Full‐length genomic sequence analysis of new subtype 3k hepatitis E virus isolates with 99.97% nucleotide identity obtained from two consecutive acute hepatitis patients in a city in northeast Japan

Miura, Masahito; Inoue, Jun; Tsuruoka, Mio; Nishizawa, Tsutomu; Nagashima, Shigeo; Takahashi, Masaharu; Shimosegawa, Tooru; Okamoto, Hiroaki

doi:10.1002/jmv.24743

Cited by 23 publications

(24 citation statements)

References 19 publications

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“…These cut‐offs not only identified the main subtypes previously described but also minimized the number of unassigned subtypes. Accordingly, HEV‐3k strains (accession numbers: AB740232; AB369689, LC131066, and LC176492) formed a cluster . The reference genome HEV‐3j (Genbank accession number AY115488) was included in the cluster of subtypes 3a.…”

Section: Resultsmentioning

confidence: 99%

“…Accordingly, HEV-3k strains (accession numbers: AB740232; AB369689, LC131066, and LC176492) formed a cluster. 7 The reference genome HEV-3j (Genbank accession number AY115488) was included in the cluster of subtypes 3a. The 2 complete HEV-3i genomes available (accession numbers FJ998008 and KP294371) were also included in the HEV-3c subtype cluster.…”

Section: Determination Of Clusters By Automated Partition For Genotmentioning

confidence: 99%

“…Therefore, a standard reference set of complete genome sequences, including 19 near full length genomes of HEV‐3, was proposed by using a conservative pragmatic approach . Recently, a new subtype, HEV‐3k, arranged in clade HEV‐3abjchi was proposed . The first 2 clades are found in humans, pigs, wild‐boar, and deer, and the third (HEV‐3ra) in humans and rabbits .…”

Section: Introductionmentioning

confidence: 99%

“…6 Recently, a new subtype, HEV-3k, arranged in clade HEV-3abjchi was proposed. 7 The first 2 clades are found in humans, pigs, wild-boar, and List of abbreviations: DNA, deoxyribonucleic acid; GTR, general time reversible; HEV, hepatitis E virus; iTOL, interactive tree of life; ML, maximum likelihood; NJ, neighbor joining; ORF, open reading frame; PCR, polymerase chain reaction; PPR, polyproline region; RBV, ribavirin; RNA, ribonucleic acid; RT-PCR, reverse transcription polymerase chain reaction; SMRT, single molecule real time; t, threshold; UN, unassigned deer, and the third (HEV-3ra) in humans and rabbits. 4,6,8 However, we have few data on complete genome sequences of HEV-3 variants within specific areas of the world, including Europe where increasing incidence has been reported.…”

Section: Introductionmentioning

confidence: 99%

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Diversity of hepatitis E virus genotype 3

Nicot

Jeanne

Roulet

et al. 2018

Reviews in Medical Virology

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Hepatitis E virus genotype 3 (HEV-3) can lead to chronic infection in immunocompromised patients, and ribavirin is the treatment of choice. Recently, mutations in the polymerase gene have been associated with ribavirin failure but their frequency before treatment according to HEV-3 subtypes has not been studied on a large data set. We used single-molecule real-time sequencing technology to sequence 115 new complete genomes of HEV-3 infecting French patients. We analyzed phylogenetic relationships, the length of the polyproline region, and mutations in the HEV polymerase gene. Eighty-five (74%) were in the clade HEV-3efg, 28 (24%) in HEV-3chi clade, and 2 (2%) in HEV-3ra clade. Using automated partitioning of maximum likelihood phylogenetic trees, complete genomes were classified into subtypes. Polyproline region length differs within HEV-3 clades (from 189 to 315 nt). Investigating mutations in the polymerase gene, distinct polymorphisms between HEV-3 subtypes were found (G1634R in 95% of HEV-3e, G1634K in 56% of HEV-3ra, and V1479I in all HEV-3efg, clade HEV-3ra, and HEV-3k strains). Subtype-specific polymorphisms in the HEV-3 polymerase have been identified. Our study provides new complete genome sequences of HEV-3 that could be useful for comparing strains circulating in humans and the animal reservoir.

