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Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection.

Publication ,  Journal Article
Kijak, GH; Sanders-Buell, E; Chenine, A-L; Eller, MA; Goonetilleke, N; Thomas, R; Leviyang, S; Harbolick, EA; Bose, M; Pham, P; Oropeza, C ...
Published in: PLoS Pathog
July 2017

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.

Duke Scholars

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Published In

PLoS Pathog

DOI

EISSN

1553-7374

Publication Date

July 2017

Volume

13

Issue

7

Start / End Page

e1006510

Location

United States

Related Subject Headings

  • Young Adult
  • Virology
  • T-Lymphocytes, Cytotoxic
  • Middle Aged
  • Male
  • Immune Evasion
  • Humans
  • High-Throughput Nucleotide Sequencing
  • HIV-1
  • HIV Infections
 

Citation

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Chicago
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Kijak, G. H., Sanders-Buell, E., Chenine, A.-L., Eller, M. A., Goonetilleke, N., Thomas, R., … Kim, J. H. (2017). Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection. PLoS Pathog, 13(7), e1006510. https://doi.org/10.1371/journal.ppat.1006510
Kijak, Gustavo H., Eric Sanders-Buell, Agnes-Laurence Chenine, Michael A. Eller, Nilu Goonetilleke, Rasmi Thomas, Sivan Leviyang, et al. “Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection.PLoS Pathog 13, no. 7 (July 2017): e1006510. https://doi.org/10.1371/journal.ppat.1006510.
Kijak GH, Sanders-Buell E, Chenine A-L, Eller MA, Goonetilleke N, Thomas R, et al. Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection. PLoS Pathog. 2017 Jul;13(7):e1006510.
Kijak, Gustavo H., et al. “Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection.PLoS Pathog, vol. 13, no. 7, July 2017, p. e1006510. Pubmed, doi:10.1371/journal.ppat.1006510.
Kijak GH, Sanders-Buell E, Chenine A-L, Eller MA, Goonetilleke N, Thomas R, Leviyang S, Harbolick EA, Bose M, Pham P, Oropeza C, Poltavee K, O’Sullivan AM, Billings E, Merbah M, Costanzo MC, Warren JA, Slike B, Li H, Peachman KK, Fischer W, Gao F, Cicala C, Arthos J, Eller LA, O’Connell RJ, Sinei S, Maganga L, Kibuuka H, Nitayaphan S, Rao M, Marovich MA, Krebs SJ, Rolland M, Korber BT, Shaw GM, Michael NL, Robb ML, Tovanabutra S, Kim JH. Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection. PLoS Pathog. 2017 Jul;13(7):e1006510.

Published In

PLoS Pathog

DOI

EISSN

1553-7374

Publication Date

July 2017

Volume

13

Issue

7

Start / End Page

e1006510

Location

United States

Related Subject Headings

  • Young Adult
  • Virology
  • T-Lymphocytes, Cytotoxic
  • Middle Aged
  • Male
  • Immune Evasion
  • Humans
  • High-Throughput Nucleotide Sequencing
  • HIV-1
  • HIV Infections