Multitypic Hepatitis C Virus Infection Identified by Real-Time Nucleotide Sequencing of Minority Genotypes

Buckton, Andrew J.; Ngui, Siew-Lin; Arnold, Catherine; Boast, Katie; Kovacs, Joanne; Klapper, Paul E.; Patel, Bharat; Ibrahim, Imad; Rangarajan, Savita; Ramsay, Mary; Teo, Chong–Gee

doi:10.1128/jcm.01638-05

Cited by 22 publications

(21 citation statements)

References 26 publications

(28 reference statements)

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“…In addition, clonal sequence analysis identified dual infection of HCV genotypes in one case (HPA017). The frequency of dual infection and/or recombination in this study was higher than expected; however, it was within the range reported in other countries (3.8% in Australia [Bowden et al, 2005] [Buckton et al, 2006]; 20% in USA [Herring et al, 2004]). The efficiency of detecting multiple infections may depend on the number of HCV genotypes circulating in the study population.…”

Section: Considering That Genotype 6e Is Thought To Have Emerged Insupporting

confidence: 72%

Multiple routes of hepatitis C virus transmission among injection drug users in Hai Phong, Northern Vietnam

Tanimoto

Cuong

Ishizaki

et al. 2010

Journal of Medical Virology

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To identify hepatitis C virus (HCV) transmission routes among injection drug users inNorthern Vietnam, plasma samples were collected from 486 drug users in Hai Phong.Plasma viral RNA was extracted from 323 (66.5%) samples that were positive for anti-HCV antibodies. Portions of the HCV 5'-untranslated (5'UTR)-Core and NS5B genes were amplified by reverse-transcriptase polymerase chain reaction, sequenced directly, and genotyped in 194 and 195 specimens, respectively. Both regions were genotyped in 137 specimens. In the 5'UTR-Core region, genotype 6a was predominant (32.5%), followed by genotype 1a (23.7%), genotype 1b (20.6%), and genotype 6e (14.4%). In the NS5B region, genotype 1a was predominant (42.6%), followed by genotype 1b

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Section: Considering That Genotype 6e Is Thought To Have Emerged Insupporting

confidence: 72%

Multiple routes of hepatitis C virus transmission among injection drug users in Hai Phong, Northern Vietnam

Tanimoto

Cuong

Ishizaki

et al. 2010

Journal of Medical Virology

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“…This is supported by a recent modeling study (26) suggesting that HCV reinfections frequently result in spontaneous clearance and by empirical data from a number of studies showing reinfection rates in PWID of 2 to 9% (27)(28)(29)(30). Other studies have suggested that reinfection is much more common in PWID (20 to 39% [31][32][33]), and differences may be due to needle exchange programs in the regions studied or sensitivities of the assays used.…”

Section: Gt3supporting

confidence: 60%

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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“…Suspected multiple-genotype infections were confirmed for previously genotyped sera by use of the methodology described in detail in a previous study (4). Briefly, after amplification of a fragment from the 5ЈNC region, products were checked by gel electrophoresis and treated with genotype-specific restriction endonucleases to digest the dominant genotype.…”

Section: Methodsmentioning

confidence: 99%

Evaluation of a New Assay in Comparison with Reverse Hybridization and Sequencing Methods for Hepatitis C Virus Genotyping Targeting Both 5′ Noncoding and Nonstructural 5b Genomic Regions

Martró

González

Buckton³

et al. 2008

J Clin Microbiol

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We report the evaluation of a new real-time PCR assay for hepatitis C virus (HCV) genotyping. The assay design is such that genotype 1 isolates are typed by amplification targeting the nonstructural 5b (NS5b) subgenomic region. Non-genotype 1 isolates are typed by type-specific amplicon detection in the 5 noncoding region (5NC) (method 1; HCV genotyping analyte-specific reagent assay). This method was compared with 5NC reverse hybridization (method 2; InnoLiPA HCV II) and 5NC sequencing (method 3; Trugene HCV 5NC). Two hundred ninety-five sera were tested by method 1; 223 of them were also typed by method 2 and 89 by method 3. Sequencing and phylogenetic analysis of an NS5b fragment were used to resolve discrepant results. Suspected multiple-genotype infections were confirmed by PCR cloning and pyrosequencing. Even though a 2% rate of indeterminates was obtained with method 1, concordance at the genotype level with results with methods 2 and 3 was high. Among eight discordant results, five mixed infections were confirmed. Genotype 1 subtyping efficiencies were 100%, 77%, and 74% for methods 1, 2, and 3, respectively; there were 11/101 discordants between methods 1 and 2 (method 1 was predominantly correct) and 2/34 between methods 2 and 3. Regarding genotype 2, subtyping efficiencies were 100%, 45%, and 92% by methods 1, 2, and 3, respectively; NS5b sequencing of discordants (16/17) revealed a putative new subtype within genotype 2 and that most subtype calls were not correct. Although only sequencing-based methods provide the possibility of identifying new variants, the real-time PCR method is rapid, straightforward, and simple to interpret, thus providing a good single-step alternative to more-time-consuming assays.Hepatitis C virus (HCV) is the most important cause of chronic liver disease and is the leading indication for liver transplantation (2). It is estimated that HCV infects 3% (170 million people) of the world's population (26). HCV possesses a positive-sense single-stranded RNA genome of approximately 9.5 kb, which is flanked by noncoding (NC) regions. The HCV genome encodes at least 11 proteins, which include both structural and nonstructural (NS) proteins (5, 7).HCV is known to have a high rate of genetic heterogeneity. This has allowed HCV strains to be classified into a number of genetically distinct groups, known as genotypes, subtypes, isolates, and quasispecies (5). Genome sequence heterogeneity arises due to poor fidelity of the viral polymerase during replication. Sequence variability is not evenly distributed throughout the genome. The lowest sequence variability is found in the 5ЈNC region, which is the target of choice for many molecular diagnostics assays, including genotyping tests. Nevertheless, nucleotide sequencing coupled with phylogenetic analysis of more-variable genomic regions has been recommended for HCV genotyping in consensus proposals (27). As patients infected with different genotypes respond differently to antiviral drug therapy, identification of the infecting genotype ha...

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Multitypic Hepatitis C Virus Infection Identified by Real-Time Nucleotide Sequencing of Minority Genotypes

Cited by 22 publications

References 26 publications

Multiple routes of hepatitis C virus transmission among injection drug users in Hai Phong, Northern Vietnam

Multiple routes of hepatitis C virus transmission among injection drug users in Hai Phong, Northern Vietnam

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

Evaluation of a New Assay in Comparison with Reverse Hybridization and Sequencing Methods for Hepatitis C Virus Genotyping Targeting Both 5′ Noncoding and Nonstructural 5b Genomic Regions

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