An introduction to a novel population genetic approach for HIV characterization

Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases
Beatriz Perez-SweeneyJohn L Ho

Abstract

The rapid evolution of the HIV genome is influenced in part by host selection pressure, which may cause parallel evolution among strains under shared selection pressures. To understand the mechanisms behind HIV-host immune escape across host populations, researchers have compared signatures of positive selection pressure on HIV codons across HIV subtypes and across phylogenetic groups of isolates within major subtypes, all relying on a criterion of phylogenetic separation. The HIV codon sites that retain diversity, evolve convergently among sets of hosts (cohorts) and diverge between cohorts may be phylogenetically undiagnostic (reveal little information about the relationship of the strains) and thus undetectable on a tree. We propose a new approach to characterizing genetic divergence among isolates using existing population genetic methods to better understand HIV response to host selection pressures. The approach combines population genetic statistical methods with codon analysis to identify putative amino acid sites evolving convergently. To illustrate the approach, we compared the C2-V3-C3 region of the envelope protein of HIV-1 clade B isolates between Haiti and USA hosts. This region showed no phylogenetic separation be...Continue Reading

References

Oct 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·T ShiodaC Cheng-Mayer
Jan 1, 1985·Journal of Molecular Evolution·M HasegawaT Yano
Oct 20, 1983·The New England Journal of Medicine·J W PapeW D Johnson
Jul 13, 1995·Nature·S BonhoefferM A Nowak
Feb 18, 1997·Proceedings of the National Academy of Sciences of the United States of America·Y Yamaguchi, T Gojobori
Jan 27, 1999·Bioinformatics·D Posada, K A Crandall
Nov 24, 1999·Molecular Biology and Evolution·Y Suzuki, T Gojobori
Feb 10, 2000·Molecular Biology and Evolution·Z Yang, R Nielsen
Jun 10, 2000·Science·B KorberT Bhattacharya
Jan 1, 1996·Cladistics : the International Journal of the Willi Hennig Society·D AgostiR DeSalle
Jun 29, 2002·Science·Brian GaschenBette Korber
Jan 14, 2003·Annual Review of Immunology·Daniel C DouekRichard A Koup
Mar 20, 2003·Proceedings of the National Academy of Sciences of the United States of America·Douglas D RichmanChristos J Petropoulos
Mar 21, 2003·Nature·Xiping WeiGeorge M Shaw
Jun 5, 2003·Molecular Biology and Evolution·Scott Williamson
Aug 13, 2003·Bioinformatics·Fredrik Ronquist, John P Huelsenbeck
Oct 18, 2003·Journal of Molecular Evolution·Wa YangZiheng Yang
Jan 7, 2004·Nature Reviews. Genetics·Andrew RambautEdward C Holmes
Jul 23, 2004·Evolution; International Journal of Organic Evolution·Rafael SanjuánSantiago F Elena
Jan 14, 2005·Bioinformatics·Federico AbascalDavid Posada
Feb 11, 2005·Molecular Biology and Evolution·Sergei L Kosakovsky Pond, Simon D W Frost
Feb 17, 2005·Bioinformatics·Sergei L Kosakovsky Pond, Simon D W Frost
Jul 20, 2005·Expert Review of Vaccines·Karen S SlobodJulia L Hurwitz
Jun 23, 2006·PLoS Computational Biology·Sergei L Kosakovsky PondAndrew J Leigh Brown
May 1, 2007·PLoS Computational Biology·David C NickleNebojsa Jojic
Nov 6, 2007·Proceedings of the National Academy of Sciences of the United States of America·M Thomas P GilbertMichael Worobey

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Citations

Jun 14, 2012·PloS One·Manon Ragonnet-CroninJames Brooks

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