Hepatitis C virus genotype 3a with phylogenetically distinct origin is circulating in Pakistan

Rehman, Irshad-ur; Idrees, Muhammad; Ali, Muhammad; Ali, Liaqat; Butt, Sadia; Hussain, Abrar; Akbar, Haji; Afzal, Samia

doi:10.1186/1479-0556-9-2

Cited by 30 publications

(24 citation statements)

References 14 publications

(17 reference statements)

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“…There was a wide range of ages for the commencement of IDU (14 to 39 years of age), although the mean, median, and mode (21,19, and 19 years, respectively) ages of these individuals confirmed that older age groups were unusual. This was applied to all other samples in the Scottish data set to give the estimated year of infection (EYI) for these individuals and used in the phylogeographical analysis within Scotland.…”

Section: Methodsmentioning

confidence: 97%

Spatiotemporal Reconstruction of the Introduction of Hepatitis C Virus into Scotland and Its Subsequent Regional Transmission

McNaughton

Cameron

Wignall-Fleming

et al. 2015

J Virol

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A more comprehensive understanding of hepatitis C virus (HCV) transmission dynamics could facilitate public health initiatives to reduce the prevalence of HCV in people who inject drugs. We aimed to determine how HCV sequences entered and spread throughout Scotland and to identify transmission hot spots. A Scottish data set with embedded demographic data was created by sequencing the NS5B of 125 genotype 1a (Gt1a) samples and 166 Gt3a samples and analyzed alongside sequences from public databases. Applying Bayesian inference methods, we reconstructed the global origin and local spatiotemporal dissemination of HCV in Scotland. Scottish sequences mainly formed discrete clusters interspersed between sequences from the rest of the world; the most recent common ancestors of these clusters dated to 1942 to 1952 (Gt1a) and 1926 to 1942 (Gt3a), coincident with global diversification and distribution. Extant Scottish sequences originated in Edinburgh (Gt1a) and Glasgow (Gt3a) in the 1970s, but both genotypes spread from Glasgow to other regions. The dominant Gt1a strain differed between Edinburgh (cluster 2 [C2]), Glasgow (C3), and Aberdeen (C4), whereas significant Gt3a strain specificity occurred only in Aberdeen. Specific clusters initially formed separate transmission zones in Glasgow that subsequently overlapped, occasioning city-wide cocirculation. Transmission hot spots were detected with 45% of samples from patients residing in just 9 of Glasgow's 57 postcode districts. HCV was introduced into Scotland in the 1940s, concomitant with its worldwide dispersal likely arising from global-scale historical events. Cluster-specific transmission hubs were identified in Glasgow, the key Scottish city implicated in HCV dissemination. This fine-scale spatiotemporal reconstruction improves understanding of HCV transmission dynamics in Scotland. IMPORTANCEHCV is a major health burden and the leading cause of hepatocellular carcinoma. Public health needle exchange and "treatment as prevention" strategies targeting HCV are designed to reduce prevalence of the virus in people who inject drugs (PWID), potentially mitigating the future burden of HCV-associated liver disease. Understanding HCV transmission dynamics could increase the effectiveness of such public health initiatives by identifying and targeting regions playing a central role in virus dispersal. In this study, we examined HCV transmission in Scotland by analyzing the genetic relatedness of strains from PWID alongside data inferring the year individuals became infected and residential information at a geographically finer-scale resolution than in previous studies. Clusters of Scotland-specific strains were identified with regional specificity, and mapping the spread of HCV allowed the identification of key areas central to HCV transmission in Scotland. This research provides a basis for identifying HCV transmission hot spots. H epatitis C virus (HCV) currently infects an estimated 180 million people throughout the world. Following a short acute phase, the virus ...

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Section: Methodsmentioning

confidence: 97%

Spatiotemporal Reconstruction of the Introduction of Hepatitis C Virus into Scotland and Its Subsequent Regional Transmission

McNaughton

Cameron

Wignall-Fleming

et al. 2015

J Virol

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“…The current standard is the INNO-LiPA, a line probe reverse hybridization assay that uses probes to the 5' untranslated region (UTR) and part of the core sequence to discern HCV type (12,13).…”

Section: Discussionmentioning

confidence: 99%

“…Previous investigations have shown that HCV GT distribution varies worldwide (10,11), though less is known about HCV subtypes. HCV subtype sequences have been shown to cluster on phylogenetic trees based on region of origin (12)(13)(14). Potentially, the diversification of HCV in local epidemics could affect SVR rates if resistance associated substitutions (RASs) emerge.…”

Section: Introductionmentioning

confidence: 99%

Global epidemiology of HCV subtypes and resistance-associated substitutions evaluated by sequencing-based subtype analyses

Welzel

Bhardwaj

Hedskog

et al. 2017

Journal of Hepatology

119

111

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“…In other subtypes, HCV-2a and 2b subtypes are mostly common in North America, Europe and Japan, and subtype 2c is found commonly in northern Italy [9]. HCV subtype 3a is the most common genotype circulating in India, Nepal and Pakistan [20]. In the other types of HCV, genotype 4 is common in the Middle East, and in Africa, HCV genotype 5 and HCV genotype 6 are establish only in South Africa and Hong Kong, respectively [9,10].…”

Section: Discussionmentioning

confidence: 99%

“…While genotype 3a is very sensitive to interferon medication compared to the other genotypes, genotype 1b is more resistant to interferon in HCV genotypes [20,21]. In Europe and in North and South America, HCV subtypes 1a and 1b have been reported as the most prevalent genotype, likewise subtype 1b is responsible in most of HCV infection in Japan [9,13].…”

Section: Discussionmentioning

confidence: 99%

The Different Distribution of Hepatitis C Virus Genotypes in Eastern Black Sea Region of Turkey

Dilek¹,

Sahin²,

Bahçeci³

et al. 2013

Microb Biochem Technol

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Hepatitis C virus (HCV) has infected about 170-200 million people worldwide and HCV genotypes have been related with a particular geographic distribution. The information of genotypes in chronic hepatitis C is critical for the decision of the pharmaceutical regimen, and for the therapeutic outcome. The aim of the study was determining the dispersion of hepatitis C Virus genotype in our area. The study was conducted on 42 patients who referred from various clinics infected with HCV. Serum HCV RNA levels were quantified by using the COBAS AMPLICOR HCV Monitor 2.0. An 851 bp long fragment spanning codons 63 to 347 of the RNA-dependent RNA polymerase in the NS5b part of the HCV genome was amplified. PCR amplifications were conducted in a BioRad DNA Engine using Quantitect SYBR Green PCR mix. Purified PCR products expressively sequenced with the ABI PRISM 310 Genetic Analyzer appliance utilizing DYEnamic ET Terminator Cycle Sequencing Kit. The most prevalent genotype was type 1b (90.4%) in our study. In the other types, type 3 and 4 were detected.We believe that distribution of HCV genotype in this region should be followed strictly due to difference from reports, which reported other parts of Turkey.

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Hepatitis C virus genotype 3a with phylogenetically distinct origin is circulating in Pakistan

Cited by 30 publications

References 14 publications

Spatiotemporal Reconstruction of the Introduction of Hepatitis C Virus into Scotland and Its Subsequent Regional Transmission

Spatiotemporal Reconstruction of the Introduction of Hepatitis C Virus into Scotland and Its Subsequent Regional Transmission

Global epidemiology of HCV subtypes and resistance-associated substitutions evaluated by sequencing-based subtype analyses

The Different Distribution of Hepatitis C Virus Genotypes in Eastern Black Sea Region of Turkey

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