Characterization of partial and near full-length genomes of HIV-1 strains sampled from recently infected individuals in São Paulo, Brazil.
BACKGROUND
Genetic variability is a major feature of human immunodeficiency virus type 1 (HIV-1) and is considered the key factor frustrating efforts to halt the HIV epidemic. A proper understanding of HIV-1 genomic diversity is a fundamental prerequisite for proper epidemiology, genetic diagnosis, and successful drugs and vaccines design. Here, we report on the partial and near full-length genomic (NFLG) variability of HIV-1 isolates from a well-characterized cohort of recently infected patients in São Paul, Brazil.


METHODS
HIV-1 proviral DNA was extracted from the peripheral blood mononuclear cells of 113 participants. The NFLG and partial fragments were determined by overlapping nested PCR and direct sequencing. The data were phylogenetically analyzed.


RESULTS
Of the 113 samples (90.3% male; median age 31 years; 79.6% homosexual men) studied, 77 (68.1%) NFLGs and 32 (29.3%) partial fragments were successfully subtyped. Of the successfully subtyped sequences, 88 (80.7%) were subtype B sequences, 12 (11%) BF1 recombinants, 3 (2.8%) subtype C sequences, 2 (1.8%) BC recombinants and subclade F1 each, 1 (0.9%) CRF02 AG, and 1 (0.9%) CRF31 BC. Primary drug resistance mutations were observed in 14/101 (13.9%) of samples, with 5.9% being resistant to protease inhibitors and nucleoside reverse transcriptase inhibitors (NRTI) and 4.9% resistant to non-NRTIs. Predictions of viral tropism were determined for 86 individuals. X4 or X4 dual or mixed-tropic viruses (X4/DM) were seen in 26 (30.2%) of subjects. The proportion of X4 viruses in homosexuals was detected in 19/69 (27.5%).


CONCLUSIONS
Our results confirm the existence of various HIV-1 subtypes circulating in São Paulo, and indicate that subtype B account for the majority of infections. Antiretroviral (ARV) drug resistance is relatively common among recently infected patients. The proportion of X4 viruses in homosexuals was significantly higher than the proportion seen in other study populations.
Division of Clinical Immunology and Allergy, Faculty of Medicine, University of São Paulo, São Paulo, Brazil. sabyem_63@yahoo.com
Sabri Saeed
SS
Sanabani
Évelyn Regina de Souza
ÉR
Pastena
Antonio Charlys
AC
da Costa
Vanessa Pouza
VP
Martinez
Walter
W
Kleine-Neto
Ana Carolina Soares
AC
de Oliveira
Mariana Melillo
MM
Sauer
Katia Cristina
KC
Bassichetto
Solange Maria Santos
SM
Oliveira
Helena Tomoko Iwashita
HT
Tomiyama
Ester Cerdeira
EC
Sabino
Esper Georges
EG
Kallas
D000328:Adult; D019380:Anti-HIV Agents / Q000627:therapeutic use; D001483:Base Sequence; D001938:Brazil / Q000453:epidemiology; D024882:Drug Resistance, Viral / Q000235:genetics; D005260:Female; D016679:Genome, Viral / Q000235:genetics*; D015658:HIV Infections / Q000188:drug therapy / Q000453:epidemiology / Q000821:virology*; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D016013:Likelihood Functions; D008297:Male; D009154:Mutation / Q000235:genetics; D010802:Phylogeny; D011995:Recombination, Genetic / Q000235:genetics; D017422:Sequence Analysis, DNA; D018523:Tropism / Q000235:genetics
D019380:Anti-HIV Agents