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


METHODS
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.
Louwagie
J
J
Henry M. Jackson Foundation Research Laboratory, Rockville, Maryland 20850.
McCutchan
F E
FE
Peeters
M
M
Brennan
T P
TP
Sanders-Buell
E
E
Eddy
G A
GA
van der Groen
G
G
Fransen
K
K
Gershy-Damet
G M
GM
Deleys
R
R
D000349:Africa; D000465:Algorithms; D000595:Amino Acid Sequence; D000940:Antigenic Variation / Q000235:genetics*; D001483:Base Sequence; D001938:Brazil; D036022:Capsid Proteins; D005060:Europe; D005787:Gene Frequency; D015683:Gene Products, gag / Q000235:genetics; D015750:Genes, gag; D014644:Genetic Variation; D005838:Genotype; D015488:HIV Antigens / Q000235:genetics*; D016655:HIV Core Protein p24 / Q000235:genetics; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D010679:Philippines; D010802:Phylogeny; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D013785:Thailand; D014764:Viral Proteins; D054301:gag Gene Products, Human Immunodeficiency Virus
D036022:Capsid Proteins; D015683:Gene Products, gag; D015488:HIV Antigens; D016655:HIV Core Protein p24; C071884:NCP7 protein, Human immunodeficiency virus 1; D014764:Viral Proteins; D054301:gag Gene Products, Human Immunodeficiency Virus; C054858:p17 protein, Human Immunodeficiency Virus Type 1; C083002:p6 gag protein, Human immunodeficiency virus 1