A re-evaluation of the origin of hepatitis C virus genotype 2 in West Africa

Purdy, Michael A.; Forbi, Joseph C.; Sue, Amanda; Layden, Jennifer E.; Switzer, William M.; Opare-Sem, Ohene; Phillips, Richard Odame; Khudyakov, Yury

doi:10.1099/vir.0.000153

Cited by 17 publications

(15 citation statements)

References 21 publications

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“…The observations of long tips and lack of tight clustering in the phylogenetic tree for the Ghanaian sequences ( Fig 2 ) indicate a significant variety of HCV-2 strains circulating in a single locale in Ghana, which may be explained by either a single massive introduction of HCV strains or introduction of numerous viral lineages over a long period of time. Alternatively, this observation suggests that Ghana is, or a part of, the geographic origin of HCV-2, which is consistent with the earlier hypothesis on the origin of this genotype in West Africa [ 39 , 41 ].…”

Section: Discussionsupporting

confidence: 90%

“…When the available HCV variants sampled from West Africa were analyzed, HCV-1 and HCV-2 variants from central Africa were found to form tight clusters while the HCV variants from Ghana and other West African countries were found intermixed ( Fig 2 ). Lack of country-specific clusters and dispersion of the Ghanaian HCV variants across the entire HCV-2 in the phylogenetic tree suggest that the sample of HCV NS5B sequences in this study was obtained from a very large and heterogeneous HCV-2 population that has been circulating in Ghana [ 41 ].…”

Section: Discussionmentioning

confidence: 99%

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Next-Generation Sequencing Reveals Frequent Opportunities for Exposure to Hepatitis C Virus in Ghana

et al. 2015

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Globally, hepatitis C Virus (HCV) infection is responsible for a large proportion of persons with liver disease, including cancer. The infection is highly prevalent in sub-Saharan Africa. West Africa was identified as a geographic origin of two HCV genotypes. However, little is known about the genetic composition of HCV populations in many countries of the region. Using conventional and next-generation sequencing (NGS), we identified and genetically characterized 65 HCV strains circulating among HCV-positive blood donors in Kumasi, Ghana. Phylogenetic analysis using consensus sequences derived from 3 genomic regions of the HCV genome, 5'-untranslated region, hypervariable region 1 (HVR1) and NS5B gene, consistently classified the HCV variants (n = 65) into genotypes 1 (HCV-1, 15%) and genotype 2 (HCV-2, 85%). The Ghanaian and West African HCV-2 NS5B sequences were found completely intermixed in the phylogenetic tree, indicating a substantial genetic heterogeneity of HCV-2 in Ghana. Analysis of HVR1 sequences from intra-host HCV variants obtained by NGS showed that three donors were infected with >1 HCV strain, including infections with 2 genotypes. Two other donors share an HCV strain, indicating HCV transmission between them. The HCV-2 strain sampled from one donor was replaced with another HCV-2 strain after only 2 months of observation, indicating rapid strain switching. Bayesian analysis estimated that the HCV-2 strains in Ghana were expanding since the 16th century. The blood donors in Kumasi, Ghana, are infected with a very heterogeneous HCV population of HCV-1 and HCV-2, with HCV-2 being prevalent. The detection of three cases of co- or super-infections and transmission linkage between 2 cases suggests frequent opportunities for HCV exposure among the blood donors and is consistent with the reported high HCV prevalence. The conditions for effective HCV-2 transmission existed for ~ 3–4 centuries, indicating a long epidemic history of HCV-2 in Ghana.

