The Virology Core is primarily responsible for supporting the clinical research effort of the HIV Drug Resistance Program by developing and applying new technologies to quantify low-level viremia, to detect low-frequency drug-resistant mutants, and to characterize the genetic diversity of HIV-1 in infected individuals.  The Virology Core has developed several assays for application to projects within the Host-Virus Interaction Branch and other sections of the HIV Drug Resistance Program:

Single-Copy Assay (SCA) for Detection of HIV-1 RNA in Plasma.  Potent antiretroviral therapy is effective in suppressing, but not eradicating, HIV-1 infection.  Persistent viremia can be detected in patients on antiretroviral therapy despite suppression of plasma HIV-1 RNA to <50 copies/ml.  The Virology Core developed the SCA for detection of HIV-1 RNA, which has a dynamic range of 10⁶ to 0.3 copies/ml.  This technology is now being applied to characterize the prevalence, level, and change over time of persistent viremia.

Single-Genome Sequencing (SGS) for Genetic Analysis of HIV-1 Populations.  Characterization of the genetic diversity of HIV-1, including the prevalence of rare drug-resistant variants, in patients with acute infection or chronic untreated infection and in patients initiating antiretroviral therapy can provide important insights into the effective population size of HIV-1, and the likelihood of emergence of drug-resistant variants.  Standard population-based DNA sequencing methods cannot reliably detect HIV-1 variants that comprise <20% of the virus population.  Furthermore, these methods cannot distinguish whether alleles are present on the same genome or different genomes.  The Virology Core developed the SGS assay for detecting sequences derived from individual viral genomes in plasma.  Using the SGS assay, the Core has studied HIV-1 diversity and divergence in recently infected patients followed for up to 5 years after infection, in patients who were chronically infected with HIV-1 for 5 years and longer, and in HIV-1-infected patients initiating therapy.

Allele-Specific PCR (ASP) for Detection of Low-Frequency Mutations.  Low-frequency drug-resistant mutants are hypothesized to contribute to antiretroviral treatment failure.  The Virology Core developed the ASP assay for quantifying drug-resistant HIV-1 variants at reverse transcriptase amino acid codon positions 103, 181, 184, and 190 at frequencies as low as 0.1%.  The Core is applying the ASP assay to plasma samples from treatment-naïve and experienced patients to assess the frequency of mutant alleles and their relation to virologic response to antiretroviral treatment.