Molecular evolutionary analyses implicate injection treatment for schistosomiasis in the initial hepatitis C epidemics in Japan

Tanaka, Yasuhito; Hanada, Kousuke; Orito, Etsuro; Akahane, Yoshihiro; Chayama, Kazuaki; Yamada, Hiroshi; Sata, Michio; Ohta, Nobuhiro; Miyakawa, Yuzo; Gojobori, Takashi; Mizokami, Masashi

doi:10.1016/j.jhep.2004.09.023

Cited by 45 publications

(31 citation statements)

References 22 publications

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“…This estimate was subsequently used to calculate R 0 values for the CRF01_1b2k strain under a plausible range of average durations of infectiousness (D), using the equation R 0 ϭ rD ϩ 1 (46). Both the estimated growth rate (r ϭ 0.1 year Ϫ1 ) and the estimated R 0 values (R 0 , ϳ2 to 4) are compatible with a number of equivalent estimates for other HCV subtypes, including those from IDU risk groups (46)(47)(48)66).…”

Section: Phylogenetic Analysismentioning

confidence: 72%

“…Evolutionary analysis of viral genomes using methods based on molecular clocks and coalescent theory has previously proved useful in reconstructing the epidemic history of various HCV strains, including subtypes 1a and 1b worldwide (33,46) and subtype 1b in Japan (66). Similar analyses of HCV genotype 4 in Egypt have estimated the timescale of the large HCV epidemic in that country and have confirmed its iatrogenic cause (48,65).…”

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confidence: 99%

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Origin and Evolution of the Unique Hepatitis C Virus Circulating Recombinant Form 2k/1b

Raghwani

Thomas

Koekkoek

et al. 2012

J Virol

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Since its initial identification in St. Petersburg, Russia, the recombinant hepatitis C virus (HCV) 2k/1b has been isolated from several countries throughout Eurasia. The 2k/1b strain is the only recombinant HCV to have spread widely, raising questions about the epidemiological background in which it first appeared. In order to further understand the circumstances by which HCV recombinants might be formed and spread, we estimated the date of the recombination event that generated the 2k/1b strain using a Bayesian phylogenetic approach. Our study incorporates newly isolated 2k/1b strains from Amsterdam, The Netherlands, and has employed a hierarchical Bayesian framework to combine information from different genomic regions. We estimate that 2k/1b originated sometime between 1923 and 1956, substantially before the first detection of the strain in 1999. The timescale and the geographic spread of 2k/1b suggest that it originated in the former Soviet Union at about the time that the world's first centralized national blood transfusion and storage service was being established. We also reconstructed the epidemic history of 2k/1b using coalescent theory-based methods, matching patterns previously reported for other epidemic HCV subtypes. This study demonstrates the practicality of jointly estimating dates of recombination from flanking regions of the breakpoint and further illustrates that rare genetic-exchange events can be particularly informative about the underlying epidemiological processes. Hepatitis C virus (HCV) infection presents a major global health burden, with the WHO estimating that 170 million chronic carriers are at risk of developing severe clinical outcomes such as cirrhosis and hepatic cellular carcinoma (56, 71). The virus belongs to the single-stranded positive-sense RNA virus family Flaviviridae and is characterized by considerable genetic diversity. HCV diversity is classified into six main genotypes (genotypes 1 to 6), each of which is further divided into numerous subtypes, and the virus exhibits nucleotide sequence divergences of 30 and 20% at the genotype and subtype levels, respectively (58). The high genomic heterogeneity of HCV is a result of both its high rate of evolution and its long-term association with human populations (60). Although there is no indication for a zoonotic virus reservoir, a related virus has recently been discovered in dogs (22).The greatest diversity of HCV is found in West and Central Africa and in Southeast Asia, where the virus appears to have persisted endemically for at least several centuries (49, 60). The current distribution of HCV genotypes and subtypes is geographically structured, reflecting differences in the rates and routes of transmission of the various subtypes and genotypes. Epidemic strains, exemplified by subtypes 1a, 1b, and 3a, are characterized by high prevalence, low genetic diversity, and a global distribution and are typically associated with transmission via infected blood products and injecting drug use (IDU) during the 20th century (13, 4...

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Section: Phylogenetic Analysismentioning

confidence: 72%

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confidence: 99%

Origin and Evolution of the Unique Hepatitis C Virus Circulating Recombinant Form 2k/1b

Raghwani

Thomas

Koekkoek

et al. 2012

J Virol

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“…Coalescent 3These authors contributed equally to this work. , 2003Tanaka et al, 2002Tanaka et al, , 2004Tanaka et al, , 2005Nakano et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

“…It therefore enables us to reconstruct the past history of virus transmission from observed virus gene sequences and phylogenies. Coalescent methods have proved particularly useful in reconstructing the history of HCV infection prior to the identification of the virus in 1989 (Pybus et al, , 2003Tanaka et al, 2002Tanaka et al, , 2004Tanaka et al, , 2005Nakano et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

