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Short Communication |
1 Department of Clinical Molecular Informative Medicine, Nagoya City University Graduate School of Medical Sciences, Kawasumi, Mizuho, Nagoya 467-8601, Japan
2 Department of Medical Sciences, Toshiba General Hospital, Tokyo 140-8522, Japan
3 Department of Hepatology, Sapporo Kosei General Hospital, Sapporo 060-0033, Japan
4 Center for Gastroenterology, Teine Keijinkai Hospital, Sapporo 006-8555, Japan
5 First Department of Internal Medicine, Iwate Medical University, Iwate 020-8505, Japan
6 Department of Gastroenterology and Hepatology, Saitama Medical University, Saitama 350-0495, Japan
7 Department of Internal Medicine, Kokuho Central Hospital, Nara 636-0302, Japan
8 Department of Internal Medicine, Tottori Red Cross Hospital, Tottori 680-8517, Japan
9 Transfusion Section, University of the Ryukyus School of Medicine, Okinawa 903-0215, Japan
10 Division of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo 180-8610, Japan
11 Department of Gastroenterology, Juntendo University School of Medicine, Urayasu Hospital, Chiba 279-0021, Japan
Correspondence
Masashi Mizokami
mizokami{at}med.nagoya-cu.ac.jp
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ABSTRACT |
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The GenBank/EMBL/DDBJ accession numbers for the HEV nucleotide sequences reported in this paper are shown in Fig. 1
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Supplementary tables are available in JGV Online.
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TOPABSTRACTMAIN TEXTREFERENCES |
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). Additionally, increasing evidence has indicated that hepatitis E is a zoonosis (Harrison, 1999; Kabrane-Lazizi et al., 1999; Meng et al., 1997, 1998, 2002; Nishizawa et al., 2003; Okamoto et al., 2001; Tei et al., 2003; Yazaki et al., 2003). It has recently been suggested that zoonotic, food-borne transmission of HEV from domestic pigs, wild boars or wild deer to humans plays an important role in the occurrence of domestic infections of hepatitis E in Japan, where people have unique habits of ingesting raw fish (sushi or sashimi) and uncooked or undercooked meat (also organ meats, such as raw liver) (Matsuda et al., 2003; Tamada et al., 2004). Thus, it seems that HEV infection is now autochthonous in Japan. It remains unclear, however, when and from where the ancestral HEV strains made inroads and have spread in Japan. In this study, we first estimated the evolutionary rate of HEV by using Japan-indigenous genotype 3 and genotype 4 strains, which were phylogenetically distinct from the other strains in foreign countries. Then, based on this evolutionary rate, we traced the demographic history of HEV in Japan.
For linear-regression analyses within significant clusters, two independent datasets were applied: one was a Hyogo cluster (genotype 3) with JMO-Hyo03L, JTH-Hyo03L, JSO-Hyo03L, JYO-Hyo03L, JDEER-Hyo03L (these five isolates were obtained in April 2003) and JBOAR1-Hyo04 (April 2004) (Takahashi et al., 2004a), and another was a Sapporo cluster (genotype 4) with JSM-Sap95 (March 1995), JKK-Sap00 (November 2000), JYWSap02 (August 2002) and JTS-Sap02 (September 2002) (Takahashi et al., 2004b). GenBank accession numbers for these strains are given in Fig. 1. To elucidate the epidemiological history of the HEV population in Japan, 48 known and newly sequenced HEV strains (n=24 for each of genotype 3 and 4) were used for molecular-evolutionary analyses. The nucleotide sequences of 28 strains for the molecular-clock analyses were determined in this study (the other 20 sequences dealt with in this paper were available from GenBank).
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A reconstructed tree was built on the RNA polymerase region by using a heuristic maximum-likelihood (ML) topology search with stepwise addition and nearest neighbour-interchange algorithms. Tree likelihood scores were calculated by using the HKY85 model (Hasegawa et al., 1985) with the molecular clock enforced, using PAUP version 4.0b8. Using the estimated topology, all possible root positions were evaluated under a single-rate dated-tips (SRDT) model with the computer software TipDate v1.2 and the root that yielded the highest likelihood was adopted (Rambaut, 2000). The program provided an ML estimate of the rate and also the associated date of the most recent common ancestor of the sequences, using a model that assumed a constant rate of nucleotide substitution. The molecular clock was tested by a likelihood-ratio test between the SRDT model and a general unconstrained branch-length model [different-rate (DR) model].
