%0 Journal Article
%T Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection
%A Agnes-Laurence Chenine
%A Anne Marie O¡¯Sullivan
%A Bette T. Korber
%A Bonnie Slike
%A Celina Oropeza
%A Claudia Cicala
%A Elizabeth A. Harbolick
%A Eric Sanders-Buell
%A Erik Billings
%A Feng Gao
%A George M. Shaw
%A Gustavo H. Kijak
%A Hannah Kibuuka
%A Hui Li
%A James Arthos
%A Jerome H. Kim
%A Joanna A. Warren
%A Kristina K. Peachman
%A Kultida Poltavee
%A Leigh A. Eller
%A Lucas Maganga
%A Mangala Rao
%A Margaret C. Costanzo
%A Mary A. Marovich
%A Meera Bose
%A Melanie Merbah
%A Merlin L. Robb
%A Michael A. Eller
%A Morgane Rolland
%A Nelson L. Michael
%A Nilu Goonetilleke
%A Phuc Pham
%A Rasmi Thomas
%A Robert J. O¡¯Connell
%A Samuel Sinei
%A Shelly J. Krebs
%A Sivan Leviyang
%A Sodsai Tovanabutra
%A Sorachai Nitayaphan
%A Will Fischer
%J -
%D 2017
%R 10.1371/journal.ppat.1006510
%X In order to inform the rational design of HIV-1 preventive and cure interventions it is critical to understand the events occurring during acute HIV-1 infection (AHI). Using viral deep sequencing on six participants from the early capture acute infection RV217 cohort, we have studied HIV-1 evolution in plasma collected twice weekly during the first weeks following the advent of viremia. The analysis of infections established by multiple transmitted/founder (T/F) viruses revealed novel viral profiles that included: a) the low-level persistence of minor T/F variants, b) the rapid replacement of the major T/F by a minor T/F, and c) an initial expansion of the minor T/F followed by a quick collapse of the same minor T/F to low frequency. In most participants, cytotoxic T-lymphocyte (CTL) escape was first detected at the end of peak viremia downslope, proceeded at higher rates than previously measured in HIV-1 infection, and usually occurred through the exploration of multiple mutational pathways within an epitope. The rapid emergence of CTL escape variants suggests a strong and early CTL response. Minor T/F viral strains can contribute to rapid and varied profiles of HIV-1 quasispecies evolution during AHI. Overall, our results demonstrate that early, deep, and frequent sampling is needed to investigate viral/host interaction during AHI, which could help identify prerequisites for prevention and cure of HIV-1 infection
%K Viremia
%K HIV-1
%K Cloning
%K Microbial genetics
%K Sequence analysis
%K Viral evolution
%K Genetic polymorphism
%K T cells
%U https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1006510