Investigating the Consequences of Interference between Multiple CD8+ T Cell Escape Mutations in Early HIV Infection

PLoS Computational Biology
Victor GarciaRoland R Regoes

Abstract

During early human immunodeficiency virus (HIV) infection multiple CD8+ T cell responses are elicited almost simultaneously. These responses exert strong selective pressures on different parts of HIV's genome, and select for mutations that escape recognition and are thus beneficial to the virus. Some studies reveal that the later these escape mutations emerge, the more slowly they go to fixation. This pattern of escape rate decrease(ERD) can arise by distinct mechanisms. In particular, in large populations with high beneficial mutation rates interference among different escape strains--an effect that can emerge in evolution with asexual reproduction and results in delayed fixation times of beneficial mutations compared to sexual reproduction--could significantly impact the escape rates of mutations. In this paper, we investigated how interference between these concurrent escape mutations affects their escape rates in systems with multiple epitopes, and whether it could be a source of the ERD pattern. To address these issues, we developed a multilocus Wright-Fisher model of HIV dynamics with selection, mutation and recombination, serving as a null-model for interference. We also derived an interference-free null model assuming i...Continue Reading

References

Feb 1, 1971·Journal of Theoretical Biology·J M Smith
Dec 1, 1966·Genetical Research·W G Hill, A Robertson
Apr 1, 1983·Theoretical Population Biology·J H Gillespie
Mar 4, 1997·Proceedings of the National Academy of Sciences of the United States of America·A J Brown
Mar 3, 1999·Proceedings of the National Academy of Sciences of the United States of America·A G RodrigoJ I Mullins
Sep 11, 1999·Science·R MirallesS F Elena
Sep 15, 1999·Proceedings of the National Academy of Sciences of the United States of America·I M Rouzine, J M Coffin
Jan 11, 2000·Journal of Virology·A E JetztJ P Dougherty
Mar 29, 2001·Neuroscience Research·T InoueN Osumi
May 10, 2001·Cell Structure and Function·Y Sato
Jul 12, 2002·Nature·Andreas JungAndreas Meyerhans
Oct 22, 2002·Journal of Virology·Jianling ZhuangJoseph P Dougherty
Jan 15, 2003·Proceedings of the National Academy of Sciences of the United States of America·Igor M RouzineJohn M Coffin
Feb 18, 2004·Nature Medicine·Thomas C FriedrichDavid I Watkins
May 26, 2004·Proceedings of the National Academy of Sciences of the United States of America·Rafael SanjuánSantiago F Elena
Jun 25, 2004·Molecular Biology and Evolution·G AchazJ Wakeley
Aug 3, 2004·Nature Reviews. Immunology·Philip J R Goulder, David I Watkins
Feb 18, 2005·Genetics·Joachim Hermisson, Pleuni S Pennings
Jun 7, 2005·Trends in Microbiology·Stephen J KentMiles P Davenport
Nov 7, 2007·Proceedings of the National Academy of Sciences of the United States of America·Su-Chan Park, Joachim Krug
May 6, 2008·BMC Evolutionary Biology·Yi Liu, John E Mittler
May 21, 2008·Proceedings of the National Academy of Sciences of the United States of America·Brandon F KeeleGeorge M Shaw
Jul 12, 2008·Nature Reviews. Immunology·Philip J R Goulder, David I Watkins
Jul 19, 2008·PLoS Computational Biology·Christian L Althaus, Rob J De Boer

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Citations

Feb 24, 2018·Frontiers in Immunology·Yiding Yang, Vitaly V Ganusov
Dec 1, 2017·Journal of the Royal Society, Interface·Kyle B Gustafson, Joshua L Proctor
Feb 28, 2019·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Subhasish BaralNarendra M Dixit
Jun 4, 2020·PLoS Pathogens·Christopher J R IllingworthKatrina A Lythgoe
May 17, 2017·Frontiers in Immunology·Victor Garcia, Marcus W Feldman
Mar 23, 2018·Journal of the Royal Society, Interface·Victor GarciaMarcus W Feldman
Jun 19, 2019·Proceedings of the National Academy of Sciences of the United States of America·Martin VögeleGerhard Hummer
Jun 28, 2018·Proceedings of the National Academy of Sciences of the United States of America·Lynsey BunnefeldKonrad Lohse
Mar 13, 2020·The Journal of Experimental Biology·Fabian SteinbeckPaul Graham
Mar 21, 2020·Proceedings of the National Academy of Sciences of the United States of America·Simeon CarstensMichael Habeck
Aug 8, 2019·Proceedings of the National Academy of Sciences of the United States of America·Matthias SteinrückenYun S Song
Mar 11, 2020·Cancer Research·Yvonne A EvrardUNKNOWN NCI PDXNet Consortium
Feb 3, 2021·Proceedings of the National Academy of Sciences of the United States of America·Camille Simonet, Luke McNally
Aug 30, 2019·Current Opinion in Systems Biology·Jessica M Conway, Ruy M Ribeiro
Apr 3, 2021·Proceedings of the National Academy of Sciences of the United States of America·Giulio IsacchiniArmita Nourmohammad
May 22, 2021·Proceedings of the National Academy of Sciences of the United States of America·William S DeWittKelley Harris
Oct 26, 2021·Frontiers in Immunology·Brittany Rife MagalisMarco Salemi

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