salmonella~virus~SPC35

Salmonella~phage~NR01

Vibrio~phage~pVp-1


Yersinia~phage~phiR201




Escherichia~virus~AKFV33










































Rhodococcus~phage~ReqiPepy6







































Bacillus~phage~Grass

Pseudomonas~phage~Lu11

Bacillus~phage~TsarBomba




Salmonella~phage~100268_sal2







Lactobacillus~phage~Lb338-1

Staphylococcus~phage~812

Staphylococcus~phage~phiIPLA-C1C

Staphylococcus~virus~G1

Staphylococcus~virus~SA11

Bacillus~phage~BCP78

Bacillus~phage~Eldridge

Bacillus~phage~Spock

Bacillus~phage~Evoli

Bacillus~phage~phiAGATE

Bacillus~phage~Eyuki

Staphylococcus~phage~MCE-2014

Bacillus~phage~Nemo

Listeria~phage~LP-048

Bacillus~phage~AvesoBmore

Bacillus~phage~CAM003

Bacillus~phage~BCP8-2

Bacillus~phage~BobbBacillus~phage~SP-10

Bacillus~phage~Deep~Blue

Bacillus~phage~JBP901

Bacillus~phage~DirtyBetty

Staphylococcus~phage~vB_SauM_Romulus

Staphylococcus~phage~vB_SauM_Remus

Bacillus~phage~Shbh1


Staphylococcus~phage~Twort



Escherichia~virus~EPS7


Enterococcus~phage~EFRM31

Salmonella~phage~FSLSP030
















Listeria~phage~P40


Listeria~phage~P35






VIRSorter_NODE_4609_length_1071_cov_3_834-cat_2VIRSorter_NODE_3_length_32693_cov_668_41-circular-cat_2

Bacillus~phage~Palmer

Salmonella~phage~FSLSP088

Enterococcus~phage~IME-EFm5








Salmonella~phage~SPN19

Bacillus~phage~Page

Proteus~phage~pPM_01


Salmonella~phage~37











Staphylococcus~phage~vB_SepS_SEP9



Providencia~phage~Redjac

Bacillus~phage~Pony

Salmonella~phage~BP12C

Enterobacter~phage~Enc34


Salmonella~phage~Chi

Salmonella~phage~iEPS5

























Lactobacillus~phage~LP65Bacillus~phage~CampHawk








































Arthrobacter~phage~KellEzio

Cellulophaga~phage~phi12a:1 Arthrobacter~phage~KitkatVIRSorter_NODE_145_length_2081_cov_6_59182-cat_2

Cellulophaga~phage~phi12:2

Microcystis~phage~MaMV-DC

Methanothermobacter~phage~psiM100Enterobacteria~phage~P4

Escherichia~virus~MS2Microcystis~aeruginosa~phage~Ma-LMM01Escherichia~virus~BZ13

Halorubrum~pleomorphic~virus~3

Methanobacterium~phage~psiM2 Halogeometricum~pleomorphic~virus~1

Pseudomonas~phage~119XPuniceispirillum~phage~HMO-2011

Polaribacter~phage~P12002S

Sulfolobus~turreted~icosahedral~virus~1 Propionibacterium~phage~PFR1Pyrobaculum~spherical~virusThermus~phage~P7426 Polaribacter~phage~P12002L


Vibrio~phage~CHOED

Thermus~thermophilus~bacteriophage~P23-77

Sulfolobus~turreted~icosahedral~virus~2

Propionibacterium~phage~PFR2

Thermoproteus~tenax~spherical~virus~1


VIRSorter_NODE_690_length_1200_cov_23_6883-cat_2 Thermus~phage~phiYS40VIRSorter_NODE_103_length_3013_cov_10_6434-cat_2

Thermus~phage~TMA

Thermus~thermophilus~phage~IN93VIRSorter_NODE_107_length_3747_cov_5_13488_GC022966_GC022966-cat_2 VIRSorter_NODE_805_length_1270_cov_2_79631-cat_2


Thermus~phage~P2345


VIRSorter_NODE_133_length_3476_cov_10_9853_GC025894_GC025894-cat_2VIRSorter_NODE_135_length_2753_cov_3_59828_GC021842_GC021842-cat_2 VIRSorter_NODE_130_length_6245_cov_1186_37-circular-cat_2














VIRSorter_NODE_302_length_2797_cov_4_32279-cat_2 VIRSorter_NODE_138_length_2763_cov_9_81906_GC022963_GC022963-cat_2




VIRSorter_NODE_116_length_6791_cov_26_2365-cat_2VIRSorter_NODE_1195_length_1296_cov_3_89089-cat_2VIRSorter_NODE_119_length_2904_cov_3_7294-cat_2VIRSorter_NODE_80_length_4184_cov_5_24203-cat_2VIRSorter_NODE_2177_length_1815_cov_4_1916-cat_2VIRSorter_NODE_597_length_1552_cov_5_03864-cat_2



Microviridae~Bog9017_22

Bacillus~virus~Andromeda

Bacillus~virus~Eoghan

Bacillus~virus~Blastoid

Microviridae~Fen418_41

Bacillus~virus~Curly





VIRSorter_NODE_28_length_10296_cov_8_56532_GC025894_GC025894-cat_1 VIRSorter_NODE_183_length_4017_cov_9_70914-cat_2

Enterobacteria~phage~ID2~Moscow/ID/2001

Enterobacteria~phage~WA13~sensu~lato

Enterobacteria~phage~St-1

Halovirus~HRTV-7

Halorubrum~phage~HF2 Vibrio~phage~fs1Acidianus~rod-shaped~virus~1 VIRSorter_NODE_789_length_2124_cov_11_3327-cat_2 VIRSorter_NODE_1329_length_1393_cov_4_82827-cat_2

Leuconostoc~phage~phiLNTR3

Staphylococcus~phage~66Staphylococcus~aureus~phage~P68


Streptococcus~phage~C1Leuconostoc~phage~phiLN12

Sulfolobus~islandicus~rudivirus~3

Sulfolobus~islandicus~rod-shaped~virus~2

Stygiolobus~rod-shaped~virus

Sulfolobus~islandicus~rod-shaped~virus~1

Acidianus~rod-shaped~virus~2

Sulfolobales~Mexican~rudivirus~1

Acidianus~filamentous~virus~1

Gordonia~phage~GTE7

Parabacteroides~phage~YZ-2015b

Gordonia~phage~Kvothe

Gordonia~phage~GMA7

Ralstonia~phage~RSS0



Gordonia~phage~Orchid

Gordonia~phage~Gmala1

Rhodococcus~phage~ReqiDocB7

Gordonia~phage~GordDuk1

Gordonia~phage~Hotorobo

Gordonia~phage~Woes

Gordonia~phage~GMA3

Tsukamurella~phage~TIN2Gordonia~phage~Jumbo


Parabacteroides~phage~YZ-2015a

Tsukamurella~phage~TIN3

Gordonia~phage~Demosthenes

Gordonia~phage~Monty

Gordonia~phage~GordTnk2









Enterobacteria~phage~Ike

Haloarcula~hispanica~pleomorphic~virus~2


Haloarcula~hispanica~pleomorphic~virus~1


VIRSorter_NODE_1873_length_1725_cov_2_88532-cat_2 Enterobacteria~phage~I2-2


Enterobacteria~phage~fd



Enterobacteria~phage~M13

Enterobacteria~phage~If1










Stenotrophomonas~phage~phiSMA9

Stenotrophomonas~phage~phiSMA7

Ralstonia~phage~1~NP-2014

Ralstonia~phage~RSM3

Ralstonia~phage~RS603

Xanthomonas~phage~Cf1c

Ralstonia~phage~p12J

Ralstonia~phage~RSM1

Stenotrophomonas~phage~phiSHP2










VIRSorter_NODE_75_length_4747_cov_7_04433-cat_2 VIRSorter_NODE_210_length_2334_cov_49_7692_ID_1237218-cat_2VIRSorter_NODE_82_length_5943_cov_11_8454-cat_2

VIRSorter_NODE_204_length_2487_cov_7_16058-cat_2 VIRSorter_NODE_88_length_5284_cov_10_0634-cat_2 VIRSorter_NODE_192_length_3117_cov_4_20329-cat_2 VIRSorter_NODE_183_length_5055_cov_11_497-cat_2VIRSorter_NODE_42_length_4426_cov_6_05932_GC021842_GC021842-cat_2VIRSorter_NODE_700_length_1299_cov_5_49018-cat_2












VIRSorter_NODE_17_length_5839_cov_24_2386_ID_33_GC022959_GC022959-cat_2 VIRSorter_NODE_1707_length_1137_cov_3_4-cat_2


VIRSorter_NODE_19_length_12517_cov_12_5272_GC022966_GC022966-cat_2 VIRSorter_NODE_19_length_12429_cov_9_68232-cat_2 VIRSorter_NODE_729_length_2816_cov_5_04746-cat_2


















Lactococcus~phage~bIBB29

Lactococcus~phage~jj50


Lactococcus~phage~jm3

Lactococcus~phage~SK1

Lactococcus~phage~SL4





Lactococcus~phage~CB13

Lactococcus~phage~CB14

Lactococcus~phage~phi7

Lactococcus~phage~jm2


Lactococcus~phage~ASCC191 Sulfolobus~virus~Kamchatka~1

Sulfolobus~spindle-shaped~virus~1 VIRSorter_NODE_74_length_6985_cov_17_2396-cat_2


Sulfolobus~spindle-shaped~virus~4

Acidianus~spindle-shaped~virus~1

Sulfolobales~Mexican~fusellovirus~1

Sulfolobus~virus~Ragged~Hills


Sulfolobus~spindle-shaped~virus~7 Sulfolobus~spindle-shaped~virus~5




Lactococcus~phage~M6162



Lactococcus~phage~D4410

Lactococcus~phage~GE1


Lactococcus~phage~c2

Lactococcus~phage~Q54

Lactococcus~phage~D4412

Sulfolobus~virus~STSV1

Sulfolobales~virus~YNP1

Sulfolobus~monocaudavirus~SMV2

Acidianus~tailed~spindle~virus


Sulfolobales~Virus~YNP2


Sulfolobus~virus~STSV2

Acidianus~two-tailed~virus



Sulfolobus~islandicus~filamentous~virus


Ralstonia~phage~PE226






















Rhodococcus~phage~RRH1


Gordonia~phage~GRU3

Gordonia~phage~GMA5

Arthrobacter~phage~Decurro

Gordonia~phage~McGonagall



















Clavibacter~phage~CN1A

Pseudoalteromonas~phage~PH1

Edwardsiella~phage~KF-1

Microbacterium~phage~vB_MoxS-ISF9

Clavibacter~phage~CMP1Vibrio~phage~VPMS1

Enterobacteria~phage~FI~sensu~lato


Escherichia~virus~FIVIRSorter_NODE_48_length_4876_cov_18_1404-cat_1

Haloarcula~hispanica~virus~PH1

Escherichia~virus~Qbeta

Haloarcula~hispanica~virus~SH1

Haloarcula~hispanica~icosahedral~virus~2Microviridae~Fen7940_21



























Pseudomonas~phage~Pf3






Persicivirga~phage~P12024S



uncultured~phage~WW-nAnB

Persicivirga~phage~P12024L



VIRSorter_NODE_299_length_4148_cov_8_5748-cat_2 Uncultured~phage~WW-nAnB~strain~3Spiroplasma~phage~SVTS2 Pseudomonas~phage~phi6

Spiroplasma~kunkelii~virus~SkV1_CR2-3x

Pseudomonas~phage~phi13

Spiroplasma~phage~1-R8A2B

Spiroplasma~phage~1-C74


Natrialba~phage~PhiCh1Pseudomonas~phage~phi2954

Acidianus~bottle-shaped~virus~3


Acidianus~bottle-shaped~virus

Vibrio~phage~VFJ VIRSorter_NODE_816_length_1439_cov_4_70117-cat_1




Acidianus~bottle-shaped~virus~2 Vibrio~phage~fs2Cellulophaga~phage~phi12:1 VIRSorter_NODE_702_length_2662_cov_3_86306-cat_1VIRSorter_NODE_70_length_5916_cov_13_2682-cat_2


VIRSorter_NODE_461_length_2912_cov_4_73651-cat_1VIRSorter_NODE_91_length_3926_cov_26_988-cat_2 VIRSorter_NODE_495_length_1539_cov_2_88714-cat_2 VIRSorter_NODE_612_length_1526_cov_6_13182-cat_2




VIRSorter_NODE_78_length_7783_cov_6_40332-cat_2VIRSorter_NODE_97_length_5738_cov_212_352-cat_1 VIRSorter_NODE_543_length_3065_cov_10_7557-cat_2




VIRSorter_NODE_427_length_1710_cov_10_147_GC021830_GC021830-cat_2 VIRSorter_NODE_419_length_1821_cov_12_289-cat_2




VIRSorter_NODE_398_length_3650_cov_9_88357-cat_2VIRSorter_NODE_414_length_3092_cov_4_90348-cat_2VIRSorter_NODE_417_length_2299_cov_4_4766-cat_1VIRSorter_NODE_534_length_2022_cov_4_55219-cat_2











Burkholderia~virus~DC1


Burkholderia~virus~Bcepmigl


Burkholderia~virus~Bcep22





















Prochlorococcus~phage~MED4-184


























Xanthomonas~phage~OP2

Burkholderia~virus~BcepNY3





Rhodobacter~phage~RcRhea



Rhizobium~phage~RR1-BVIRSorter_NODE_5_length_19800_cov_29_4493_ID_9_GC022959_GC022959-cat_2




