In–Depth Characterization of Viral Isolates from Plasma and Cells Compared with Plasma Circulating Quasispecies in Early HIV-1 Infection

• DOI: 10.1371/journal.pone.0032714
• Publication Date: 2012-02-29T22:42:33Z
• Authors: Judith Dalmau; Francisco M. Codoñer; Itziar Erkizia; Maria Pino; Christian Pou; Roger Paredes; Bonaventura Clotet; Javier Martinez-P...; Julia G. Prado
• Keywords: Viral quasispecies; Viral evolution

Background The use of in vitro models to unravel the phenotypic characteristics circulating viral variants is key understanding HIV-1 pathogenesis but limited by availability primary isolates from biological samples. However, overall vivo genetic variability within a subject may not be reflected viable population obtained after isolation. Although several studies have tried determine whether populations expanded are representative findings, answer remains unclear due reduced number clonal sequences analyzed or samples compared. In order overcome previous experimental limitations, here we applied Deep Pyrosequencing (DPS) technology combination with experiments analyze and compare unprecedented detail composition quasispecies. Methodology/Principal Findings We amplified DPS genomic regions covering gag, protease, integrase env-V3 characterize paired plasma peripheral blood mononuclear cells them total RNA four recently infected subjects. Our study demonstrated presence unique haplotypes scattered between sample types conservation major variants. addition, no differences intra- inter-population encoded protein were found different when these compared Additionally, similarities terms replicative capacity co-receptor usage RNA. Conclusion This first in-depth comparison characterization sources quasispecies using data supports regardless their cellular origin define traits