Characteristics of transmitted viruses in acute and early HIV

infection

Eric Hunter

IAC 2010

Hypothesis

• An effective prophylactic vaccine or microbicide against HIV-1 must protect against those viruses that initiate infection at the mucosal surface.

• These may be distinct from the bulk of the variants that have evolved to survive during their growth in the chronically infected host.

What is the nature of these viruses and where do they come from?

Genetic bottleneck during transmission of HIV

Genetic bottleneck during transmission of HIV

Re-emergence of viral diversity

Diverse virus population in chronically infected “donor”

Transmission

Zhu et. Al. Science, 1993; Derdeyn et. al., Science, 2004; Keele et. al., PNAS, 2008; Salazar et. al., J. Virol., 2008; Haaland et. al., PLoS Path., 2009; Abrahams et. al., J. Virol., 2009;

HIV-1 transmission in discordant couples allows analysis of both ‘donor’ and ‘recipient’ viruses

80-85% of transmissions

Recipient Plasma

Recipient PBMC

Donor Plasma

Donor PBMC

An Extreme Genetic Bottleneck occurs

during Transmission

• In this linked transmission pair the recipient virus is relatively homogeneous and originates from a single branch of the donor phylogenetic tree - thus a single genetic variant has established infection.

Haaland et. al., PLoS Path., 2009

The virus population in the acutely

infected recipient is remarkably

homogeneous

27/40 = 67% identical11/40 - one base change2/40 - two base changes

Modeling of virus replication and evolution in the absence of selection would predict:76% identical at 13 days58% identical at 26 days 45% identical at 40 days to transmitted variant

Where does the bottleneck originate

• In the donor? –through limited heterogeneity in the

genital fluids• In the recipient?

–at the mucosal surface–selection during virus outgrowth

Z216 F->MEDI = 31p24/ab+ve

Highlighter analysis of SGA V1-V4 sequences allows identification of closest donor variant in PBMC,

Plasma and Genital Fluid derived sequences

Z216 F to M transmissionAg+ EDI=31days

Color Codes:Donor PBMCDonor PLDonor GTRecipient PBMCRecipient PL

GT variant closest to Recipient branch

Phylogenetic analyses show compartmentalized lineages in genital fluids

Origin of the genetic bottleneck• Based on SGA analysis of genital fluids from 6

FTM and 3 MTF transmission pairs– Both male and female genital tract-derived viruses appear

to be comprised of stable sub-populations (clades) some of which exhibit very limited diversity (clonal populations).

– Because the variant that establishes infection is generally not derived from the predominant GT clades, it is unlikely that the limited diversity in the donor GT is the reason for a single genetic variant being transmitted in a majority of cases.

– These data also argue against a purely stochastic mechanism for transmission and for selection of a variant with specific traits that favor systemic spread.

In our initial analysis of eight heterosexual transmission pairs in Lusaka, compared to viruses in the donor quasispecies, the viruses that established infection in the recipients encoded Env molecules exhibited:•Shorter V1-V4 regions (recapitulated in 10 additional subtype C transmission pairs – Haaland et al PLoS Path 2009)•Fewer N-linked Gly sites in V1-V4 (supported by CHAVI analysis of acute and chronic cohorts – Swanstrom – AIDS 2010 )

– Possible requirement for exposure of the a4b7 binding site – (Fauci –AIDS 2010)

Hypothesized that envelope of these viruses might bind CD4 and CCR5 better.

Derdeyn et al., Science 2004

Can we define a unique characteristic of viruses that initiate infection?

Subtype C HIV-1 variants that establish infection exhibit a high requirement for CCR5

Alexander et al. J. Virol. 2010

Infection of both donor and recipient virus is decreased 30-fold on JC-10 cells which express 50-fold less CCR5 relative to JC-53 cells

N=6 N=6

Subtype C HIV-1 variants that establish infection exhibit a high requirement for CD4

Alexander et al. J. Virol 2010

Infection of both donor and recipient virus is decreased 1000-fold on RC-55 cells which express 10-fold less CD4 relative to JC-53 cells

N=6 N=6

Characteristics of subtype C HIV-1 variants that establish infection

• Inefficient entry into macrophages relative to Bal strain of HIV-1

Isaacman-Beck et al., J. Virol. 2009

D R D R

Characteristics of the viruses that establish infection

• The envelope glycoproteins of founder viruses show a high dependency on CD4 and CCR5 for mediating entry into cells expressing different levels of these receptors– Consistent with efficient replication in mucosal T

cells, but very inefficient infection of macrophages

• The differences in glycosylation and V1-V4 lengths may reflect tropism determinants such as a4b7 binding or a requirement for dendritic cell interactions currently under study.

AcknowledgementsEmory UniversityHunter LabMelissa Alexander, Ph.D.Jon AllenDebi Boeras, Ph.D. Mona ChatterjeeRich Haaland, Ph.D. McKenzie HurlestonMalinda Schaefer, Ph.D.Ling Yue, M.D.Paul Farmer, Ph.D.

Derdeyn LabCynthia Derdeyn, Ph.D.

Los Alamos National LaboratoryBette Korber, Ph.D.Peter HraberLANL Team

Emory/RZHRG cohortsThe Staff and ParticipantsEtienne Karita, M.D.Elwyn Chomba, M.D.Joseph Mulenga, M.D.William Kilembe, M.D.Mubiana Inambao, M.D.Amanda Tichacek, MPHSusan Allen, M.D., MPH

Funding:NIH R37 AI-51321 (Hunter/Derdeyn)NIH R01 AI-58706 (Derdeyn)Gates Grand Challenge (Shaw)NIH P30 AI-050409 Emory Center for AIDS ResearchIAVI (Allen)

Univ. Alabama at BirminghamShaw/Hahn LabJesus Salazar, Ph.D.Joshua Baalwa, M.D.Brandon Keele, Ph.D.Beatrice Hahn, M.D.George Shaw, M.D., Ph.D.

Univ. of PennsylvaniaCollman LabJesse Isaacman-Beck