Vibrio~phage~CP-T1

Edwardsiella~phage~MSW-3


Klebsiella~phage~JD001VIRSorter_NODE_86_length_7371_cov_10_0333-cat_1












Vibrio~phage~SHOU24




Enterobacteria~phage~P88




Agrobacterium~phage~7-7-1




















Vibrio~phage~VP585

Vibrio~phage~VHML

Mannheimia~phage~vB_MhM_587AP1



Pseudomonas~phage~phiCTX



Vibrio~phage~K139

Escherichia~virus~P2



Enterobacteria~phage~fiAA91-ssVibrio~phage~vB_VpaM_MAR

Escherichia~phage~pro483

Escherichia~phage~pro147


Escherichia~phage~vB_EcoM-ep3Burkholderia~phage~KL3



Ralstonia~phage~RSY1

Burkholderia~phage~KS5

Ralstonia~phage~RSA1

Haemophilus~phage~HP1

Burkholderia~virus~phiE122



VIRSorter_NODE_1788_length_1258_cov_2_55546-cat_2Aeromonas~virus~phiO18P

Pasteurella~phage~F108

Pseudomonas~phage~PPpW-3









Vibrio~phage~VP882

Enterobacteria~phage~WPhi

Halomonas~phage~phiHAP-1VIRSorter_NODE_157_length_3058_cov_15_698-cat_2

Mannheimia~phage~phiMHaA1Burkholderia~phage~ST79

Salmonella~phage~SEN5

Yersinia~phage~L-413C

Erwinia~phage~ENT90


Vibrio~phage~VPUSM~8





















Cellulophaga~phage~phi39:1VIRSorter_NODE_20_length_9796_cov_10_8183-cat_2


Cyanophage~MED4-117
























Vibrio~phage~X29























Yersinia~phage~PY54




Pseudomonas~phage~F116


Vibrio~phage~douglas~12A4




Erwinia~phage~PEp14VIRSorter_NODE_3_length_72233_cov_121_234-cat_2

Edwardsiella~phage~GF-2

Rhizobium~phage~16-3VIRSorter_NODE_234_length_3371_cov_10_5686-cat_2








Salmonella~phage~IME207


Vibrio~phage~pYD38-A







Pectobacterium~phage~ZF40






Iodobacteriophage~phiPLPE

Vibrio~phage~VBM1

Sinorhizobium~phage~PBC5


Azospirillum~phage~Cd

Burkholderia~virus~Bcepil02












Acinetobacter~phage~YMC-13-01-C62


Acinetobacter~phage~phiAC-1

Acinetobacter~bacteriophage~AP22


Burkholderia~virus~BcepMu

Acinetobacter~phage~YMC11/12/R2315









Haemophilus~phage~HP2



















Rhizobium~phage~RR1-A






Leuconostoc~phage~phiLN34


Leuconostoc~phage~P793














Vibrio~phage~Vf33

Halovirus~HRTV-5

Vibrio~phage~VfO3K6

Halovirus~HGTV-1

Halovirus~HRTV-8

Vibrio~phage~VSK

Halovirus~HF1

Enterobacteria~phage~M

Pseudomonas~phage~PRR1

Helicobacter~phage~1961P Enterobacteria~phage~Hgal1

Bacillus~phage~GIL16c

Helicobacter~phage~phiHP33

Helicobacter~phage~KHP40

Enterobacteria~phage~C-1~INW-2012

Bacillus~phage~Wip1

Helicobacter~phage~KHP30



VIRSorter_NODE_356_length_2682_cov_7_16775-cat_2 VIRSorter_NODE_315_length_1882_cov_7_96898-cat_2VIRSorter_NODE_711_length_2637_cov_4_34102-cat_2VIRSorter_NODE_45_length_6837_cov_11_6386-cat_2







Anabaena~phage~A-4L

Phormidium~phage~Pf-WMP3

Archaeal~BJ1~virus

Bacillus~phage~Bam35c

Halovirus~HRTV-4

Cyanophage~PP

Bacillus~phage~AP50

Phormidium~phage~Pf-WMP4

Halorubrum~phage~CGphi46

Uncultured~phage~WW-nAnB~strain~2









Halovirus~HVTV-1

Halovirus~HSTV-1

Halovirus~HCTV-5

Halovirus~HCTV-1

Halovirus~HCTV-2

Halovirus~HHTV-2

Enterococcus~phage~vB_EfaP_IME195


Staphylococcus~phage~SAP-2

Staphylococcus~phage~SLPW

Staphylococcus~phage~44AHJD

Leuconostoc~phage~phiLNTR2

Leuconostoc~phage~Lmd1

Leuconostoc~phage~1-A4

Leuconostoc~phage~Ln-8


Leuconostoc~phage~Ln-9

Leuconostoc~phage~phiLN6B

Staphylococcus~phage~BP39

Enterococcus~phage~vB_Efae230P-4

Lactoccocus~phage~WP-2

Staphylococcus~phage~GRCS









Bacillus~virus~Riggi


Microviridae~Fen685_11 Bacillus~virus~Finn


Bacillus~virus~Glittering







Cellulophaga~phage~phiST






Lactococcus~phage~KSY1









Enterobacteria~phage~ID18~sensu~lato

Enterobacteria~phage~alpha3

Enterobacteria~phage~phiX174~sensu~lato

Enterobacteria~phage~G4~sensu~lato

Enterobacteria~phage~phiK

Halovirus~HSTV-2


Vibrio~phage~VEJphi

Vibrio~phage~VGJphi

Eel~River~basin~pequenovirus

Vibrio~phage~VfO4K68

Vibrio~phage~VCY-phi

Vibrio~phage~KSF-1phi

Vibrio~phage~CTX







Aurantimonas~phage~AmM-1







Burkholderia~virus~phi52237



Enterobacter~phage~Arya

Salmonella~phage~RE-2010


Salmonella~phage~SEN1Salmonella~phage~FSL~SP-004

Escherichia~virus~186

Salmonella~virus~PsP3








Tetrasphaera~phage~TJE1








Streptomyce~phage~TG1




Mycobacterium~phage~Catera


Mycobacterium~phage~Rizal


Pseudomonas~phage~PB1

Mycobacterium~phage~Cali

Streptomyces~phage~phiC31

Mycobacterium~phage~Myrna


Arthrobacter~phage~BarretLemon




Pseudomonas~phage~NH-4

Pseudomonas~phage~14-1





Pseudomonas~phage~vB_Pae_PS44


Burkholderia~virus~BcepF1






Pseudomonas~phage~SN


Pseudomonas~phage~LBL3




Escherichia~phage~ECML-117


Pseudomonas~phage~vB_PaeM_PAO1_Ab27

Pseudomonas~phage~JG024


Pseudomonas~phage~LMA2



VIRSorter_NODE_89_length_4617_cov_9_96388_GC025894_GC025894-cat_2VIRSorter_NODE_87_length_4658_cov_6_26697_GC025894_GC025894-cat_2VIRSorter_NODE_131_length_3513_cov_7_25378_GC025894_GC025894-cat_2



Pseudomonas~phage~H70

Pseudomonas~phage~vB_PaeS_PAO1_Ab30

Pseudomonas~phage~D3112












Mycobacterium~phage~ArcherS7


Streptomyces~phage~phiSASD1


Mycobacterium~phage~HyRo

Mycobacterium~phage~ScottMcG



Mycobacterium~phage~Pleione


Mycobacterium~phage~Bxz1


Mycobacterium~phage~MoMoMixon


Mycobacterium~phage~Gizmo

Mycobacterium~phage~Tonenili



Mycobacterium~phage~Breeniome

Mycobacterium~phage~ET08 VIRSorter_NODE_1_length_45849_cov_160_572-cat_2

Mycobacterium~phage~LinStu



Mycobacterium~phage~Spud




Rhodococcus~phage~E3



Pseudomonas~phage~JBD5Pseudomonas~phage~MP38VIRSorter_NODE_48_length_12194_cov_19_9894-cat_2VIRSorter_NODE_285_length_2422_cov_6_08955-cat_2

Pseudomonas~phage~LPB1

Pseudomonas~phage~JD024


Pseudomonas~phage~PA1phi


















Acinetobacter~phage~LZ35VIRSorter_NODE_821_length_1759_cov_9_98692-cat_2



Escherichia~phage~vB_EcoM_ECO1230-10

Aeromonas~phage~vB_AsaM-56

Stenotrophomonas~phage~Smp131




Bdellovibrio~phage~phi1422


















Edwardsiella~phage~PEi21



Vibrio~phage~vB_VchM-138















Rhodobacter~phage~RcapNL










































Pseudomonas~phage~JBD30

Staphylococcus~phage~PT1028

Pseudomonas~phage~vB_PaeS_PM105


Pseudomonas~phage~B3




Pseudomonas~phage~MP42



Pseudomonas~phage~JBD88a



Pseudomonas~phage~DMS3

Phage~MP22

















Rhizobium~phage~vB_RleM_PPF1

















Ralstonia~phage~RS138



Rhodovulum~phage~vB_RhkS_P1







Rhodovulum~phage~RS1

Rhodobacter~phage~RcapMu

Rhodobacter~phage~RC1Vibrio~phage~martha~12B12






Escherichia~phage~D108







Arthrobacter~phage~vB_ArtM-ArV1











Escherichia~virus~Mu

Enterobacteria~phage~SfMu






Mannheimia~phage~vB_MhM_3927AP2

Haemophilus~phage~SuMu


Achromobacter~phage~JWF
























Burkholderia~phage~BcepB1A







Stenotrophomonas~phage~S1





Propionibacterium~phage~PHL171M01Propionibacterium~phage~P100_APropionibacterium~phage~PHL041M10

Propionibacterium~phage~Attacne

Propionibacterium~phage~BruceLethal

Propionibacterium~phage~PAS50

Propionibacterium~phage~MrAK










Mycobacterium~phage~Dandelion

Mycobacterium~phage~Nappy



Mycobacterium~phage~Alice






Streptomyces~phage~phiBT1





Propionibacterium~phage~PHL060L00

Propionibacterium~phage~PAC1

Propionibacterium~phage~PHL111M01


Propionibacterium~phage~PA6


Propionibacterium~phage~PA1-14

Propionibacterium~phage~PHL114L00

Propionibacterium~phage~Pacnes~2012-15


Shigella~phage~SfIV



Salmonella~phage~ST64B

Pseudomonas~phage~PMG1

Mannheimia~phage~vB_MhS_1152AP2



Salmonella~enterica~bacteriophage~SE1


Salmonella~phage~vB_SemP_Emek

Salmonella~phage~c341

Enterobacteria~phage~mEp460

Salmonella~phage~epsilon34

Enterobacterial~phage~mEp390 Stx2~converting~phage~II


Stx2~converting~phage~vB_EcoP_24B




Enterobacteria~phage~933W



Escherichia~virus~HK97

Enterobacteria~phage~HK140

Escherichia~virus~HK022



Stx2-converting~phage~1717


Enterobacteria~phage~mEpX2

Burkholderia~virus~phi6442


Salmonella~phage~ST64T


Stx2-converting~phage~86


Enterobacteria~phage~SfI


Enterobacteria~phage~ST104


Ralstonia~phage~RSK1



Pseudomonas~phage~D3


Serratia~phage~Eta

Sodalis~phage~phiSG1

Cronobacter~phage~ENT47670


Enterobacteria~phage~Min27

Enterobacteria~phage~ES18

VIRSorter_NODE_152_length_3125_cov_36_1188-cat_2Enterobacteria~phage~VT2-Sakai

Salmonella~phage~vB_SosS_Oslo

Enterobacterial~phage~mEp234


Pseudomonas~phage~PS-1

Escherichia~phage~HK75


Pseudoalteromonas~phage~H103


Shigella~phage~75/02~Stx


Salmonella~phage~SPN3UB

Shigella~phage~POCJ13

Enterobacteria~phage~YYZ-2008

Escherichia~Stx1~converting~phage


Enterobacteria~phage~BP-4795

Escherichia~phage~PA2

Enterobacteria~phage~Sf101

Salmonella~phage~ST160

Enterobacteria~phage~Sf6


Salmonella~phage~SPN9CC



Burkholderia~virus~phi1026b

Enterobacteria~phage~UAB_Phi20Salmonella~virus~P22

Enterobacteria~phage~mEp235


Thalassomonas~phage~BA3





Shigella~phage~EP23

Escherichia~virus~JL1


Sodalis~phage~SO1


Escherichia~phage~HK578

Enterobacteria~phage~EK99P-1


Salmonella~phage~36


Cyanophage~KBS-S-2A

Salmonella~phage~SSU5Shigella~phage~pSf-1Klebsiella~phage~1513

Shigella~virus~Shfl1


Shigella~phage~pSf-2

Citrobacter~phage~Stevie

Escherichia~virus~TLS

Escherichia~phage~ADB-2

Cronobacter~virus~ESP29491

Escherichia~virus~RtpVIRSorter_NODE_1_length_64633_cov_56_7676-cat_2Klebsiella~phage~Sushi








