About: 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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About: Recent Evolutionary History of Human Immunodeficiency Virus Type 1 Subtype B: Reconstruction of Epidemic Onset Based on Sequence Distances to the Common Ancestor Goto Sponge NotDistinct Permalink

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Recent Evolutionary History of Human Immunodeficiency Virus Type 1 Subtype B: Reconstruction of Epidemic Onset Based on Sequence Distances to the Common Ancestor
Creator	Goudsmit, Jaap Lukashov, Vladimir
source	Medline; PMC
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.
has issue date	2002-01-01(xsd:dateTime)
bibo:doi	10.1007/s00239-001-0070-5
bibo:pmid	11965440
has license	no-cc
sha1sum (hex)	13ce60d39ae49f779e91769ad1a1bf00259abd49
schema:url	https://doi.org/10.1007/s00239-001-0070-5
resource representing a document's title	Recent Evolutionary History of Human Immunodeficiency Virus Type 1 Subtype B: Reconstruction of Epidemic Onset Based on Sequence Distances to the Common Ancestor
has PubMed Central identifier	PMC7087360
has PubMed identifier	11965440
schema:publication	J Mol Evol
resource representing a document's body	covid:13ce60d39ae49f779e91769ad1a1bf00259abd49#body_text
is schema:about of	named entity 'RETROSPECTIVE' named entity 'NUCLEOTIDE' named entity 'INDIVIDUAL' named entity 'DIFFERENT' named entity 'ACCURACY' named entity 'SAMPLING' named entity '1992' named entity 'COMMON' named entity 'SEQUENCE' named entity 'maximum-likelihood' named entity 'recent evolution' named entity 'molecular clock' named entity 'HIV-1' named entity 'HIV-1' named entity 'United States' named entity 'homosexual' named entity 'virus' named entity 'Common Ancestor' named entity 'Human Immunodeficiency Virus Type 1' named entity 'U.S.' named entity 'recent common ancestor' named entity 'phylogenetic' named entity 'nonsynonymous' named entity 'epidemic' named entity 'epidemic' named entity 'serological' named entity 'molecular clock' named entity 'HIV-1' named entity 'HIV' named entity 'nucleotide' named entity 'reverse transcriptase' named entity 'HIV-1' named entity 'nonsynonymous' named entity 'HIV-1' named entity 'HIV-1' named entity 'weighted least-squares' named entity 'HIV' named entity 'epidemiological studies' named entity 'Amsterdam' named entity 'synonymous substitutions' named entity 'evolutionary history' named entity 'Dutch' named entity 'drug-resistant' named entity 'HIV-1' named entity 'HIV-1' named entity 'evolution' named entity '95% CI' named entity 'molecular evolution' named entity 'HIV-1' named entity 'epidemiological data' named entity 'nucleotide' named entity 'common ancestor' named entity 'env' named entity 'phylogenetic tree' named entity 'nonsynonymous' named entity 'U.S.' named entity 'Baltimore' named entity 'env gene' named entity 'Chicago' named entity 'drug-resistant' named entity 'statistically independent' named entity 'United States' named entity 'HIV-1' named entity 'virus strain' named entity 'HIV-1' named entity 'env' named entity 'virus' named entity 'reverse transcriptase' named entity 'HIV-1' named entity 'HIV-1' named entity 'hepadnavirus family' named entity 'common ancestor' named entity 'phylogenetic method' named entity 'HIV-1' named entity 'HIV-1' named entity 'virus' named entity 'recent common ancestor' named entity 'env' named entity 'nonsynonymous' named entity 'confidence intervals'

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