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Section: Discussionsupporting

confidence: 90%

Section: Discussionmentioning

confidence: 99%

Next-Generation Sequencing Reveals Frequent Opportunities for Exposure to Hepatitis C Virus in Ghana

et al. 2015

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“…Genotype 2 with a general frequency of 40.0% (211/528) was the main genotype found in Benin, Burkina Faso, Ghana, Guinea-Bissau and Mali (Figure 2 ). Indeed, several previous studies have reported a predominance of HCV genotype 2 in West Africa[ 75 ]. Most authors suggest a West African genotype 2 origin of HCV in the region, including The Gambia and Guinea-Bissau[ 46 ].…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity of hepatitis viruses in West-African countries from 1996 to 2018

Assih

Ouattara

Diarra

et al. 2018

WJH

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The severity of hepatic pathology and the response to treatment depend on the hepatitis virus genotype in the infected host. The objective of this review was to determine the distribution of hepatitis virus genotypes in West African countries. A systematic review of the literature in PubMed, Google Scholar and Science Direct was performed to identify 52 relevant articles reporting hepatitis A, B, C, D, E and G viruses genotypes. Hepatitis B virus (HBV) genotype E with a prevalence of 90.6% (95%CI: 0.891-0.920) found in this review, is characterized by low genetic diversity. Hepatitis C virus (HCV) genotypes 1 and 2 represented 96.4% of HCV infections in West African countries, while hepatitis delta virus, hepatitis A virus, hepatitis G virus genotypes 1 and HEV genotype 3 were reported in some studies in Ghana and Nigeria. HBV genotype E is characterized by high prevalence, low genetic diversity and wide geographical distribution. Further studies on the clinical implications of HBV genotype E and HCV genotypes 1 and 2 are needed for the development of an effective treatment against this viral hepatitis in West African countries. Surveillance of the distribution of different genotypes is also needed to reduce recombination rates and prevent the emergence of more virulent viral strains.

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“…Bayesian coalescent analysis was performed in BEAST software (v1.8.3). The GTR+I+gamma substitution model, uncorrected exponential clock model and Bayesian skygrid coalescent model were selected [ 20 ], and 5.0*10 −4 substitution/site*year was set as the prior rate [ 21 ]. The XML file was generated by BEUTi program and ran in BEAST software, with MCMC run for 300,000,000 states and sampled every 10,000 states.…”

Section: Methodsmentioning

confidence: 99%

Molecular epidemiology of hepatitis C infections in Ningxia, China: genotype, phylogeny and mutation analysis

Cui

Zhao

et al. 2016

Virol J

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BackgroundCurrent prevalence and genotype distribution of hepatitis C virus (HCV) infection remain unknown in Ningxia, northwest China.MethodsFrom June to December 2013, 13,022 individuals were screened in Ningxia HIV/AIDS Sentinel Surveillance System, with their demographic features collected and serum samples tested for HCV antibody. Sero-positive drug users were further subjected to sequencing of NS5B and Core regions of HCV.ResultsThe anti-HCV prevalence was 0.34 % among individuals without history of drug use, while it was 15.80 % among drug users. Of 79 NS5B sequences amplified from drug users, 64 (81.0 %) were male and 51 (64.0 %) were injection drug users (IDUs). Subtype 3a (40.5 %) and 1b (25.3 %) were the most predominant subtypes, followed in frequency by 3b (10.1 %) and 2a (7.6 %). Subtype distribution has no significant difference between injection and non-injection drug users. Based on phylogeographic analysis, HCV strains in Ningxia IDUs were mainly originated from two sites, Yunnan province (in southwest China bordering Myanmar, also known as Burma) and Xinjiang Autonomous Region (in northwest China on the border of Central Asia), which are the two major drug trafficking originates in China. Previously reported drug-resistance mutations were also scanned in this treatment-naïve population. Amino acid substitutions (C316N) associated with direct anti-viral agents (DAA) resistance were identified in the NS5B region in seven samples.ConclusionThis study is the first to reveal the existence of multiple genotypes of HCV in Ningxia, an inland province in northwest China, suggesting the rapid spreading of the virus.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-016-0635-y) contains supplementary material, which is available to authorized users.

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A re-evaluation of the origin of hepatitis C virus genotype 2 in West Africa

Cited by 17 publications

References 21 publications

Next-Generation Sequencing Reveals Frequent Opportunities for Exposure to Hepatitis C Virus in Ghana

Next-Generation Sequencing Reveals Frequent Opportunities for Exposure to Hepatitis C Virus in Ghana

Genetic diversity of hepatitis viruses in West-African countries from 1996 to 2018

Molecular epidemiology of hepatitis C infections in Ningxia, China: genotype, phylogeny and mutation analysis

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