MOLECULAR PHYLOGENY OF PART OF THE ENV GENE OF HIV-1 STRAINS ISOLATEDIN COTE-DIVOIRE

Objectives: To examine the genetic variation of HIV-1 isolates in Abid jan, Cote 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. Design: Phylogenetic comparison of 13 HIV-1 strai ns isolated from patients in Abidjan with previously documented HIV-1 strains of different geographic origin. Methods: To sequence a 900 bas e-pair fragment of the env gene containing V3, V4, V5 and the beginnin g of gp41 of three to four clones per isolate. Phylogenetic tree analy sis was performed with the software package TREECON. Results: Eleven H IV-1 isolates of Abidjan were classified as genotype A, while two were classed as genotypes B and D. Intra-genotype A distances at the nucle otide 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%. Phylog enetic trees, based on sequence data of a 300 base-pair fragment conta ining 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 Cote d'Ivo ire HIV-1 strains, which comprise 11 out of 13 isolates, predominate i n Abidjan, which may indicate a local burst of particular variants. Ph ylogenetic trees should be interpreted with caution when based on a mo re limited number of nucleotides, such as the V3 region.