For estimates of demographic history, a non-parametric function N(t), also known as a skyline plot, was obtained by transforming the coalescent intervals of an observed genealogy into a piecewise plot that represented an effective population size through time (Pybus et al., 2001; Pybus & Rambaut, 2002). A parametric ML was estimated by several models with the computer software GENIE v3.5 to build a statistical framework for inferring the demographic history of a population on phylogenies reconstructed from sampled DNA sequences (Pybus & Rambaut, 2002). This model assumes a continuous epidemic process in which the viral transmission parameters remain constant through time. Model fitting was evaluated by likelihood-ratio tests of the parametric ML estimates (Lemey et al., 2003; Pybus et al., 2003; Tanaka et al., 2005). Approximate 95 % confidence intervals for the parameters were estimated by using the likelihood-ratio test statistics.
A phylogenetic tree in the partial RNA polymerase region of the HEV genome is represented in Fig. 1. A functional gene, such as the RNA polymerase gene, is suitable for molecular-evolutionary analyses based on the neutral theory, because the substitution of functional genes is based on the neutral theory. The 24 genotype 3 and 24 genotype 4 strains in Japan showed a significant cluster with a high bootstrap value, which was the major Japanese cluster distinct from other strains found in foreign countries by molecular-evolutionary analyses. Such a significant cluster is suitable for the following coalescent analysis. Additionally, the tree topology based on the RNA polymerase region, including functional genes, was quite similar to that based on complete genomes (data not shown).
To determine the evolutionary rate of HEV, the 48 Japan-indigenous HEV strains (Fig. 1) were subjected to further molecular-evolutionary analyses. The molecular-evolutionary rate was estimated by two independent methods. In brief, linear-regression analyses using highly similar strains, i.e. six genotype 3 strains in Hyogo and four genotype 4 strains in Sapporo, indicated that a molecular-evolutionary rate was (0·81–0·88)x10–3 nucleotide substitutions per site per year (Fig. 2). Second, TipDate (v1.2) was used to compare the DR model with the single-rate (SR) and SRDT models. The SRDT model provided an adequate fit to the data (P>0·05; see Supplementary Table S1, available in JGV Online). Based on the SRDT model, the mean rate of nucleotide substitutions was estimated to be (0·81–0·94)x10–3 nucleotide substitutions per site per year, which was similar to the rate for Hepatitis C virus (Ina et al., 1994; Tanaka et al., 2002). When we used 0·84x10–3 nucleotide substitutions per site per year, which was based on all 48 sequences (24 genotype 3 and 24 genotype 4), the time of the most recent common ancestor of Japan-indigenous genotype 3 was estimated to be in the 1900s (95 % confidence interval, 1902–1917) and that of genotype 4 was approximately in the 1880s (1881–1898) (Fig. 1).
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shows the skyline plots and population growth for the HEV strains, according to a specific demographic model in GENIE v3.5 with three parameters and a piecewise-expansion growth model, which was evaluated by likelihood-ratio testing (Ina et al., 1994; Lemey et al., 2003; Pybus et al., 2003; Tanaka et al., 2005). Our estimates of the effective numbers of HEV infections showed a transition from constant size to exponential growth in the 1920s (95 % confidence interval, 1916–1930) among the genotype 3 population (Fig. 3a), whereas the rapid exponential growth among the genotype 4 population was dated in the 1980s (1978–1990) (Fig. 3b).
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. The estimated ks values from HAV strains isolated from a clam-associated outbreak varied from 0·038 for VP0 to 0·29 for VP1. Similarly, we estimated the evolutionary rate of HEV by using Japan-indigenous genotype 3 and genotype 4 strains isolated over time. The rate was estimated to be approximately 0·8x10–3 nucleotide substitutions per site per year by two independent methods, which was around half of our previously estimated rate (Takahashi et al., 2004b). One of the reasons is that the molecular-evolutionary rate would depend on estimated genes; the previous report (Takahashi et al., 2004b) used complete sequences, whereas this study used only RNA polymerase sequences. Another reason is that the previous extrapolation of substitution rate on pairwise (direct) comparisons can give overestimates of the molecular clock and hence divergent times of HEV species, as reported previously (Ina et al., 1994). Based on the molecular clock, we traced the demographic history of HEV in Japan and the indigenization time was suggested to be similar (approx. 1900), but the spread time was quite different, between HEV genotypes 3 and 4 (1920s versus 1980s). Interestingly, in addition, the evolutionary growth of genotype 3 has been quite slow since the 1920s, whereas genotype 4 strains have spread rapidly in Sapporo since the 1980s.
