Gastroenteric viruses: Current status Jim Gray Professor of Clinical Virology, UEA & Consultant Virologist, NNUH

Gastroenteric viruses:Current status

Jim GrayProfessor of Clinical Virology,UEA &Consultant Virologist, NNUH

Viruses infecting the gutViruses associated with gastroenteritis

• rotaviruses• caliciviruses

• noroviruses • sapoviruses

• astroviruses• adenoviruses 40, 41

Noroviruses

Sapoviruses

Rotaviruses

Astroviruses

Adenoviruses

Viruses infecting the gut

Presumptive gastroenteric viruses

• Torovirus• Coronavirus• Parvovirus: Bocavirus• Picobirnavirus• Aichi virus

Torovirus

Coronavirus

Parvovirus

Kobuvirus

Noroviruses

• Family : Caliciviridae

• Non-enveloped small round structured viruses (27-32 nm diameter)

• Genome: pos sense ssRNA ~ 7.5kb

• Endemic and epidemic in the community

• The most common cause of outbreaks of gastroenteritis

Noroviruses

NorovirusClinical manifestations

Nausea - 79%Vomiting - 69%Diarrhoea - 66%Fever - 37%Chills - 32%Abdominal cramps - 30%Myalgias -26%Headache - 22%Sore throat - 18%

• Incubation period: 10-50h• Duration of symptoms: 24-48h• Excrete >106 particles/g or ml • Infectious dose: 10 virus particles

Infects enterocytes of the duodenum and jejunum resulting in malabsorption and increased secretion

SeasonalitySeasonality

0

10

20

30

40

50

60

% d

ete

cti

on

case

cont

rols

case

cont

rols

case

cont

rols

case

cont

rols

case

cont

rols

case

cont

rols

case

cont

rols

case

cont

rols

case

cont

rols

case

cont

rols

case

cont

rols

case

cont

rols

<1 1 to 4 5 to 9 10 to19

20 to29

30 to39

40 to49

50 to59

60 to69

70 to79

80 to93

Allage

Age and specimens

Norovirus detection

Age distribution of norovirus infection in cases of gastroenteritis and age-matched controls (IID study: Amar et al)

Temperature inactivation of norovirus

Fort LauderdaleSaint Cloud

Alphatron

Jena

NewburyCH126

Blakemore

Winchester

DSV

Stavanger

KY89Norwalk

HesseSindlesham

SouthamptonWhiteRose

Musgrove318/S05/95

Thistle

Chiba

Malta

Koblenz

BristolLordsdale

TorontoMexico

Seacroft

Sw43Limburg

Leeds273/Gwyned

M7

Amsterdam

VA97207Idaho Fall

FayettevilleKashiwa47

Erfurt 546

Snow MountainMelkshamHillingdon

290/White River

GirlingtonHawaii

Wortley/90314/S19/94

GGII

GGIII

GGI

GGIV

MNV-1

GGV

Phylogenetic grouping among noroviruses

Mechanisms for generating genomic and antigenic diversity

Noroviruses• Genetic recombination during dual infection of a single cell• Accumulation of point mutations

Rotaviruses• Genetic reassortment during dual infection of a single cell• Accumulation of point mutations• Genome rearrangement

Inter- and Intra-seasonal diversity of NoV genotypes during 2003 to 2006. Early, mid and late season outbreaks characterised.

Genotype 2003/04 2004/05 2005/06

Early Mid Late Early Mid Late Early Mid Late

GI-1 0 0 0 0 0 0 0 1 (5%) 0

GI-2 1 (5%) 0 0 0 0 0 0 0 0

GI-3 1 (5%) 0 0 0 0 0 0 1 (5%) 0

GI-4 0 0 0 0 0 0 0 3 (15%) 0

GI-6 2 (10%) 0 0 0 0 0 0 0 0

GII-1 0 0 0 0 0 1 (5%) 0 1 (5%) 0

GII-2 3 (15%) 1 (5%) 0 4 (20%) 2 (10%) 0 0 1 (5%) 0

GII-3 7 (35%) 3 (15%) 2 (10%) 0 0 0 0 2 (10%) 0

GII-4 1 (5%) 14 (70%) 18 (90%) 14 (70%) 18 (90%) 18* (90%) 9 (45%) 7 (35%) 18 (90%)

GII-6 1 (5%) 0 0 2 (10%) 1 (5%) 0 2 (10%) 0 1 (5%)

GII-7 3 (15%) 2 (10%) 0 0 0 1(5%) 6 (30%) 3 (15%) 1 (5%)

