1995 Host-pathogen (co-)evolution

Virus A

Primate B

Primate C

Primate A

Virus C

Virus B

Host-pathogen co-evolution

Divergent lineages of SIV have also been found in African green monkeys

Host-pathogen co-evolution in other SIV

These primates have a broad distribution throughout sub-Saharan Africa and have been classified based on phenotypic differences into four major species:

African green monkeys

1. vervet (Chlorocebus pygerythrus).ETYMOLOGY:French: vert = green

2. grivet (C. aethiops)3. sabaeus (C. sabaeus) 4. tantalus (C. tantalus).

The many SIVagm strains infecting these animals cluster into four distinct phylogenetic lineages according to their species origin, indicating ancient infection followed by co-evolution of virus and host.

Virus A

Primate B

Primate C

Primate A

Virus C

Virus B

Host-pathogen co-evolution in other SIV

One possibility is that the ancestor of human and chimp had a virus, and that the virus split with the human-chimp split…

(1990)

Co-evolution between HIV-1 and SIVcpz?

1999

1999. Nature

There are several doubts casting the theory that chimpanzees are the natural host and reservoir for HIV-1

1. There is a wide spectrum of diversity between HIV-1 and SIVcpz.

2. An apparent low prevalence of SIVcpz infection in wild-living animals.

3. The presence of chimpanzees in geographic regions of Africa where AIDS was not initially recognized.

The natural host of HIV-1

Rather, it has been suggested that another, yet unidentified, primate species could be the natural host for SIVcpz and HIV-1.

Unidentified virus as the origin?

“We recently identified a fourth chimpanzee with natural SIVcpz infection.

This animal (Marilyn) was wild-caught in Africa (county of origin unknown), exported to the United States as an infant, and used as a breeding female in a primate facility until her death at age 26.”

Marilyn

During a serosurvey in 1985, Marilyn was the only chimpanzee of 98 tested who had antibodies strongly reactive with HIV-1 by enzyme-linked immunosorbent assay (ELISA) and western immunoblot.

How this SIV was found?

Maybe she was infected with HIV during her stay in the STATES?

“She has never been used in AIDS research and had not received human blood products after 1969. She died in 1985 after giving birth to still-born twins.”

An alternative explanation

Endometritis: דלקת רירית הרחםSepsis: אלח דם

“An autopsy revealed endometritis, retained placental elements and sepsis as the final cause of death. Depletion of lymhoid tissues was not noted.”

To convince that she did not have AIDS…

Chimps do not develop AIDS

An ultimate proof that the virus is SIV could be the isolation of the virus and infecting chimpanzee cells in the lab.

However, virus isolation from the autopsy tissues was unsuccessful…

Failed…

No virus could be isolated

PCR was used to amplify a complete proviral genome.

The genome was termed SIVcpzUS.

But sequencing worked!

Provirus

The "provirus" is the form of the virus which is capable of being integrated into the host genome. In the case of HIV it means the DNA "copy" of the HIV genome (HIV normally carries its genes around in RNA form).

•Analysis of potential coding regions revealed the presence of a vpu gene. Vpu is only found in HIV-1 and SIVcpz viruses

•Promoter and enhancer elements of the SIVcpzUS long terminal repeat (LTR) were indistinguishable from those of other members of the HIV-1/SIVcpz group.

HIV-1 and SIVcpz have similar genomes

Only three other SIVcpz strains have been reported:

Two from animals wild-caught in Gabon (SIVcpzGAB1 and SIVcpzGAB2)

One from a chimpanzee exported to Belgium from Zaire (SIVcpzANT).

(1990 paper)

(SIVcpzGAB1 and SIVcpzANT have been sequenced completely, but only 280bp of the pol sequence are available for SIVcpzGAB2)

NJ tree

0.1 amino-acid replacements per site

HIV-1 + SIVcpz are monophyletic

Only bootstrap values >80% are shown

Phylogenetic tree

NJ tree

There are at least two different HIV-1 clades, and two different SIVcpz clades

Phylogenetic tree

From which chimpanzee subspecies the virus came from? [chimp = Pan troglodytes].

Four chimpanzee subspecies with non-overlapping geographic ranges are known:

1. The western P. t. verus.2. Nigerian P. t. vellerosus.3. Central P. t. troglodytes.4. Eastern P. t. schweinfurthii.

Zooming in – chimpanzee subspecies

Geographic distribution of chimpanzee subspecies

Question: how to find the chimpanzee subspecies from which HIV-1 was transferred to human?

This is important, as it can tell us where the epedimic started…

Zooming in – chimpanzee subspecies

The idea:

Sequence Marilyn (the HOST) and test to which subspecies she belongs.

This can be done by comparing the DNA of the infected chimps to the DNA of characterized chimp subspecies…

Marilyn again!

1. A fragment of the mitochondrial control region (D-loop) was sequenced.

2. It was sequenced from all four infected chimps.

3. Sequences were compared to sequences from the 4 chimp subspecies.

Marilyn again!

The three chimpanzees infected with the more closely related SIVcpzGAB1 (GAB1), SIVcpzGAB2 (GAB2), and SIVcpzUS (Marilyn) strains all belonged to the P. t. troglodytes subspecies.

SIVcpzANT strain (Noah) was identified as a member of the P. t. schweinfurthii subspecies

Marilyn (SIVcpzUS) and GAB1 are close to HIV-1 and belong to P.t.t -> probably HIV-1 originated from P.t.t

Conclusions

GAB1GAB2Marilyn

NOA

Origin - geography

Globally circulating strains of HIV-1 have been classified into three major phylogenetic groups, termed M, N and O.