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Section: Resultsmentioning

confidence: 99%

Section: Determination Of Clusters By Automated Partition For Genotmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Diversity of hepatitis E virus genotype 3

Nicot

Jeanne

Roulet

et al. 2018

Reviews in Medical Virology

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“…MEGA7 software 2 was used for the alignment. Reference HEV-3 sequences of established and recently proposed subtypes (n = 15) (Smith et al, 2016;Miura et al, 2017;De Sabato et al, 2018) and 130 sequences showing closest relatedness (≥93.0% nt. identity) to the novel Italian sequences were included in phylogenetic analysis, for a total of 145 sequences included in the analysis ( Table 1).…”

Section: Dataset Of Italian and Worldwide Sequencesmentioning

confidence: 94%

Molecular Characterization of HEV Genotype 3 in Italy at Human/Animal Interface

et al. 2020

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Hepatitis E virus (HEV) is an emerging public health issue in industrialized countries. In the last decade the number of autochthonous human infections has increased in Europe. Genotype 3 (HEV-3) is typically zoonotic, being foodborne the main route of transmission to humans, and is the most frequently detected in Europe in both humans and animals (mainly pigs and wild boars). In Italy, the first autochthonous human case was reported in 1999; since then, HEV-3 has been widely detected in both humans and animals. Despite the zoonotic characteristic of HEV-3 is well established, the correlation between animal and human strains has been poorly investigated in Italy. In the present study, we compared the subtype distribution of HEV-3 in humans and animals (swine and wild boar) in the period 2000-2018 from Italy. The dataset for this analysis included a total of 96 Italian ORF2 sequences (300 nt long), including both NCBI databasederived (n = 64) and recent sequences (2016-2018, n = 32) obtained in this study. The results show that subtype 3f is the most frequent in humans and pigs, followed by the HEV-3e, HEV-3c and other unassignable HEV-3 strains. Diversely, in wild boar a wider group of HEV-3 subtypes have been detected, including HEV-3a, which has also been detected for the first time in a human patient in Central Italy in 2017, and a wide group of unassignable HEV-3 strains. The phylogenetic analysis including, besides Italian strains, also sequences from other countries retrieved from the NCBI database, indicated that human Italian sequences, in particular those of HEV-3f and HEV-3e, form significant clusters mainly with sequences of animal origin from the same country. Nevertheless, for HEV-3c, rarely detected in Italian pigs, human sequences from Italy are more correlated to human sequences from other European countries. Furthermore, clusters of nearidentical human strains identified in a short time interval in Lazio Region (Central Italy) can be recognized in the phylogenetic tree, suggesting that multiple infections originating from a common source have occurred, and confirming the importance of sequencing support to HEV surveillance.

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Nationwide epidemiologic and genetic surveillance of hepatitis E in Japan, 2014–2021

Sugiyama

Takahara

Yahata

et al. 2023

Journal of Medical Virology

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Hepatitis E virus (HEV) is an emerging causative agent of acute hepatitis. To clarify the epidemiology of HEV and characterize the genetic diversity of the virus in Japan, nationwide enhanced surveillance and molecular characterization studies of HEV in Japan were undertaken from 2014 to 2021. In total, 2770 hepatitis E cases were reported, of which 88% were domestic cases, while only 4.1% represented cases following infection abroad. In addition, 57% of domestic infections occurred in males aged in their 40s–70s. For domestic cases, infection via pork meat consumption continued to be the most reported route. Analysis of the 324 sequences detected between 2016 and 2021 showed that the majority of domestic HEV strains belong to Genotype 3a (G3a) and G3b. In contrast, six of eight cases of G1 HEV reflected infection abroad. Our results suggest that HEV is circulating widely in Japan, with genotypes G3a and G3b being most prevalent. Continued surveillance is necessary to monitor future trends and changes in the epidemiology of HEV in Japan.

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Full‐length genomic sequence analysis of new subtype 3k hepatitis E virus isolates with 99.97% nucleotide identity obtained from two consecutive acute hepatitis patients in a city in northeast Japan

Cited by 23 publications

References 19 publications

Diversity of hepatitis E virus genotype 3

Diversity of hepatitis E virus genotype 3

Molecular Characterization of HEV Genotype 3 in Italy at Human/Animal Interface

Nationwide epidemiologic and genetic surveillance of hepatitis E in Japan, 2014–2021

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