Near full-length genome analysis of HCV genotype 5 strains from South Africa

Gededzha, Maemu P.; Selabe, Selokela G.; Blackard, Jason T.; Kyaw, Thanda; Mphahlele, M. Jeffrey

doi:10.1016/j.meegid.2013.10.022

Cited by 17 publications

(14 citation statements)

References 27 publications

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“…However, the proportions of certain genotypes seem to have increased: genotype 3 increased from 8% to 18% and genotype 4 increased from 2% to 14%. The cumulative presence of intergenotypic viral populations in this study was found to be higher than previous studies; 7% compared to 6% and 0% . As in other studies, our sampling was biased to those who seek care but another possible explanation is the change in technology used to identify genotypes.…”

Section: Discussioncontrasting

confidence: 90%

“…However, the proportions of certain genotypes seem to have increased: genotype 3 increased from 8% to 18% and genotype 4 increased from 2% to 14%. The cumulative presence of intergenotypic viral populations in this study was found to be higher than previous studies; 7% compared to 6% 33 and 0%. 14 When we looked at the association of gender with HCV genotypes, we found that males comprised overall a higher proportion than females for each genotype for both study groups, except for genotype 5a in blood donors.…”

Section: Discussioncontrasting

confidence: 88%

“…Genotypes may differ in geographic locations within countries . Previously, a predominance of 19% for genotype 4 was seen in a hospital in the north‐western part of Pretoria, bordering North West Province . In our study, genotypes 1 and 5 were at highest proportions across all provinces compared to other genotypes.…”

Section: Discussionsupporting

confidence: 50%

“…Province. 33 In our study, genotypes 1 and 5 were at highest proportions across all provinces compared to other genotypes. Genotype 4 was prevalent in North West (14%) and Limpopo (21%) provinces.…”

Section: Discussionmentioning

confidence: 42%

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Hepatitis C genotype distribution in patient and blood donor samples in South Africa for the period 2008–2012

Prabdial-Sing

Chirwa

Thaver

et al. 2016

Journal of Viral Hepatitis

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There are limited molecular epidemiological studies of hepatitis C at a national level in South Africa. The introduction of newer treatment modalities for hepatitis C requires knowledge of the genotypes as these may have different prognostic and therapeutic implications. This retrospective study describes genotype distributions of patients attending specialist clinics and a blood donor group studied during the period 2008-2012 in South Africa. Residual samples from diagnostic viral load testing from specialist clinics in South Africa (n=941) and from the South African National Blood Service (n=294) were analysed quantitatively by real-time PCR and genotyped using the Versant line probe assay or sequencing. Genotype 1 was predominant in blood donors (34%), whilst genotype 5a was prevalent in patients (36%). In the blood donor group, genotype 4 was detected for the first time. Genotype 2 was rare in the patient group and not detected in blood donors. Genotype 1 was the predominant genotype in the younger age groups (less than 30 years), whereas genotype 5a was found at higher proportions in the older age groups for both the patient and blood donor groups, comprising more than 60% of genotypes in those older than 50 years. Genotypes 1 and 5 were at highest proportions across all provinces compared to other genotypes. In blood donors, genotype 1 was predominant among Caucasians (43%) and genotype 5a among Blacks (54%). Such information is required for planning the impact on the health sector with regard to newly emerging therapies for hepatitis C and burden of disease.

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Section: Discussioncontrasting

confidence: 90%

“…However, the proportions of certain genotypes seem to have increased: genotype 3 increased from 8% to 18% and genotype 4 increased from 2% to 14%. The cumulative presence of intergenotypic viral populations in this study was found to be higher than previous studies; 7% compared to 6% 33 and 0%. 14 When we looked at the association of gender with HCV genotypes, we found that males comprised overall a higher proportion than females for each genotype for both study groups, except for genotype 5a in blood donors.…”

Section: Discussioncontrasting

confidence: 88%

Section: Discussionsupporting

confidence: 50%

Section: Discussionmentioning

confidence: 42%

See 2 more Smart Citations

Hepatitis C genotype distribution in patient and blood donor samples in South Africa for the period 2008–2012

Prabdial-Sing

Chirwa

Thaver

et al. 2016

Journal of Viral Hepatitis

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“…Patients’ demographics and genotyping based on 5’UTR were previously described in detail ( 25 ). Six of 18 samples were sequenced as part of the genotype 5a near-full length analysis previously described ( 26 ). DGMAH is an academic hospital serving a population of around 4 million from both rural and urban areas.…”

Section: Methodsmentioning

confidence: 99%

Characterization of HCV Genotype 5a Envelope Proteins: Implications for Vaccine Development and Therapeutic Entry Target

2014

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Background:Hepatitis C virus (HCV) is one of the major causes of cirrhosis and hepatocellular carcinoma with an estimation of 185 million people with infection. The E2 is the main target for neutralizing antibody responses and the variation of this region is related to maintenance of persistent infection by emerging escape variants and subsequent development of chronic infection. While both E1 and E2 are hypervariable in nature, it is difficult to design vaccines or therapeutic drugs against them.Objectives:The objective of this study was to characterize genotype 5a E1 and E2 sequences to determine possible glycosylation sites, conserved B-cell epitopes and peptides in HCV that could be useful targets in design of vaccine and entry inhibitors.Patients and Methods:This study was conducted through PCR amplification of E1 and E2 regions, sequencing, prediction of B-cell epitopes, analysis of N-linked glycosylation and peptide design in 18 samples of HCV genotype 5a from South African.Results:Differences in the probability of glycosylation in E1 and E2 regions were observed in this study. Three conserved antigenic B-cell epitopes were predicted in the E2 regions and also 11 short peptides were designed from the highly conserved residues.Conclusions:This study provided conserved B-cell epitopes and peptides that can be useful for designing entry inhibitors and vaccines able to cover a global population, especially where genotype 5a is common.

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Comparison of Three Different Hepatitis C Virus Genotyping Methods: 5′NCR PCR‐RFLP, Core Type‐Specific PCR, and NS5b Sequencing in a Tertiary Care Hospital in South India

Daniel

David

Raghuraman

et al. 2016

Clinical Laboratory Analysis

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Near full-length genome analysis of HCV genotype 5 strains from South Africa

Cited by 17 publications

References 27 publications

Hepatitis C genotype distribution in patient and blood donor samples in South Africa for the period 2008–2012

Hepatitis C genotype distribution in patient and blood donor samples in South Africa for the period 2008–2012

Characterization of HCV Genotype 5a Envelope Proteins: Implications for Vaccine Development and Therapeutic Entry Target

Comparison of Three Different Hepatitis C Virus Genotyping Methods: 5′NCR PCR‐RFLP, Core Type‐Specific PCR, and NS5b Sequencing in a Tertiary Care Hospital in South India

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