Molecular phylogeny of part of the env gene of HIV-1 strains isolated in Côte d'Ivoire.
OBJECTIVE
To examine the genetic variation of HIV-1 isolates in Abidjan, Côte d'Ivoire, and to determine the extent to which phylogenetic trees based on sequence information of part of the env gene containing the principal neutralizing domain are representative for documenting genetic variability.


METHODS
Phylogenetic comparison of 13 HIV-1 strains isolated from patients in Abidjan with previously documented HIV-1 strains of different geographic origin.


METHODS
To sequence a 900 base-pair fragment of the env gene containing V3, V4, V5 and the beginning of gp41 of three to four clones per isolate. Phylogenetic tree analysis was performed with the software package TREECON.


RESULTS
Eleven HIV-1 isolates of Abidjan were classified as genotype A, while two were classed as genotypes B and D. Intra-genotype A distances at the nucleotide level were a maximum of 14.1%. Inter-genotype distances between genotype A and genotypes B, C, and D varied from 16.0 to 22.6%. Phylogenetic trees, based on sequence data of a 300 base-pair fragment containing the V3 loop, showed significant differences in tree topology and statistical confidence with phylogenetic trees based on sequence data of the 900 base-pair env fragment.


CONCLUSIONS
Genotype A Côte d'Ivoire HIV-1 strains, which comprise 11 out of 13 isolates, predominate in Abidjan, which may indicate a local burst of particular variants. Phylogenetic trees should be interpreted with caution when based on a more limited number of nucleotides, such as the V3 region.
Janssens
W
W
Department of Infection and Immunity, University of Antwerp, Belgium.
Heyndrickx
L
L
Van de Peer
Y
Y
Bouckaert
A
A
Fransen
K
K
Motte
J
J
Gershy-Damet
G M
GM
Peeters
M
M
Piot
P
P
van der Groen
G
G
D001483:Base Sequence; D007560:Cote d'Ivoire; D004279:DNA, Viral; D015752:Genes, env; D014644:Genetic Variation; D015699:HIV Envelope Protein gp120 / Q000235:genetics*; D015658:HIV Infections / Q000382:microbiology*; D015497:HIV-1 / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000235:genetics*; D010802:Phylogeny
D004279:DNA, Viral; D015699:HIV Envelope Protein gp120; C059762:HIV envelope protein gp120 (305-321); D010446:Peptide Fragments