HIV-1 molecular diversity in Brazil unveiled by 10\xa0years of sampling by the national genotyping network

Tiago Gräf,Alexandre Bonfim Pinheiro Da Silva,David A Rasmussen,Lídia Theodoro Boullosa,Gonzalo Bello,Paula Andrade,João Marcos Pereira,Ighor Arantes,Mônica B Arruda,Amilcar Tanuri,Diana Mariani,Ann M Dennis,Rafael V Veiga,José Carlos Couto Fernandez

doi:10.1038/s41598-021-94542-5

Abstract

HIV-1 has diversified into several subtypes and recombinant forms that are heterogeneously spread around the world. Understanding the distribution of viral variants and their temporal dynamics can help to design vaccines and monitor changes in viral transmission patterns. Brazil has one of the largest HIV-1 epidemics in the western-world and the molecular features of the virus circulating in the country are still not completely known. Over 50,000 partial HIV-1 genomes sampled between 2008 and 2017 by the Brazilian genotyping network (RENAGENO) were analyzed. Sequences were filtered by quality, duplicate sequences per patient were removed and subtyping was performed with online tools and molecular phylogeny. Association between patients’ demographic data and subtypes were performed by calculating the relative risk in a multinomial analysis and trends in subtype prevalence were tested by Pearson correlation. HIV-1B was found to be the most prevalent subtype throughout the country except in the south, where HIV-1C prevails. An increasing trend in the proportion of HIV-1C and F1 was observed in several regions of the country, while HIV-1B tended to decrease. Men and highly educated individuals were more frequently infected by HIV-1B and non-B variants were more prevalent among women with lower education. Our results suggest that socio-demographic factors partially segregate HIV-1 diversity in Brazil while shaping viral transmission networks. Historical events could explain a preferential circulation of HIV-1B among men who have sex with men (MSM) and non-B variants among heterosexual individuals. In view of an increasing male/female ratio of AIDS cases in Brazil in the last 10–15 years, the decrease of HIV-1B prevalence is surprising and suggests a greater penetrance of non-B subtypes in MSM transmission chains.

Highlights

HIV-1 has diversified into several subtypes and recombinant forms that are heterogeneously spread around the world
A steep increase in the number of HIV-1 sequences per year can be observed in the RENAGENO dataset (Fig. 1a), closely mirroring the increment of patients on antiretroviral therapy (ART) in Brazil
To characterize the current picture of the HIV-1 molecular diversity in Brazil, we compared data from patients sampled in the last triennium (2015–2017) to data of all AIDS diagnosed individuals from the same period, as reported by the Brazilian Ministry of Health (Table 1)

Summary

Introduction

HIV-1 has diversified into several subtypes and recombinant forms that are heterogeneously spread around the world. Founder effects can explain much of the heterogeneous distribution of HIV-1 subtypes around the world (i.e. the first to arrive dominates the local epidemic), several inherent viral factors, such as the rate of disease progression, efficiency of transmission and response to antiretroviral therapy (ART), may influence the successful spread of particular subtypes or CRFs1. These factors are not well understood yet and a better comprehension of HIV-1 diversity and its implications on viral transmission and disease onset would greatly help pandemic control efforts. We present a comprehensive analysis of the HIV-1 molecular diversity in the Brazilian Genotyping Network (RENAGENO) databank that contains information on 46,877 patients in therapeutic failure, pregnant women and children born with HIV that were sampled for routine genotyping service between 2008 and 2017

Methods

Results

Discussion

Conclusion