Distribution of human immunodeficiency virus type 1 subtypes in the state of Amazonas, Brazil, and subtype C identification

L.K.H Cunha,S Kashima,E.S Rodrigues,M.F.C Amarante,K.L.T Silva,D.B Castro,A Malheiro,T.A Lima,D.T Covas,R Haddad,F.C Brito,E.G Almeida

doi:10.1590/s0100-879x2012007500003

Abstract

Few studies have reported the molecular epidemiological characterization of HIV-1 in the Northern region of Brazil. The present study reports the molecular and epidemiological characterization of 31 HIV-1 isolates from blood donors from the State of Amazonas who donated blood between April 2006 and March 2007. Serum/plasma samples from all donors were screened for HIV antibodies by ELISA and the results confirmed by Western blot analysis. Genomic DNA was extracted from the buffy coat using the Super Quik-Gene-DNA Isolation kit. Nested PCR was performed on the env, gag, and pol regions of HIV-1 using the Gene Amp PCR System 9700. Sequencing reactions were performed using the inner PCR primers and the DYEnamic™ ET Dye Terminator Kit, and phylogenetic analysis was performed using the gag, pol, and env gene sequences. We collected samples from 31 blood donors who tested positive for HIV-1 in confirmatory experiments. The male:female ratio of blood donors was 3.4:1, and the mean age was 32.4 years (range: 19 to 61 years). Phylogenetic analysis showed that subtype B is the most prevalent among Northern Brazilian HIV-1-seropositive blood donors. One HIV-1 subtype C and one circulating recombinant form (CRF_BF) of HIV-1 were identified in the State of Amazonas. This is the first study showing the occurrence of a possible “homogenous” subtype C in this region of Brazil. This finding could contribute to a better characterization of the HIV-1 strains that circulate in the country. Key words: HIV-1; Subtypes; Phylogenetic analysis; Blood donors; Molecular and epidemiological characterization

Highlights

Two major reasons for the extensive genetic diversity of HIV-1 are high levels of viral replication and error-prone reverse transcription, which incorporates mutations into the viral genome
Analyses of similarity were performed to compare the env sequences found in the Southern region of Brazil (DQ358770, DQ358766, DQ358763, DQ358761, DQ358757, DQ358756, and U52953) and env sequences from different geographic regions, including Venezuela (AY456916 and AY456917), South Africa (AY772699), India (AF067155), and Ethiopia (U46016) (Table 4). This genomic region was selected for similarity analysis because it is the most variable region of HIV-1. These analyses showed that Amazonian C subtype isolates show high similarity to sequences from the Southern region, suggesting that HIV-1 subtype C may have disseminated to the North following a South to North gradient pattern
Most of the molecular and epidemiological characterization of HIV-1 in Brazil has concentrated in the Southeast, where HIV-1 subtype B is prevalent

Summary

Introduction

Two major reasons for the extensive genetic diversity of HIV-1 are high levels of viral replication and error-prone reverse transcription, which incorporates mutations into the viral genome. Based on phylogenetic analyses of env and gag gene sequences, HIV-1 is classified into three main groups: the major (M), outlier (O), and new (N) groups [1,2,3,4]. Nine genetic subtypes have been identified in the M group: A-D, F-H, J, and K; at least 34 circulating recombinant forms (CRFs) have been recognized [5,6,7]. These genetic subtypes may have an impact on drug susceptibility, the emergence of new drug resistance mutations, and the performance of laboratory tests for diagnostics and measurements of viral loads [8]

Methods

Results

Conclusion