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La Bella G, Basanisi MG, Nobili G, Coppola R, Damato AM, Donatiello A, Occhiochiuso G, Romano AC, Toce M, Palazzo L, Pellegrini F, Fanelli A, Di Martino B, Suffredini E, Lanave G, Martella V, La Salandra G. Evidence of Circulation and Phylogenetic Analysis of Hepatitis E Virus (HEV) in Wild Boar in South-East Italy. Viruses 2023; 15:2021. [PMID: 37896798 PMCID: PMC10611066 DOI: 10.3390/v15102021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/21/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023] Open
Abstract
Hepatitis E virus (HEV) is an important cause of acute viral hepatitis in humans worldwide. The food-borne transmission of HEV appears to be a major route in Europe through the consumption of pork and wild boar meat. HEV epidemiology in wild boars has been investigated mainly in Northern and Central Italian regions, whilst information from Southern Italy is limited. We investigated the occurrence of HEV in wild boar in the Apulia and Basilicata regions (Southern Italy). Thirteen (10.4%) out of one hundred and twenty-five wild boar samples tested positive for HEV using a quantitative reverse transcription PCR. HEV prevalence was 12% in Apulia and 9.3% in Basilicata. Seven samples were genotyped, and different subtypes (c, f, m) of genotype 3 were identified. The complete genome of a 3m strain was determined, and the virus showed the highest nucleotide identity to a human HEV strain identified in France in 2017. These findings demonstrate the substantial circulation of HEV in the wild boar population in Italian Southern regions. Gathering information on the HEV strains circulating in different geographical areas is useful for tracking the origin of HEV outbreaks and assessing the epidemiological role of wild boar as a potential virus reservoir for domestic pigs.
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Affiliation(s)
- Gianfranco La Bella
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy
| | - Maria Grazia Basanisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy
| | - Gaia Nobili
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy
| | - Rosa Coppola
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy
| | - Annita Maria Damato
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy
| | - Adelia Donatiello
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy
| | - Gilda Occhiochiuso
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy
| | | | - Mariateresa Toce
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy
| | - Lucia Palazzo
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy
| | - Francesco Pellegrini
- Department of Veterinary Medicine, University of Bari Aldo Moro, 70010 Bari, Italy
| | - Angela Fanelli
- Department of Veterinary Medicine, University of Bari Aldo Moro, 70010 Bari, Italy
| | - Barbara Di Martino
- Department of Veterinary Medicine, Università degli Studi di Teramo, 64100 Teramo, Italy
| | - Elisabetta Suffredini
- Department of Food Safety Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Gianvito Lanave
- Department of Veterinary Medicine, University of Bari Aldo Moro, 70010 Bari, Italy
| | - Vito Martella
- Department of Veterinary Medicine, University of Bari Aldo Moro, 70010 Bari, Italy
| | - Giovanna La Salandra
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy
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2
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Battistini R, Serracca L, Razzuoli E, Listorti V, Guardone L, Dellepiane M, Pussini N, Brunelli F, Peletto S, Beltramo C, Ercolini C, Masotti C. Hepatitis E Virus (HEV): Identification of Subtypes 3b and 3m in Wild Boar Population in Liguria Region, Italy. Pathogens 2022; 11:1236. [PMID: 36364986 PMCID: PMC9694157 DOI: 10.3390/pathogens11111236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/21/2022] [Accepted: 10/22/2022] [Indexed: 10/20/2023] Open
Abstract
The wild boar is an important natural reservoir for the zoonotic transmission of the hepatitis E virus (HEV) around the world. In particular, HEV genotypes 3 and 4 are an emerging problem in industrialized countries, as the number of wild boars has increased, and their territory is ever closer to farms and populated areas. This study describes the HEV prevalence and geographic circulation among wild boar populations in the Ligurian region (Italy) during the period 2019-2022. Liver samples from 849 wild boars were analyzed for HEV RNA using real-time RT-PCR; positive samples were then subjected to sequencing and phylogenetic analysis. Overall, 6.7% of the wild boars were positive for HEV RNA; however, in the last two years, the percentage of positive animals almost doubled. Phylogenetic analysis showed that wild boar HEV sequences belonged to genotype 3 and clustered within subtypes 3a and 3c, and, for the first time in Italy, subtypes 3b and 3m were identified. Interestingly, 13 sequences could not be assigned to a recognized subtype. Furthermore, the results showed different circulations of identified subtypes across the territory. These findings increase the knowledge of HEV-3 heterogeneity in Italy and describe the role of wild boars in maintaining an active viral circulation in the environment.
