Genetic History of Hepatitis C Virus in East Asia

Pybus, Oliver G.; Barnes, Eleanor; Taggart, Rachel; Lemey, Philippe; Markov, Peter V.; Rasachak, Bouachan; Syhavong, Bounkong; Phetsouvanah, Rattanaphone; Sheridan, Isabelle; Humphreys, Isla; Lü, Ling; Newton, Paul N.; Klenerman, Paul

doi:10.1128/jvi.01501-08

Cited by 195 publications

(241 citation statements)

References 60 publications

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“…However, this should only be regarded as a minimum estimate given the difficulties associated with extrapolating short-term substitution rates to longer evolutionary periods (39,40). We estimated the TMRCA between CHV and HCV using a substitution rate previously used to infer the divergence times within HCV genotypes/subtypes (37,38). However, whether these rates can be reliably applied to much more divergent CHV and HCV sequences is unclear.…”

Section: Resultsmentioning

confidence: 99%

“…To determine the evolutionary relation between CHV and other hepaciviruses, a Bayesian Markov chains Monte Carlo (MCMC) estimation of the time to most recent common ancestor (TMRCA) for the HCV genotypes, GBV-B, and CHV was performed by using an external rate calibration based on the evolutionary rates estimated for (i) HCV subtypes 1a and 1b (37) and (ii) HCV subtype 6 (38). The mean estimated TMRCA for the Hepacivirus clade and CHV is 341 y before present (ybp) 1 calibration and 1,680 ybp (521-3,291 ybp) based on the HCV subtype 6 calibration (Fig.…”

Section: Resultsmentioning

confidence: 99%

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Characterization of a canine homolog of hepatitis C virus

Kapoor

Simmonds

Qaisar

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

244

282

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An estimated 3% of the world's population is chronically infected with hepatitis C virus (HCV). Although HCV was discovered more than 20 y ago, its origin remains obscure largely because no closely related animal virus homolog has been identified; furthermore, efforts to understand HCV pathogenesis have been hampered by the absence of animal models other than chimpanzees for human disease. Here we report the identification in domestic dogs of a nonprimate hepacivirus. Comparative phylogenetic analysis of the canine hepacivirus (CHV) confirmed it to be the most genetically similar animal virus homolog of HCV. Bayesian Markov chains Monte Carlo and associated time to most recent common ancestor analyses suggest a mean recent divergence time of CHV and HCV clades within the past 500-1,000 y, well after the domestication of canines. The discovery of CHV may provide new insights into the origin and evolution of HCV and a tractable model system with which to probe the pathogenesis, prevention, and treatment of diseases caused by hepacivirus infection.flavivirus | zoonosis

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Characterization of a canine homolog of hepatitis C virus

Kapoor

Simmonds

Qaisar

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

244

282

View full text Add to dashboard Cite

show abstract

“…For example, the origins of subtype 6 in East Asia have been traced back to approximately 1000 CE by evolutionary analysis of sequence data [32]. Similarly, the origin of the genotype 4 epidemic in Africa has been traced back to the 17th century [33].…”

Section: Discussionmentioning

confidence: 99%

Historical Trends in the Hepatitis C Virus Epidemics in North America and Australia

Rodrigo¹,

Eltahla²,

Bull³

et al. 2016

J Infect Dis.

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Background. Bayesian evolutionary analysis (coalescent analysis) based on genetic sequences has been used to describe the origins and spread of rapidly mutating RNA viruses, such as influenza, Ebola, human immunodeficiency virus (HIV), and hepatitis C virus (HCV).Methods. Full-length subtype 1a and 3a sequences from early HCV infections from the International Collaborative of Incident HIV and Hepatitis C in Injecting Cohorts (InC3), as well as from public databases from a time window of 1977-2012, were used in a coalescent analysis with BEAST software to estimate the origin and progression of the HCV epidemics in Australia and North America. Convergent temporal trends were sought via independent epidemiological modeling.Results. The epidemic of subtype 3a had more recent origins (around 1950) than subtype 1a (around 1920) in both continents. In both modeling approaches and in both continents, the epidemics underwent exponential growth between 1955 and 1975, which then stabilized in the late 20th century.Conclusions. Historical events that fuelled the emergence and spread of injecting drug use, such as the advent of intravenous medical therapies and devices, and growth in the heroin trade, as well as population mixing during armed conflicts, were likely drivers for the cross-continental spread of the HCV epidemics.

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“…PCR primers and thermal profile were described elsewhere (16). Duplicate tests were performed to ensure the accuracy of positive results.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Diverse Genotypes of Hepatitis C Virus in Voluntary Blood Donors in Shanghai, China

Wang

Gong

et al. 2017

Hepat Mon

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Background: Prevalence of hepatitis C virus (HCV) in voluntary blood donors (VBD) in China has decreased progressively. However, it was still higher than those in developed countries and some developing countries. Methods: A total of 38952 VBD in Shanghai, China, were recruited in the study. The donated blood specimens were examined for anti-HCV antibody by ELISA. Hepatitis B virus DNA, HCV RNA, or HIV-1 RNA was subsequently tested by nucleic acid test (NAT) in the specimens negative for anti-HCV. A 377-nt partial sequence in HCV NS5B region was amplified in the specimens positive for anti-HCV or positive by NAT. To conduct a phylogenetic analysis, 179 sequences most phylogenetically identical to the VBD strains with BLAST search were retrieved in the GenBank and thirty nine 377-nt partial sequences isolated contemporaneously in local intravenous drug users (IDU) were included. Results: Overall prevalence of anti-HCV antibody in VBD was 0.46% (179/38952). Varying along demographics, the prevalence was higher in those aged 18-30 years and first donors. A total of thirty seven 377-nt partial sequences were amplified in the specimens positive for anti-HCV, whereas they were not seen in those negative for anti-HCV while positive by NAT. HCV genotype 1b was most predominant in VBD, followed by 2a, 3a, 1a, 3b, 6n, and 6a; in contrast, genotypes 3a and 3b were dominant in IDU. In genotypes 3a, 3b, 6a, and 6n, VBD and IDU strains shared high sequence identities and clustered together. In genotype 1b, VBD strains were phylogenetically identical to the sequences isolated across China, of which some were clustered more closely with IDU strains than the retrieved sequences. Conclusions: HCV prevalence in VBD in Shanghai remained low. However, there were diverse genotypes of HCV that were identified in VBD. HCV transmission from high-risk population to general population is likely to occur.

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Genetic History of Hepatitis C Virus in East Asia

Cited by 195 publications

References 60 publications

Characterization of a canine homolog of hepatitis C virus

Characterization of a canine homolog of hepatitis C virus

Historical Trends in the Hepatitis C Virus Epidemics in North America and Australia

Diverse Genotypes of Hepatitis C Virus in Voluntary Blood Donors in Shanghai, China

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