Laboratory of Molecular Virology

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Feng Gao, MD
Professor
fgao@duke.edu

One of the unique features of human immunodeficiency viruses (HIV) is the extraordinary variation in the genome. Based on genetic variation, the HIV-1 group M viruses have been classified into nine subtypes. Genetic analyses of viral genomes have played a significant role in many important findings in HIV research but the high level of genetic variation also poses a major hurdle for the development of broadly reactive vaccines. Dr. Gao’s laboratory has a long-standing interest in elucidating the genetic variation and evolution of HIV and SIV and in studying HIV/SIV gene function and pathogenic mechanisms from an evolutionary perspective. Research in Dr. Gao’s laboratory focuses on three major areas:
 
1. Study of drug resistance mechanisms.
 
Highly active antiretroviral therapy (HAART) has been effective in reducing HIV-related mortality and morbidity. However, many HIV-infected patients still fail HAART. Emergence of drug-resistant viruses plays a fundamental role in treatment failure and the development of resistance to antiretroviral drugs can eventually comprise the efficacy of HIV-1 treatment. It is important to delineate mechanisms of multiple-drug resistance in order to more effectively control HIV infection. To address this important issue, Dr Gao’s laboratory is currently studying population genetics, fitness, and evolution of minority linked multiple drug resistant viruses using a highly sensitive parallel allele-specific sequencing method. Results from these studies may lead to a better understanding of the role of minority drug-resistant populations in drug resistance, drug-resistance mechanisms, better treatment regimens, and assays that can accurately predict treatment outcomes.
 
2. Development of broadly reactive HIV vaccines.
 
AIDS vaccine development has been hindered by two main obstacles: the high level of genetic variation among HIV-1 strains and weak immune responses induced by current vaccines. With genetic variation as high as 30% in the envelope protein among different subtypes of HIV-1 group M viruses, it is overly optimistic to believe that cross-subtype protection will occur equally well among all subtypes.  Dr Gao’s laboratory is developing a novel centralized gene (consensus and ancestor) strategy to decrease the genetic distance between candidate immunogens and field virus strains and to induce cross-reactive immune responses to all subtypes. The first generation group M consensus env gene (CON6) is equidistant from contemporary HIV-1 subtypes and recombinants and is as biologically functional as contemporary Env proteins. Most importantly, CON6 can elicit broader and more potent T cell responses than wild type HIV-1 env genes. Further modifications of the group M consensus envelope immunogen show that glycosylation on the consensus envelope protein has a significant impact on its processing in mammalian cells and envelope immunogens with minimum glycosylation and deletion of variable regions can induce T cell responses that are different from those induced by wild type envelope proteins. Work is continuing to explore other possibilities to develop HIV-1 vaccines that can induce more potent and broadly reactive immune responses.
 
3. Study of HIV-1 genetic variation and sequence/biological signatures.
 
Functional HIV-1 env clones have been widely used for vaccine development, neutralization assays, and pathogenesis studies. Dr Gao’s laboratory characterizes a large number of functional env genes obtained by a single genome amplification (SGA) method to avoid artificial recombination and resampling during PCR amplification. A recently developed promoter addition PCR (pPCR) method was developed in this laboratory allowing quick functional analysis of a large number of quasispecies HIV-1 env genes from each individual. It is being investigated if acute HIV infection viruses have sequence and biological signatures that differ from chronic infection viruses. On going studies focus on mapping of nAb epitiopes using Env pseudoviruses, patient sera and monoclonal antibodies. Dr Gao’s laboratory also determines escape mutations in T cell epitopes by analyzing full HIV-1 genomes from different time points of infection using the SGA method. Detailed analysis of viral sequences and their correlation with immune response and escape may assist in more effective vaccine designs.