GII-8 1 (5%) 0 0 0 0 0 0 1 (5%) 0

Total 20 20 20 20 20 20 20 20 20

Total of

genotypes

3 GI

6 GII

4 GII 2 GII 3 GII 3 GII 2 GII 4 GII 3 GI

6 GII

3 GII

Early = September/October, Middle = December, Late = March, GII = Genogroup II, GI = Genogroup I, * = February and March

Highlights the fitness of GII-4 to infect the human population against a background of herd immunity

Emergence of GII-4 variants

0%

20%

40%

60%

80%

100%

Sep

-03

Nov

-03

Jan-

04

Mar

-04

May

-04

Jul-0

4

Sep

-04

Nov

-04

Jan-

05

Mar

-05

May

-05

Jul-0

5

Sep

-05

Nov

-05

Jan-

06

Mar

-06

May

-06

Jul-0

6

Sep

-06

Nov

-06

Jan-

07

Mar

-07

May

-07

Jul-0

7

Sep

-07

v11

v10

v8

v6

v5

v4

v3

v2

GII-4 variants: September 2003 to September 2007

Norovirus [Norwalk]

Norovirus [Grimsby]

Sapovirus

Vesivirus (SMSV)

Calicivirus structure

Protruding domain

Autumn Winter Spring Summer Autumn Winter Spring Summer

GII4 variant is selected, out of season outbreaks occur, becomes epidemic

Normal winter season

Narrowing diversity: GII4 predominates

GII4 variants emerge

Return to normal season, wide diversity at the beginning, narrowing as season progresses.

Autumn Winter Spring Summer

Normal winter seasonNormal summer activity

Lack of short-term herd immunity to a new variant

Epidemic winter seasonUnusual summer activity

2002/03 epidemic

A E J

A

B

A

B

A

B

A E J

A

B

A

B

A

B

A

B

A E J

A

B

A

B

A

B

A

B

Pre-2002 2002 epidemic

Structural changes on the P2 domain between GII-4 variants

Molecular surface

Electrostatic surface

Monoclonal antibodies raised against thepre-2002 GII-4 strains do not react with the 2002 GII-4 strain and vice versa.

Pre-2002 2002

Food/ water-bornespread

Environmentalspread

Person to personspread

Modes of

transmission

Food/ water-bornespread

Environmentalspread

Person to personspread

Modes of

transmission

Similarity among NoV GII-4 outbreaks reported between December/06 and September/07 from different regions of England and Wales. NE = North East, NW

= North West, SW = South West.

Similarity among NoV GII-4 outbreaks reported between December/06 and September/07 from different regions of England and Wales. NE = North East, NW

= North West, SW = South West.

