Paleovirology

How did HIV-1 and HIV-2 adapt to humans?

AGM RCM Mandrill Colobus

Why are humans infected with some lentiviruses and not others?

Sooty Mangabey Chimpanzee Human

HIV-2

4X >7X

Years from present

102 103 104 105 106 >107

Change(s) in the specificity of antiviral genes

Antiviral genes

Modern viruses Paleovirus

Ancient viral pathogens of humans and human ancestors have shaped our immunity to modern viruses

?

nucleus

Primates encode antiviral factors that limit virus replication

nuclear import

integration

uncoating

reverse transcription assembly

budding

APOBEC3

Tetherin

SAMHD1

Viruses encode proteins to evade the antiviral factors

Vif

Vpu

Vpx

nucleus

nuclear import

integration

uncoating

reverse transcription assembly

budding

APOBEC3

Tetherin

SAMHD1

Vif

Vpu

Vpx

Host susceptibility = sum of the interactions between host antiviral factors and viral antagonists

Leading to an evolutionary “arms race” between host genomes and viruses

Viral-host ‘arms race’ and Species barriers

Host antiviral gene

Viral antagonist Host antiviral gene Viral antagonist

Host evasion

Viral adaptation

Host wins

Virus wins

Viral cross-species transmission

Host wins

Viral adaptation to recover the antagonism

… …

(Emerman and Malik, Plos Biol 2010)

Species 1 Species 1

= Successful jump

REPLACEMENT (dN) SYNONYMOUS (dS)

PURIFYING SELECTION

dN

dS < 1

dN

dS > 1 POSITIVE

SELECTION

Virus-host interactions drive positive selection

The ancient origins of HIV-1

SIVgor

SIVmus

SIVrcm

SIVcol

SIVgsn SIVsmm

SIVlho SIVagm

SIVmnd

SIVcpz

HIV-1

Old World monkeys Hominids

How long have HIV-like viruses been in primates?

What allowed the virus to jump to chimpanzees?

Why are humans so susceptible to HIV?

Target cell

Producer cell

APOBEC3G

APOBEC3G inhibits HIV/SIV during reverse transcription

Packaging Reverse transcription

G > A hypermutations

Cytidine deaminase C > U

G G G

C U U

G A A

Inactivated viral genome

Viral RNA

Target cell

Producer cell

APPBEC3G

Lentiviral Vif antagonizes APOBEC3G (A3G)

Packaging Reverse transcription

G G G

C C C

G G G

Viral infection

Viral Vif

Viral RNA Recruitment of Ub ligase complex

Proteasome degradation

Using the virus-host interaction sites to identify ancient pathogens

time

Infection by pathogenic

virus

time

Primate species phylogeny

Virus-encoded Antagonist

virus-encoded antagonist

Antiviral Factor

126FWKPDYQ132

Species-specific mutations in A3G govern sensitivity to Vif

A3G CD1 CD2

Vif binding

African Green Monkey A3G

Human A3G HIV-1 Vif

SIVagm Vif 126FWDPDYQ13 2

• Residue 128 of A3G is a critical determinant of Vif sensitivity

• Positive selection in this region of A3G driven by viral interactions

126FWEPDYQ132

126FWKPHYQ132

126FWKPDYQ132

Ancient and ongoing co-evolution of AGMs and their lentiviruses

AGM Ancestor Vervet

Tantalus

Grivet

Sabaeus

126FWKPDYQ132

126FWKPDYQ132

126FWKPDYQ132

126FWKPDYQ132

A3G variants:

*

*

Adaptive evolution of A3G in deep time: inferring ancient viruses

CD1 CD2 A3G

Have ‘escape‘ mutations in A3G emerged in other primate species?

Old World Monkeys

Compton and Emerman, PLOS Pathogens, 2013

0

1

10

100 %

Infe

ctiv

ity

No Vif SIVdeb SIVagm.Ver

De Brazza’s A130D

A3G:

Vif:

126FWKPAYQ132

Mustached Wolf’s Guenon De Brazza’s

Compton and Emerman, PLOS Pathogens, 2013

• D130A allows escape from Vif • SIV Vif infecting Cercopithecus genus has counter-evolved

A mutation common to Cercopithecus genus allows evasion of Vif

126FWKPAYQ132

126FWKPAYQ132

126FWKPAYQ132

126FWKPAYQ132

126FWKPDYQ132

A pathogenic lentivirus infected the Cercopithecus ancestor at least 5 MYA

Ancestor

126FWKPAYQ132

Cercopithecus

Allenopithecus

A3G variants:

Compton and Emerman PLOS Pathogens, 2013

How old are the primate lentiviruses?

