Accurate reconstruction of a known HIV-1 transmission history by phylogenetic tree analysis.
- 1 October 1996
- journal article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences
- Vol. 93 (20) , 10864-10869
- https://doi.org/10.1073/pnas.93.20.10864
Abstract
Phylogenetic analyses are increasingly used in attempts to clarify transmission patterns of human immunodeficiency virus type 1 (HIV-1), but there is a continuing discussion about their validity because convergent evolution and transmission of minor HIV variants may obscure epidemiological patterns. Here we have studied a unique HIV-1 transmission cluster consisting of nine infected individuals, for whom the time and direction of each virus transmission was exactly known. Most of the transmissions occurred between 1981 and 1983, and a total of 13 blood samples were obtained approximately 2-12 years later. The p17 gag and env V3 regions of the HIV-1 genome were directly sequenced from uncultured lymphocytes. A true phylogenetic tree was constructed based on the knowledge about when the transmissions had occurred and when the samples were obtained. This complex, known HIV-1 transmission history was compared with reconstructed molecular trees, which were calculated from the DNA sequences by several commonly used phylogenetic inference methods [Fitch-Margoliash, neighbor-joining, minimum-evolution, maximum-likelihood, maximum-parsimony, unweighted pair group method using arithmetic averages (UPGMA), and a Fitch-Margoliash method assuming a molecular clock (KITSCH)]. A majority of the reconstructed trees were good estimates of the true phylogeny; 12 of 13 taxa were correctly positioned in the most accurate trees. The choice of gene fragment was found to be more important than the choice of phylogenetic method and substitution model. However, methods that are sensitive to unequal rates of change performed more poorly (such as UPGMA and KITSCH, which assume a constant molecular clock). The rapidly evolving V3 fragment gave better reconstructions than p17, but a combined data set of both p17 and V3 performed best. The accuracy of the phylogenetic methods justifies their use in HIV-1 research and argues against convergent evolution and selective transmission of certain virus variants.Keywords
This publication has 25 references indexed in Scilit:
- Selective Transmission of Human Immunodeficiency Virus Type-1 Variants from Mothers to InfantsScience, 1992
- Experimental Phylogenetics: Generation of a Known PhylogenyScience, 1992
- Bidirectional solid-phase sequencing of in vitro-amplified plasmid DNA.1991
- Molecular clock of viral evolution, and the neutral theory.Proceedings of the National Academy of Sciences, 1990
- PHYLOGENIES FROM MOLECULAR SEQUENCES: INFERENCE AND RELIABILITYAnnual Review of Genetics, 1988
- Relative efficiencies of the maximum parsimony and distance-matrix methods in obtaining the correct phylogenetic tree.Molecular Biology and Evolution, 1988
- Property and efficiency of the maximum likelihood method for molecular phylogenyJournal of Molecular Evolution, 1988
- The neighbor-joining method: a new method for reconstructing phylogenetic trees.Molecular Biology and Evolution, 1987
- Mitochondrial DNA and human evolutionNature, 1987
- Construction of Phylogenetic TreesScience, 1967