Pairwise (OG:100%,UG:0%) (FAST:2,10) Gapcost:0%

100

9998979695949392

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04/01/07

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GII-4

GII-4

GII-4

GII-4

GII-4

GII-4

GII-4

GII-4

GII-4

GII-4

GII-4

GII-4

GII-4

GII-4

GII-4

GII-4

GII-4

GII-4

NE

NE

Wales

London

Wales

Wales

NW

London

London

NW

NE

NW

SW

NE

SE

NW

London

SW

Gene encoding the P2 domain

Outbreak tracking

DateCluster

WardP2

10

0

99

98

97

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94

93

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88

III

III

III

III

III

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VI

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IV

I

I

I

I

I

I

I

I

I

I

I

VIII

VIII

VIII

VIII

VIII

VIII

VIII

V

V

V

VII

VII

II

II

II

II

II

II

II

II

Kilverston

Holt

Kimberley

Kimberley

Holt

Holt

Holt

Kimberley

Kilverstone

Kilverstone

Kilverstone

Kilverstone

Kimberley

Knapton

Knapton

Knapton

Kimberley

Holt

Heydon

Heydon

Kimberley

Holt

Guist

Guist

Docking

Mulbarton

Mulbarton

Hethel

Mulbarton

Mulbarton

Holt

Holt

Hethel

Guist

Knapton

Knapton

Heydon

Brundall

Holt

Holt

Knapton

Knapton

Brundall

Heydon

Knapton

Knapton

Gateley

Gateley

Langley

Dunston

Hethel

Dunston

Hethel

Gunthorpe

Gunthorpe

Gunthorpe

13.01.10

13.01.10

08.02.10

26.02.10

18.01.10

25.01.10

15.02.10

19.02.10

19.01.10

26.01.10

28.01.10

28.01.10

06.03.10

01.02.10

08.02.10

18.02.10

07.03.10

27.03.10

17.03.10

13.04.10

08.04.10

22.03.10

25.02.10

08.03.10

14.03.10

13.01.10

12.01.10

18.01.10

05.01.10

08.01.10

04.01.10

08.01.10

10.02.10

18.01.10

04.01.10

18.01.10

26.04.10

28.04.10

25.04.10

27.04.10

29.04.10

01.05.10

28.04.10

04.05.10

17.03.10

22.03.10

21.04.10

18.04.10

12.01.10

12.01.10

11.01.10

18.01.10

18.01.10

11.01.10

20.01.10

26.01.10

Phylogenetic analysis of NNUH strainsrevealed 8 genetic clusters of NoVwere introduced into the hospital in the 2009/ 2010 NoV season

NNUH NoV Outbreaks, 2010

Sequencing the hypervariable region encoding the P2 domain revealed 8 distinct genetic clusters circulating or co-circulating in the hospital.

0

1

2

3

4

5

6

7

8

9

10

21/12/2

009

28/12/200

9

04/01/2

010

11/01

/2010

18/0

1/2010

25/01

/201

0

01/0

2/2010

08/02

/201

0

15/0

2/2010

22/02

/201

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01/0

3/2010

08/03

/2010

15/03/20

10

22/03/2

010

29/03/201

0

05/04/20

10

12/04

/2010

19/0

4/2010

26/04

/201

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03/0

5/2010

10/05

/201

0

Date of onset

Number of Cases

Moving average of suspected and confirmed cases of norovirus gastroenteritis: Dec 2009 to May 2010

GII-4Variant 1

GII-4Variant 2

GII-4Variant 3

GII-4Variant 4

GII-4Variant 5Variant 6

GII-4Variant 7

GII-4Variant 8

0

1

2

3

4

5

6

7

8

9

10

21/12/2

009

28/12/200

9

04/01/2

010

11/01

/2010

18/0

1/2010

25/01

/201

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01/0

2/2010

08/02

/201

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15/0

2/2010

22/02

/201

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08/03

/2010

15/03/20

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22/03/2

010

29/03/201

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10

12/04

/2010

19/0

4/2010

26/04

/201

0

03/0

5/2010

10/05

/201

0

Date of onset

Number of Cases

Moving average of suspected and confirmed cases of norovirus gastroenteritis: Dec 2009 to May 2010

GII-4Variant 1

GII-4Variant 2

GII-4Variant 3

GII-4Variant 4

GII-4Variant 5Variant 6

GII-4Variant 7

GII-4Variant 8

Date Ward Cluster I Cluster II Cluster III Cluster IV Cluster V Cluster VI Cluster VII Cluster VIII02.01.10 KNAPTON I03.01.10 HOLT I05.01.10 MULBARTON I07.01.10 HOLT I07.01.10 MULBARTON I10.01.10 GUNTHORPE II11.01.10 DUNSTON II11.01.10 HETHEL II12.01.10 LANGLEY II12.01.10 MULBARTON I12.01.10 MULBARTON I13.01.10 HOLT III13.01.10 KILVERSTONE III17.01.10 DUNSTON II17.01.10 HETHEL I17.01.10 HETHEL II17.01.10 HOLT III18.01.10 GUIST I18.01.10 KNAPTON I19.01.10 KILVERSTONE III20.01.10 GUNTHORPE II25.01.10 GUNTHORPE II25.01.10 HOLT III26.01.10 KILVERSTONE III27.01.10 KILVERSTONE III28.01.10 KILVERSTONE III01.02.10 KNAPTON III05.02.10 KIMBERLEY III08.02.10 KNAPTON III10.02.10 HETHEL I14.02.10 HOLT III17.02.10 KIMBERLEY III17.02.10 KNAPTON III23.02.10 GUIST IV23.02.10 KIMBERLEY III06.03.10 KIMBERLEY III07.03.10 KIMBERLEY III08.03.10 GUIST IV14.03.10 DOCKING IV17.03.10 KNAPTON V17.03.10 HEYDON VI22.03.10 HOLT VI22.03.10 KNAPTON V27.03.10 HOLT III08.04.10 KIMBERLEY VI14.04.10 HEYDON VI18.04.10 GATELEY VII21.04.10 GATELEY VII21.04.10 HOLT VIII25.04.10 HOLT VIII27.04.10 HEYDON VIII27.04.10 HOLT VIII28.04.10 BRUNDALL VIII29.04.10 KNAPTON VIII01.05.10 KNAPTON VIII04.05.10 HEYDON V

