HIV Type 1 molecular epidemiology in cuba: high genetic diversity, frequent mosaicism, and recent expansion of BG intersubtype recombinant forms.
Highly diverse HIV-1 genetic forms are circulating in Cuba, including subtypes B and G and two recombinant forms of African origin (CRF18_cpx and CRF19_cpx). Here we phylogenetically analyze pol sequences from a large collection of recent samples from Cuba, corresponding to 425 individuals from all Cuban provinces, which represents approximately 12% of prevalent infections in the country. RNA from plasma was used to amplify a pol segment by reverse transcription-polymerase chain reaction; phylogenetic analyses were performed with neighbour-joining trees and bootscanning. The distribution of genetic forms was subtype B, 41.2%; CRF19_cpx, 18.4%; BG recombinants, 11.6%; CRF18_cpx, 7.1%; subtype C, 6.1%; subtype G, 3.8%; B/CRF18 recombinants, 2.6%; subtype H, 2.1%; B/CRF19 recombinants, 1.7%; and others, 5.4%. Seventy-five (17.6%) viruses were recombinant between genetic forms circulating in Cuba. In logistic regression analyses, adjusting by gender and region, subtype B was more prevalent (OR 5.0, 95% CI 2.0-12.3) and subtype G less prevalent (OR 0.1, 95% CI 0.0-0.5) among men who have sex with men (MSM) than among heterosexuals. Within the main genetic forms of Cuba there were phylogenetic subclusters, several of which correlated with risk exposure or region. BG recombinants formed three phylogenetically related subclusters, corresponding to three different mosaic structures; most of these recombinants were from MSM from Havana City, among whom they have expanded recently, reaching 31% HIV-1 infections diagnosed in 2003. This study confirms the high HIV-1 diversity and frequent recombination in Cuba and reveals the recent expansion of diverse related BG recombinant forms in this country.
Pérez
Lissette
L
Instituto de Medicina Tropical 'Pedro Kourí', La Habana, Cuba.
Thomson
Michael M
MM
Bleda
María J
MJ
Aragonés
Carlos
C
González
Zoila
Z
Pérez
Jorge
J
Sierra
María
M
Casado
Gema
G
Delgado
Elena
E
Nájera
Rafael
R
D003462:Cuba / Q000453:epidemiology; D005260:Female; D015751:Genes, pol / Q000235:genetics*; D014644:Genetic Variation; D015658:HIV Infections / Q000453:epidemiology* / Q000821:virology; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D006801:Humans; D016015:Logistic Models; D008297:Male; D008969:Molecular Sequence Data; D010802:Phylogeny; D011995:Recombination, Genetic / Q000235:genetics; D017422:Sequence Analysis, DNA; D013045:Species Specificity