Characteristics of transmitted viruses in acute and early HIV infection

1. Characteristics of transmitted viruses in acute and early HIV infection Eric Hunter IAC 2010

2. 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?

3. Genetic bottleneck during transmission of HIV

4. Genetic bottleneck during transmission of HIV Transmission Re-emergence of viral diversity Diverse virus population in chronically infected “donor” 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;

5. HIV-1 transmission in discordant couples allows analysis of both ‘donor’ and ‘recipient’ viruses 80-85% of transmissions

6. 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

7. The virus population in the acutely infected recipient is remarkably homogeneous 27/40 = 67% identical 11/40 - one base change 2/40 - two base changes Modeling of virus replication and evolution in the absence of selection would predict: 76% identical at 13 days 58% identical at 26 days 45% identical at 40 days to transmitted variant

8. 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

9. Highlighter analysis of SGA V1-V4 sequences allows identification of closest donor variant in PBMC, Plasma and Genital Fluid derived sequences Z216 F->M EDI = 31 p24/ab+ve

10. Phylogenetic analyses show compartmentalized lineages in genital fluids Z216 F to M transmission Ag+ EDI=31days Color Codes: Donor PBMC Donor PL Donor GT Recipient PBMC Recipient PL GT variant closest to Recipient branch

11. 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.

12. Can we define a unique characteristic of viruses that initiate infection? 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., Science2004

13. Subtype C HIV-1 variants that establish infection exhibit a high requirement for CCR5 N=6 N=6 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 Alexander et al. J. Virol. 2010

14. Subtype C HIV-1 variants that establish infection exhibit a high requirement for CD4 N=6 N=6 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 Alexander et al. J. Virol 2010

15. Characteristics of subtype C HIV-1 variants that establish infection • Inefficient entry into macrophages relative to Bal strain of HIV-1 D D R R Isaacman-Beck et al., J. Virol. 2009

16. 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.

17. Acknowledgements Emory University Hunter Lab Melissa Alexander, Ph.D. Jon Allen Debi Boeras, Ph.D. Mona Chatterjee Rich Haaland, Ph.D. McKenzie Hurleston Malinda Schaefer, Ph.D. Ling Yue, M.D. Paul Farmer, Ph.D. Derdeyn Lab Cynthia Derdeyn, Ph.D. Emory/RZHRG cohorts The Staff and Participants Etienne Karita, M.D. Elwyn Chomba, M.D. Joseph Mulenga, M.D. William Kilembe, M.D. Mubiana Inambao, M.D. Amanda Tichacek, MPH Susan Allen, M.D., MPH Univ. of Pennsylvania Collman Lab Jesse Isaacman-Beck Los Alamos National Laboratory Bette Korber, Ph.D. Peter Hraber LANL Team Univ. Alabama at Birmingham Shaw/Hahn Lab Jesus Salazar, Ph.D. Joshua Baalwa, M.D. Brandon Keele, Ph.D. Beatrice Hahn, M.D. George Shaw, M.D., Ph.D. Funding: NIH R37 AI-51321 (Hunter/Derdeyn) NIH R01 AI-58706 (Derdeyn) Gates Grand Challenge (Shaw) NIH P30 AI-050409 Emory Center for AIDS Research IAVI (Allen)