VIRSorter_NODE_581_length_1707_cov_13_4031-cat_2Salmonella~phage~phSE-2


Klebsiella~phage~KP36

Klebsiella~phage~KLPN1

Klebsiella~phage~PKP126


uncultured~phage~crAssphage











Xanthomonas~phage~vB_XveM_DIBBI

Escherichia~phage~e4/1cEnterobacteria~phage~vB_EcoS_Rogue1

Escherichia~phage~vB_EcoS_AHP42

Escherichia~phage~vB_EcoS_AKS96












Enterobacteria~phage~vB_EcoS_NBD2




Escherichia~phage~Jk06Escherichia~phage~vB_Eco_ACG-M12

Escherichia~phage~vB_EcoS_AHS24




Synechococcus~phage~S-CBS4




Pseudoalteromonas~phage~Pq0



Listeria~phage~P70

VIRSorter_NODE_29_length_17826_cov_23_1448-cat_2Synechococcus~phage~P60


Enterobacteria~phage~K1F

Cyanophage~SS120-1

Pseudomonas~phage~Phi-S1

Enterobacteria~phage~K30

Citrobacter~phage~SH3


Pseudomonas~phage~PPpW-4

Pseudomonas~phage~PPPL-1





Vibrio~phage~SIO-2

Pseudomonas~phage~phiIBB-PF7A


VIRSorter_NODE_3_length_40652_cov_1063_38_ID_1561464-circular-cat_2












Pectobacterium~phage~PP1




Erwinia~amylovora~phage~Era103



Enterobacter~phage~phiEap-1


Morganella~phage~MmP1

Yersinia~phage~phiA1122

Klebsiella~phage~K5

Pseudomonad~phage~gh-1

Yersinia~phage~Yep-phi


Vibrio~phage~phi-A318

Proteus~phage~vB_PmiP_Pm5460

Salmonella~phage~BP12B

Proteus~phage~PM~85

Salmonella~virus~SP6

VIRSorter_NODE_373_length_2570_cov_9_72563-cat_2Enterobacteria~phage~UAB_Phi78


Proteus~phage~PM~93

Pseudomonas~phage~YMC11/06/C171_PPU_BP

Ralstonia~phage~RSB3


Pantoea~phage~LIMElight

Pseudomonas~phage~phi-2




Ralstonia~phage~RSJ5


Ralstonia~phage~RSJ2

Enterobacteria~phage~BA14

Erwinia~phage~FE44Delftia~phage~IME-DE1

Klebsiella~phage~K11Escherichia~phage~64795_ec1

Yersinia~phage~BerlinYersinia~phage~Yepe2

Citrobacter~phage~CR44b


Enterobacteria~phage~13a

Pseudomonas~phage~LKA1

Lelliottia~phage~phD2B



Enterobacteria~phage~vB_EcoP_ACG-C91

Escherichia~virus~K1-5

Escherichia~virus~K1E

Klebsiella~phage~NTUH-K2044-K1-1

Escherichia~phage~vB_EcoP_GA2AVIRSorter_NODE_2301_length_1326_cov_2_59247-cat_2

Salmonella~phage~BP12A

Citrobacter~phage~phiCFP-1

Erwinia~phage~vB_EamP-L1

Enterobacter~phage~E-2

Enterobacteria~phage~T7Escherichia~phage~PE3-1

Stenotrophomonas~phage~IME15

Escherichia~phage~P483

Escherichia~phage~CICC~80001

Pseudomonas~phage~PT2


Pseudomonas~phage~vB_PaeP_PAO1_Ab05

Pantoea~phage~LIMEzero




Pseudomonas~phage~phikF77

Pseudomonas~phage~vB_PaeP_PPA-ABTNL

Xylella~phage~Prado

Pseudomonas~phage~vB_Pae-TbilisiM32


Pseudomonas~phage~phiKMVVIRSorter_NODE_347_length_2613_cov_7_52326-cat_1

VIRSorter_NODE_373_length_2545_cov_2_69327-cat_2Ralstonia~phage~RSB1

Pseudomonas~phage~LKD16

Enterobacteria~phage~J8-65








Burkholderia~phage~JG068

Xanthomonas~phage~CP1


Acinetobacter~phage~Fri1







Klebsiella~phage~vB_Kp2

Klebsiella~phage~vB_KpnP_SU552A

Pseudomonas~phage~MPK7

Acinetobacter~phage~AB3


Acinetobacter~phage~vB_AbaP_Acibel007

Yersinia~phage~phi80-18


Pseudomonas~phage~MPK6


Acinetobacter~phage~vB_AbaP_PD-AB9


Acinetobacter~phage~vB_AbaM_IME200

Xanthomonas~phage~OP1


Klebsiella~phage~vB_KpnP_KpV41



Xylella~phage~Paz


Acinetobacter~phage~Petty

Acinetobacter~phage~Abp1

Vibrio~phage~VP93

Cronobacter~phage~Dev-CD-23823


Klebsiella~phage~F19


Yersinia~phage~vB_YenP_ISAO8



Pseudomonas~phage~Bf7



Acinetobacter~phage~phiAB6


Cronobacter~phage~vB_CskP_GAP227


Proteus~phage~PM~75




Escherichia~phage~phiKT




Pseudomonas~phage~Andromeda











Xanthomonas~phage~phiL7


Xanthomonas~phage~Xp10

Xanthomonas~phage~Xop411




Escherichia~phage~LM33_P1

Salmonella~phage~Vi06

Morganella~phage~vB_MmoP_MP2

Citrobacter~phage~CR8


Salmonella~phage~phiSG-JL2




Klebsiella~phage~vB_Kp1

Enterobacteria~phage~285P


Vibrio~phage~ICP3

Cronobacter~phage~Dev2 Pseudomonas~phage~Pf-10



Escherichia~phage~EB49

Escherichia~virus~N15


Cyanophage~PSS2


Cronobacter~phage~phiES15

Edwardsiella~phage~eiAU-183


Enterobacteria~phage~mEp043~c-1

Escherichia~phage~TL-2011c





Pseudomonas~phage~YMC11/02/R656



Escherichia~phage~phi191

Enterobacteria~phage~cdtI

Pseudomonas~phage~YMC11/07/P54_PAE_BP


Salmonella~phage~Vi~II-E1

Klebsiella~phage~phiKO2

Enterobacteria~phage~VT2phi_272

Enterobacterial~phage~mEp213

Enterobacteria~phage~mEpX1

Erwinia~phage~phiEt88

Enterobacteria~phage~HK629Enterobacteria~phage~HK630

Escherichia~virus~Lambda

Psychrobacter~phage~Psymv2

Listonella~phage~phiHSIC

Acinetobacter~phage~vB_AbaS_TRS1


Pseudomonas~phage~PAJU2


Escherichia~phage~YD-2008.s

Escherichia~phage~Envy

Burkholderia~phage~Bcep176

Escherichia~phage~GluttonyEscherichia~virus~SSL2009a

Vibrio~phage~VvAW1


Escherichia~phage~K1-dep(4)

Salmonella~phage~MA12

Salmonella~phage~f18SE

Salmonella~phage~SETP3

Salmonella~phage~SE2 Salmonella~phage~LSPA1

Enterobacter~phage~phiEap-2

Salmonella~phage~vB_SenS-Ent3

Salmonella~phage~SS3e

Escherichia~phage~HK639VIRSorter_NODE_52_length_8920_cov_4_01029-cat_2


Enterobacteria~phage~phi80

Shigella~phage~Ss-VASDEnterobacteria~phage~mEp237


Cronobacter~phage~ENT39118































Synechococcus~phage~S-RIP1







VIRSorter_NODE_3496_length_1469_cov_3_86782-cat_2Riemerella~phage~RAP44





Pseudomonas~phage~AF





Enterobacteria~phage~epsilon15



Escherichia~phage~phiV10

Xanthomonas~citri~phage~CP2




VIRSorter_NODE_151_length_1878_cov_116_108_ID_301_GC022959_GC022959-cat_1VIRSorter_NODE_85_length_8370_cov_15_7844-cat_1







Enterobacter~phage~Tyrion





Bordetella~virus~BPP1





Cyanophage~NATL1A-7




Liberibacter~phage~SC1


Liberibacter~phage~SC2




Escherichia~phage~TL-2011b


Salmonella~phage~SPN1S








Acinetobacter~phage~phiAB1

Klebsiella~phage~vB_KpnP_SU503VIRSorter_NODE_1_length_43078_cov_20_0369_GC021825_GC021825-cat_2










Acinetobacter~phage~vB_AbaP_PD-6A3

Pectobacterium~phage~Peat1

Proteus~phage~PM16









Cyanophage~9515-10a


Prochlorococcus~phage~P-SSP3

Cyanophage~P-SSP2


Podovirus~Lau218


Synechococcus~phage~S-CBP4




Enterobacteria~phage~T3

Synechococcus~phage~Syn5

Kluyvera~phage~Kvp1

Yersinia~phage~phiYeO3-12

Yersinia~phage~vB_YenP_AP10

Yersinia~phage~vB_YenP_AP5


Marinomonas~phage~P12026

Enterobacteria~phage~EcoDS1Pseudomonas~phage~phiPSA2




Ralstonia~phage~RSB2

Enterobacter~phage~E-3

Mesorhizobium~phage~vB_MloP_Lo5R7ANS


Vibriophage~VP4


Vibrio~phage~N4


Listeria~phage~LP-037Cyanophage~KBS-P-1A

Brucella~phage~Tb




Synechococcus~phage~S-RIP2



Streptococcus~phage~SPQS1


Enterococcus~phage~VD13





Colwellia~phage~9AEnterococcus~phage~BC611


Idiomarinaceae~phage~1N2-2

Vibrio~phage~pYD38-B



Pseudoalteromonas~phage~BS5VIRSorter_NODE_5_length_67441_cov_26_2734-cat_2

Xylella~phage~Xfas53




Prochlorococcus~phage~P-GSP1

Cyanophage~NATL2A-133






Burkholderia~virus~BcepC6B



Salmonella~phage~vB_SenS-Ent2

Rhizobium~phage~vB_RleS_L338C

Salmonella~phage~L13



VIRSorter_NODE_45_length_7755_cov_7_76426-cat_2Pseudomonas~phage~vB_PaeP_Tr60_Ab31

Brucella~phage~Pr


Salmonella~phage~Jersey

Escherichia~phage~K1-dep(1)



Salmonella~phage~Ent1

Salmonella~phage~BPS11Q3





Enterococcus~phage~vB_EfaS_IME198





















Myxococcus~phage~Mx8




















































Clostridium~phage~phiCD38-2


















Clostridium~phage~phiCP13OVIRSorter_NODE_1128_length_1091_cov_2_26036-cat_2















































Streptomyces~phage~phiHau3



Streptomyces~phage~SF1


Streptomyces~phage~R4

Streptomyces~phage~Amela





















VIRSorter_NODE_54_length_6148_cov_5_99555-cat_2VIRSorter_NODE_32_length_9049_cov_61_2692_ID_1233962-cat_2





Pseudomonas~phage~vB_PaeS_PAO1_Ab18




Roseobacter~phage~RDJL~Phi~1








Pseudoalteromonas~phage~H105/1






Salicola~phage~CGphi29



Idiomarinaceae~phage~Phi1M2-2








Lactobacillus~phage~LLKu








Pseudomonas~phage~MD8

Aggregatibacter~phage~S1249



Haemophilus~phage~Aaphi23



Sinorhizobium~phage~phiLM21


Vibrio~phage~pYD21-A

Shigella~phage~SfII

Enterobacteria~phage~SfV


Enterobacteria~phage~phiP27



VIRSorter_NODE_12_length_18337_cov_26_2012-cat_2Rhizobium~phage~vB_RglS_P106B


Brucella~phage~BiPBO1





Acinetobacter~phage~Bphi-B1251

Bacteriophage~Lily





Enterobacteria~phage~IME10



Vibrio~phage~PVA1


Rhizobium~phage~RHEph06


Salmonella~phage~9NA

Pseudomonas~phage~phiPSA1






Salmonella~phage~BP63





Gordonia~phage~GMA6

Paenibacillus~phage~PG1




Xanthomonas~phage~Xp15





Psychrobacter~phage~pOW20-A


































Mycobacterium~phage~Astraea






Propionibacterium~phage~P105

Propionibacterium~phage~ATCC29399B_C

Propionibacterium~phage~P14.4


Propionibacterium~phage~PHL092M00Propionibacterium~phage~PHL116M00

Propionibacterium~phage~Wizzo


Propionibacterium~phage~Stormborn

Propionibacterium~phage~Ouroboros

Propionibacterium~phage~Kubed

Propionibacterium~phage~PHL055N00

Propionibacterium~phage~P100_1


Propionibacterium~phage~P100D



Propionibacterium~phage~QueenBey

Propionibacterium~phage~Pirate

Propionibacterium~phage~ATCC29399B_T




Propionibacterium~phage~Moyashi


Propionibacterium~phage~SKKY

Propionibacterium~phage~P104A




Propionibacterium~phage~P101A


Propionibacterium~phage~PHL025M00 VIRSorter_NODE_105_length_5940_cov_5_06942-cat_2

Propionibacterium~phage~Solid

Propionibacterium~phage~Procrass1





Arthrobacter~phage~vB_ArS-ArV2


Propionibacterium~phage~Enoki


Propionibacterium~phage~PAD20

Propionibacterium~phage~LauchellyPropionibacterium~phage~PHL132N00


Gordonia~phage~BachitaGordonia~phage~NyceiraeGordonia~phage~ClubL

Mycobacterium~phage~Cambiare

Mycobacterium~phage~Halo

Streptomyces~phage~SF3

Mycobacterium~phage~Kratio

Gordonia~phage~Cucurbita

Mycobacterium~phage~Angel

Mycobacterium~phage~FlagStaff


Streptococcus~phage~M102


Lactococcus~phage~ul36

Lactobacillus~phage~iLp84

Lactobacillus~phage~PLE3


Lactobacillus~phage~CL2


Lactococcus~phage~P335~sensu~lato


Lactococcus~phage~PLgT-1

Listeria~phage~B054

Lactococcus~phage~TP901-1

Lactobacillus~prophage~Lj928

Streptococcus~phage~SMP


Enterococcus~phage~phiFL2A

Lactobacillus~phage~phiadh



Streptococcus~phage~YMC-2011


Brochothrix~phage~BL3

Streptococcus~phage~O1205

Streptococcus~phage~7201




Streptococcus~phage~TP-778L




Streptococcus~virus~9872

Weissella~phage~WCP30

Streptococcus~phage~Alq132









Streptococcus~phage~DT1Lactococcus~phage~Tuc2009

Streptococcus~phage~M102AD

Lactobacillus~phage~iLp1308

Streptococcus~phage~Sfi19





Streptococcus~phage~TP-J34




Lactobacillus~phage~phijl1









Streptococcus~phage~APCM01


Enterobacteria~phage~9g

Stenotrophomonas~phage~vB_SmaS-DLP_2



Burkholderia~phage~KL1

Pseudomonas~phage~vB_PaeS_SCH_Ab26


Pseudomonas~phage~73

Pseudomonas~phage~vB_Pae-Kakheti25

Enterobacteria~phage~JenP1



Enterobacteria~phage~JenP2

Paracoccus~phage~vB_PmaS_IMEP1Pseudomonas~phage~PaMx42


Acinetobacter~phage~IME_AB3

Enterobacteria~phage~JenK1




Achromobacter~phage~JWX






Escherichia~phage~CAjan


Vibrio~phage~VpKK5

Pseudomonas~phage~PaMx11










Vibrio~phage~vB_VpaS_MAR10





VIRSorter_NODE_170_length_2425_cov_4_76405-cat_2Achromobacter~phage~83-24

Pseudomonas~phage~PAE1

Pseudomonas~phage~M6













Rhodobacter~phage~RcTitan

Pseudomonas~phage~NP1



Phage~phiJL001

Pseudomonas~phage~YuA

Burkholderia~phage~BcepGomr

Burkholderia~phage~AH2



Streptococcus~phage~IC1



Pediococcus~phage~clP1





Streptococcus~phage~phiARI0468-1

Enterococcus~phage~phiEf11



Lactobacillus~phage~CL1

Streptococcus~phage~Abc2



Lactobacillus~phage~LfeSau

Streptococcus~phage~A25

























Oenococcus~phage~phiS11


VIRSorter_NODE_703_length_1772_cov_3_67906-cat_2Oenococcus~phage~phiS13

Oenococcus~phage~phi9805


Lactobacillus~phage~ATCC8014












Aeromonas~phage~pAh6-C













































Enterobacteria~phage~phiEcoM-GJ1





VIRSorter_NODE_121_length_7606_cov_38_426-cat_2Pseudomonas~phage~UFV-P2

Pseudomonas~phage~tf














Erwinia~phage~vB_EamM-Y2VIRSorter_NODE_592_length_3284_cov_11_218-cat_1



Pseudomonas~phage~PhiCHU



Pseudomonas~phage~vB_PaeP_p2-10_Or1VIRSorter_NODE_1972_length_1006_cov_1_83854-cat_2