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Affiliation(s)
- Roberta Battistini
- Department of La Spezia, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via degli Stagnoni 96, 19100 La Spezia, Italy
| | - Laura Serracca
- Department of La Spezia, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via degli Stagnoni 96, 19100 La Spezia, Italy
| | - Elisabetta Razzuoli
- Department of Genoa, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Piazza Borgo Pila 39/24, 16129 Genoa, Italy
| | - Valeria Listorti
- Department of Genoa, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Piazza Borgo Pila 39/24, 16129 Genoa, Italy
| | - Lisa Guardone
- Department of Genoa, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Piazza Borgo Pila 39/24, 16129 Genoa, Italy
| | - Monica Dellepiane
- Department of Savona, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Martiri 6, 17056 Savona, Italy
| | - Nicola Pussini
- Department of Imperia, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Nizza 4, 18100 Imperia, Italy
| | - Francesco Brunelli
- Department of Imperia, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Nizza 4, 18100 Imperia, Italy
| | - Simone Peletto
- Department of Turin, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Turin, Italy
| | - Chiara Beltramo
- Department of Turin, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Turin, Italy
| | - Carlo Ercolini
- Department of La Spezia, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via degli Stagnoni 96, 19100 La Spezia, Italy
| | - Chiara Masotti
- Department of La Spezia, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via degli Stagnoni 96, 19100 La Spezia, Italy
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3
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Yoon J, Park T, Sohn Y, Lee SK, Park BJ, Ahn HS, Go HJ, Kim DH, Lee JB, Park SY, Song CS, Lee SW, Choi IS. Surveillance of hepatitis E virus in the horse population of Korea: A serological and molecular approach. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 103:105317. [PMID: 35738550 DOI: 10.1016/j.meegid.2022.105317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/08/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
Hepatitis E virus (HEV) is an emerging zoonotic pathogen causing hepatitis worldwide. Despite the prevalent evidence of interspecies HEV infection in various animal species, the role of horses in HEV epidemiology remains unclear. In this study, we investigated the prevalence of HEV infection in 283 blood and 114 fecal samples from 397 horses using sandwich enzyme-linked immunosorbent assay and nested reverse transcription-polymerase chain reaction. Among the 283 serum samples, 35 were positive for anti-HEV antibodies (12.4%; 95% confidence interval: 8.8-16.8), and four of the five sampling regions (80%) had these seropositive individuals. Analyses of the potential risk factors for HEV infection revealed that racing horses had a significantly higher risk of infection (P = 0.01). However, HEV RNA was not detected in any of the tested serum and fecal samples. To the best of our knowledge, this is the first epidemiological HEV study on horses in Republic of Korea, thereby providing evidence of HEV exposure in the horse population in Korea and specifying the risk factors for HEV infection.
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Affiliation(s)
- Jungho Yoon
- Equine Clinic, Jeju Stud Farm, Korea Racing Authority, Jeju-si, Jeju 63346, Republic of Korea; Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Taemook Park
- Equine Clinic, Jeju Stud Farm, Korea Racing Authority, Jeju-si, Jeju 63346, Republic of Korea
| | - Yongwoo Sohn
- Equine Clinic, Jeju Stud Farm, Korea Racing Authority, Jeju-si, Jeju 63346, Republic of Korea
| | - Sang-Kyu Lee
- Equine Clinic, Jeju Stud Farm, Korea Racing Authority, Jeju-si, Jeju 63346, Republic of Korea
| | - Byung-Joo Park
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Hee-Seop Ahn
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Hyeon-Jeong Go
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Dong-Hwi Kim
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Joong-Bok Lee
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Seung-Yong Park
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Chang-Seon Song
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Sang-Won Lee
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - In-Soo Choi
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea; KU Center for Animal Blood Medical Science, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea.
