Our laboratory is involved in determining the links between viral sequence variation and viral disease pathogenesis. The major focus is on sequence variation of hepatitis C virus (HCV) during acute infection, and the degree to which that sequence variation is linked to eventual persistence versus spontaneous clearance of infection. These investigations are in turn linked to our studies of the cellular and humoral immune responses to HCV infection, including Elispot assays, in vitro cytokine staining, and dendritic cell maturation. The sequence analysis has required development of novel sequence analysis software, as well as long-amplicon RT-PCR and cloning techniques.

We also collaborate in analyses of sequence variation of other pathogens, including human immunodeficiency virus (collaboration with Dr. Siliciano), hepatitis B virus (collaborators in other institutions), enteroviruses (collaboration with Dr. Ticehurst in Pathology), and ehrlichial endosymbionts (collaboration with Dr. Dumler in Pathology).

Cox AL, Mosbruger T, Mao Q, Liu Z, Wang XH, Yang HC, Sidney J, Sette A, Pardoll D, Thomas DL, Ray SC. (2005) Cellular immune selection with hepatitis C virus persistence in humans. J. Exp. Med. 183:2373-2378 [PubMed]

Ray SC, Fanning L, Wang XH, Netski DM, Kenny-Walsh E, Thomas DL. (2005) Divergent and convergent evolution after a common-source outbreak of hepatitis C virus. J. Exp. Med. 23:13731-13738 [PubMed]

Cox AL, Mosbruger T, Lauer GM, Pardoll D, Thomas DL, Ray SC. (2005) Comprehensive analyses of CD8+ T cell responses during longitudinal study of acute human hepatitis C. Hepatology 77:116-127 [PubMed]

Hermankova M, Ray SC, Ruff C, Powell Davis M, Ingersoll R, D'Aquila RT, Quinn TC, Siliciano JD, Siliciano RF, Persaud D. (2001) Stasis in the drug resistance profiles of HIV-1 in the plasma of infected children and adults on protease inhibitor-containing combination therapy with <50 copies/ml of plasma HIV-1 RNA. JAMA 9:331 [PubMed]

Ray SC, Quinn TC. (2000) Sex and the genetic diversity of HIV-1. Nature Medicine 9:412-20 [PubMed]

Ray SC, Wang Y-M, Laeyendecker O, Ticehurst JR, Villano SA, Thomas DL. (1999) Acute Hepatitis C Virus structural gene sequences as predictors of persistent viremia: Hypervariable region 1 as a decoy. J. Virol. 9:619-624, [PubMed]