TY - JOUR
T1 - The evolution of HIV
T2 - Inferences using phylogenetics
AU - Castro-Nallar, Eduardo
AU - Pérez-Losada, Marcos
AU - Burton, Gregory F.
AU - Crandall, Keith A.
PY - 2012/2
Y1 - 2012/2
N2 - Molecular phylogenetics has revolutionized the study of not only evolution but also disparate fields such as genomics, bioinformatics, epidemiology, ecology, microbiology, molecular biology and biochemistry. Particularly significant are its achievements in population genetics as a result of the development of coalescent theory, which have contributed to more accurate model-based parameter estimation and explicit hypothesis testing. The study of the evolution of many microorganisms, and HIV in particular, have benefited from these new methodologies. HIV is well suited for such sophisticated population analyses because of its large population sizes, short generation times, high substitution rates and relatively small genomes. All these factors make HIV an ideal and fascinating model to study molecular evolution in real time. Here we review the significant advances made in HIV evolution through the application of phylogenetic approaches. We first examine the relative roles of mutation and recombination on the molecular evolution of HIV and its adaptive response to drug therapy and tissue allocation. We then review some of the fundamental questions in HIV evolution in relation to its origin and diversification and describe some of the insights gained using phylogenies. Finally, we show how phylogenetic analysis has advanced our knowledge of HIV dynamics (i.e., phylodynamics).
AB - Molecular phylogenetics has revolutionized the study of not only evolution but also disparate fields such as genomics, bioinformatics, epidemiology, ecology, microbiology, molecular biology and biochemistry. Particularly significant are its achievements in population genetics as a result of the development of coalescent theory, which have contributed to more accurate model-based parameter estimation and explicit hypothesis testing. The study of the evolution of many microorganisms, and HIV in particular, have benefited from these new methodologies. HIV is well suited for such sophisticated population analyses because of its large population sizes, short generation times, high substitution rates and relatively small genomes. All these factors make HIV an ideal and fascinating model to study molecular evolution in real time. Here we review the significant advances made in HIV evolution through the application of phylogenetic approaches. We first examine the relative roles of mutation and recombination on the molecular evolution of HIV and its adaptive response to drug therapy and tissue allocation. We then review some of the fundamental questions in HIV evolution in relation to its origin and diversification and describe some of the insights gained using phylogenies. Finally, we show how phylogenetic analysis has advanced our knowledge of HIV dynamics (i.e., phylodynamics).
KW - Drug resistance
KW - HIV
KW - HIV origins
KW - Molecular epidemiology
KW - Phylodynamics
KW - Phylogenetics
KW - Reservoir
KW - Vaccine resistance
KW - Viral transmission
KW - Virus evolution
UR - http://www.scopus.com/inward/record.url?scp=84855194563&partnerID=8YFLogxK
U2 - 10.1016/j.ympev.2011.11.019
DO - 10.1016/j.ympev.2011.11.019
M3 - Review article
C2 - 22138161
AN - SCOPUS:84855194563
SN - 1055-7903
VL - 62
SP - 777
EP - 792
JO - Molecular Phylogenetics and Evolution
JF - Molecular Phylogenetics and Evolution
IS - 2
ER -