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Muñoz-Chimeno M, Bartúren S, García-Lugo MA, Morago L, Rodríguez Á, Galán JC, Pérez-Rivilla A, Rodríguez M, Millán R, Del Álamo M, Alonso R, Molina L, Aguinaga A, Avellón A. Hepatitis E virus genotype 3 microbiological surveillance by the Spanish Reference Laboratory: geographic distribution and phylogenetic analysis of subtypes from 2009 to 2019. EURO SURVEILLANCE : BULLETIN EUROPEEN SUR LES MALADIES TRANSMISSIBLES = EUROPEAN COMMUNICABLE DISEASE BULLETIN 2022; 27. [PMID: 35686567 PMCID: PMC9198656 DOI: 10.2807/1560-7917.es.2022.27.23.2100542] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Background Hepatitis E virus genotype 3 (HEV-3) is widely distributed throughout Europe, with incidence of infections increasing in many countries. Belgium, Bulgaria, France, Germany, Italy, the Netherlands and the United Kingdom have reported the distribution of HEV-3 subtypes in cohorts of patients with hepatic disease. Aim To describe the distribution of the HEV-3 subtypes in Spain at national and autonomous community (AC) levels between 2009 and 2019. The study was also extended to Andorra. Methods Of 5,197 samples received by the National Reference Laboratory during the study, 409 were HEV-RNA-positive. Among these, 294 (71.9%) were further typed based on an ORF2 sequence fragment, or, for a subset of 74, based on the full-coding genome sequence. Results HEV-3 was detected in 291 samples. The dominant subtype in Spain was HEV-3f (88.3%; 257/291), which occurred in all ACs, with no change in detection level over time. Within this subtype, three subclusters were characterised: HEV-3f-B, HEV-3f-A1 and HEV-3f-A2. The second most common HEV subtype was the recently described HEV-3m (7%; 21/291), with two subclusters identified: HEV-3m-A, which has been known since 2010, and HEV-3m-B, since 2014. The third most encountered subtype was HEV-3c (4.1%; 12/291), with a frequency not increasing over time, unlike observations in some European countries. Conclusion The importance of the surveillance of HEV-3 subtype and subcluster circulation is yet to be assessed. This surveillance together with the comprehensive epidemiological characterisation of clinical cases, could support the identification of sources of transmission and the establishment of control measures nationally and internationally.
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Affiliation(s)
- Milagros Muñoz-Chimeno
- Hepatitis Unit, National Centre of Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Silvia Bartúren
- Hepatitis Unit, National Centre of Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | | | - Lucia Morago
- Hepatitis Unit, National Centre of Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Álvaro Rodríguez
- Hepatitis Unit, National Centre of Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Juan Carlos Galán
- CIBERESP, Madrid, Spain.,Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | | | - Mercedes Rodríguez
- Hospital Universitario Central de Asturias, Grupo de Microbiología Traslacional (ISPA) Oviedo, Asturias, Spain
| | - Rosario Millán
- Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | | | - Roberto Alonso
- Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Laura Molina
- Hospital Universitario de Fuenlabrada, Madrid, Spain
| | | | - Ana Avellón
- CIBERESP, Madrid, Spain.,Hepatitis Unit, National Centre of Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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5
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Nicot F, Dimeglio C, Migueres M, Jeanne N, Latour J, Abravanel F, Ranger N, Harter A, Dubois M, Lameiras S, Baulande S, Chapuy-Regaud S, Kamar N, Lhomme S, Izopet J. Classification of the Zoonotic Hepatitis E Virus Genotype 3 Into Distinct Subgenotypes. Front Microbiol 2021; 11:634430. [PMID: 33584599 PMCID: PMC7875884 DOI: 10.3389/fmicb.2020.634430] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 12/30/2020] [Indexed: 12/27/2022] Open
Abstract
Hepatitis E virus (HEV) genotype 3 is the most common genotype linked to HEV infections in Europe and America. Three major clades (HEV-3.1, HEV-3.2, and HEV-3.3) have been identified but the overlaps between intra-subtype and inter-subtype p-distances make subtype classification inconsistent. Reference sequences have been proposed to facilitate communication between researchers and new putative subtypes have been identified recently. We have used the full or near full-length HEV-3 genome sequences available in the Genbank database (April 2020; n = 503) and distance analyses of clades HEV-3.1 and HEV-3.2 to determine a p-distance cut-off (0.093 nt substitutions/site) in order to define subtypes. This could help to harmonize HEV-3 genotyping, facilitate molecular epidemiology studies and investigations of the biological and clinical differences between HEV-3 subtypes.
