AIDS RESEARCH AND HUMAN RETROVIRUSES Volume 18, Number 17, 2002, pp. 1261–1269 © Mary Ann Liebert, Inc. High Frequency of Recombinant Genomes in HIV Type 1 Samples from Brazilian Southeastern and Southern Regions MONICK LINDENMEYER GUIMARÃES, 1 ALINE DOS SANTOS MOREIRA, 1 REGINA LOUREIRO, 2 BERNARDO GALVÃO-CASTRO, 3 THE BRAZILIAN NETWORK FOR HIV ISOLATION AND CHARACTERIZATION, and MARIZA GONÇALVES MORGADO 1 ABSTRACT We describe the genetic variability of HIV-1 subtypes and recombinant genomes in samples from southeast- ern and southern Brazilian regions. Phylogenetic analysis of a subset of 34 samples (8F, 7B, 7C, 2D, 1A, and 9B0 variant) based on the DNA sequencing of the env gp120 and gp41, gag p17, and nef regions confirmed the presence of nine (26.5%) potentially HIV-1 recombinant genomes. From the eight C2–V3 gp120 subtype F samples, only two seem to be pure F. One of the samples, classified as B0 in the C2–V3 gp120 and as B in gp41 had the gag and nef regions clustering with subtype C. Two of seven C2–V3 subtype C samples pre- sented distinct recombinant patterns as Bgag/Cenv/Bnef and Bgag/Cenv/Cnef. Putative recombinant break- points were obtained for three samples presenting discordant subtypes (F/B) between gp120 and gp41 env fragments showing that similar breakpoints could be observed between two unlinked samples (95BRRJ014 and 96BRRJ101). A higher degree of polymorphism was verified in the analysis of a subtype A sample (98BRRS058) in the C2–V3/gp41 env fragment. The intrasubtype C distance was found to be lower than that found for the other subtypes for all genomic regions. These data confirm that distinct HIV-1 subtypes and recombinant forms are actively participating in the Brazilian AIDS epidemic, and that the subtype C was in- troduced more recently into southern Brazil. 1261 INTRODUCTION T HE HIV/AIDS PANDEMIC is highly heterogeneous and dy- namic and composed of distinct microepidemics occurring in different regions of the world. As of September 2001, 222,356 AIDS cases have been reported to the Brazilian Min- istry of Health and, on average, 597,443 people are estimated to be living with HIV/AIDS in the country. 1 The human immunodeficiencyvirus type 1 (HIV-1) exhibits an extraordinarydegree of genetic variabilityand has been clas- sified, based on phylogenetic relationships, into groups, sub- types, subsubtypes,and circulating recombinant forms (CRFs). Three distinct groups were described: M (major), which con- tains the majority of the pandemic HIV-1 strains; group O (out- lier), with very highly divergent strains, 2 and group N (new or non-M non-O), found in Cameroon 3 and strongly related to SIV CPZ from chimpanzees from this country. 4,5 Based on phy- logenetic relationships, the M group has been further divided into nine subtypes (A–D, F–H, J, and K) and, more recently, the F 6 and A 7 subtypes were divided into two subclades. Re- combination events are responsible for the formation of HIV- 1 mosaic genomes, with distinct subtype signatures in different genomic regions. Some of them, designated as CRFs, were ob- tained from apparently unlinked isolates with the same inter- subtype breakpointsand are actively participating in the global AIDS epidemic. 8 Subtype B has been described as the predominant HIV-1 subtype in Brazil followed by F and C subtypes, respectively, occurring in high frequency in the southeastern and southern regions. 9–13 Moreover, the V3 loop GWGR HIV-1 B0 variant and potential mosaic genomes involving the recombination or dual infections between B/F, B/C, and F/D subtypes have been previously described by our group and other groups. 14–17 The presence of D and A subtypes has already been demonstrated as isolated cases in the country. 18,19 The aim of this study was to evaluate HIV-1 samples, ob- 1 Department of Immunology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil. 2 Public Healthy Secretariat of RS State, Porto Alegre, RS, Brazil. 3 Advanced Public Health Laboratory, Gonçalo Muniz Research Center, FIOCRUZ, Bahia, Brazil.