Pseudomonas~phage~vB_PaeP_C2-10_Ab22VIRSorter_NODE_136_length_3977_cov_9_3759-cat_1

Enterobacteria~phage~NJ01



Escherichia~phage~172-1




Pseudomonas~phage~PA11




Phage~vB_EcoP_SU10

Escherichia~virus~phiEco32VIRSorter_NODE_66_length_3374_cov_10_5839-cat_2

Pseudoalteromonas~phage~RIO-1





VIRSorter_NODE_1853_length_1738_cov_3_04455-cat_2Pseudomonas~phage~TL



Escherichia~phage~KBNP1711




Pseudomonas~phage~phiIBB-PAA2
















Salinivibrio~phage~CW02


























Vibrio~phage~VpV262

Vibrio~phage~ICP2_2013_A_Haiti


Pseudomonas~phage~O4


Citrobacter~phage~CVT22



















Pectobacterium~phage~PM1


Clostridium~phage~phiCTP1








































































Vibrio~phage~ICP2





Celeribacter~phage~P12053L









Sulfitobacter~phage~pCB2047-C


Sulfitobacter~phage~pCB2047-A






























VIRSorter_NODE_404_length_2208_cov_6_09855-cat_2Streptococcus~phage~Dp-1
























Roseobacter~phage~SIO1




































Vibrio~phage~phiVC8

















Vibrio~phage~VP5



Streptococcus~phage~DCC1738



Streptococcus~phage~phiARI0462





Streptococcus~phage~K13




Streptococcus~phage~SpSL1




Streptococcus~phage~phiARI0746VIRSorter_NODE_10_length_34876_cov_52_3248-cat_2






VIRSorter_NODE_275_length_2040_cov_3_12481_GC021830_GC021830-cat_1VIRSorter_NODE_2_length_55450_cov_60_6792-circular-cat_2



Streptococcus~phage~phiARI0468-4Temperate~phage~phiNIH1.1


Streptococcus~phage~MM1




Lactobacillus~phage~phiJBStreptococcus~phage~EJ-1



























Lactobacillus~phage~phiLdb









Clostridium~phage~phiCDHM13




Clostridium~phage~phiMMP04






Clostridium~virus~phiCD27



Hamiltonella~virus~APSE1

Bacillus~phage~BalMu-1








Paenibacillus~phage~Tripp
















Bacillus~phage~BCD7




Croceibacter~phage~P2559Y














VIRSorter_NODE_17_length_10153_cov_52_2661-cat_2 Ruegeria~phage~DSS3-P1



Bacillus~phage~phiCM3









Clostridium~phage~phiCP26F





Paenibacillus~phage~Vegas






Bacillus~phage~Gamma

Clostridium~phage~phiCT19406C


Bacillus~virus~Wbeta

Bacillus~phage~Fah

Bacillus~virus~250



Bacillus~phage~phi105



Bacillus~phage~BtCS33


Bacillus~phage~phIS3501

Bacillus~phage~vB_BtS_BMBtp3

Bacillus~phage~Waukesha92














Clostridium~phage~phiCP39-O

Staphylococcus~phage~80Staphylococcus~phage~StauST398-4

Staphylococcus~phage~StauST398-3

Staphylococcus~phage~phinm4

Staphylococcus~phage~StauST398-1VIRSorter_NODE_261_length_4346_cov_10_5306-cat_1

Staphylococcus~phage~phi5967PVL

Staphylococcus~phage~ROSAStaphylococcus~phage~StauST398-5

Staphylococcus~phage~B166Deep-sea~thermophilic~phage~D6E

Staphylococcus~phage~phiSa119


Staphylococcus~phage~52A

Staphylococcus~phage~phiPVL-CN125Staphylococcus~phage~77

Staphylococcus~phage~phiMR11

Staphylococcus~phage~3MRA


Staphylococcus~phage~42E

Staphylococcus~phage~Slt

Staphylococcus~phage~EW

Staphylococcus~phage~YMC/09/04/R1988



Bacillus~phage~PM1


Bacillus~phage~vB_BhaS-171

Bacillus~phage~PBC1

Bacillus~phage~PfEFR-5

Paenibacillus~phage~Fern

Paenibacillus~phage~SitaraPaenibacillus~phage~Diva

Paenibacillus~phage~Rani


Paenibacillus~phage~phiIBB_Pl23Paenibacillus~phage~Harrison

VIRSorter_NODE_34_length_9174_cov_107_608_GC025894_GC025894-cat_2 Paenibacillus~phage~HB10c2 Lactobacillus~phage~Ldl1


