Phylogenetic analysis of gag genes from 70 international... : AIDS (original) (raw)

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Phylogenetic analysis of gag genes from 70 international HIV-1 isolates provides evidence for multiple genotypes

Louwagie, Joost; McCutchan, Francine E.; Peeters, Martine; Brennan, Terrence P.; Sanders-Buell, Eric; Eddy, Gerald A.; van der Groen, Guido; Fransen, Katrien; Gershy-Damet, Guy-Michel; Deleys, Robert; Burke, Donald S.

Henry M. Jackson Foundation Research Laboratory, Rockville, Maryland, USA, the Prince Leopold institute of Tropical Medicine, Antwerp, Belgium, the Institut Pasteur de Côte d'lvoire, Abidjan, Côte d'lvoire, NV Innogenetics, Ghent, Belgium, the Walter Reed Army Institute of Research, Washington, District of Columbia and the Military Medical Consortium for Applied Retroviral Research, USA.

Abstract

Objective

To determine the extent of genetic variation among internationally collected HIV-1 isolates, to analyse phylogenetic relationships and the geographic distribution of different variants.

Design

Phylogenetic comparison of 70 HIV-1 isolates collected in 15 countries on four continents.

Methods

To sequence the complete gag genome of HIV-1 isolates, build multiple sequence alignments and construct phylogenetic trees using distance matrix methods and maximum parsimony algorithms.

Results

Phylogenetic tree analysis identified seven distinct genotypes. The seven genotypes were evident by both distance matrix methods and maximum parsimony analysis, and were strongly supported by bootstrap resampling of the data. The intra-genotypic gag distances averaged 7%, whereas the inter-genotypic distances averaged 14%. The geographic distribution of variants was complex. Some genotypes have apparently migrated to several continents and many areas harbor a mixture of genotypes. Related variants may cluster in certain areas, particularly isolates from a single city collected over a short time.

Conclusions

The genetic variation among HIV-1 isolates is more extensive than previously appreciated. At least seven distinct HIV-1 genotypes can be identified. Diversification, migration and establishment of local, temporal ‘blooms' of particular variants may all occur concomitantly.