GII-4 genetic clusters

23d

20d

34d

Environmental NoV sampling

At the conclusion of the outbreak and after clinical cleaning

• Cleansers/ disinfectants • Equipment• Nurses station• Bedside environment• Furniture, fixtures and fittings

Site

No

. tested

No

. po

sitive

perce

nt p

os

itive

Cleansers and disinfectantsSoap dispensers 13 6 46.2Alcohol dispensers 7 3 42.9Sub-total 20 9 45.0

EquipmentNon-invasive ventilator 1 1 100.0IV pump 1 1 100.0Pulse oximeter 6 4 66.7BP machine (handles, cuffs, buttons) 24 10 41.7Tympanic thermometer 3 1 33.3Temporal thermometer 1 0 0.0Tourniquet 1 0 0.0Sub-total 37 17 45.9

Notes trolley 6 4 66.7Computer keyboards 10 4 40.0Computer mouse 8 1 12.5Telephone 10 1 10.0

Patients' bowls 2 2 100.0Bedspace basket 1 1 100.0Patients' lockers 2 2 100.0Bed frame 1 1 100.0Bed controls 2 1 50.0Patientline equipment 5 1 20.0Patients' call bells 8 1 12.5

Chairs 1 1 100.0Carpet 1 1 100.0Remote control 1 1 100.0Zimmer frame 1 1 100.0Shelf 1 1 100.0Shower fitments 8 4 50.0Hand rails/ grab rails 26 9 34.6Taps 26 5 19.2Cupboard/ drawer handles 12 2 16.7Toilet flush handles 6 1 16.7Door handles 24 3 12.5Light switches 11 1 9.1Fridge handles 3 0 0.0Tables 2 0 0.0Commode 1 0 0.0Fan 1 0 0.0Toilet seat 1 0 0.0TV switch 1 0 0.0

Environmental norovirus sampling6 wards post-cleaning

Site

No

. teste

d

No

. po

sitiv

e

pe

rce

nt p

os

itive

Soap dispensers 13 6 46.2Alcohol dispensers 7 3 42.9

Non-invasive ventilator 1 1 100.0IV pump 1 1 100.0Pulse oximeter 6 4 66.7BP machine (handles, cuffs, buttons) 24 10 41.7Tympanic thermometer 3 1 33.3Temporal thermometer 1 0 0.0Tourniquet 1 0 0.0

Nurses stationNotes trolley 6 4 66.7Computer keyboards 10 4 40.0Computer mouse 8 1 12.5Telephone 10 1 10.0Sub-total 34 10 29.4

Bedside environmentPatients' bowls 2 2 100.0Bedspace basket 1 1 100.0Patients' lockers 2 2 100.0Bed frame 1 1 100.0Bed controls 2 1 50.0Patientline equipment 5 1 20.0Patients' call bells 8 1 12.5Sub-total 21 9 42.9


Site

No

. teste

d

No

. po

sitiv

e

perc

en

t po

sitiv

e






Site

No

. teste

d

No

. po

sitiv

e

pe

rce

nt p

os

itive






Site

No

. tested

No

. po

sitive

pe

rcen

t po

sitiv

e





Furniture, fixtures and fittingsChairs 1 1 100.0Carpet 1 1 100.0Remote control 1 1 100.0Zimmer frame 1 1 100.0Shelf 1 1 100.0Shower fitments 8 4 50.0Hand rails/ grab rails 26 9 34.6Taps 26 5 19.2Cupboard/ drawer handles 12 2 16.7Toilet flush handles 6 1 16.7Door handles 24 3 12.5Light switches 11 1 9.1Fridge handles 3 0 0.0Tables 2 0 0.0Commode 1 0 0.0Fan 1 0 0.0Toilet seat 1 0 0.0TV switch 1 0 0.0Sub-total 127 30 23.6

Total (all sites) 239 75 31.4

Norovirus:Environmental contamination

• Two wards re-cleaned and re-sampled

Kimberley Ward After 1st clinical clean After 2nd clinical clean

Site

No

. tested

No

. po

sitive

percen

t po

sitive

No

. tested

No

. po

sitive

percen

t po

sitive

Cleansers and disinfectantsSoap dispensers 2 1 50.0 2 0 0Alcohol dispensers 1 0 0 1 0 0Sub-total 3 1 33.3 3 0 0

