Potential overestimation of HIV-1 sub-subtype F1 circulation in Rio de Janeiro, Brazil

Abstract

In Brazil, detection of the HIV-1 sub-subtype F1 has decreased with a simultaneous increase in detection of the recombinant FB and FC forms. In previous HIV-1 env molecular epidemiology studies in Rio de Janeiro, 11.4% of the detected sequences were of the F1 sub-subtype. With the goal of re-estimating the prevalence of the HIV-1 F1 sub-subtype, we performed extended analyses of these samples by examining five genomic regions, resulting in 3.3% being confirmed as F1. Moreover, genomic analysis of 11 of the 21 samples identified as F1 confirmed that nine were F1 and two were BF1. Considering the number of samples assayed, the prevalence of F1 was quite low, which supports the use of different genomic regions for the assessment of HIV-1 classification in countries where several subtypes and recombinant forms co-circulate.

Estimating HIV-1 Genetic Diversity in Brazil Through Next-Generation Sequencing

“…An important study conducted by Pessôa et al evaluated the complete genomes of HIV-1 strains by NGS previously sequenced by Alencar et al assigned to subtype F1 and showed that 23 of the 24 samples analyzed were BF recombinants, with 4 CRF70_BF1 and 11 CRF71_BF1 novel recombinant types (Alencar et al, 2013; Pessoa et al, 2014b). The same was observed by Marques et al (2018) where 34 of the 55 sequences analyzed were classified as recombinants. In our cohort, only one sequence was classified as subtype F1 and three as URF-BF1, which corroborates to literature and highlights the higher prevalence of recombinants forms comprising subtype F1.…”

“…Through the progress of next-generation sequencing (NGS) techniques it became possible to expand the study of HIV genetic diversity, evolutionary and epidemic processes, allowing the generation of HIV complete or near full-length genomes (NFLG) and improving the characterization of intra- and interhost diversity of viral populations. Greater sensitivity and accuracy in the detection of viral recombinant forms represents one of the major improvements associated with this development, since most of the previous studies were based on partial HIV genomic sequences, mainly within the pol gene region due to the interest in determining drug resistance mutational patterns, resulting in underestimation of the frequency of recombinant forms (Thomson and Najera, 2005; Hemelaar et al, 2011; Marques et al, 2018). It also permits the characterization of multiple viral infections within individual hosts.…”

“…It also permits the characterization of multiple viral infections within individual hosts. Previous Brazilian studies using NGS to analyze HIV diversity were able to identify several distinct unique and circulating recombinant forms and evidenced dual infections (Pessoa et al, 2014b, 2015, 2016; Alves et al, 2017; Marques et al, 2018). In the pooled analysis depicted in this report, we pooled publically available Brazilian sequences obtained by NGS and new genetic data from HIV-positive patients in five states of Brazil with some of the highest HIV prevalence, three in the Southeast (Rio de Janeiro, São Paulo, and Minas Gerais), one in the Northeast (Pernambuco) and one in the South (Rio Grande do Sul).…”

Identification of New HIV-1 Circulating Recombinant Forms CRF81_cpx and CRF99_BF1 in Central Western Brazil and of Unique BF1 Recombinant Forms

“…So far, among the 15 CRF_BF reported at the Los Alamos HIV Sequence Database, the majority was described in different geographic regions of Brazil: CRF28_BF, CRF29_BF, CRF39_BF, CRF40_BF, CRF46_BF, CRF70_BF, CRF71_BF, CRF72_BF, and the CRF90_BF1 which was recently described by our group in the Central Western region (Sanabani et al, 2006, 2010; Guimarães et al, 2008; Pessôa et al, 2014a,b; Reis et al, 2017). Several URFs BF1 and URFs BC have been described by full and near-full-length genome sequencing studies in Brazil and this approach is necessary to define the real contribution of these mosaic forms in the Brazilian epidemic (Barreto et al, 2006; Sanabani et al, 2006, 2010; Passaes et al, 2009; Pessôa et al, 2016; Marques et al, 2018).…”

Ações De Educação Em Saúde Do Pet-Saúde/Interprofissionalidade:um Relato De Experiência

“…O subtipo A fica subdividido em A1, A2, A3, A4, A5, A6, o subtipo F fica subdividido em F1 e F2. 14,15 Alguns estudos sugerem que o subtipo viral pode afetar a progressão e a evolução da doença como também potencialmente afetar a resistência às drogas antirretrovirais. 15 A epidemia brasileira é composta pelo subtipo B, com menor circulação do recombinante BF1 e do subtipo C. 16. O subtipo B está relacionado com a transmissão predominante por homens que fazem sexo com homens.…”