Zoonosis has been implicated in HEV transmission. The first animal strain of HEV to be isolated and characterized was a swine HEV from a pig in the USA in 1997 (Meng et al., 1997). Since then, many swine HEV strains, which exhibit extensive genetic heterogeneity, have been identified worldwide and shown to be genetically related closely to strains of human HEV (Chandler et al., 1999; Hsieh et al., 1999; Huang et al., 2002; Okamoto et al., 2001; Wang et al., 2002). Recent findings suggested an interspecies HEV transmission between boar and deer in their wild life (Takahashi et al., 2004a) and that both animals might serve as an infection source for human beings. More recently, wild mongoose was newly added to the list of HEV-reservoir animals in Japan (Nakamura et al., 2006). Notwithstanding the importance of these wild animals, pigs for food must be the major reservoirs of HEV: a recent Japanese study indicated that anti-HEV antibodies were detected in 1448 (58 %) of 2500 pigs from 2 to 6 months of age at 25 commercial swine farms in Japan (Takahashi et al., 2003). The importance of transmission of HEV from pigs to humans was further supported by a recent field study in Indonesia: Muslim people, for whom it is a taboo to eat or contact pigs, were significantly less frequently positive for anti-HEV than Hindu people (2·0 vs 20 %) (Surya et al., 2005).
Our molecular-evolutionary analyses suggested that HEV entered Japan around 1900. If we have traced the origin of Japan-indigenous HEV correctly back to about 100 years ago, what happened at that time in relevance to HEV's indigenization? Several kinds of Yorkshire pig were imported for the first time in the history of Japan from the UK in 1900, by the Japanese government's policy to introduce excellent domestic animals for food in Western countries to Japan, as a measure to nutritionally strengthen the people (especially soldiers) of this formerly vegetarian country. Since then, the Yorkshire pigs have been propagated in Japan and, in the 1930s, thousands of pigs were reported all over Japan (http://okayama.lin.go.jp/history/2-3-1-2.htm), suggesting that the domestic spread of HEV might have been associated with the popularization of pigs for food in Japan. Indeed, a previous phylogenetic analysis of a 304 bp nucleotide sequence (ORF2) obtained from the two UK swine strains showed a close relationship with Japanese swine strains in genotype 3 (Banks et al., 2004), indicating that Japanese genotype 3 may have been imported from the UK. On the other hand, Japanese genotype 4 strains were related phylogenetically to Asian strains in Taiwan and China. As the HEV found in wild boars living in the Iriomote Island, near Taiwan, was of genotype 4 (unpublished results), the source of Japanese genotype 4 might be from Taiwan or the mainland of China. Note that a phylogenetic analysis showed that the Japanese swine and human HEV strains segregated into four clusters [three genotype 3 clusters (one major Japanese and two minor clusters) and one genotype 4 cluster], with the highest nucleotide identity being 94·4–100 % between swine and human strains in each cluster (Takahashi et al., 2003), suggesting that swine have served as one of the most important reservoirs for HEV to be transmitted to humans. The possible risk factor for transmission of HEV was to have eaten uncooked or undercooked pig liver and/or intestine 1–2 months before the onset of hepatitis E in Hokkaido, Japan (Mizuo et al., 2005). Such eating habits, which are particularly unique to those living in Hokkaido (Sapporo is one of the big cities there) in recent decades, might be one of the reasons that HEV has been widespread in this area since 1990, as supported by our molecular-evolutionary analyses in this study.
In conclusion, based on our present data, the indigenization and domestic spread of HEV in Japan are proposed to have been associated with the importation and popularization of pigs for food in Japan. However, there still remains a possibility of different scenarios. Another animal(s) might have carried the virus to Japan: for example, mongoose was imported from India to Japan in 1910 (Nakamura et al., 2006).
