title: Estimating selection pressures on HIV-1 using phylogenetic likelihood models.
abstract: Human immunodeficiency virus (HIV-1) can rapidly evolve due to selection pressures exerted by HIV-specific immune responses, antiviral agents, and to allow the virus to establish infection in different compartments in the body. Statistical models applied to HIV-1 sequence data can help to elucidate the nature of these selection pressures through comparisons of non-synonymous (or amino acid changing) and synonymous (or amino acid preserving) substitution rates. These models also need to take into account the non-independence of sequences due to their shared evolutionary history. We review how we have developed these methods and have applied them to characterize the evolution of HIV-1 in vivo. To illustrate our methods, we present an analysis of compartment-specific evolution of HIV-1 env in blood and cerebrospinal fluid and of site-to-site variation in the gag gene of subtype C HIV-1.
authors.affiliation: Department of Pathology, University of California, San Diego, CA 92093, USA.
authors.forename: S L
authors.initials: SL
authors.lastname: Kosakovsky Pond
authors.forename: A F Y
authors.initials: AF
authors.lastname: Poon
authors.forename: S
authors.initials: S
authors.lastname: Zárate
authors.forename: D M
authors.initials: DM
authors.lastname: Smith
authors.forename: S J
authors.initials: SJ
authors.lastname: Little
authors.forename: S K
authors.initials: SK
authors.lastname: Pillai
authors.forename: R J
authors.initials: RJ
authors.lastname: Ellis
authors.forename: J K
authors.initials: JK
authors.lastname: Wong
authors.forename: A J
authors.initials: AJ
authors.lastname: Leigh Brown
authors.forename: D D
authors.initials: DD
authors.lastname: Richman
authors.forename: S D W
authors.initials: SD
authors.lastname: Frost
mesh_terms: D015497:HIV-1 / Q000378:metabolism / Q000472:pathogenicity*; D006801:Humans; D016013:Likelihood Functions; D015233:Models, Statistical; D010802:Phylogeny; D012641:Selection, Genetic; D054301:gag Gene Products, Human Immunodeficiency Virus / Q000235:genetics
chemical_list: D054301:gag Gene Products, Human Immunodeficiency Virus