Abstract
The intra-host evolutionary and population dynamics of the human immunodeficiency virus type 1 (HIV-1), the cause of the acquired immunodeficiency syndrome, have been the focus of one of the most extensive study efforts in the field of molecular evolution over the past three decades. As HIV-1 is among the fastest mutating organisms known, viral sequence data sampled over time from infected patients can provide, through phylogenetic analysis, significant insights about the tempo and mode of evolutionary processes shaped by complex interaction with the host milieu. Five main aspects are discussed: the patterns of HIV-1 intra-host diversity and divergence over time in relation to different phases of disease progression; the impact of selection on the temporal structure of HIV-1 intra-host genealogies inferred from longitudinally sampled viral sequences; HIV-1 intra-host sub-population structure; the potential relationship between viral evolutionary rate and disease progression and the central evolutionary role played by recombination occurring in super-infected cells.
Highlights
Abstract swarm that infects most HIV-1seropositive individuals fits the definition of a measurably evolving population, i.e. a population from which molecular sequences taken at different
The intra-host evolutionary and population words, HIV-1 evolution in vivo is an observable dynamics of the human immunodeficiency virus type 1 (HIV-1), the cause of the acquired ly immunodeficiency syndrome, have been the focus of one of the most extensive study efforts n in the field of molecular evolution over the past o three decades
As HIV-1 is among the fastest mutating organisms known, viral sequence e data sampled over time from infected patients s can provide, through phylogenetic analysis, significant insights about the tempo and mode u of evolutionary processes shaped by complex l interaction with the host milieu
Summary
Influence of random genetic drift on o human immunodeficiency virus type 1 env evolution during chronic infection. Poss M, Rodrigo AG, Gosink JJ, et al Evolution of envelope sequences from the genital tract and peripheral blood of women infected with clade A human immunodeficiency virus type 1. Investigation of the dynamics of the spread of human immunodeficiency virus to brain and other tissues by evolutionary analysis of sequences from the p17gag and env genes. Likelihood models for and visualizing temporal clustering in Genetic and functional analysis of fulldetecting positively selected amino acid genealogies inferred from serially sampled length human immunodeficiency virus sites and applications to the HIV-1 enveviral sequences.
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