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

AI Article Synopsis

  • * A new computational tool called RAPR has been developed to analyze in vivo viral recombination using near-full-length HIV-1 genome sequences from repeated samples.
  • * The study reveals that recombinant genomes quickly replace the original transmitted lineages, enhancing genetic complexity and potentially aiding the virus in evading the immune response by preserving resistance mutations.

Article Abstract

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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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5954121PMC
http://dx.doi.org/10.1038/s41467-018-04217-5DOI Listing

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