Diversity of hepatitis E virus genotype 3

Nicot, Florence; Jeanne, Nicolas; Roulet, Alain; Lefèbvre, Caroline; Carcenac, Romain; Manno, Maxime; Dubois, Martine; Kamar, Nassim; Lhomme, Sébastien; Abravanel, Florence; Izopet, Jacques

doi:10.1002/rmv.1987

Cited by 40 publications

(48 citation statements)

References 33 publications

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“…Interestingly, here is a clear difference in the distribution of genotypes observed in pigs and in human cases. Although genotype 3c was predominant in our study, human cases reported were more frequently due to strains belonging to genotype 3f (Nicot et al, ; Suin et al, ); recently genotype 3c strains are increasingly reported in human cases (Lhomme et al, ). Since both genotypes hold a similar pathogenicity (Smith et al, ), this suggests that in Corsica human infections are not acquired from consumption of pig products produced by the traditional breeding system.…”

Section: Discussionmentioning

confidence: 46%

Drastic decline of hepatitis E virus detection in domestic pigs after the age of 6 months, Corsica, France

Capai

Maestrini

Casabianca

et al. 2019

Transbound Emerg Dis

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Suidae is an important reservoir of hepatitis E virus (HEV) and a source of transmission to humans (direct contact or via consumption of meat products). Our goal was to characterize the epidemiology of HEV infecting domestic pigs in Corsica Island, a French region hyperendemic for HEV. In Corsica, traditional extensive (or semi‐extensive) outdoor pig farming system is common. Sixteen farms were selected according to location and breeding system. Individual pig faeces samples were collected and qRT‐PCR for detecting HEV RNA was performed. Nucleic acids from HEV‐positive samples were amplified using specific ORF2 genotyping system. The genotype and subtype of the Corsican HEV sequences were determined by phylogenetic analysis. Among the 919 porcine faeces samples tested 9.2% (n = 85) were positive. The presence of viral RNA was correlated with (a) age (>6 months) Adjusted Odd Ratio (AOR) 0.25 [0.068–0.90] p = .032; 3–4 months AOR = 4.94 [2.30–10.62] p = .000043) with the logistic regression model with a random effect at the farm level. Among the 85 positive samples, 83 belonged to genotype 3c and two to genotype 3f. The highest prevalence was observed in the 3–4 months age group and older age (>6 months) was negatively related to HEV infection and this suggests that traditional breeding with a late slaughter age may limit the risk of transmission to humans. A kinetic study of pigs from birth to slaughtering would allow to ensure that the type of traditional breeding reported here is very favourable to the absence of the virus in slaughtered pigs and in pork products.

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Section: Discussionmentioning

confidence: 46%

Drastic decline of hepatitis E virus detection in domestic pigs after the age of 6 months, Corsica, France

Capai

Maestrini

Casabianca

et al. 2019

Transbound Emerg Dis

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“…Full length sequences of the HEV genomic RNA were generated as previously described (Nicot et al, 2018). Briefly, two long amplicons (4,500 and 4,200 bp) with an overlap of around 1,450 bp were amplified and then sequenced using P6-C4 chemistry on the PacBio RSII sequencer [at the Toulouse genomic platform 1 ] to obtain the entire 7,250 bp HEV genome.…”

Section: Single Molecular Real-time Sequencing Of the Complete Hepatimentioning

confidence: 99%

“…Several consensus sequences were sometimes obtained for a single strain indicating the possible presence of different variants in the virus quasispecies. The HEV genotype was determined by analyzing the complete genome sequence by maximum likelihood phylogenetic analysis (Nicot et al, 2018); all the samples contained HEV genotype 3 (HEV-3). The proportion of each variant was estimated using the count related to each consensus read after the processing on Long Amplicon Analysis v2.0.…”

Section: Single Molecular Real-time Sequencing Of the Complete Hepatimentioning

confidence: 99%

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Insertions and Duplications in the Polyproline Region of the Hepatitis E Virus

et al. 2020

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Recombinant strains of hepatitis E virus (HEV) with insertions of human genomic fragments or HEV sequence duplications in the sequence encoding the polyproline region (PPR) were previously described in chronically infected patients. Such genomic rearrangements confer a replicative advantage in vitro but little is known about their frequency, location, or origin. As the sequences of only a few virus genomes are available, we analyzed the complete genomes of 114 HEV genotype 3 strains from immunocompromised (n = 85) and immunocompetent (n = 29) patients using the single molecular real-time sequencing method to determine the frequency, location, and origin of inserted genomic fragments, plus the proportions of variants with genomic rearrangements in each virus quasispecies. We also examined the amino acid compositions and post-translational modifications conferred by these rearrangements by comparing them to sequences without human gene insertions or HEV gene duplications. We found genomic rearrangements in 7/114 (6.1%) complete genome sequences (4 HEV-3f, 1 HEV-3e, 1 HEV-3 h, and 1 HEV-3chi-new), all from immunocompromised patients, and 3/7 were found at the acute phase of infection. Six of the seven patients harbored virus-host recombinant variants, including one patient with two different recombinant variants. We also detected three recombinant variants with genome duplications of the PPR or PPR + X domains in a single patient. All the genomic rearrangements (seven human fragment insertions of varying origins and three HEV genome duplications) occurred in the PPR. The sequences with genomic rearrangements had specific characteristics: increased net load ( p < 0.001) and more ubiquitination ( p < 0.001), phosphorylation ( p < 0.001), and acetylation ( p < 0.001) sites. The human fragment insertions and HEV genome duplications had slightly different characteristics. We believe this is the first description of HEV strains with genomic rearrangements in patients at the acute phase of infection; perhaps these strains are directly transmitted. Clearly, genomic rearrangements produce a greater net load with duplications and insertions having different features. Further studies are needed to clarify the mechanisms by which such modifications influence HEV replication.

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“…Of the hitherto identified seven genotypes (HEV1 to HEV7), HEV1, 2, 3, 4 and 7 are known to infect humans. The genotypes belong to a single serotype and are further subdivided into subtypes [5] . Notably, while HEV1 and 2 are restricted to human (anthroposis), HEV3 and 4 infect both humans and swine as well other mammalian species (anthropozoonosis) [6] .…”

Section: Introductionmentioning

confidence: 99%

The Hepatopathogenesis of Hepatitis E Virus Genotype 3

Parvez

2019

Journal of Gastroenterology and Hepatology Research

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Of the zoonotic genotypes of hepatitis E virus, the genotype 3 (HEV3) has emerged as the most pathogenic strain causing chronic hepatitis in immunosuppressed patients in industrialized nations. The epidemiology of HEV3 is rather complex because of its hitherto well recognized sources and routes of transmission. Currently, ribavirin is the only effective drug that however, induces mutations in viral polymerase gene leading to drug-resistance or-nonresponse, and teratogenic effects in pregnant women.

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Diversity of hepatitis E virus genotype 3

Cited by 40 publications

References 33 publications

Drastic decline of hepatitis E virus detection in domestic pigs after the age of 6 months, Corsica, France

Drastic decline of hepatitis E virus detection in domestic pigs after the age of 6 months, Corsica, France

Insertions and Duplications in the Polyproline Region of the Hepatitis E Virus

The Hepatopathogenesis of Hepatitis E Virus Genotype 3

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