Staphylococcus~phage~SpaA1



Paenibacillus~phage~Xenia

Clostridium~phage~phi3626


Rhodoferax~phage~P26218



Staphylococcus~phage~Ipla35

Staphylococcus~phage~vB_SauS_phi2

Staphylococcus~phage~StauST398-2


Staphylococcus~phage~Phi12

Staphylococcus~phage~tp310-2

Staphylococcus~phage~PH15Staphylococcus~phage~CNPH82


Bacillus~phage~SPP1Streptococcus~phage~phi3396



Staphylococcus~phage~SMSAP5



Staphylococcus~phage~CNPx


Staphylococcus~phage~phiNM3

Staphylococcus~phage~phiBU01

Staphylococcus~phage~23MRA

Staphylococcus~phage~P954

Staphylococcus~phage~B236

Staphylococcus~phage~TEM123



Bacillus~virus~1

Clostridium~virus~phiC2



Geobacillus~phage~GBSV1


Clostridium~phage~phiCT9441A

Bacillus~phage~BCJA1c






Clostridium~phage~CDMH1

Bacillus~phage~TP21-L













Clostridium~phage~phi8074-B1


Bacillus~virus~BMBtp2




Clostridium~virus~phiCD119

Clostridium~phage~phiCD481-1






Lactobacillus~phage~Ld17










Bacteriophage~APSE-2







Clostridium~phage~PhiS63








Lactobacillus~phage~Ld25A

Lactobacillus~phage~c5



Lactobacillus~phage~Ld3

Listeria~phage~LP-030-2

Listeria~phage~2389



Erysipelothrix~phage~SE-1

Geobacillus~virus~E2



Bacillus~virus~IEBH

Brevibacillus~phage~Davies

Thermus~phage~phi~OH2


Brevibacillus~phage~Abouo


Brevibacillus~phage~Jimmer1



VIRSorter_NODE_78_length_5137_cov_17_9613-cat_1Brevibacillus~phage~Osiris


Staphylococcus~phage~StB12Streptococcus~phage~P9



Listeria~phage~A006

Staphylococcus~phage~StB27Listeria~phage~B025

Lactobacillus~phage~JCL1032



Streptococcus~phage~PH10

Lactobacillus~phage~iA2


Streptococcus~phage~PH15

Streptococcus~phage~phiNJ2

Streptococcus~phage~phiBHN167

Streptococcus~phage~T12

Enterococcus~phage~EFC-1



Lactobacillus~phage~LL-H

Lactobacillus~phage~phig1eListeria~phage~A118

Lactobacillus~phage~phiAQ113

Lactobacillus~phage~KC5a

Listeria~phage~A500



Listeria~phage~LP-030-3Listeria~phage~vB_LmoS_293


Lactobacillus~phage~phi~jlb1


Listeria~phage~vB_LmoS_188


Mycobacterium~phage~Conspiracy

Mycobacterium~phage~Smeadley

Mycobacterium~phage~Tiffany

Mycobacterium~phage~CatalinaMycobacterium~phage~UnionJack

Mycobacterium~phage~40AC

Mycobacterium~phage~Severus

Mycobacterium~phage~Phantastic

Mycobacterium~phage~Jobu08Mycobacterium~phage~Anubis

Gordonia~phage~Emalyn

Mycobacterium~phage~Blue7

Mycobacterium~phage~Pioneer

Mycobacterium~phage~Alma

Gordonia~phage~JSwag

Mycobacterium~phage~MarQuardt

Mycobacterium~phage~BellusTerra

Mycobacterium~phage~PeachesMycobacterium~phage~Obama12

Mycobacterium~phage~AnnaL29

Mycobacterium~phage~Chy5

Mycobacterium~phage~BTCU-1

Mycobacterium~phage~D29

Mycobacterium~phage~RedRock

Mycobacterium~phage~Chy4

Mycobacterium~phage~RhynO

Mycobacterium~phage~LadyBird

Mycobacterium~phage~Pukovnik

Mycobacterium~phage~EagleEye

Mycobacterium~phage~Wile

Mycobacterium~phage~Kampy

Mycobacterium~phage~Sheen

Mycobacterium~phage~Serenity

Gordonia~phage~Rosalind

Mycobacterium~phage~Iracema64

Gordonia~phage~Schwabeltier

Gordonia~phage~Ghobes

Gordonia~phage~Hedwig

Mycobacterium~phage~Dori

Gordonia~phage~Splinter

Gordonia~phage~Yeezy

Gordonia~phage~Guacamole

Gordonia~phage~CarolAnn

Gordonia~phage~Utz

Gordonia~phage~Gsput1


Gordonia~phage~CaptainKirk2

Gordonia~phage~Blueberry


Gordonia~phage~Zirinka

Gordonia~phage~Kita

Gordonia~phage~Bowser

Corynebacterium~phage~BFK20

Gordonia~phage~BaxterFox

Gordonia~phage~UmaThurman

Gordonia~phage~Nymphadora


Mycobacterium~phage~MOOREtheMARYer

Mycobacterium~phage~32HC

Gordonia~phage~Eyre

Gordonia~phage~SoilAssassin

Mycobacterium~phage~Jolie2


Mycobacterium~phage~Trouble

Mycobacterium~phage~PhrostyMug

Mycobacterium~phage~Doom

Mycobacterium~phage~Gompeii16

Mycobacterium~phage~Turj99

Mycobacterium~phage~PattyP

Mycobacterium~phage~Nerujay

Gordonia~phage~KatherineG

Mycobacterium~phage~Swirley

Mycobacterium~phage~HanShotFirstMycobacterium~phage~RidgeCB

Mycobacterium~phage~Phlei

Mycobacterium~phage~ArcherNM



Mycobacterium~phage~CASbigMycobacterium~phage~Euphoria

Mycobacterium~phage~Makemake

Mycobacterium~phage~Seabiscuit

Mycobacterium~phage~Pepe

Mycobacterium~phage~Perseus

Mycobacterium~phage~EdthersonMycobacterium~phage~Lockley


Mycobacterium~phage~Omega

Mycobacterium~phage~Redno2

Mycobacterium~phage~Jabbawokkie

Mycobacterium~phage~Courthouse

Mycobacterium~phage~Wanda

Mycobacterium~phage~Thibault


Mycobacterium~phage~Lolly9

Mycobacterium~phage~bron

Mycobacterium~phage~MiaZeal

Mycobacterium~phage~Minerva

Mycobacterium~phage~244

Mycobacterium~phage~Cjw1

Mycobacterium~phage~Dusk

Mycobacterium~phage~Corndog

Mycobacterium~phage~Phaux

Mycobacterium~phage~Phrux

Mycobacterium~phage~DrDrey

Mycobacterium~phage~Contagion

Mycobacterium~phage~Phatniss

Mycobacterium~phage~Drago

Mycobacterium~phage~Inventum

Mycobacterium~phage~Dylan

Mycobacterium~phage~Hades

Mycobacterium~phage~Hamulus

Mycobacterium~phage~Pacc40

Mycobacterium~phage~DeadP

Mycobacterium~phage~SaalMycobacterium~phage~Tweety

Mycobacterium~phage~Taj

Mycobacterium~phage~Toto

Mycobacterium~phage~NelitzaMV


Mycobacterium~phage~Mindy

Mycobacterium~phage~Lilac


Mycobacterium~phage~Porky

Mycobacterium~phage~Dumbo

Mycobacterium~phage~Murphy






Streptomyces~phage~mu1/6




Mycobacterium~phage~Bruin

Mycobacterium~phage~Quink

Mycobacterium~phage~PhatBacter

Mycobacterium~phage~HufflyPuff

Mycobacterium~phage~Nala





Arthrobacter~phage~Mudcat































Rhodococcus~phage~ReqiPoco6





Mycobacterium~phage~Llij

Mycobacterium~phage~Florinda

Mycobacterium~phage~Estave1

Mycobacterium~phage~Goku

Mycobacterium~phage~Cabrinians

Mycobacterium~phage~DanteMycobacterium~phage~Sparkdehlily

Mycobacterium~phage~Llama

Mycobacterium~phage~Wee

Mycobacterium~phage~Gardann

Mycobacterium~phage~CrossroadsMycobacterium~phage~Faith1

Mycobacterium~phage~QuicoMycobacterium~phage~PMC

Mycobacterium~phage~Bipolar

Mycobacterium~phage~Archie

Mycobacterium~phage~Boomer

Mycobacterium~phage~RamseyMycobacterium~phage~SeagreenRhodococcus~phage~REQ3

Mycobacterium~phage~Kostya

Mycobacterium~phage~Wildcat

Mycobacterium~phage~Job42

Mycobacterium~phage~BuzzLyseyear

Mycobacterium~phage~Brujita

Mycobacterium~phage~Fishburne

Mycobacterium~phage~Shipwreck

Mycobacterium~phage~Brocalys

Mycobacterium~phage~MichelleMyBell

Mycobacterium~phage~Brusacoram

Mycobacterium~phage~Phayonce

Mycobacterium~phage~Carcharodon

Mycobacterium~phage~Sbash

Mycobacterium~phage~BigNuz

Gordonia~phage~GMA1Mycobacterium~phage~Panchino

Mycobacterium~phage~Che9c

Mycobacterium~phage~Butters

Mycobacterium~phage~Babsiella

Mycobacterium~phage~Redi

Mycobacterium~phage~Cerasum

Mycobacterium~phage~Ardmore

Mycobacterium~phage~Enkosi

Mycobacterium~phage~Liefie

Mycobacterium~phage~PegLegMycobacterium~phage~Larva

Mycobacterium~phage~Sneeze

Gordonia~phage~Smoothie Mycobacterium~phage~Bipper

Mycobacterium~phage~Velveteen

Mycobacterium~phage~Gengar

Mycobacterium~phage~Phrann

Mycobacterium~phage~CharlieMycobacterium~phage~XenoMycobacterium~phage~Donovan

Gordonia~phage~GAL1

Mycobacterium~phage~Squirty

Mycobacterium~phage~Sparky


Gordonia~phage~BetterKatz

Mycobacterium~phage~Malithi

Mycobacterium~phage~Giles


Gordonia~phage~Lucky10

Gordonia~phage~GMA4

Gordonia~phage~Yvonnetastic

Streptomyces~phage~VWB

Gordonia~phage~BritBrat

Mycobacterium~phage~Eremos

Mycobacterium~phage~SuffolkMycobacterium~phage~Newman

Mycobacterium~phage~Oline

Mycobacterium~phage~Badfish

Mycobacterium~phage~Orion

Mycobacterium~phage~Vortex

Mycobacterium~phage~ShiVal

Mycobacterium~phage~JacAttac

Mycobacterium~phage~Phipps

Mycobacterium~phage~ApiziumMycobacterium~phage~Swish

Gordonia~phage~Phinally

Mycobacterium~phage~NigelMycobacterium~phage~Colbert

Mycobacterium~phage~Vista

Mycobacterium~phage~Phlyer

Mycobacterium~phage~Rosebush

Mycobacterium~phage~Gadjet

Mycobacterium~phage~39HC

Mycobacterium~phage~Adawi

Mycobacterium~phage~JAMaL

Tsukamurella~phage~TPA2

Rhodococcus~phage~ReqiPine5

Mycobacterium~phage~OSmaximus

Mycobacterium~phage~Manad


Actinoplanes~phage~phiAsp2

Gordonia~phage~Vivi2

Mycobacterium~phage~Acadian

Mycobacterium~phage~Qyrzula

Mycobacterium~phage~Pipefish

Mycobacterium~phage~Bernardo Mycobacterium~phage~Bane1

Mycobacterium~phage~BrownCNA

Mycobacterium~phage~KayaCho

Mycobacterium~phage~Soto

Mycobacterium~phage~Pops

Mycobacterium~phage~UncleHowie

Mycobacterium~phage~Kikipoo

Mycobacterium~phage~Phelemich

Mycobacterium~phage~Vincenzo

Microbacterium~phage~Min1


VIRSorter_NODE_45_length_6842_cov_19_1861-cat_1Gordonia~phage~GTE6


Mycobacterium~phage~Cooper

VIRSorter_NODE_73_length_4944_cov_7_2104-cat_1VIRSorter_NODE_381_length_2599_cov_8_24108-cat_2Mycobacterium~phage~Phaedrus

Mycobacterium~phage~Baee




Nocardia~phage~NBR1


Gordonia~phage~Wizard

Gordonia~phage~Twister6

Mycobacterium~phage~GUmbie

Mycobacterium~phage~SiSi

Mycobacterium~phage~Rumpelstiltskin

Mycobacterium~phage~SG4

Mycobacterium~phage~KimberliumMycobacterium~phage~Che9d

Mycobacterium~phage~Che8

Mycobacterium~phage~CaptainTrips

Mycobacterium~phage~MosMoris

Mycobacterium~phage~Daenerys

Mycobacterium~phage~Ariel

Mycobacterium~phage~Bobi

Mycobacterium~phage~Snenia

Mycobacterium~phage~Avani

Mycobacterium~phage~Whirlwind

Mycobacterium~phage~Fruitloop

Mycobacterium~phage~PopTart

Mycobacterium~phage~OkiRoe

Gordonia~phage~Bantam

Mycobacterium~phage~Ovechkin

Mycobacterium~phage~Catdawg

Mycobacterium~phage~Angelica

Mycobacterium~phage~DS6A

Mycobacterium~phage~WIVsmall

Mycobacterium~phage~Firecracker

Mycobacterium~phage~Omnicron

Mycobacterium~phage~Mufasa

Mycobacterium~phage~TM4

Mycobacterium~phage~BarrelRoll

Mycobacterium~phage~XFactor

Mycobacterium~phage~CrimD

Tsukamurella~phage~TPA4

Mycobacterium~phage~Bernal13

Mycobacterium~phage~Gaia

Mycobacterium~phage~TheloniousMonkMycobacterium~phage~Solon

Mycobacterium~phage~KBG

Mycobacterium~phage~Graduation

Mycobacterium~phage~Dreamboat

Mycobacterium~phage~Alsfro

Mycobacterium~phage~vB_MapS_FF47

Gordonia~phage~GTE2

Gordonia~phage~OneUp


Mycobacterium~phage~Cheetobro

Mycobacterium~phage~Muddy

Mycobacterium~phage~Validus

Mycobacterium~phage~Bruns

Mycobacterium~phage~fionn

Mycobacterium~phage~ZoeJ

Mycobacterium~phage~Bethlehem

Mycobacterium~phage~Milly

Mycobacterium~phage~Aeneas

Mycobacterium~phage~L5

Mycobacterium~phage~DD5

Mycobacterium~phage~U2

Mycobacterium~phage~Jasper

Mycobacterium~phage~Lamina13

Mycobacterium~phage~Barriga

Mycobacterium~phage~Larenn

Mycobacterium~phage~CRB1

Mycobacterium~phage~Turbido

Mycobacterium~phage~SweetiePie

Mycobacterium~phage~Che12

Mycobacterium~phage~Piro94

Mycobacterium~phage~Luchador

Mycobacterium~phage~EvilGenius

Mycobacterium~phage~Pinto

Mycobacterium~phage~Bactobuster

Mycobacterium~phage~Mulciber

Mycobacterium~phage~Loser

Mycobacterium~phage~Bxb1

Mycobacterium~phage~Wheeler

Mycobacterium~phage~BillKnuckles

Mycobacterium~phage~Alvin

Mycobacterium~phage~Abrogate

Mycobacterium~phage~Sarfire

Mycobacterium~phage~Nhonho

Mycobacterium~phage~Adzzy

Mycobacterium~phage~Equemioh13Mycobacterium~phage~Trike

Mycobacterium~phage~SWU1

Gordonia~phage~RemusMycobacterium~phage~Echild

Mycobacterium~phage~20ESMycobacterium~phage~First

Rhodococcus~phage~CosmicSans

Gordonia~phage~Soups

Mycobacterium~phage~Nyxis

Mycobacterium~phage~HINdeR

Mycobacterium~phage~Trixie

Mycobacterium~phage~Artemis2UCLA

Mycobacterium~phage~Jovo

Mycobacterium~phage~VohminGhazi

Mycobacterium~phage~Bxz2

Mycobacterium~phage~KugelMycobacterium~phage~Tasp14

Mycobacterium~phage~Pari

Mycobacterium~phage~Rufus

Mycobacterium~phage~Violet

Mycobacterium~phage~SkiPole

Mycobacterium~phage~Papez

Mycobacterium~phage~CloudWang3

Mycobacterium~phage~Chadwick

Mycobacterium~phage~FredwardMycobacterium~phage~LittleCherry

Streptomyces~phage~LikaStreptomyces~phage~Sujidade

Gordonia~phage~Cozz

Streptomyces~phage~Nanodon

Streptomyces~phage~CaliburnStreptomyces~phage~LannisterStreptomyces~phage~Zemlya

Streptomyces~phage~Izzy

Mycobacterium~phage~Keshu

Mycobacterium~phage~MurucutumbuMycobacterium~phage~ShedlockHolmes

Mycobacterium~phage~Leo



Mycobacterium~phage~Hosp

Mycobacterium~phage~Jolie1


Mycobacterium~phage~Stinger

Mycobacterium~phage~Zaka

Rhodococcus~phage~RGL3VIRSorter_NODE_2_length_36052_cov_56_7074_GC022966_GC022966-cat_2

Mycobacterium~phage~Theia

Rhodococcus~phage~RER2

Rhodococcus~phage~REQ2

Gordonia~phage~Obliviate

Gordonia~phage~Vendetta









Enterococcus~phage~SANTOR1


Enterococcus~phage~IME-EF4

Enterococcus~phage~EfaCPT1


Bacillus~phage~Pavlov

Streptococcus~phage~SM1


Lactobacillus~phage~LBR48



Lactococcus~phage~BK5-T


Streptococcus~phage~Str-PAP-1









Lactococcus~phage~r1t



Lactococcus~phage~phiLC3


















Staphylococcus~phage~X2


Staphylococcus~phage~Sap26

Staphylococcus~phage~DW2

Staphylococcus~phage~phiETA3



Enterococcus~phage~EFAP-1VIRSorter_NODE_305_length_3204_cov_4_48097-cat_1


Enterococcus~phage~Ec-ZZ2

Enterococcus~phage~IME-EFm1


Lactobacillus~phage~Lv-1

Lactobacillus~phage~Sha1





Staphylococcus~prophage~phiPV83


Staphylococcus~phage~JS01


Staphylococcus~phage~PVL

Staphylococcus~phage~StB20-like

Staphylococcus~phage~StB20

Staphylococcus~phage~phiJB

Staphylococcus~phage~Pvl108


Staphylococcus~phage~phiETA


Staphylococcus~phage~IME-SA4

Staphylococcus~phage~phiRS7



Loktanella~phage~pCB2051-A









Burkholderia~phage~BcepNazgul

VIRSorter_NODE_10_length_40982_cov_79_9576-cat_2 Enterococcus~phage~IME_EF3


Lactobacillus~phage~Lrm1



Lactobacillus~phage~J-1

Lactobacillus~phage~PL-1

Geobacillus~phage~GBK2

Lactobacillus~phage~LF1

Lactobacillus~phage~phiPYB5

Lactobacillus~phage~A2

Lactococcus~phage~BM13



Staphylococcus~phage~phiNMStaphylococcus~phage~phiETA2

Staphylococcus~phage~80alpha

Lactobacillus~phage~PLE2



Staphylococcus~phage~phinm2


Staphylococcus~phage~phiMR25

Brochothrix~phage~NF5




Lactobacillus~phage~phiAT3



Lactobacillus~phage~Lc-Nu























Streptomyces~phage~SV1



























































































































Sulfitobacter~phage~NYA-2014a

























Flavobacterium~phage~2A


Flavobacterium~phage~6H

Flavobacterium~phage~11b

Flavobacterium~phage~1H
























































































Viral RefSeq

Human phage contigs

Bat phage contigs

FIG 9 Network analysis of the phageome of the bat and human pools with the prokaryotic and archaeal viral RefSeq viruses (in light sky blue). In yellow andred are viral contigs shown identified in Cameroonian humans and bat samples, respectively. Gray filled ovals, clusters containing only novel phages; gray openovals, clusters where a large fraction of the phages were identified in this study; brown filled ovals, clusters of novel bat and human phages only.

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family were identified most frequently (Fig. 1B). This is partly because it is one of thelargest viral families and is made up of at least 29 genera, many of which aretransmitted through the fecal-oral or respiratory route (28). Most of these infectionswere in pools of individuals less than 20 years of age (Fig. 1C). This finding is consistentwith previous findings from Cameroon, where a high prevalence of EV in children wasreported using PCR-based approaches (65). Furthermore, most of the EVs here were ofgenotype C, also supporting a recent study that identified a high rate of EV Cs in thenorthern regions of Cameroon (31). Therefore, the high prevalence of EV C is probablynational. However, the absence of genetic relatedness between the Cameroonianhuman EV strains and animal strains (from chimp and gorilla [66]) does not indicateinterspecies transmission of EVs from animals. Additionally, we report for the first time(nearly) complete genomes of picornaviruses of the genera Parechovirus, Cardiovirus,Hepatovirus A, and Cosavirus from Cameroonian patients. This broadens the range ofpicornaviruses found in the Cameroonian population, indicating that picornavirusesmight be playing a vital role in gastroenteric viral infection in the Cameroonianpopulation, especially given that most of these were from samples of sick children.

Rotavirus A (RVA), a common viral gastroenteritis-causing agent, was identified onlyin a limited number of pools. This was previously observed in Cameroon, and possiblereasons for the low prevalence could include the acute nature of rotavirus infections orseasonal changes in rotavirus infections (6). Of note, rotavirus vaccination was intro-duced in Cameroon in April 2014, coinciding with the period of sample collection of thisstudy (February to September 2014); however, the vaccination campaign had notstarted in the sampling locations within this period, and therefore, the result representsa prevaccination rotavirus prevalence status. The identified rotavirus strain showed 3%nt differences with the vaccine strain, further suggesting that this was a wild-type RVAstrain, rather than a vaccine-derived strain.

Uncommon human gastroenteric virus: mammalian orthoreovirus (MORV). This

first MORV strain from Cameroon showed topological incongruence in its phylogeny,thereby pointing to possible reassortment events in the past. The phylogenetic clus-tering of some segments to strains from animals (rodents and bats) could be anindication of a zoonotic event or could also be due to the absence of related strains indatabases from an unknown host. Given that this strain was from a pool of samplesfrom two children suffering from severe diarrhea, it is not unlikely that this strain mighthave contributed to the disease. Therefore, MORV might be playing a greater role indiarrheal diseases in this region than was previously known. Hence, extensive epide-miological studies in different regions and in different hosts are required to fullydelineate the prevalence, genomics, and interspecies transmissibility of MORV.

Viruses not (yet) associated with gastroenteritis: Picobirnaviridae, smacovirus,and Anelloviridae. Apart from the above-mentioned gastroenteritis-related viruses,

several other viruses with unelucidated gastroenteric roles were also identified in thisstudy. First, we observed fewer reads of picobirnaviruses (PBVs) in pools from childrenthan in adults. Previous studies also detected a relatively low percentage of childrenwith PBVs (67, 68). This therefore adds up to the notion that PBVs are likely to be absentin infants and young children and only start to increase with age and potentially achanging diet, though this needs to be further proven (69, 70). Interestingly, thegenetic relatedness of a human picobirna-like virus with one that was found in a batpool from the same region suggests an interspecies transmission. However, thesepicobirna-like sequences are translated using an alternative mitochondrial codon,indicating that their hosts may not be mammals. A principal component analysis of thecodon usage bias of different known mitochondrial genome sequences, mitoviruses,and PBVs seems to suggest that they may have the same lifestyle as mitoviruses knownto infect fungal mitochondria (71). However, the recent identification of a bacterialribosomal binding site in PBV genomes suggests prokaryotes as a potential host (72).Given that the mitochondria have descended from ancient eubacterial endosymbionts




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(73), this may explain the clustering of these PBVs with mitoviruses. Therefore, thequestion about the true host of PBVs remains controversial.