HIV-1

SIVcpz

SIVcpz

SIVcpz

SIVgor SIVmus SIVrcm SIVcol

SIVagm SIVgsn SIVsmm

SIVlho SIVmnd

SIVagm SIVmnd

A pathogenic lentivirus was present in some simian primates at least 5 million years ago. Probably longer.

Sometimes exogenous retroviruses enter the germline

exogenous virus endogenous virus

where they become inherited and fixed within the species

Viral fossils also point to ancient pathogenic viruses

baboon

New World monkeys

human

chimpanzee

gorilla

orangutan

gibbon

Myr 5 10 15 20 25 30 35 40 45 50 55 60 65 80-100

HERV-K

Germline acquisition of retroviral elements

MaLR

Most HERV families

few ~70 HERV-K

Human endogenous retroviruses are all defective.

8% of human genome

100,000 integrants of 31 families of retroviruses

Large numbers of Retroviral fossils in the human genome

Implications of endogenous retroviruses in the human genome

• There have been many retroviral infections of human ancestors

• Retroviral lineages go extinct in their host

• Host wins!

An endogenous lentivirus in the genome of a prosimian

Gifford, Katzourakis et al. PNAS, 2008

Grey mouse lemur

There was a distantly related lentivirus in a prosimian at least 4 million years ago

The ancient origins of HIV-1

SIVgor

SIVmus

SIVrcm

SIVcol

SIVgsn SIVsmm

SIVlho SIVagm

SIVmnd

SIVcpz

HIV-1

Old World monkeys Hominids

At least 5 Mya Adaptation of an HIV-like virus to hominids

SIVrcm SIVmus/mon/gsn

SIVcpz

Red-capped mangabeys Guenons

Chimpanzees

SIVcpz is a recombinant between two viruses from old world monkeys

23

HIV-1

Restricted

Dendritic cells Monocytes Resting T-cells

VPX HIV-1

Not Restricted

Vpx antagonizes the host SAMHD1 protein

DCAF DDB1 CUL4

SAMHD1 VPX

dNTP

The capacity to antagonize SAMHD1 was lost during the genesis of SIVcpz

25

vif

vif

vpr

vpr SIVrcm

SAMHD1

APOBEC3G

APOBEC3G

SAMHD1 SIVcpz

gag

pol

env

gag

pol env

vpx

The deletion of Vpx from SIVcpz also altered Vif

Acquisition of 60-75bp

1 2 3 Vpx

109aa Vpr 101aa

Vif 223aa Fr

ames

1 2 3

Vpr 99aa

Vif 190aa

vif-vpr 61bp

Fram

es …PLP…

Loss of ~380bp

*

*

*

…SLQYLA

…SLQYLA

26

SIVrcm

SIVcpz

Loss of vpx was driven by selection for changes in vif to gain APOBEC3 antagonism

0

1

10

100

1000

chimpA3G chimpA3D chimpA3F chimpA3H

SIVcpz Vif No Vif SIVrcm Vif

SIVcpz Vif PLP *

% v

irus

infe

ctiv

ity

SIVrcm SIVmus

Red-capped mangabeys 5’LTR gag

pol

vif

vpr

vpu tat

env

nef

3’LTR rev

5’LTR gag

pol

vif vpr

vpx

tat env

nef

3’LTR

rev

Guenons

SIVcpz epidemic in chimpanzees

HIV-1 in humans SIVgor in gorillas

SIVcpz Vif was pre-equipped to degrade humA3G

SIVcpz

Recombination between distant SIVs

5’LTR gag

pol

vif

vpr

vpu tat

env

nef

3’LTR rev

Loss of Vpx Reconstruction of Vif

5’LTR gag

pol

vif

vpr

vpu tat

env

nef

3’LTR rev Adaptation of Vif to

chimpA3G and A3D

Hominoids

The ancient origins of HIV-1

SIVgor

SIVmus

SIVrcm

SIVcol

SIVgsn SIVsmm

SIVlho SIVagm

SIVmnd

SIVcpz

HIV-1

Old World monkeys Hominids

~100 years ago

Perez-Caballero et al. Cell, 30 October 2009

Tetherin directly tethers virions to cells

Counter-acted by HIV-1 Vpu which removes Tetherin from the cell surface

Virus release is inhibited by Tetherin

No Tetherin + Tetherin

1

10

100

No Vpu HIV Vpu SIVcpz Vpu SIVgor Vpu

Rela

tive

Infe

ctiv

ity (%

)

