Dataset Information

Monitoring HIV-1 Group M Subtypes in Yaounde, Cameroon Reveals Broad Genetic Diversity and a Novel CRF02_AG/F2 Infection.

ABSTRACT: Broad HIV-1 genetic diversity in Cameroon provides a unique opportunity to monitor HIV-1 evolution and allows the detection of novel strains. We have genetically characterized the HIV-1 subtypes found in 156 samples from 90 drug-naive subjects in Yaoundé, Cameroon collected from 2011 to 2013, using phylogenetic analysis of regions in gag and pol. We identified subtypes CRF02_AG (64.9%), CRF22_01A1 (7.1%), D (4.5%), F2 (3.9%), G (3.2%), CRF18_cpx (3.2%), CRF37_cpx (3.2%), CRF11_cpx (2.6%), CRF13_cpx (1.9%), A1 (1.3%), CRF01_AE (1.3%), CRF09_cpx (1.3%), A2 (0.6%), and H (0.6%). Sequence data for both the gag and pol regions were obtained from 62 subjects; for 59 of these subjects the two regions were identified as the same viral subtype while three subjects were discordant, A1/CRF02_AG (subject MDC006), CRF02_AG/F2 (subject MDC179), and a dual infection with CRF02_AG/F2 (subject MDC131). Longitudinal sequence data were obtained for 28 of these 62 subjects and confirmed the cross-sectional results. These data update subtype information for this area and highlight the necessity of such studies due to the numerous circulating subtypes, the ongoing superinfection, and the risk of emerging novel recombinant viruses.

SUBMITTER: Courtney CR

PROVIDER: S-EPMC4817561 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature

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Monitoring HIV-1 Group M Subtypes in Yaoundé, Cameroon Reveals Broad Genetic Diversity and a Novel CRF02_AG/F2 Infection.

Courtney Colleen R CR Agyingi Lucy L Fokou Arlette A Christie Stephanie S Asaah Bladine B Meli Josephine J Ngai Johnson J Hewlett Indira I Nyambi Phillipe N PN

AIDS research and human retroviruses 20151217 4

Broad HIV-1 genetic diversity in Cameroon provides a unique opportunity to monitor HIV-1 evolution and allows the detection of novel strains. We have genetically characterized the HIV-1 subtypes found in 156 samples from 90 drug-naive subjects in Yaoundé, Cameroon collected from 2011 to 2013, using phylogenetic analysis of regions in gag and pol. We identified subtypes CRF02_AG (64.9%), CRF22_01A1 (7.1%), D (4.5%), F2 (3.9%), G (3.2%), CRF18_cpx (3.2%), CRF37_cpx (3.2%), CRF11_cpx (2.6%), CRF13_ ...[more]

PMID: 26681241

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Project description:IntroductionIn Cameroon, a manifold diversity of HIV strains exists with CRF02_AG and unique recombinant forms (URFs) being the predominant strains. In recent years, a steady increase in URFs and clade F2 viruses has been monitored through partial genome sequencing. There is an information gap in the characterization of emerging URFs along the full genome, which is needed to address the challenges URFs pose towards diagnosis, treatment and HIV-1 vaccine design.MethodEighteen Cameroonian URFs from samples collected between the years 2000 and 2015 were studied using a newly developed near full genome sequencing (NFGS) protocol based on variable nested RT-PCRs with a versatile primer set. Near full genomes were characterized for recombination patterns and sequence signatures with possible impact on antiretroviral treatment or Env-directed immune responses. Third-generation sequencing (3GS) of near full or half genomes (HGs) gave insight into intra-patient URF diversity.ResultsThe characterized URFs were composed of a broad variety of subtypes and recombinants including A, F, G, CRF01_AE, CRF02_AG and CRF22_01A1. Phylogenetic analysis unveiled dominant CRF02_AG and F2 recombination patterns. 3GS indicated a high intra-patient URF diversity with up to four distinct viral sub-populations present in plasma at the same time. URF pol genomic analysis revealed a number of accessory drug resistance mutations (DRMs) in the ART-naïve participants. Genotypic env analysis suggests CCR5 usage in 14/18 samples and identified deviations at residues, critical for gp120/gp41 interphase and CD4 binding site broadly neutralizing antibodies in more than half of the studied URFs. V1V2 sites of immune pressure in the human RV144 vaccine study varied in more than a third of URFs.ConclusionsThis study identified novel mosaic patterns in URFs in Cameroon. In line with the regional predominance of CRF_02AG and the increased prevalence of clade F2, prominent CRF_02AG and F2 background patterns were observed underlying the URFs. In the context of the novel mosaic genomes, the impact of the identified accessory DRMs and Env epitope variations on treatment and immune control remains elusive. The evolving diversity of HIV-1 URFs in Cameroon requires continuous monitoring to respond to the increasing challenges for diagnosis, antiretroviral treatment and prevention.

Project description:IntroductionThe purpose of this study was to examine the relationship between socio-demographic characteristics, risky sexual behaviour, alcohol use and transactional sex among female bar workers in Yaounde, Cameroon.Materials and methodsA cross-sectional survey was conducted among a representative sample of 410 female bar workers, recruited through a modified version of venue-based cluster sampling technique from May to June 2017. Transactional sex was defined as having received money/gifts in exchange for sex with any sexual partner in the past 12 months. Logistic regression models were performed to identify the factors associated with transactional sex. The level of statistical significance was set at p< = 0.05.ResultsAbout 14.9% (n = 61) of respondents reported to have engaged in transactional sex, 83.7% (n = 338) had multiple sexual partners at the time of the study, 14.4% (n = 55) had sex with one or more of their male customers in the past 6 months. Almost 73.4% (n = 301) reported alcohol use. Of these, 37.2% (n = 112) were frequent alcohol consumers. About 17.6% (n = 72) reported to have had unprotected sex under the influence of alcohol in the past 6 months. Multivariate logistic regression analysis showed that those who engaged in transactional sex were more likely to have had sex with a male customer in the past 6 months (aOR = 7.34; 95% CI, 3.63-16.98), had sex under the influence of alcohol in the past 6 months (aOR = 2.42; 95% CI, 1.18-4.96) and frequent alcohol consumers (aOR = 2.06; 95%CI, 1.04-4.10). Respondents who had their last sexual intercourse 4 weeks or more prior to the study (aOR = 0.26; 95% CI, 0.08-0.84) were less likely to have engaged in transactional sex.ConclusionsOur study concludes that female bar workers are exposed to male customers and engage in risky sexual practices including transaction sex. Most of them also consume alcohol which increases their risk of HIV and STI acquisition. They are a high-risk group that need to be targeted with HIV prevention interventions.

Dataset Information

Monitoring HIV-1 Group M Subtypes in Yaounde, Cameroon Reveals Broad Genetic Diversity and a Novel CRF02_AG/F2 Infection.

Publications

Monitoring HIV-1 Group M Subtypes in Yaoundé, Cameroon Reveals Broad Genetic Diversity and a Novel CRF02_AG/F2 Infection.

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