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ACKNOWLEDGEMENTS |
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REFERENCES |
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TOPABSTRACTMAIN TEXTREFERENCES |
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Chandler, J. D., Riddell, M. A., Li, F., Love, R. J. & Anderson, D. A. (1999). Serological evidence for swine hepatitis E virus infection in Australian pig herds. Vet Microbiol 68, 95–105.[CrossRef][Medline]
Harrison, T. J. (1999). Hepatitis E virus – an update. Liver 19, 171–176.[Medline]
Hasegawa, M., Kishino, H. & Yano, T. (1985). Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22, 160–174.[CrossRef][Medline]
Hsieh, S.-Y., Meng, X.-J., Wu, Y.-H., Liu, S.-T., Tam, A. W., Lin, D.-Y. & Liaw, Y.-F. (1999). Identity of a novel swine hepatitis E virus in Taiwan forming a monophyletic group with Taiwan isolates of human hepatitis E virus. J Clin Microbiol 37, 3828–3834.
Huang, F. F., Haqshenas, G., Guenette, D. K., Halbur, P. G., Schommer, S. K., Pierson, F. W., Toth, T. E. & Meng, X. J. (2002). Detection by reverse transcription-PCR and genetic characterization of field isolates of swine hepatitis E virus from pigs in different geographic regions of the United States. J Clin Microbiol 40, 1326–1332.
Ina, Y., Mizokami, M., Ohba, K. & Gojobori, T. (1994). Reduction of synonymous substitutions in the core protein gene of hepatitis C virus. J Mol Evol 38, 50–56.[Medline]
Kabrane-Lazizi, Y., Fine, J. B., Elm, J. & 7 other authors (1999). Evidence for widespread infection of wild rats with hepatitis E virus in the United States. Am J Trop Med Hyg 61, 331–335.[Abstract]
Lemey, P., Pybus, O. G., Wang, B., Saksena, N. K., Salemi, M. & Vandamme, A.-M. (2003). Tracing the origin and history of the HIV-2 epidemic. Proc Natl Acad Sci U S A 100, 6588–6592.
Matsuda, H., Okada, K., Takahashi, K. & Mishiro, S. (2003). Severe hepatitis E virus infection after ingestion of uncooked liver from a wild boar. J Infect Dis 188, 944.[CrossRef][Medline]
Meng, X.-J., Purcell, R. H., Halbur, P. G., Lehman, J. R., Webb, D. M., Tsareva, T. S., Haynes, J. S., Thacker, B. J. & Emerson, S. U. (1997). A novel virus in swine is closely related to the human hepatitis E virus. Proc Natl Acad Sci U S A 94, 9860–9865.
Meng, X.-J., Halbur, P. G., Shapiro, M. S., Govindarajan, S., Bruna, J. D., Mushahwar, I. K., Purcell, R. H. & Emerson, S. U. (1998). Genetic and experimental evidence for cross-species infection by swine hepatitis E virus. J Virol 72, 9714–9721.
Meng, X. J., Wiseman, B., Elvinger, F., Guenette, D. K., Toth, T. E., Engle, R. E., Emerson, S. U. & Purcell, R. H. (2002). Prevalence of antibodies to hepatitis E virus in veterinarians working with swine and in normal blood donors in the United States and other countries. J Clin Microbiol 40, 117–122.
Mizuo, H., Yazaki, Y., Sugawara, K., Tsuda, F., Takahashi, M., Nishizawa, T. & Okamoto, H. (2005). Possible risk factors for the transmission of hepatitis E virus and for the severe form of hepatitis E acquired locally in Hokkaido, Japan. J Med Virol 76, 341–349.[CrossRef][Medline]
Nakamura, M., Takahashi, K., Taira, K., Taira, M., Ohno, A., Sakugawa, H., Arai, M. & Mishiro, S. (2006). Hepatitis E virus infection in wild mongooses of Okinawa, Japan: demonstration of anti-HEV antibodies and a full-genome nucleotide sequence. Hepatol Res (in press).
Nishizawa, T., Takahashi, M., Mizuo, H., Miyajima, H., Gotanda, Y. & Okamoto, H. (2003). Characterization of Japanese swine and human hepatitis E virus isolates of genotype IV with 99 % identity over the entire genome. J Gen Virol 84, 1245–1251.
