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

Nature Communications
Hongshuo SongFeng Gao

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.

References

Nov 1, 1995·AIDS Research and Human Retroviruses·A C SiepelB T Korber
Jun 11, 1996·Proceedings of the National Academy of Sciences of the United States of America·L MoutouhD D Richman
Nov 22, 2001·Proceedings of the National Academy of Sciences of the United States of America·D Posada, K A Crandall
Feb 16, 2002·Journal of Molecular Evolution·David Posada, Keith A Crandall
Mar 22, 2002·Nature Reviews. Immunology·Alan S Perelson
Oct 22, 2002·Journal of Virology·Jianling ZhuangJoseph P Dougherty
Jan 22, 2004·Bioinformatics·Emmanuel ParadisKorbinian Strimmer
Sep 3, 2004·Genetics·Daniel ShrinerJames I Mullins
Oct 14, 2005·Molecular Biology and Evolution·Daniel H Huson, David Bryant
Feb 21, 2006·Bioinformatics·Jochen Maydt, Thomas Lengauer
Sep 28, 2006·Nucleic Acids Research·Heather A BairdMatteo Negroni
May 21, 2008·Proceedings of the National Academy of Sciences of the United States of America·Brandon F KeeleGeorge M Shaw
Jul 16, 2008·The Journal of Experimental Medicine·Hendrik StreeckTodd M Allen
Sep 13, 2008·PLoS Computational Biology·John ArcherDavid L Robertson
Jun 3, 2009·The Journal of Experimental Medicine·Jesus F Salazar-GonzalezGeorge M Shaw
Dec 4, 2009·PLoS Computational Biology·Sergei L Kosakovsky PondSimon D W Frost
Feb 4, 2010·PLoS Computational Biology·Richard A Neher, Thomas Leitner
May 6, 2010·PLoS Computational Biology·Timothy E SchlubMiles P Davenport
Oct 27, 2010·BMC Bioinformatics·Elena E GiorgiTanmoy Bhattacharya
Mar 26, 2011·Proceedings of the National Academy of Sciences of the United States of America·Rebecca BatorskyJohn M Coffin
Jul 5, 2011·Nature Reviews. Microbiology·Etienne Simon-Loriere, Edward C Holmes
Oct 14, 2011·Viruses·Krista Delviks-FrankenberryWei-Shau Hu
Jan 1, 2001·Indian Journal of Clinical Biochemistry : IJCB·A RayB K Sharma
Jan 24, 2013·PLoS Computational Biology·Mikael SunnåkerChristophe Dessimoz
Feb 15, 2013·Journal of Virology·Penny L MooreLynn Morris
Apr 5, 2013·Nature·Hua-Xin LiaoBarton F Haynes
Apr 10, 2013·Journal of Theoretical Biology·Elena E GiorgiTanmoy Bhattacharya
Oct 18, 2013·Molecular Biology and Evolution·Koichiro TamuraSudhir Kumar
Mar 5, 2014·Nature·Nicole A Doria-RoseJohn R Mascola
Jan 1, 2013·Journal of Statistical Mechanics : Theory and Experiment·Vitaly V GanusovAlan S Perelson

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Citations

Aug 4, 2018·The Journal of Experimental Medicine·Yehuda Z CohenMichel C Nussenzweig
Mar 19, 2019·Current Opinion in HIV and AIDS·Nicholas BbosaDeogratius Ssemwanga
Jan 10, 2020·AIDS Research and Human Retroviruses·Adam A CapoferriUNKNOWN Rakai Health Sciences Program and the PANGEA Consortium
Sep 7, 2018·Journal of the Royal Society, Interface·Joëlle Barido-SottaniTanja Stadler
Apr 29, 2020·Annual Review of Immunology·Kathryn E StephensonDan H Barouch
May 13, 2020·Virus Evolution·Heather E GrantAndrew J Leigh Brown
Oct 23, 2019·Virus Evolution·Pakorn AiewsakunAris Katzourakis
Feb 2, 2021·PLoS Computational Biology·Bethany DearloveUNKNOWN RV217 Study Team
Jan 22, 2021·The Journal of Immunology : Official Journal of the American Association of Immunologists·David A SpencerAnn J Hessell
Dec 30, 2020·Pathogens·Marta GiovanettiAlessandra Borsetti
Feb 16, 2021·Molecular Biology and Evolution·Juan Ángel Patiño-GalindoRaul Rabadan
Mar 23, 2021·Open Forum Infectious Diseases·Hongshuo SongJintanat Ananworanich
Apr 4, 2021·International Journal of Molecular Sciences·Sayuri SakuragiJun-Ichi Sakuragi
Jul 10, 2021·Cell Host & Microbe·Will FischerBette Korber

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Methods Mentioned

BETA
SGA
glycosylation
PCR
ELISA
RAPR

Software Mentioned

MEGA6
CLUSTAL
RAT
Highlighter
Recombination Analysis PRogram ( RAPR )
Poisson Fitter
SGA
RECCO
R
RAPR

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