Characterization of HIV-1 genetic diversity and antiretroviral resistance in the state of Maranhão, Northeast Brazil.

Élcio Leal,Daniel Duarte Costa,Kledoaldo Lima,Marta Barreiros,Antonia Iracilda E Silva Viana,Francisco Dimitre Rodrigo Pereira Santos,Nilviane Pires Silva Sousa,Allan Kardec Barros,Antonio Dantas Silva,Claudia Regina Arrais,Jessyca Kalynne Farias Rodrigues

doi:10.1371/journal.pone.0230878

Abstract

The HIV-1 epidemic in Brazil has been growing in northeast and north regions, particularly an increase in AIDS cases among the younger male population has been observed. This study aims to characterize the HIV-1 genetic diversity and to evaluate its antiretroviral resistance profile among individuals presenting virological failure in the state of Maranhão—Brazil. HIV-1 pol gene sequences from 633 patients on antiretroviral therapy were obtained from the Department of Surveillance, Prevention and Control of Sexually Transmitted Infections, HIV/AIDS and Viral Hepatitis of the Brazilian Ministry of Health. Phylogenetic and recombination analyses were performed to characterize viral genetic diversity. The presence of antiretroviral resistance mutations was assessed using the HIV Drug Resistance Database online platform of Stanford University. A predominance of subtype B (84.5%) was observed, followed by recombinant BF (9.5%), where more than half of the sequences were dispersed in 3 clusters. Antiretroviral resistance was detected in 74.1% of the sequences, and it was significantly higher for nucleoside analogue reverse-transcriptase inhibitors (NRTIs) than for non-nucleoside analogue reverse-transcriptase inhibitors (NNRTIs) and protease inhibitors (PIs). Inference of putative transmissions clusters identified 11 clusters with 22 query sequences (22/633, 3.5%). Thus, we conclude that continuous monitoring of the molecular epidemiology of HIV-1 is essential for prevention strategies, epidemic control, and treatment adequacy.

Highlights

The HIV epidemic in Brazil was reported as the number of AIDS cases per 100,000 inhabitants
Brazil is a country of continental dimensions, with economic, social, and cultural differences, which may interfere with the dynamics of the epidemics
Some regions of Northeast Brazil have a high proportion of subtype F (~30%) [5] and recombinant BF (18%) [3], as well as circulation of recently identified recombinant circulating forms (CRFs) such as the CRF70 and 71BF [8]

Summary

Introduction

The HIV epidemic in Brazil was reported as the number of AIDS cases per 100,000 inhabitants. AIDS cases in the country have been stable over the past decade, with a rate of 18.3 cases per 100,000 individuals in 2018, while the number of reported HIV infection rose sharply from seven to 42,000 cases between 2007 and 2017, mainly due to the improvement of information systems [1]. Some regions of Northeast Brazil have a high proportion of subtype F (~30%) [5] and recombinant BF (18%) [3], as well as circulation of recently identified recombinant circulating forms (CRFs) such as the CRF70 and 71BF [8]. HIV-1 subtype C and its recombinant forms, mainly CRF31_BC, are predominant [9]. In the Midwest, 2 new CRFs were identified, CRF 90_BF [12] and CRF_99BF [13]

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