EquipmentPulse oximeter 1 1 100 1 0 0BP machine (handles, cuffs, buttons) 6 5 83.3 6 1 16.7Tympanic thermometer 2 1 50.0 2 1 50.0Sub-total 9 7 77.8 9 2 22.2

Nurses stationComputer keyboards 2 2 100 2 1 50.0Computer mouse 2 1 50.0 2 0 0Telephone 3 0 0 3 0 0Sub-total 7 3 42.9 7 1 14.3

Bedside environmentPatients' call bells 1 0 0 1 0 0.0Sub-total 1 0 0 1 0 0.0

Furniture, fixtures and fittingsShower fitments 3 3 100 3 1 33.3Hand rails/ grab rails 5 1 20.0 5 0 0.0Taps 4 1 25.0 4 1 25.0Toilet flush handles 1 0 0 1 0 0.0Door handles 4 0 0 4 0 0.0Light switches 1 0 0 1 0 0.0Sub-total 18 5 27.8 18 2 11.1

Total (all sites) 38 16 42.1 38 5 13.2

Date 14/12/2010 20/01/2011 08/02/2011 15/03/2011Ward: Holt

Soap dispenser NoV detected NoV detected NoV detected NoV detectedBed frame Neg NoV detected Neg NegPatient's locker Neg Neg Neg NoV detectedPatients line equip Neg Neg Neg NoV detectedCall bell Neg Neg Neg NegNotes trolley Neg Neg Neg NoV detectedComputer keyboard Neg Neg Neg NoV detectedComputer mouse Neg Neg Neg NoV detectedTelephone Neg Neg Neg NoV detectedShower fitment Neg NoV detected Neg NoV detectedHand rails/ Grab rails Neg Neg NoV detected NegTap Neg Neg Neg NegToilet flush handle Neg Neg Neg NegDoor handle Neg Neg Neg NoV detectedLight switch NoV detected Neg Neg NoV detectedSoap dispenser Neg Neg Neg NegSoap dispenser Neg Neg Neg NoV detectedBlood pressure machine Neg Neg NoV detected NoV detectedBlood pressure cuff Neg Neg Neg NoV detectedPulse oximeter Neg Neg No swab NoV detectedTympanic thermometer Neg Neg Neg NegPatient washbowl Neg Neg Neg NegBay door handle Neg Neg No swab NoV detectedHand wash basin No swab Neg Neg NegDigital thermometer No swab No swab Neg No swab

Environmental monitoring: 2011

surveillance outbreak

Also consider:• Bed occupancy rates• Built environment• Infection control procedures• Admission Units

Risk of norovirus spread within the hospital environment

Patients

Environment

Reduced risk of spread Increased risk of spread

Cohortnursing

Adherence tohand washingpractices, soap and water

Elbow/automatictaps onhandbasins

Single roomswith en suite

Surface finishesallowing decontamination

Projectilevomiting

Staff affected

Reduced staffing

Soft furnishingscontaminated

Open wards

Ward closure

High attack rate

Low infectious dose

Unrestrictedvisiting/admissions

Virusvariant/ mutant

Hand contactsurfacescontaminated

Potential vaccines

• Low infectious dose ~ 10-100 virus particles• Noroviruses 107 particles per gram/ml• Rotaviruses 1011 particles per gram/ml

• Stability in the environment• Norovirus survives up to 80oC• Rotavirus survives in the environment for months

• Protected by the matrix – faeces and vomit, which also inactivate chlorine-based disinfectants• Non-enveloped viruses – resistant to many disinfectants and alcohol• Short term immunity ~ 6 months• 16% of the population excrete NoV in the absence of symptoms• 14% of the population excrete rotavirus in the absence of symptoms

Keys to the success of gastroenteric viruses

• Multiple routes of transmission - person to person contact, through ingestion of contaminated water or food or by contact with contaminated environmental surfaces• RNA genome replication results in the accumulation of point mutations• Segmented rotavirus genome replication results in reassortment• Dual infections can result in recombination or reassortment• Rotaviruses are associated with zoonotic infection• Hospital-acquired infections are predominantly associated with GII-4• There are multiple introductions into hospitals, of variants of GII-4, throughout the NoV season and many rotavirus strains co-circulate in the human population• Antibody-escape mutants and rotavirus reassortants are selected and driven by herd immunity resulting in epidemics in an immunologically naive population

Documents

Gastroenteric viruses: Current status Jim Gray Professor of Clinical Virology, UEA & Consultant Virologist, NNUH