Okamoto, H., Takahashi, M., Nishizawa, T., Fukai, K., Muramatsu, U. & Yoshikawa, A. (2001). Analysis of the complete genome of indigenous swine hepatitis E virus isolated in Japan. Biochem Biophys Res Commun 289, 929–936.[CrossRef][Medline]
Purcell, R. H. & Emerson, S. U. (2001). Hepatitis E virus. In Fields Virology, 4th edn, pp. 3051–3061. Edited by D. M. Knipe, P. M. Howley, D. E. Griffin, R. A. Lamb, M. A. Martin, B. Roizman & S. E. Straus. Philadelphia, PA: Lippincott Williams & Wilkins.
Pybus, O. G. & Rambaut, A. (2002). GENIE: estimating demographic history from molecular phylogenies. Bioinformatics 18, 1404–1405.
Pybus, O. G., Charleston, M. A., Gupta, S., Rambaut, A., Holmes, E. C. & Harvey, P. H. (2001). The epidemic behavior of the hepatitis C virus. Science 292, 2323–2325.
Pybus, O. G., Drummond, A. J., Nakano, T., Robertson, B. H. & Rambaut, A. (2003). The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approach. Mol Biol Evol 20, 381–387.
Rambaut, A. (2000). Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies. Bioinformatics 16, 395–399.
Sánchez, G., Bosch, A. & Pintó, R. M. (2003). Genome variability and capsid structural constraints of hepatitis A virus. J Virol 77, 452–459.
Surya, I. G. P., Kornia, K., Suwardewa, T. G. A., Mulyanto Tsuda, F. & Mishiro, S. (2005). Serological markers of hepatitis B, C, and E viruses and human immunodeficiency virus type-1 infections in pregnant women in Bali, Indonesia. J Med Virol 75, 499–503.[Medline]
Takahashi, M., Nishizawa, T., Miyajima, H., Gotanda, Y., Iita, T., Tsuda, F. & Okamoto, H. (2003). Swine hepatitis E virus strains in Japan form four phylogenetic clusters comparable with those of Japanese isolates of human hepatitis E virus. J Gen Virol 84, 851–862.
Takahashi, K., Kitajima, N., Abe, N. & Mishiro, S. (2004a). Complete or near-complete nucleotide sequences of hepatitis E virus genome recovered from a wild boar, a deer, and four patients who ate the deer. Virology 330, 501–505.[CrossRef][Medline]
Takahashi, K., Toyota, J., Karino, Y., Kang, J.-H., Maekubo, H., Abe, N. & Mishiro, S. (2004b). Estimation of the mutation rate of hepatitis E virus based on a set of closely related 7.5-year-apart isolates from Sapporo, Japan. Hepatol Res 29, 212–215.[Medline]
Tamada, Y., Yano, K., Yatsuhashi, H., Inoue, O., Mawatari, F. & Ishibashi, H. (2004). Consumption of wild boar linked to cases of hepatitis E. J Hepatol 40, 869–870.[CrossRef][Medline]
Tanaka, Y., Hanada, K., Mizokami, M., Yeo, A. E. T., Shih, J. W.-K., Gojobori, T. & Alter, H. J. (2002). A comparison of the molecular clock of hepatitis C virus in the United States and Japan predicts that hepatocellular carcinoma incidence in the United States will increase over the next two decades. Proc Natl Acad Sci U S A 99, 15584–15589.
Tanaka, Y., Hanada, K., Orito, E. & 8 other authors (2005). Molecular evolutionary analyses implicate injection treatment for schistosomiasis in the initial hepatitis C epidemics in Japan. J Hepatol 42, 47–53.[Medline]
Tei, S., Kitajima, N., Takahashi, K. & Mishiro, S. (2003). Zoonotic transmission of hepatitis E virus from deer to human beings. Lancet 362, 371–373.[CrossRef][Medline]
Wang, Y.-C., Zhang, H.-Y., Xia, N.-S. & 11 other authors (2002). Prevalence, isolation, and partial sequence analysis of hepatitis E virus from domestic animals in China. J Med Virol 67, 516–521.[CrossRef][Medline]
Yazaki, Y., Mizuo, H., Takahashi, M., Nishizawa, T., Sasaki, N., Gotanda, Y. & Okamoto, H. (2003). Sporadic acute or fulminant hepatitis E in Hokkaido, Japan, may be food-borne, as suggested by the presence of hepatitis E virus in pig liver as food. J Gen Virol 84, 2351–2357.
Received 6 November 2005;
accepted 7 December 2005.
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