SIVcpz Vpu cannnot antagonize Tetherin

Lim ES, Malik HS and Emerman M. JV, 2010

Virus production in the presence of

Tetherin

SIVsm LTR gag

pol

vif

env vpr

rev

vpx

HIV-1 LTR gag

pol

vif

env LTR

nef vpr

rev

tat

vpu

Most SIVs use Nef, not Vpu, to counteract Tetherin

LTR gag

pol

vif

env LTR

vpr

rev

tat

vpu SIVcpz

tat

nef

LTR

nef

Primate phylogeny Codon alignment

Host-virus arms race

Positive selection “hot spot” Identifies the

Target binding surface

Evolution-guided identification of host-virus interaction sites

Purifying selection (dN/dS < 1) Positive selection (dN/dS > 1)

Strong signal of positive selection

RVPMDDIWKKDGDKRC RVPMDDIWKKDGDKRC RVPMDAILKKDGDKRC RVPMGDICKKDGDKRC RGPMDDIWKKDGDKRC RVPMDGIWKKDGDKRC KMPMYDSCKEDGDKRC KMPMDDICKEDRDKCC KMPMDDICKEDGDKCC KMLMDDIWKEDGDKHC KMPMDDIWKEDGDKRC KMPMDDNLKEDGDKCC KMPMDDIWKEDGDKRC KMSMDDICKEDGGKRC PVPMDDFLKHERKERC PVPMDDFLKHERKERC LVPMDDFPKHERKERC LVPMDDFLKHESKERC LVPMDDFLKHERKERC

Hominoids Chimp Bonobo Gorilla Orangutan Gibbon Agile gibbon Old World Monkeys Cephus AGM Patas Talapoin Rhesus Francois leaf Douc Langur Kik Colobus New World Monkeys Woolly Howler Saki PygmyMarm Tamarin

9 17 43

TM Coiled-coil C. Tail GPI Tetherin Nef

RVPME-----DGDKRC RVPMDDIWKKDGDKRC RVPMDDIWKKDGDKRC RVPMDAILKKDGDKRC RVPMGDICKKDGDKRC RGPMDDIWKKDGDKRC RVPMDGIWKKDGDKRC KMPMYDSCKEDGDKRC KMPMDDICKEDRDKCC KMPMDDICKEDGDKCC KMLMDDIWKEDGDKHC KMPMDDIWKEDGDKRC KMPMDDNLKEDGDKCC KMPMDDIWKEDGDKRC KMSMDDICKEDGGKRC PVPMDDFLKHERKERC PVPMDDFLKHERKERC LVPMDDFPKHERKERC LVPMDDFLKHESKERC LVPMDDFLKHERKERC

Hominoids Human Chimp Bonobo Gorilla Orangutan Gibbon Agile gibbon Old World Monkeys Cephus AGM Patas Talapoin Rhesus Francois leaf Douc Langur Kik Colobus New World Monkeys Woolly Howler Saki PygmyMarm Tamarin

9 17 43

LGVPLIIFTIKANSEAC LGVPLIIFTIKANSEAC LGVPLIIFTIKANSEAC LGVPLIIFTIKANSEAC LGVPLIIFTIKANSEAC LGVPLIIFTIKANSEAC LGVPLIIFTIKANSEA LGVLLIFFIIKANSEAC LGVPLIFFIIKANSEAC MGVPLIFFIIKASSEAC LGVPLIFFIIKANSEAC LGVPLIFFIIKANSEAC LGVLLTFFIIKANSEAC LGVLLIFFIIKANSEAC LGVLLIFFIIKANSEAC LGVLLIVYVKRANSEAC LGVFLIIYVKKANSEAC LGALLIVYVKRANSEAC LGVLLIFYVKRANSEAC LGVLLIIYVQRANSEAC

Vpu Nef TM Coiled-coil C. Tail GPI Tetherin

Human

Viral Antagonist Tetherin

HIV-1 adapted to humans by evolution of Vpu towards the unique form of human Tetherin

Nef

Evolution of Vpu

Vpu Vpu

Rapid adaptive evolution

Nef Cannot work against human Tetherin

Only occurred in the pandemic HIV-1 (group M)

The ancient origins of HIV-1

SIVgor

SIVmus

SIVrcm

SIVcol

SIVgsn SIVsmm

SIVlho SIVagm

SIVmnd

SIVcpz

HIV-1

Old World monkeys Hominids

The pandemic form of HIV- 1 acquired a final adaptation to humans

Viruses similar to HIV are ancient pathogens of primates

Adaptation of an HIV-like virus to hominids by gene deletion and d t ti

Years from present

102 103 104 105 106 >107

SARS HIV DEN measles smallpox

Paleoviruses

HERV-K PtERV? Other ERV

Modern and ancient viral pathogens of humans and human ancestors

Episodic selections by ancient pathogenic viruses has driven the evolution of current innate immunity genes

genetic evidence

Modern viruses

Ancient infections influence modern virus susceptibility

Fred Hutchinson Cancer Research Center