Estimating selection pressures on HIV-1 using phylogenetic likelihood models.
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.
Kosakovsky Pond
S L
SL
Department of Pathology, University of California, San Diego, CA 92093, USA.
Poon
A F Y
AF
Zárate
S
S
Smith
D M
DM
Little
S J
SJ
Pillai
S K
SK
Ellis
R J
RJ
Wong
J K
JK
Leigh Brown
A J
AJ
Richman
D D
DD
Frost
S D W
SD
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
D054301:gag Gene Products, Human Immunodeficiency Virus