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Genetic diversity of rotavirus genome segment 6 (encoding VP6) in Pretoria, South Africa.

ABSTRACT: BACKGROUND:Rotavirus viral protein 6 (VP6), encoded by genome segment (GS) 6, is the primary target for rotavirus diagnosis by serological and some molecular techniques. Selected full length nucleotide sequences of GS 6 of rotavirus strains from South Africa were sequenced and analysed to determine genetic diversity and variations within the circulating rotaviruses. FINDINGS:The VP6 amplicons were sequenced using the Sanger ABI 3130xl. Phylogenetic and pairwise analysis revealed that the VP6 genes of the study strains belonged to two different VP6 [I] genotypes. Five sequences were assigned genotype I1 and seven as genotype I2. Comparison of the group specific antigenic regions of the South African strains to the reference strains, shows that the South African VP6 sequences belonging to the VP6 genotype I2 were highly conserved, with only two amino acids changes at positions 239 (T›N) and 261(I›V). On the other hand, South African VP6 sequences belonging to I1 genotypes revealed several amino acid variations mostly within the antigenic region III. CONCLUSIONS:Rotavirus strains with I1 and I2 genotype are predominantly circulating within the South African communities of which the later seems to be more conserved within the antigenic regions. The observed genetic variations observed within GS 6 of rotaviruses analysed in the current study are unlikely to impact negatively on the performance of the current VP6-based detection methods. Nevertheless, investigators should continually consider this diversity and adapt the primer design for the detection and characterization of the VP6 gene accordingly.

SUBMITTER: Nyaga MM

PROVIDER: S-EPMC4000354 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Genetic diversity of rotavirus genome segment 6 (encoding VP6) in Pretoria, South Africa.

Nyaga Martin M MM Esona Mathew D MD Jere Khuzwayo C KC Peenze Ina I Seheri Mapaseka L ML Mphahlele M Jeffrey MJ

SpringerPlus 20140405

<h4>Background</h4>Rotavirus viral protein 6 (VP6), encoded by genome segment (GS) 6, is the primary target for rotavirus diagnosis by serological and some molecular techniques. Selected full length nucleotide sequences of GS 6 of rotavirus strains from South Africa were sequenced and analysed to determine genetic diversity and variations within the circulating rotaviruses.<h4>Findings</h4>The VP6 amplicons were sequenced using the Sanger ABI 3130xl. Phylogenetic and pairwise analysis revealed t ...[more]

PMID: 24790824

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Project description:South Africa has 6.4 million adults over the age of 15 living with HIV. Gender inequality issues continue to drive the HIV epidemic in South Africa, where Black African women bear the greatest HIV burden. Limited access to services; little capacity to negotiate sex and condom use; and other legal, social, and economic inequities make women highly vulnerable to HIV infection. Behavioral interventions have been shown to decrease risk behaviors, but they have been less successful in reducing HIV incidence. Conversely, biomedical prevention strategies have proven to be successful in reducing HIV incidence, but require behavioral interventions to increase uptake and adherence. Consequently, there is a need for integrated approaches that combine biomedical and behavioral interventions. Effective combination prevention efforts should comprise biomedical, behavioral, and structural programming proven in randomized trials that focuses on the driving forces and key populations at higher risk of HIV infection and transmission.This prospective, geographically clustered randomized field experiment is enrolling participants into two arms: a control arm that receives standard HIV testing and referral for treatment; and an intervention arm that receives an evidence-based, woman-focused behavioral intervention that emphasizes risk reduction and retention, the Women's Health CoOp. We divided the city of Pretoria into 14 mutually exclusive geographic zones and randomized these zones into either the control arm or the intervention arm. Outreach workers are recruiting drug-using women from each zone. At baseline, eligible participants complete a questionnaire and biological testing for HIV, recent drug use, and pregnancy. Follow-up interviews are completed at 6 and 12 months.The biobehavioral intervention in this study merges an efficacious behavioral HIV prevention intervention for women with biomedical prevention through HIV treatment as prevention using a Seek, Test, Treat and Retain strategy. This combination biobehavioral intervention is designed to (1) improve the quality of life and reduce HIV infectiousness among women who are HIV positive, and (2) reduce HIV risk behaviors among women regardless of their HIV status. If efficacious, this intervention could help control the HIV epidemic in South Africa.Trial registration no: NCT01497405.

Dataset Information

Genetic diversity of rotavirus genome segment 6 (encoding VP6) in Pretoria, South Africa.

Publications

Genetic diversity of rotavirus genome segment 6 (encoding VP6) in Pretoria, South Africa.

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