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Tracking HIV-1 recombination to resolve its contribution to HIV-1 evolution in natural infection.

Publication ,  Journal Article
Song, H; Giorgi, EE; Ganusov, VV; Cai, F; Athreya, G; Yoon, H; Carja, O; Hora, B; Hraber, P; Romero-Severson, E; Jiang, C; Li, X; Wang, S ...
Published in: Nat Commun
May 15, 2018

Recombination in HIV-1 is well documented, but its importance in the low-diversity setting of within-host diversification is less understood. Here we develop a novel computational tool (RAPR (Recombination Analysis PRogram)) to enable a detailed view of in vivo viral recombination during early infection, and we apply it to near-full-length HIV-1 genome sequences from longitudinal samples. Recombinant genomes rapidly replace transmitted/founder (T/F) lineages, with a median half-time of 27 days, increasing the genetic complexity of the viral population. We identify recombination hot and cold spots that differ from those observed in inter-subtype recombinants. Furthermore, RAPR analysis of longitudinal samples from an individual with well-characterized neutralizing antibody responses shows that recombination helps carry forward resistance-conferring mutations in the diversifying quasispecies. These findings provide insight into molecular mechanisms by which viral recombination contributes to HIV-1 persistence and immunopathogenesis and have implications for studies of HIV transmission and evolution in vivo.

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Published In

Nat Commun

DOI

EISSN

2041-1723

Publication Date

May 15, 2018

Volume

9

Issue

1

Start / End Page

1928

Location

England

Related Subject Headings

  • Recombination, Genetic
  • Phylogeny
  • Male
  • Longitudinal Studies
  • Humans
  • HIV-1
  • HIV Infections
  • Genotype
  • Genetic Variation
  • Evolution, Molecular
 

Citation

APA
Chicago
ICMJE
MLA
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Song, H., Giorgi, E. E., Ganusov, V. V., Cai, F., Athreya, G., Yoon, H., … Gao, F. (2018). Tracking HIV-1 recombination to resolve its contribution to HIV-1 evolution in natural infection. Nat Commun, 9(1), 1928. https://doi.org/10.1038/s41467-018-04217-5
Song, Hongshuo, Elena E. Giorgi, Vitaly V. Ganusov, Fangping Cai, Gayathri Athreya, Hyejin Yoon, Oana Carja, et al. “Tracking HIV-1 recombination to resolve its contribution to HIV-1 evolution in natural infection.Nat Commun 9, no. 1 (May 15, 2018): 1928. https://doi.org/10.1038/s41467-018-04217-5.
Song H, Giorgi EE, Ganusov VV, Cai F, Athreya G, Yoon H, et al. Tracking HIV-1 recombination to resolve its contribution to HIV-1 evolution in natural infection. Nat Commun. 2018 May 15;9(1):1928.
Song, Hongshuo, et al. “Tracking HIV-1 recombination to resolve its contribution to HIV-1 evolution in natural infection.Nat Commun, vol. 9, no. 1, May 2018, p. 1928. Pubmed, doi:10.1038/s41467-018-04217-5.
Song H, Giorgi EE, Ganusov VV, Cai F, Athreya G, Yoon H, Carja O, Hora B, Hraber P, Romero-Severson E, Jiang C, Li X, Wang S, Li H, Salazar-Gonzalez JF, Salazar MG, Goonetilleke N, Keele BF, Montefiori DC, Cohen MS, Shaw GM, Hahn BH, McMichael AJ, Haynes BF, Korber B, Bhattacharya T, Gao F. Tracking HIV-1 recombination to resolve its contribution to HIV-1 evolution in natural infection. Nat Commun. 2018 May 15;9(1):1928.

Published In

Nat Commun

DOI

EISSN

2041-1723

Publication Date

May 15, 2018

Volume

9

Issue

1

Start / End Page

1928

Location

England

Related Subject Headings

  • Recombination, Genetic
  • Phylogeny
  • Male
  • Longitudinal Studies
  • Humans
  • HIV-1
  • HIV Infections
  • Genotype
  • Genetic Variation
  • Evolution, Molecular