Second, for the first time, two strains of African smacovirus (SCV) were identified inCameroonian samples. Their genetic relatedness to a chimpanzee strain (isolated froma captive chimp in a zoo in San Francisco) and a strain from a child from the UnitedStates (54, 55) indicates either an interspecies transmission event or the presence of ashared viral host in both humans and chimps. Although the role of smacovirus ingastroenteritis has not been elucidated, their presence in cases of unexplained diarrheain French patients seems to indicate a potential role in gastroenteritis (54); hence, thesecould be instances of interspecies transmissions.

The percentages of pools positive for anelloviruses were higher in age categories ofchildren and the old and lower for the middle-aged groups. Given the well-establishednotion that infants and the elderly have reduced immunity (74, 75), this could be in linewith previous studies that suggest a link between the burden of anelloviruses and hostimmune competence (76–78). Despite their ubiquity, Anelloviridae have an undefinedimplication in hosts’ health and are thought to be probably asymptomatic (harmless)or even beneficial. However, they have been associated with hepatitis, pulmonarydiseases, hematologic disorders, myopathy, and lupus, but it is not clear if theirpresence is the cause or the result of disease progression (79–82).

Human viruses and interspecies transmission from bats. In bats from the samearea, we were able to identify gastroenteritis-related and nonrelated viruses. Here, thecorresponding viruses identified from the families Astroviridae (astrovirus), Caliciviridae(sapovirus), and Reoviridae (RVA) are genetically diverse from those identified in batsfrom the same region, indicating no evidence of recent interspecies transmissionsbetween bats and humans (63). However, genetic relatedness of human MORV toanimal strains showed the possibility of zoonosis between humans and not only batsbut animals in general. Additionally, the presence of some Cameroonian strains of SCVand PBV in bats or other animals would indicate interspecies transmissions if theirinfectivity in these animals is fully elucidated.

Human and bat phageome. In this study, we detected a huge phage communitywith a great diversity beyond the range of known bacteriophages in reference data-bases, potentially representing the gut microbiome diversity in the patients (83, 84).Overall, this further supports the idea that the full phageome richness is still to becompletely elucidated (85). Furthermore, network analysis indicates the presence ofcompletely novel phage groups and that phage genera in the gut microbiota might beshared between humans and bats.

Conclusion. Several diverse viruses were discovered in the gut virome of Camer-oonians. Some of these were already known to be the causative agent of gastroen-teritis, whereas others are likely to be the cause of gastroenteric problems in thepatients. Further screening of patients for these viruses will be needed to establish theirprevalence in the population, allowing for more appropriate measures and treatmentand prevention of viral gastroenteritis. Also, to be able to completely elucidate the roleof the novel viruses like pecovirus and smacovirus, more studies are required. Furtherattention should also be given to newly identified viruses (for example, MORV) andtheir potential as emerging pathogens in the human population.

MATERIALS AND METHODSEthical authorization. Ethical authorization for the use of human samples was obtained from the

Cameroon National Ethics Committee, Yaoundé. All human experiments were performed in accordancewith the Ministry’s National Ethics Committee guidelines.

Sample collection and preparation. Human fecal samples were collected between February andSeptember 2014, after informed consent was obtained from patients in two different hospitals (LysokaHealth District and Kumba District Hospital of the Southwest region of Cameroon). This region waschosen because here bats are hunted, sold, and eaten. Diarrheic patients and/or people who came intocontact with bats directly (by eating, hunting, or handling) or indirectly (if a family member was directlyexposed to bats) were eligible for sampling. A total of 221 samples were collected from subjects betweenage 0 and �3 years (age group A, 80 samples), 3 and �20 (age group B, 63 samples), 20 and �60 (agegroup C, 65 samples), and 60 and older (age group D, 13 samples). All the samples were from people who

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had symptoms of gastroenteritis, except 2 from age group C who had contact with bats. Samples werethen placed into labeled tubes containing universal transport medium (UTM), placed on dry ice, andstored at �20°C, until being shipped to the Laboratory of Viral Metagenomics, Leuven, Belgium. Thesamples were stored at �80°C until used (63).

Fecal samples were first diluted using UTM, and equal volumes of the dilutions were pooled basedon the location, age, and bat contact status (direct, indirect, or none). Each pool contained two to fivesamples, and for the different age groups (A to D) we had 22, 17, 20, and 4 pools, respectively. The poolswere then treated according to the NetoVIR protocol (86). Briefly, the pools (10% [wt/vol] fecalsuspensions) were homogenized for 1 min at 3,000 rpm with a Minilys homogenizer (Bertin Technolo-gies) and filtered using an 0.8-�m PES filter (Sartorius). The filtrate was then treated with a cocktail ofBenzonase (Novagen) and micrococcal nuclease (New England Biolabs) at 37°C for 2 h to digestfree-floating nucleic acids. Total nucleic acids (both RNA and DNA) were extracted using the QIAamp viralRNA minikit (Qiagen) according to the manufacturer’s instructions but without addition of carrier RNA tothe lysis buffer. First- and second-strand synthesis and random PCR amplification for 17 cycles wereperformed using a slightly modified whole-transcriptome amplification (WTA2) kit procedure (Sigma-Aldrich). WTA2 products were purified with MSB Spin PCRapace spin columns (Stratec), and the librarieswere prepared for Illumina sequencing using a slightly modified version of the Nextera XT librarypreparation kit (Illumina), which is described in detail in reference 86. Samples were pooled in an attemptto obtain an average of approximately 10 million paired-end reads per pool. Sequencing was performedon a NextSeq 500 high-output platform (Illumina) for 300 cycles (2 � 150-bp paired ends).

Genomic and phylogenetic analysis. NGS reads were analyzed as described in the work of Yindaet al. (20, 63). Briefly, raw reads were trimmed using Trimmomatic (parameters: HEADCROP:19 LEAD-ING:15 TRAILING:15 SLIDINGWINDOW:4:20 MINLEN:50) and FastUniq to remove identical reads. The denovo assembly or reads and annotation of reads were performed using SPAdes (with the meta flag) andDiamond (with the sensitive option using the GenBank nonredundant database), respectively (61, 87, 88).Open reading frames (ORFs) of contigs of interest were identified and further analyzed for conservedmotifs in the amino acid sequences using NCBI’s conserved domain database (CDD) (89). Nucleotide andamino acid alignments of viral sequences were done with MUSCLE implemented in MEGA7 (90) or MAFFT(91). Substitution models were determined using ModelGenerator (92), and phylogenetic trees wereconstructed using RAxML (93), with the autoMRE flag, which enables a posteriori bootstrapping analysis.All trees were visualized in FigTree (http://tree.bio.ed.ac.uk/software/figtree/) and midpoint rooted forpurposes of clarity.

Phageome analysis. Contig annotation with DIAMOND is dependent on the accuracy of thedatabase used, and in most databases, phages are poorly annotated. However, VirSorter uses a manuallycurated database of virus reference genomes augmented with metagenomic viral sequences sampledfrom freshwater, seawater, and human gut, lung, and saliva. Hence, for further identification of bacte-riophages, scaffolds �1 kb were classified using VirSorter (decontamination mode [60]). Only scaffoldsassigned to categories 1 and 2 were considered bacteriophage contigs and were filtered for redundancyat 95% nucleotide identity over 70% of the length using Cluster Genomes (94). Then, trimmed reads fromeach pool were mapped using Bowtie 2 (95) to the bacteriophage contigs, and the generated BAM fileswere filtered to remove reads that aligned at �95% identity using BamM (http://ecogenomics.github.io/BamM/). Abundance tables were obtained and normalized for total number of reads of each sample.For the richness comparison, Mann-Whitney tests were used, and for the clustering, an Adonis test wasperformed. All downstream analyses were done in R (96) using the vegan package (97). Furthermore, toidentify the potential corresponding bacterial host, a database of these contigs was made to which anucleotide BLASTN search (100% identity without gaps) was performed using a fasta file of CRISPRsequences (98) as query. These sequences correspond to different bacterial hosts, and their presence inthe phage genome highlight the potential host of the phage.

To see if the phage community of these humans is related to those of the bats from the same locality,a visualization of the network of both human and bat phageomes was performed using vConTACT (62).Initially, proteins were predicted using Prodigal (99), and combined with the Viral RefSeq of archaeal andprokaryotic predicted proteins. A database was generated from the contigs of bat pools, human pools,and viral RefSeq proteins, and BLASTp was performed against the combined proteins. The output of blastwas used to run vConTACT, and the output network was visualized in Cytoscape (100).

Data availability. All sequences were deposited in GenBank under the following accession numbers:MH608285 to MH608287 and MH933752 to MH933860 (details in Table S3). Raw reads were submittedto the NCBI’s Short Read Archive (SRA) under the project ID PRJNA491626.

SUPPLEMENTAL MATERIALSupplemental material for this article may be found at https://doi.org/10.1128/

mSphere.00585-18.FIG S1, PDF file, 0.1 MB.FIG S2, PDF file, 0.2 MB.FIG S3, PDF file, 0.3 MB.FIG S4, PDF file, 0.2 MB.FIG S5, PDF file, 0.3 MB.FIG S6, PDF file, 0.1 MB.TABLE S1, PDF file, 0.1 MB.




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https://www.ncbi.nlm.nih.gov/nuccore/MH608285




https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA491626





TABLE S2, PDF file, 0.1 MB.TABLE S3, PDF file, 0.1 MB.

ACKNOWLEDGMENTSC.K.Y. was supported by the Interfaculty Council for Development Cooperation (IRO)

from the KU Leuven. N.C.-N. and L.B. were supported by the Flanders Innovation &Entrepreneurship (VLAIO). This work was supported by KU Leuven grant EJX-C9928-StG/15/020BF. The funders had no role in study design, data collection and interpre-tation, or the decision to submit the work for publication.

C.K.Y., S.M.G., M.V.R., and J.M. conceived and designed the study; C.K.Y. and S.M.G.collected the samples; C.K.Y., E.V., N.C.-N., and C.S. performed the experiments; C.K.Y.,E.V., N.C.-N., L.B., W.D., C.S., P.M., and J.M. analyzed the data and drafted the manuscript.All authors read and approved the final manuscript.

The authors declare no competing financial interests.

REFERENCES1. World Health Organization. 2017. Global Health Observatory data re-

pository. GHO | World— diarrhoeal diseases. World Health Organiza-tion, Geneva, Switzerland.

2. WHO. 2015. Levels and trends in child mortality 2015. World HealthOrganization, Geneva, Switzerland.

3. Fong T-T, Lipp EK. 2005. Enteric viruses of humans and animals inaquatic environments: health risks, detection, and potential water qual-ity assessment tools. Microbiol Mol Biol Rev 69:357–371. https://doi.org/10.1128/MMBR.69.2.357-371.2005.

4. Ayukekbong J, Kabayiza J-C, Lindh M, Nkuo-Akenji T, Tah F, BergströmT, Norder H. 2013. Shift of Enterovirus species among children inCameroon; identification of a new enterovirus, EV-A119. J Clin Virol58:227–232. https://doi.org/10.1016/j.jcv.2013.07.005.

5. Santosham M, Chandran A, Fitzwater S, Fischer-Walker C, Baqui AH,Black R. 2010. Progress and barriers for the control of diarrhoealdisease. Lancet 376:63– 67. https://doi.org/10.1016/S0140-6736(10)60356-X.

6. Ayukekbong JA, Andersson ME, Vansarla G, Tah F, Nkuo-AkenjI T,Lindh M, Bergström T. 2014. Monitoring of seasonality of norovirusand other enteric viruses in Cameroon by real-time PCR: an explor-atory study. Epidemiol Infect 142:1393–1402. https://doi.org/10.1017/S095026881300232X.

7. Ayukekbong J, Lindh M, Nenonen N, Tah F, Nkuo-Akenji T, Bergström T.2011. Enteric viruses in healthy children in Cameroon: viral load andgenotyping of norovirus strains. J Med Virol 83:2135–2142. https://doi.org/10.1002/jmv.22243.

8. Ayukekbong JA. 2013. PhD thesis. University of Gothenburg, Gothen-burg, Sweden.

9. Li L, Victoria J, Kapoor A, Blinkova O, Wang C, Babrzadeh F, Mason CJ,Pandey P, Triki H, Bahri O, Oderinde BS, Baba MM, Bukbuk DN, BesserJM, Bartkus JM, Delwart EL. 2009. A novel picornavirus associated withgastroenteritis. J Virol 83:12002–12006. https://doi.org/10.1128/JVI.01241-09.

10. Phan TG, Sdiri-Loulizi K, Aouni M, Ambert-Balay K, Pothier P, Deng X,Delwart E. 2014. New parvovirus in child with unexplained diarrhea,Tunisia. Emerg Infect Dis 20:1911–1913. https://doi.org/10.3201/eid2011.140428.

11. Bosch A, Guix S, Sano D, Pintó RM. 2008. New tools for the study anddirect surveillance of viral pathogens in water. Curr Opin Biotechnol19:295–301. https://doi.org/10.1016/j.copbio.2008.04.006.

12. Fenton M, Simmons N. 2015. Bats, a world of science and mystery. TheUniversity of Chicago Press, Chicago, IL.

13. Rupprecht CE, Smith JS, Fekadu M, Childs JE. 1995. The ascension ofwildlife rabies: a cause for public health concern or intervention? EmergInfect Dis 1:107–114. https://doi.org/10.3201/eid0104.950401.

14. Towner JS, Pourrut X, Albariño CG, Nkogue CN, Bird BH, Grard G,Ksiazek TG, Gonzalez J-P, Nichol ST, Leroy EM. 2007. Marburg virusinfection detected in a common African bat. PLoS One 2:e764. https://doi.org/10.1371/journal.pone.0000764.

15. Leroy EM, Kumulungui B, Pourrut X, Rouquet P, Hassanin A, Yaba P,Delicat A, Paweska JT, Gonzalez J-P, Swanepoel R. 2005. Fruit bats as

reservoirs of Ebola virus. Nature 438:575–576. https://doi.org/10.1038/438575a.

16. Lau SKP, Woo PCY, Li KSM, Huang Y, Tsoi H-W, Wong BHL, Wong SSY,Leung S-Y, Chan K-H, Yuen K-Y. 2005. Severe acute respiratory syn-drome coronavirus-like virus in Chinese horseshoe bats. Proc Natl AcadSci U S A 102:14040 –14045. https://doi.org/10.1073/pnas.0506735102.

17. Memish ZA, Mishra N, Olival KJ, Fagbo SF, Kapoor V, Epstein JH,AlHakeem R, Durosinloun A, Al Asmari M, Islam A, Kapoor A, Briese T,Daszak P, Al Rabeeah AA, Lipkin WI. 2013. Middle East respiratorysyndrome coronavirus in bats, Saudi Arabia. Emerg Infect Dis 19:1819 –1823. https://doi.org/10.3201/eid1911.131172.