All of which cause AIDS.

The 'main' group M is responsible for the global AIDS epidemic and comprises by far the majority of HIV-1 isolates.

These viruses have been further subdivided based on phylogenetic relatedness into ten distinct subtypes or clades, termed A–J.

HIV-1 subtypes

Group O (for 'outlier') is represented by many fewer isolates that originate mainly from Cameroon, Gabon and Equatorial Guinea.

Group N (for 'non-M/non-O') was discovered only very recently and is the least widespread of all HIV-1 lineages; so far, it has been documented in only two individuals from Cameroon.

HIV-1 subtypes O and N

Marylin and friends may explain subtypes M and N. Origin of O – unclear.

1999:

HIV-1 infection of humans occurred as a result of cross-species transmission of SIVcpz from P. t. troglodytes.

Probably explaining the origin of subtypes M and N.

Intermediate summary

2003

SIVcpz

2003. Science

A part of SIVcpz (the pol gene) is closer to SIVrcm,and another part (env) is closer to SIVgsn

SIVcpz origin

rcm = red-capped mangabeys (Cercocebus torquatus)

Gsn=greater spot-nosed monkeys (Cercopithecus nictitans)

A part of SIVcpz (the pol gene) is closer to SIVrcm,and another part (env) is closer to SIVgsn

Differences from the SIVcpz gene.

and in others, the red is closest (SIVgsn).

The red = SIVgsn is closest to SIVcpz

The blue = SIVrcm is closest to SIVcpz

SIVcpz origin

A recombination event at the Pol-Env junction led to the creation of SIVcpz…

SIVcpz origin – from recombination

HIV

1999Hooper, a well known scientist claimed that the AIDS virus (type 1) has crossed into humans as a result of contamination of the oral polio vaccine (OPV).

The OPV/AIDS theory claims that chimpanzees from the vicinity of Kisangani in Congo were the source of SIVcpz that was transmitted to humans when chimpanzee tissues were used in the preparation of OPV.

Nature 2004

Nature 2004

Nature 2004Nature 2004

They isolated SIV from urine samples of chimpanzees in the vicinity of Kisangani, where the polio vaccines were given.

They found that the SIV in this region is of a chimpanzee subtype called Pan troglodytes schweinfurthii (pts) and not Pan troglodytes troglodytes (ptt).

HIV-1 subtypes M, N, and O all cluster within SIVcpzPtt (green) while SIV from chimps within the red area (of Polio vaccine) clusters within SIVcpzPts (red). Conclusion: “The molecular epidemiological data presented here… should finally lay the OPV/AIDS theory to rest”.

2006

In 2006, it was already established that HIV is made of three subtypes: M, N, and O.

It was also clear that HIV-1 M and HIV-1 N were obtained from chimpanzees independently

The origin of HIV-1 O was unknown…

The origin of HIV-O

2006. Nature

“We tested 378 chimpanzees and 213 gorilla fecal samples from remote forest regions in Cameroon for HIV-1 cross-reactive antibodies”

“Surprisingly, 6 of 213 fecal samples from wild-living gorillas also gave a positive HIV-1 signal”

The origin of HIV-O

Bayesian analysis

HIV-1 O is a sister clade of SIV from Gorilla!

It seems that chimpanzee transmitted SIV to gorilla and gorilla to human type O, or

Chimpanzee transmitted to both gorilla and to human type O

Note: gorilla and chimps rarely interact + gorilla are herbivores

The origin of HIV-O

NATURE 2008 Vol 455:605-606

First description of HIV-1

HIV-1 was first described in 1981. But it is clear that the zoonotic transfer of HIV-1 from SIVcpz occurred much before that.

In 2008, genome fragments from HIV-1 were sequenced from a lymph node biopsy collected in 1960 in Kinshasa, the capital of the Democratic Republic of Congo.

Subtypes of “ancient” HIV-1 viruses

The sequenced virus from 1960 (DRC60) is related to subtype A.

Another HIV-1 ancestor from a blood plasma sample, from the same place was originally obtained in 1959 (ZR59).ZR59 was most closely related to subtype D.

Subtypes of “ancient” HIV-1 viruses

Conclusion I: the subtypes diverged more than 50 years ago.

HIV-1 early divergence

DRC60 and ZR59 have 88% sequence identity – a value similar to the maximal distance observed today between isolates from the same subtype.

If the 12% difference observed within subtypes today took 50 years to emerge, one can extrapolate that the HIV-1 ancestor is ~100 years old.

HIV-1 dating

Using advanced probabilistic based method, the HIV-1 common ancestor was found to be between 1902-1921 (95% confidence interval).

If one assumes an exponential growth curve from a few individuals in 1910 to 55 millions in 2007 – then in 1960 there were only a few thousand infected individuals.

Kinshasa

Both “ancient” subtypes were found in Kinshasa. Samples from today show many subtypes in this area, and many divergent strains that were not characterized.

It seems that early HIV-1 divergence occurred around Kinshasa.

SIVcpz

But the closest SIVcpz to HIV-1 were found in the southeast corner of Cameroon, some 700 km from Kinshasa.

HIV epidemic

700 km

For the HIV-1 epidemic – a large population is needed. Kinshasa was the biggest city in the area. In the early 1900s it was the main route of transportation out of the forest region via rivers leading to the Congo River and from their to Kinshasa.

Why 1900s?

Simply because only around that time, major cities, including Kinshasa emerged.

Kinshasa 1955

Kinshasa 1896