Recent Evolutionary History of Human Immunodeficiency Virus Type 1 Subtype B: Reconstruction of Epidemic Onset Based on Sequence Distances to the Common Ancestor |
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Authors: | Vladimir V Lukashov Jaap Goudsmit |
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Institution: | (1) Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Amsterdam, Meibergdreef 15, 1105 AZ The Netherlands, NL |
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Abstract: | We obtained and studied HIV-1 sequences with a known sampling year from three outbreaks of the HIV-1 epidemic: 141 env V3
(270 nt) sampled between 1984 and 1992 and 117 pol prot/RT (804 nt) sequences sampled between 1986 and 1999 from Dutch homosexual
men and injecting drug users (IDUs), as well as 77 env V3 sequences sampled between 1983 and 1994 in the United States. Since
retrospective serological and/or epidemiological data on these populations are available, providing estimates of the dates
of the onset of the HIV-1 epidemics, we had the opportunity to test different phylogenetic models for their accuracy in deriving
the recent evolutionary history of HIV-1 subtype B and the onset date of the HIV-1 epidemic. We observed that, in any given
year, individual sequences vary widely in their distances to the common ancestor, and sequences close to the ancestors were
found decades after the onset of the epidemic. Nevertheless, the mean evolutionary distances of virus strains to ancestors
were increasing significantly during the course of the studied epidemics, which indicates that the molecular clock is operational
in the recent evolution of HIV-1. When the relationship between the sampling years of sequences and their nucleotide distances
to the common ancestor was extrapolated to the past, analysis of pol sequences provided accurate estimates of the onset years
of the epidemics, whereas analysis of V3 sequences by the maximum-likelihood or neighbor-joining methods led to an overestimation
of the age of the epidemics. Separate analysis of nonsynonymous and synonymous distances revealed that this overestimation
results from nonsynonymous substitutions, whose numbers were not increasing significantly in all three virus populations over
the observation period. In contrast, analysis of synonymous env V3 distances provided accurate estimates of the onset years
for the outbreaks we studied.
Received: 26 October 2001 / Accepted: 8 November 2001 |
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Keywords: | : HIV-1 — AIDS epidemic — Molecular history |
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