18. Chua KB, Lek Koh C, Hooi PS, Wee KF, Khong JH, Chua BH, Chan YP, LimME, Lam SK. 2002. Isolation of Nipah virus from Malaysian Islandflying-foxes. Microbes Infect 4:145–151.

19. Wong S, Lau S, Woo P, Yuen K-YY. 2007. Bats as a continuing source ofemerging infections in humans. Rev Med Virol 17:67–91. https://doi.org/10.1002/rmv.520.

20. Yinda CK, Rector A, Zeller M, Conceição-Neto N, Heylen E, Maes P,Stephen GM, Van Ranst M, Matthijnssens J, Ghogomu SM, Van Ranst M,Matthijnssens J. 2016. A single bat species in Cameroon harbors mul-tiple highly divergent papillomaviruses in stool identified by metag-enomics analysis. Virol Rep 6:74 – 80. https://doi.org/10.1016/j.virep.2016.08.001.

21. Yinda CK, Zell R, Deboutte W, Zeller M, Conceição-Neto N, Heylen E,Maes P, Knowles NJ, Ghogomu SM, Van Ranst M, Matthijnssens J. 2017.Highly diverse population of Picornaviridae and other members of thePicornavirales, in Cameroonian fruit bats. BMC Genomics 18:249.https://doi.org/10.1186/s12864-017-3632-7.

22. Yinda CK, Conceição-Neto N, Zeller M, Heylen E, Maes P, Ghogomu SM,Van Ranst M, Matthijnssens J. 2017. Novel highly divergent sapovirusesdetected by metagenomics analysis in straw-colored fruit bats in Cam-eroon. Emerg Microbes Infect 6:e38. https://doi.org/10.1038/emi.2017.20.

23. Yinda CK, Ghogomu SM, Conceição-Neto N, Beller L, Deboutte W,Vanhulle E, Maes P, Van Ranst M, Matthijnssens J. 2018. Cameroonianfruit bats harbor divergent viruses, including rotavirus H, bastroviruses,and picobirnaviruses using an alternative genetic code. Virus Evol4:vey008. https://doi.org/10.1093/ve/vey008.

24. Steyer A, Gutiérrez-Aguire I, Kolenc M, Koren S, Kutnjak D, Pokorn M,Poljšak-Prijatelj M, Racki N, Ravnikar M, Sagadin M, Fratnik Steyer A,Toplak N. 2013. High similarity of novel orthoreovirus detected in achild hospitalized with acute gastroenteritis to mammalian orthoreo-viruses found in bats in Europe. J Clin Microbiol 51:3818 –3825. https://doi.org/10.1128/JCM.01531-13.

25. Lelli D, Moreno A, Lavazza A, Bresaola M, Canelli E, Boniotti MB, CordioliP. 2013. Identification of mammalian orthoreovirus type 3 in Italianbats. Zoonoses Public Health 60:84 –92. https://doi.org/10.1111/zph.12001.

26. Ciarlet M, Estes M. 2002. Rotaviruses: basic biology, epidemiology andmethodologies, p 2573–2773. In Britton G (ed), Encyclopedia of envi-ronmental microbiology, John Wiley & Sons, New York, NY.

Yinda et al.



sphere.asm.org/

Dow

nloaded from

https://doi.org/10.1128/MMBR.69.2.357-371.2005

https://doi.org/10.1128/MMBR.69.2.357-371.2005

https://doi.org/10.1016/j.jcv.2013.07.005

https://doi.org/10.1016/S0140-6736(10)60356-X

https://doi.org/10.1016/S0140-6736(10)60356-X

https://doi.org/10.1017/S095026881300232X

https://doi.org/10.1017/S095026881300232X

https://doi.org/10.1002/jmv.22243


https://doi.org/10.1128/JVI.01241-09

https://doi.org/10.1128/JVI.01241-09

https://doi.org/10.3201/eid2011.140428

https://doi.org/10.3201/eid2011.140428

https://doi.org/10.1016/j.copbio.2008.04.006

https://doi.org/10.3201/eid0104.950401

https://doi.org/10.1371/journal.pone.0000764


https://doi.org/10.1038/438575a

https://doi.org/10.1038/438575a

https://doi.org/10.1073/pnas.0506735102

https://doi.org/10.3201/eid1911.131172

https://doi.org/10.1002/rmv.520

https://doi.org/10.1002/rmv.520

https://doi.org/10.1016/j.virep.2016.08.001

https://doi.org/10.1016/j.virep.2016.08.001

https://doi.org/10.1186/s12864-017-3632-7

https://doi.org/10.1038/emi.2017.20

https://doi.org/10.1038/emi.2017.20

https://doi.org/10.1093/ve/vey008

https://doi.org/10.1128/JCM.01531-13

https://doi.org/10.1128/JCM.01531-13

https://doi.org/10.1111/zph.12001

https://doi.org/10.1111/zph.12001



27. Estes MK, Cohen J. 1989. Rotavirus gene structure and function. Micro-biol Rev 53:410 – 449.

28. Knowles NJ, Hovi T, Hyypiä T, King AMQ, Lindberg M, Pallansch MA,Palmenberg AC, Simmonds P, Skern T, Stanway G, Yamashita T, Zell R.2012. Picornaviridae, p 855– 880. In King AMQ, Adams MJ, Carstens EB,Lefkowitz EJ (ed), Virus taxonomy: classification and nomenclature ofviruses. Ninth report of the International Committee on Taxonomy ofViruses. Elsevier, San Diego, CA.

29. Tracy S, Chapman NM, Drescher KM, Kono K, Tapprich W. 2006. Evolu-tion of virulence in picornaviruses, p 193–209. In Domingo E (ed),Quasispecies: concept and implications for virology. Springer, Berlin,Germany.

30. Wang X, Ren J, Gao Q, Hu Z, Sun Y, Li X, Rowlands DJ, Yin W, Wang J, StuartDI, Rao Z, Fry EE. 2015. Hepatitis A virus and the origins of picornaviruses.Nature 517:85–88. https://doi.org/10.1038/nature13806.

31. Sadeuh-Mba SA, Bessaud M, Massenet D, Joffret M-L, Endegue M-C,Njouom R, Reynes J-M, Rousset D, Delpeyroux F. 2013. High frequencyand diversity of species C enteroviruses in Cameroon and neighboringcountries. J Clin Microbiol 51:759 –770. https://doi.org/10.1128/JCM.02119-12.

32. Kroneman A, Vennema H, Deforche K, Avoort HVD, Peñaranda S,Oberste MS, Vinjé J, Koopmans M. 2011. An automated genotyping toolfor enteroviruses and noroviruses. J Clin Virol 51:121–125. https://doi.org/10.1016/j.jcv.2011.03.006.

33. Tolf C, Gullberg M, Johansson ES, Tesh RB, Andersson B, LindbergAM. 2009. Molecular characterization of a novel Ljungan virus(Parechovirus; Picornaviridae) reveals a fourth genotype and indicatesancestral recombination. J Gen Virol 90:843– 853. https://doi.org/10.1099/vir.0.007948-0.

34. Sun G, Wang Y, Tao G, Shen Q, Cao W, Chang X, Zhang W, Shao C, YiM, Shao S, Yang Y. 2012. Complete genome sequence of a novel typeof human parechovirus strain reveals natural recombination events. JVirol 86:8892– 8893. https://doi.org/10.1128/JVI.01241-12.

35. Figueroa JP, Ashley D, King D, Hull B. 1989. An outbreak of acute flaccidparalysis in Jamaica associated with echovirus type 22. J Med Virol29:315–319.

36. Koskiniemi M, Paetau R, Linnavuori K. 1989. Severe encephalitis asso-ciated with disseminated echovirus 22 infection. Scand J Infect Dis21:463– 466.

37. Oberste MS, Maher K, Kilpatrick DR, Pallansch MA. 1999. Molecularevolution of the human enteroviruses: correlation of serotype with VP1sequence and application to picornavirus classification. J Virol 73:1941–1948.

38. Chuchaona W, Khamrin P, Yodmeeklin A, Saikruang W, KongsricharoernT, Ukarapol N, Okitsu S, Hayakawa S, Ushijima H, Maneekarn N. 2015.Detection and characterization of a novel human parechovirus geno-type in Thailand. Infect Genet Evol 31:300 –304. https://doi.org/10.1016/j.meegid.2015.02.003.

39. Holtz LR, Finkbeiner SR, Kirkwood CD, Wang D. 2008. Identification ofa novel picornavirus related to cosaviruses in a child with acute diar-rhea. Virol J 5:159. https://doi.org/10.1186/1743-422X-5-159.

40. Naeem A, Hosomi T, Nishimura Y, Alam MM, Oka T, Zaidi SSZ, ShimizuH. 2014. Genetic diversity of circulating Saffold viruses in Pakistan andAfghanistan. J Gen Virol 95:1945–1957. https://doi.org/10.1099/vir.0.066498-0.

41. Chiu CY, Greninger AL, Kanada K, Kwok T, Fischer KF, Runckel C, LouieJK, Glaser CA, Yagi S, Schnurr DP, Haggerty TD, Parsonnet J, Ganem D,DeRisi JL. 2008. Identification of cardioviruses related to Theiler’s mu-rine encephalomyelitis virus in human infections. Proc Natl Acad SciU S A 105:14124 –14129. https://doi.org/10.1073/pnas.0805968105.

42. Ren L, Gonzalez R, Xiao Y, Xu X, Chen L, Vernet G, Paranhos-Baccalà G,Jin Q, Wang J. 2009. Saffold cardiovirus in children with acute gastro-enteritis, Beijing, China. Emerg Infect Dis 15:1509 –1511. https://doi.org/10.3201/eid1509.081531.

43. Cristina J, Costa-Mattioli M. 2007. Genetic variability and molecularevolution of hepatitis A virus. Virus Res 127:151–157. https://doi.org/10.1016/j.virusres.2007.01.005.

44. Franco E, Meleleo C, Serino L, Sorbara D, Zaratti L. 2012. Hepatitis A:epidemiology and prevention in developing countries. World J Hepatol4:68 –73. https://doi.org/10.4254/wjh.v4.i3.68.

45. Tjon GMS, Wijkmans CJ, Coutinho RA, Koek AG, van den Hoek JAR,Leenders ACAP, Schneeberger PM, Bruisten SM. 2005. Molecular epi-demiology of hepatitis A in Noord-Brabant, The Netherlands. J Clin Virol32:128 –136. https://doi.org/10.1016/j.jcv.2004.03.008.

46. Donato C, Vijaykrishna D. 2017. The broad host range and geneticdiversity of mammalian and avian astroviruses. Viruses 9:102. https://doi.org/10.3390/v9050102.

47. Xi JN, Graham DY, Wang KN, Estes MK. 1990. Norwalk virus genomecloning and characterization. Science 250:1580 –1583.

48. McFadden N, Bailey D, Carrara G, Benson A, Chaudhry Y, Shortland A,Heeney J, Yarovinsky F, Simmonds P, Macdonald A, Goodfellow I. 2011.Norovirus regulation of the innate immune response and apoptosisoccurs via the product of the alternative open reading frame 4. PLoSPathog 7:e1002413. https://doi.org/10.1371/journal.ppat.1002413.

49. Zheng D-P, Ando T, Fankhauser RL, Beard RS, Glass RI, Monroe SS. 2006.Norovirus classification and proposed strain nomenclature. Virology346:312–323. https://doi.org/10.1016/j.virol.2005.11.015.

50. Oka T, Lu Z, Phan T, Delwart EL, Saif LJ, Wang Q. 2016. Geneticcharacterization and classification of human and animal sapoviruses.PLoS One 11:e0156373. https://doi.org/10.1371/journal.pone.0156373.

51. Olarte-Castillo XA, Hofer H, Goller KV, Martella V, Moehlman PD, EastML. 2016. Divergent sapovirus strains and infection prevalence in wildcarnivores in the Serengeti ecosystem: a long-term study. PLoS One11:e0163548. https://doi.org/10.1371/journal.pone.0163548.

52. Conceicao-Neto N, Mesquita JR, Zeller M, Yinda CK, Álvares F, Roque S,Petrucci-Fonseca F, Godinho R, Heylen E, Van Ranst M, Matthijnssens J.2016. Reassortment among picobirnaviruses found in wolves. ArchVirol 161:2859 –2862. https://doi.org/10.1007/s00705-016-2987-4.

53. Malik YS, Kumar N, Sharma K, Dhama K, Shabbir MZ, Ganesh B, Ko-bayashi N, Banyai K. 2014. Epidemiology, phylogeny, and evolution ofemerging enteric Picobirnaviruses of animal origin and their relation-ship to human strains. Biomed Res Int 2014:780752. https://doi.org/10.1155/2014/780752.

54. Ng TFF, Zhang W, Sachsenröder J, Kondov NO, da Costa AC, Vega E,Holtz LR, Wu G, Wang D, Stine CO, Antonio M, Mulvaney US, MuenchMO, Deng X, Ambert-Balay K, Pothier P, Vinjé J, Delwart E. 2015. Adiverse group of small circular ssDNA viral genomes in human andnon-human primate stools. Virus Evol 1:vev017. https://doi.org/10.1093/ve/vev017.

55. Phan TG, da Costa AC, del Valle Mendoza J, Bucardo-Rivera F, NordgrenJ, O’Ryan M, Deng X, Delwart E. 2016. The fecal virome of South andCentral American children with diarrhea includes small circular DNAviral genomes of unknown origin. Arch Virol 161:959 –966. https://doi.org/10.1007/s00705-016-2756-4.

56. Smits SL, Schapendonk CME, van Beek J, Vennema H, Schürch AC,Schipper D, Bodewes R, Haagmans BL, Osterhaus ADME, KoopmansMP. 2014. New viruses in idiopathic human diarrhea cases, the Neth-erlands. Emerg Infect Dis 20:1218 –1222. https://doi.org/10.3201/eid2007.140190.

57. Cheung AK, Ng TF, Lager KM, Alt DP, Delwart EL, Pogranichniy RM.2014. Unique circovirus-like genome detected in pig feces. GenomeAnnounc 2:e00251-14. https://doi.org/10.1128/genomeA.00251-14.

