Grant: $47,210 - National Institutes of Health - Jul. 23, 2009
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Award Description: CTL ESCAPE AND REVERSION IN LINKED PAIRS Recent studies have demonstrated that HIV immune escape follows a predictable mutational path in response to an individual?s genetic environment, specifically an individual?s HLA alleles. Since immune escape follows predictable mutational pathways, these evolutionary events are not random, and understanding the dynamics between CTL epitope escape and reversion will further our knowledge of the immune pressures that drive viral evolution and diversity at both an individual and population level. It will also allow us to better understand host/pathogen dynamics and may identify additional epitopes and viral protein sequences that may be exploited in vaccine design. The project proposed here will examine the escape and reversion rates of known CTL epitopes in a cohort of subtype C infected epidemiologically linked transmission pairs in Zambia. This project, while similar to other studies, has certain strengths that make it novel and significant. Since the project will be examining linked pairs, the transmitted sequence will be known and we will be able to overcome the limitations that have hindered previous studies. Additionally, samples are taken from our linked recipients at the time of recipient seroconversion, providing uniform baseline sampling time point. Finally, we will examine escape and reversion in African individuals infected with a subtype C virus. 1. Based on known amino acid polymorphisms and the correlating HLA allele, we will determine the kinetics of CTL escape mutations and reversion in an African subtype C cohort. Previous studies addressing this question have been hindered by limitations that this study will overcome by using epidemiologically linked transmission pairs from an African subtype C cohort. Using sequence data of gag, pol and nef from 150 Zambian linked transmission pairs from the Zambia-Emory HIV Research Project we will determine the escape and reversion rates of known CTL escape epitopes. We will also examine the frequency of epitope recognition and determine if it correlates with the rate of epitope escape. Additionally, we will examine the subtle differences in escape and reversion at a molecular level. Studies involving the well-characterized escape epitope TW10 (TSTLQEQIGW, Gag 240-249) have demonstrated that in HLA-B*57 positive individuals an escape mutation, T242N, arises and alters the interaction between capsid and cyclophilin A, resulting in a less fit virus and lower viral loads. However, subsequently, a compensatory mutation, G248A, arises and is associated with increased viral loads, presumably restoring viral fitness. We will determine if additional epitopes require compensatory mutations to overcome viral fitness costs and determine if these mutations arise prior to immune escape or are selected for after escape to restore viral fitness. 2. Determine if escape mutations in reverting epitopes are associated with a viral fitness cost. CTL escape epitopes that revert upon transmission to an individual with a different HLA type are thought to represent escape mutations that incur a fitness cost. Previous studies addressing this question have focused on epitopes presented by protective HLA alleles (HLA-B*57and HLA-B*27) presenting epitopes in Gag, specifically, epitopes TW10 and KF11 (KAFSPEVIPMF, Gag 162-172) presented by HLA-B*57 and KK10 (KRWIILGLNK, Gag 263-272) presented by HLA-B*27. We will determine if escape mutations in reverting epitopes are associated with a fitness cost. Viral fitness will be assessed through competition and in vitro replication assays.
Project Description: HIV immune escape events are not random and follow a predictable mutational path in response to the HLA alleles carried by an individual. Understanding the dynamics between CTL epitope escape and reversion will further our knowledge of the immune pressures that drive viral evolution and diversity at both an individual and population level. Recent studies have examined the kinetics of CTL epitope escape and reversion in subtype B HIV-1 infected individuals, but such studies are complicated by the absence of information about the transmitted sequence. To address the question of CTL epitope escape and reversion, where the genotype of the transmitted virus is known, we examined Gag, Pol and Nef in a large number of epidemiologically linked transmission pairs from an African subtype C cohort. Cohabiting HIV-1 discordant heterosexual couples from Lusaka, Zambia were followed longitudinally on a monthly or three-monthly schedule. Despite counseling and condom provision, approximately 7% of uninfected partners became infected each year. At the time of infection and at three-month follow-up intervals, blood and PBMC samples were collected from both the donor and recipient. To date we have amplified and sequenced the gag, pol and nef genes from 43 linked transmission pairs with follow-up out to one year. We have observed that CTL escape mutations are transmitted more frequently than previously recognized. Additionally, only 5-13% (depending on the gene) of these transmitted CTL escape mutations will revert to consensus during the first year of infection. Furthermore, we observed that of the CTL escape mutations present at one-year post transmission only 12-19% represent new escape mutations. These results indicate that transmission pairs are critical for an accurate analysis of HLA linked viral evolution in a newly infected individual.
Infrastructure Description: N/A
Jobs Summary: A postdoctoral training position was created/retained when this work was funded. A postdoctoral training position allows a doctoral graduate to receive further training in scientific research methods and develop critical thinking skills that will be essential for future career development as an independent research scientist. (Total jobs reported: 0)
Project Status: Less Than 50% Completed
This award's data was last updated on Jul. 23, 2009. Help expand these official descriptions using the wiki below.