“…Coalescent 3These authors contributed equally to this work. , 2003Tanaka et al, 2002Tanaka et al, , 2004Tanaka et al, , 2005Nakano et al, 2004).It has been estimated that 2?5-4?9 % of China's population is HCV-positive (WHO, 2000), although it is possible that some estimates reflect urban populations with higher prevalences than the country as a whole. With an estimated population of 1?3 billion, the number of HCV-infected people in China could thus potentially exceed 50 million.…”

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Population genetic history of hepatitis C virus 1b infection in China

Nakano

Lü

et al. 2006

Journal of General Virology

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Subtype 1b is the most common strain of Hepatitis C virus (HCV) in China. Here, the molecular epidemiology and epidemic history of this strain were investigated by conducting phylogenetic and population genetic analyses of E1 and NS5B gene sequences sampled from nine Chinese cities. The phylogenetic analysis indicated the presence of two clusters of Chinese strains that did not include reference strains from other countries, suggesting that these clusters represent two independent chains of HCV transmission within China. The remaining Chinese isolates were more closely related to reference strains from other countries. The date of origin and past population dynamics of the two groups were investigated using a new population genetic method, the Bayesian skyline plot. The estimated dates of origin of both groups coincide with the period of the Chinese 'Cultural Revolution' during the years [1966][1967][1968][1969][1970][1971][1972][1973][1974][1975][1976]. Both groups grew at a rapid exponential rate between~1970 and~1990, after which transmission slowed considerably. Possible explanations for the groups' fast spread and subsequent slowdown are discussed, including parenteral transmission by unsafe injection, iatrogenic transmission by infected blood or blood products and improvements in blood safety since 1990. These results shed light on HCV transmission in China and may help to predict the future burden of HCV-related disease in the country. INTRODUCTIONHepatitis C virus (HCV) is a genetically diverse RNA virus with a single-stranded, positive-sense genome. The virus is classified into six major genotypes with closely related isolates within each genotype being grouped into subtypes (Simmonds et al., 1993;Robertson et al., 1998). Partial genome sequences, particularly those from the E1 and NS5B genes, are commonly used in HCV genotyping and evolutionary analysis (e.g. Simmonds et al., 1993;Smith et al., 1997). Different HCV genotypes and subtypes have different geographical distributions, transmission routes and rates of spread (Bukh et al., 1993;Smith et al., 1997;Pybus et al., 2001). 'Epidemic' subtypes, such as 1a, 1b and 3a, are typically found at high prevalences globally having spread rapidly during the twentieth century, probably via infected blood, blood products and injecting drug use. In contrast, 'endemic' strains of HCV are usually less prevalent, found in restricted geographical areas and represent long-term, low-level endemic infection in particular populations Pybus et al., 2001).Evolutionary analysis of sampled virus sequences has advanced considerably during the past decade and is now an important tool in molecular epidemiology. In addition to standard phylogenetic analysis, population genetic methods based on coalescent theory can be used to estimate epidemiological history from viral gene sequences. Coalescent 3These authors contributed equally to this work. , 2003Tanaka et al., 2002Tanaka et al., , 2004Tanaka et al., , 2005Nakano et al., 2004).It has been estimated that 2?5-4?9 % of China's...

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Phylogenetic reconstruction of HCV genotype 1b dissemination in a small city centre: The Camporeale model

Ferraro

Genovese

Argentini

et al. 2008

Journal of Medical Virology

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Several seroepidemiological population-based surveys carried out in Italy have shown a high prevalence of hepatitis C virus (HCV) infection. Camporeale (CP), a small Sicilian town with a 10.4% prevalence of HCV mostly genotype 1b, probably represents a specific context, since intravenous drug addiction, and sexual promiscuity are almost absent. In order to reconstruct the pattern of introduction and diffusion of HCV in this ecological niche, the NS5 genomic region of 72 HCV genotype 1 isolates (39 from CP and 33 collected throughout Sicily) was amplified and sequenced. Sequences were aligned and analyzed by BioEdit, PAUP and BEAST, and their molecular evolution compared. Thirty-eight HCV genotype 1b isolates from CP were associated in a monophyletic "transmission cluster." By applying Monte Carlo Markov simulation, it was calculated that HCV was introduced between the end of the 1940s and the beginning of the 1950s. The phylogenetic distance between the CP cluster and other Sicilian isolates confirmed its uniqueness and the local diffusion from a common ancestor. The data obtained from classic phylogenetic analysis, combined with the application of the Bayesian analysis to the study of the coalescence of phylogenetic trees, have shown that, in CP, few HCV native strains have been transmitted in a limited length of time probably through iatrogenic routes, and then have not spread further.

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Molecular evolutionary analyses implicate injection treatment for schistosomiasis in the initial hepatitis C epidemics in Japan

Cited by 45 publications

References 22 publications

Origin and Evolution of the Unique Hepatitis C Virus Circulating Recombinant Form 2k/1b

Origin and Evolution of the Unique Hepatitis C Virus Circulating Recombinant Form 2k/1b

Population genetic history of hepatitis C virus 1b infection in China

Phylogenetic reconstruction of HCV genotype 1b dissemination in a small city centre: The Camporeale model

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