58. Woo PCY, Lau SKP, Teng JLL, Tsang AKL, Joseph M, Wong EYM, Tang Y,Sivakumar S, Bai R, Wernery R, Wernery U, Yuen K-Y. 2014. Metag-enomic analysis of viromes of dromedary camel fecal samples revealslarge number and high diversity of circoviruses and picobirnaviruses.Virology 471– 473:117–125. https://doi.org/10.1016/j.virol.2014.09.020.

59. Kraberger S, Argüello-Astorga GR, Greenfield LG, Galilee C, Law D,Martin DP, Varsani A. 2015. Characterisation of a diverse range ofcircular replication-associated protein encoding DNA viruses recoveredfrom a sewage treatment oxidation pond. Infect Genet Evol 31:73– 86.https://doi.org/10.1016/j.meegid.2015.01.001.

60. Roux S, Enault F, Hurwitz BL, Sullivan MB. 2015. VirSorter: mining viralsignal from microbial genomic data. PeerJ 3:e985. https://doi.org/10.7717/peerj.985.

61. Buchfink B, Xie C, Huson DH. 2015. Fast and sensitive protein alignmentusing DIAMOND. Nat Methods 12:59 – 60. https://doi.org/10.1038/nmeth.3176.

62. Bolduc B, Jang HB, Doulcier G, You Z-Q, Roux S, Sullivan MB. 2017.vConTACT: an iVirus tool to classify double-stranded DNA viruses thatinfect Archaea and Bacteria. PeerJ 5:e3243. https://doi.org/10.7717/peerj.3243.

63. Yinda CK, Zeller M, Conceicaõ-Neto N, Maes P, Deboutte W, Beller L,Heylen E, Ghogomu SM, Van Ranst M, Matthijnssens J. 2016. Novelhighly divergent reassortant bat rotaviruses in Cameroon, withoutevidence of zoonosis. Sci Rep 6:34209. https://doi.org/10.1038/srep34209.




sphere.asm.org/

Dow

nloaded from

https://doi.org/10.1038/nature13806

https://doi.org/10.1128/JCM.02119-12

https://doi.org/10.1128/JCM.02119-12



https://doi.org/10.1099/vir.0.007948-0

https://doi.org/10.1099/vir.0.007948-0

https://doi.org/10.1128/JVI.01241-12

https://doi.org/10.1016/j.meegid.2015.02.003


https://doi.org/10.1186/1743-422X-5-159

https://doi.org/10.1099/vir.0.066498-0

https://doi.org/10.1099/vir.0.066498-0

https://doi.org/10.1073/pnas.0805968105

https://doi.org/10.3201/eid1509.081531

https://doi.org/10.3201/eid1509.081531

https://doi.org/10.1016/j.virusres.2007.01.005

https://doi.org/10.1016/j.virusres.2007.01.005

https://doi.org/10.4254/wjh.v4.i3.68


https://doi.org/10.3390/v9050102

https://doi.org/10.3390/v9050102

https://doi.org/10.1371/journal.ppat.1002413

https://doi.org/10.1016/j.virol.2005.11.015



https://doi.org/10.1007/s00705-016-2987-4

https://doi.org/10.1155/2014/780752

https://doi.org/10.1155/2014/780752

https://doi.org/10.1093/ve/vev017

https://doi.org/10.1093/ve/vev017

https://doi.org/10.1007/s00705-016-2756-4

https://doi.org/10.1007/s00705-016-2756-4

https://doi.org/10.3201/eid2007.140190

https://doi.org/10.3201/eid2007.140190

https://doi.org/10.1128/genomeA.00251-14



https://doi.org/10.7717/peerj.985


https://doi.org/10.1038/nmeth.3176




https://doi.org/10.1038/srep34209




64. Clokie MRJ, Millard AD, Letarov AV, Heaphy S. 2011. Phages in nature.Bacteriophage 1:31– 45. https://doi.org/10.4161/bact.1.1.14942.

65. Ayukekbong JA, Fobisong C, Lindh M, Nkuo-Akenji T, Bergström T,Norder H. 2014. Molecular analysis of enterovirus in Cameroon bypartial 5=UTR-VP4 gene sequencing reveals a high genetic diversity andfrequency of infections. J Med Virol 86:2092–2101. https://doi.org/10.1002/jmv.23926.

66. Sadeuh-Mba SA, Bessaud M, Joffret M-L, Endegue Zanga M-C, BalanantJ, Mpoudi Ngole E, Njouom R, Reynes J-M, Delpeyroux F, Rousset D.2014. Characterization of enteroviruses from non-human primates inCameroon revealed virus types widespread in humans along withcandidate new types and species. PLoS Negl Trop Dis 8:e3052. https://doi.org/10.1371/journal.pntd.0003052.

67. Cascio A, Bosco M, Vizzi E, Giammanco A, Ferraro D, Arista S. 1996.Identification of picobirnavirus from faeces of Italian children sufferingfrom acute diarrhea. Eur J Epidemiol 12:545–547.

68. Pereira H, Linhares A, Candeias JA, Glass R. 1993. National laboratorysurveillance of viral agents of gastroenteritis in Brazil. Pan Am J PublicHeal 27:224 –233.

69. Lim ES, Wang D, Holtz LR. 2016. The bacterial microbiome and viromemilestones of infant development. Trends Microbiol 24:801– 810.https://doi.org/10.1016/j.tim.2016.06.001.

70. Lim ES, Zhou Y, Zhao G, Bauer IK, Droit L, Ndao IM, Warner BB, Tarr PI,Wang D, Holtz LR. 2015. Early life dynamics of the human gut viromeand bacterial microbiome in infants. Nat Med 21:1228 –1234. https://doi.org/10.1038/nm.3950.

71. Hong Y, Dover SL, Cole TE, Brasier CM, Buck KW. 1999. Multiple mito-chondrial viruses in an isolate of the Dutch elm disease fungus Ophios-toma novo-ulmi. Virology 258:118 –127. https://doi.org/10.1006/viro.1999.9691.

72. Krishnamurthy SR, Wang D. 2018. Extensive conservation of prokaryoticribosomal binding sites in known and novel picobirnaviruses. Virology516:108 –114. https://doi.org/10.1016/j.virol.2018.01.006.

73. Dyall SD, Brown MT, Johnson PJ. 2004. Ancient invasions: from endo-symbionts to organelles. Science 304:253–257. https://doi.org/10.1126/science.1094884.

74. Simon AK, Hollander GA, McMichael A. 2015. Evolution of the immunesystem in humans from infancy to old age. Proc R Soc B Biol Sci 282:20143085. https://doi.org/10.1098/rspb.2014.3085.

75. Katz JM, Plowden J, Renshaw-Hoelscher M, Lu X, Tumpey TM, Samb-hara S. 2004. Immunity to influenza. Immunol Res 29:113–124. https://doi.org/10.1385/IR:29:1-3:113.

76. Brodin P, Davis MM. 2017. Human immune system variation. Nat RevImmunol 17:21–29. https://doi.org/10.1038/nri.2016.125.

77. De Vlaminck I, Khush KK, Strehl C, Kohli B, Luikart H, Neff NF, OkamotoJ, Snyder TM, Cornfield DN, Nicolls MR, Weill D, Bernstein D, ValantineHA, Quake SR. 2013. Temporal response of the human virome toimmunosuppression and antiviral therapy. Cell 155:1178 –1187. https://doi.org/10.1016/j.cell.2013.10.034.

78. Béland K, Dore-Nguyen M, Gagné M-J, Patey N, Brassard J, Alvarez F,Halac U. 2014. Torque Teno virus in children who underwent ortho-topic liver transplantation: new insights about a common pathogen. JInfect Dis 209:247–254. https://doi.org/10.1093/infdis/jit423.

79. Maggi F, Pifferi M, Fornai C, Andreoli E, Tempestini E, Vatteroni M,Presciuttini S, Marchi S, Pietrobelli A, Boner A, Pistello M, Bendinelli M.2003. TT virus in the nasal secretions of children with acute respiratorydiseases: relations to viremia and disease severity. J Virol 77:2418 –2425.

80. Chung J-Y, Han TH, Koo JW, Kim SW, Seo JK, Hwang ES. 2007. Smallanellovirus infections in Korean children. Emerg Infect Dis 13:791–793.https://doi.org/10.3201/eid1305.061149.

81. Miyamoto M, Takahashi H, Sakata I, Adachi Y. 2000. Hepatitis-associatedaplastic anemia and transfusion-transmitted virus infection. Intern Med39:1068 –1070.

82. Spandole S, Cimponeriu D, Berca LM, Mihaescu G. 2015. Humananelloviruses: an update of molecular, epidemiological and clinicalaspects. Arch Virol 160:893–908. https://doi.org/10.1007/s00705-015-2363-9.

83. Minot S, Sinha R, Chen J, Li H, Keilbaugh SA, Wu GD, Lewis JD, BushmanFD. 2011. The human gut virome: inter-individual variation and dy-namic response to diet. Genome Res 21:1616 –1625. https://doi.org/10.1101/gr.122705.111.

84. Reyes A, Haynes M, Hanson N, Angly FE, Heath AC, Rohwer F, GordonJI. 2010. Viruses in the fecal microbiota of monozygotic twins and theirmothers. Nature 466:334 –338. https://doi.org/10.1038/nature09199.

85. Rohwer F. 2003. Global phage diversity. Cell 113:141.86. Conceicao-Neto N, Zeller M, Lefrere H, De Bruyn P, Beller L, Deboutte W,

Yinda CK, Lavigne R, Maes P, Van Ranst M, Heylen E, Matthijnssens J.2015. Modular approach to customise sample preparation proceduresfor viral metagenomics: a reproducible protocol for virome analysis. SciRep 5:16532. https://doi.org/10.1038/srep16532.

87. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmerfor Illumina sequence data. Bioinformatics 30:2114 –2120. https://doi.org/10.1093/bioinformatics/btu170.

88. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS,Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV,Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a newgenome assembly algorithm and its applications to single-cell se-quencing. J Comput Biol 19:455– 477. https://doi.org/10.1089/cmb.2012.0021.

89. Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, Geer LY,Geer RC, He J, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Marchler GH,Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C, BryantSH. 2015. CDD: NCBI’s conserved domain database. Nucleic Acids Res43:D222–D226. https://doi.org/10.1093/nar/gku1221.

90. Kumar S, Stecher G, Tamura K. 2016. MEGA7: molecular evolutionarygenetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870 –1874. https://doi.org/10.1093/molbev/msw054.

91. Katoh K, Misawa K, Kuma K, Miyata T. 2002. MAFFT: a novel method forrapid multiple sequence alignment based on fast Fourier transform.Nucleic Acids Res 30:3059 –3066.

92. Keane TM, Creevey CJ, Pentony MM, Naughton TJ, McInerney JO. 2006.Assessment of methods for amino acid matrix selection and their useon empirical data shows that ad hoc assumptions for choice of matrixare not justified. BMC Evol Biol 6:29. https://doi.org/10.1186/1471-2148-6-29.

93. Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysisand post-analysis of large phylogenies. Bioinformatics 30:1312–1313.https://doi.org/10.1093/bioinformatics/btu033.

94. Bolduc B, Roux S. 2017. Clustering viral genomes in iVirus. https://www.protocols.io/view/clustering-viral-genomes-in-ivirus-gwebxbe.

95. Langmead B, Salzberg SL. 2012. Fast gapped-read alignment withBowtie 2. Nat Methods 9:357–359. https://doi.org/10.1038/nmeth.1923.

96. R Core Team. 2016. R: a language and environment for statisticalcomputing. R Foundation for Statistical Computing, Vienna, Austria.

97. Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O’Hara RB,Simpson GL, Solymos P, Stevens MHH, Wagner H. 2017. vegan: Com-munity Ecology Package. https://cran.r-project.org/web/packages/vegan/index.html.

98. Grissa I, Vergnaud G, Pourcel C. 2007. The CRISPRdb database and toolsto display CRISPRs and to generate dictionaries of spacers and repeats.BMC Bioinformatics 8:172. https://doi.org/10.1186/1471-2105-8-172.

99. Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. 2010.Prodigal: prokaryotic gene recognition and translation initiation siteidentification. BMC Bioinformatics 11:119. https://doi.org/10.1186/1471-2105-11-119.

100. Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C,Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R,Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, PicoAR, Vailaya A, Wang P-L, Adler A, Conklin BR, Hood L, Kuiper M, SanderC, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD. 2007.Integration of biological networks and gene expression data usingCytoscape. Nat Protoc 2:2366 –2382. https://doi.org/10.1038/nprot.2007.324.

Yinda et al.



sphere.asm.org/

Dow

nloaded from

https://doi.org/10.4161/bact.1.1.14942



https://doi.org/10.1371/journal.pntd.0003052

https://doi.org/10.1371/journal.pntd.0003052

https://doi.org/10.1016/j.tim.2016.06.001

https://doi.org/10.1038/nm.3950

https://doi.org/10.1038/nm.3950

https://doi.org/10.1006/viro.1999.9691

https://doi.org/10.1006/viro.1999.9691


https://doi.org/10.1126/science.1094884

https://doi.org/10.1126/science.1094884

https://doi.org/10.1098/rspb.2014.3085

https://doi.org/10.1385/IR:29:1-3:113

https://doi.org/10.1385/IR:29:1-3:113

https://doi.org/10.1038/nri.2016.125

https://doi.org/10.1016/j.cell.2013.10.034

https://doi.org/10.1016/j.cell.2013.10.034

https://doi.org/10.1093/infdis/jit423

https://doi.org/10.3201/eid1305.061149

https://doi.org/10.1007/s00705-015-2363-9

https://doi.org/10.1007/s00705-015-2363-9

https://doi.org/10.1101/gr.122705.111

https://doi.org/10.1101/gr.122705.111

https://doi.org/10.1038/nature09199


https://doi.org/10.1093/bioinformatics/btu170


https://doi.org/10.1089/cmb.2012.0021

https://doi.org/10.1089/cmb.2012.0021

https://doi.org/10.1093/nar/gku1221

https://doi.org/10.1093/molbev/msw054

https://doi.org/10.1186/1471-2148-6-29

https://doi.org/10.1186/1471-2148-6-29


https://www.protocols.io/view/clustering-viral-genomes-in-ivirus-gwebxbe

https://www.protocols.io/view/clustering-viral-genomes-in-ivirus-gwebxbe


https://cran.r-project.org/web/packages/vegan/index.html

https://cran.r-project.org/web/packages/vegan/index.html

https://doi.org/10.1186/1471-2105-8-172

https://doi.org/10.1186/1471-2105-11-119

https://doi.org/10.1186/1471-2105-11-119

https://doi.org/10.1038/nprot.2007.324

https://doi.org/10.1038/nprot.2007.324



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