1. Impact of immune-driven sequence variation in HIV- 1 subtype C Gag-protease on viral fitness and clinical outcome Thumbi Ndung’u, BVM, PhD HIV Pathogenesis Programme Doris Duke Medical Research Institute Nelson R. Mandela School of Medicine University of KwaZulu-Natal

2. Distribution of HIV-1 Subtypes 47.2% 27.0 % 12.3%

3. Need for vaccine: HIV prevalence reaches >50% in some young antenatal clinic attendees, Durban, South Africa Fundisiwe Chonco, et. al., unpublished 0 0 25 50 75 Age 816243240485460 % PMMH March 2009 66%

4. CTL Pathway to HIV vaccine: Understanding of viral genetics, host genetics and immune responses

5. Experimental design: 406 chronically infected antiretroviral-naïve patients infected with HIV-1 subtype C Viral load, CD4 count and HLA type done High throughput Gag-protease-based viral replication assay Does viral replication capacity influence disease outcome?

6. High throughput Gag-protease viral replication assay abc 10 0 1 2 3 4 GXR-GFP 0 200 400 600 800 1000 Forward Scatter 0.02 10 0 1 2 3 4 GXR-GFP + HIV) 0 200 400 600 800 1000 28.4 0.1 1 10 100 234567 Day % GFP+

7. Wide range of viral replication capacities in chronically infected patients (N=406)

8. Viral fitness is associated with markers of disease progression

9. Replication capacities vary significantly across HLA-B alleles RCs varied significantly across the different HLA-B alleles, some individual alleles are associated with lower replication capacity (e.g. HLA-B*81) Individuals with the least fit viruses more frequently had protective HLA alleles.

10. Majority of non-consensus amino acids in p24 increase RC Majority of non-consensus aa in p24 decreased RC and in p17 increased RC. 17 codons associated with changes in replication capacity in a multivariate model.

11. Recombinant viruses expressing patient derived HIV-1 subtype Gag have a wide range of replication capacities Viral replication capacities vary significantly across different HLA-B alleles and some protective HLA alleles are associated with reduced viral fitness Viral replication capacity is associated with markers of disease progression Gag may be an important immunogen in vaccines designed to drive HIV to a less replicative state Discussion and conclusions

12. Acknowledgements UKZN Jaclyn Wright Mopo Radebe Sinikithemba study team HPP acute infection study team Simon Fraser University Mark Brockman Zabrina Brumme Harvard/MGH Marcus Altfeld Bruce Walker Microsoft Research David Heckerman Jonathan Carlson University of Oxford Philip Goulder Funding NIH South Africa AIDS Vaccine Initiative Ragon Institute of MGH, MIT and Harvard University South African DST/NRF