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Affiliation(s)
- Florence Nicot
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Centre National de Référence du Virus de l'Hépatite E, Toulouse, France
| | - Chloé Dimeglio
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Centre National de Référence du Virus de l'Hépatite E, Toulouse, France.,INSERM, U1043, Toulouse, France
| | - Marion Migueres
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Centre National de Référence du Virus de l'Hépatite E, Toulouse, France.,INSERM, U1043, Toulouse, France
| | - Nicolas Jeanne
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Centre National de Référence du Virus de l'Hépatite E, Toulouse, France
| | - Justine Latour
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Centre National de Référence du Virus de l'Hépatite E, Toulouse, France
| | - Florence Abravanel
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Centre National de Référence du Virus de l'Hépatite E, Toulouse, France.,INSERM, U1043, Toulouse, France.,Department of Virology, Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Noémie Ranger
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Centre National de Référence du Virus de l'Hépatite E, Toulouse, France
| | - Agnès Harter
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Centre National de Référence du Virus de l'Hépatite E, Toulouse, France
| | - Martine Dubois
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Centre National de Référence du Virus de l'Hépatite E, Toulouse, France
| | - Sonia Lameiras
- Institut Curie Genomics of Excellence Platform, Institut Curie Research Center, Paris, France
| | - Sylvain Baulande
- Institut Curie Genomics of Excellence Platform, Institut Curie Research Center, Paris, France
| | - Sabine Chapuy-Regaud
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Centre National de Référence du Virus de l'Hépatite E, Toulouse, France.,INSERM, U1043, Toulouse, France.,Department of Virology, Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Nassim Kamar
- INSERM, U1043, Toulouse, France.,Department of Virology, Université Toulouse III Paul-Sabatier, Toulouse, France.,CHU de Toulouse, Hôpital Rangueil, Service de Néphrologie, Dialyse et Transplantation d'Organe, Toulouse, France
| | - Sébastien Lhomme
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Centre National de Référence du Virus de l'Hépatite E, Toulouse, France.,INSERM, U1043, Toulouse, France.,Department of Virology, Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Jacques Izopet
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Centre National de Référence du Virus de l'Hépatite E, Toulouse, France.,INSERM, U1043, Toulouse, France.,Department of Virology, Université Toulouse III Paul-Sabatier, Toulouse, France
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6
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Development and Clinical Validation of a Pangenotypic PCR-Based Assay for the Detection and Quantification of Hepatitis E Virus ( Orthohepevirus A Genus). J Clin Microbiol 2021; 59:JCM.02075-20. [PMID: 33148702 DOI: 10.1128/jcm.02075-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 10/22/2020] [Indexed: 01/01/2023] Open
Abstract
The objective of this study was to design a pangenotypic PCR-based assay for the detection and quantification of hepatitis E virus (HEV) RNA from across the entire spectrum of described genotypes belonging to the Orthohepevirus A genus. The optimal conditions and the performance of the assay were determined by testing the WHO standard strain (6219/10) and the WHO HEV panel (8578/13). Similarly, performance comparisons were made with two commercial assays (Real Star HEV RT-PCR 2.0 and ampliCube HEV 2.0 Quant) to detect HEV RNA at concentrations below 1,000 IU/ml with viral strains from the WHO and to test samples from 54 patients with acute hepatitis. The assay presented in this study was able to detect the entire spectrum of described genotypes belonging to the Orthohepevirus A genus, demonstrating better performance than both commercial kits. This procedure may represent a significant improvement in the molecular diagnosis of HEV infection.
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7
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Muñoz-Chimeno M, Cenalmor A, Garcia-Lugo MA, Hernandez M, Rodriguez-Lazaro D, Avellon A. Proline-Rich Hypervariable Region of Hepatitis E Virus: Arranging the Disorder. Microorganisms 2020; 8:microorganisms8091417. [PMID: 32942608 PMCID: PMC7564002 DOI: 10.3390/microorganisms8091417] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 08/21/2020] [Accepted: 09/11/2020] [Indexed: 12/15/2022] Open
Abstract
The hepatitis E virus (HEV) hypervariable region (HVR) presents the highest divergence of the entire HEV genome. It is characteristically rich in proline, and so is also known as the “polyproline region” (PPR). HEV genotype 3 (HEV-3) exhibits different PPR lengths due to insertions, PPR and/or RNA-dependent RNA polymerase (RdRp) duplications and deletions. A total of 723 PPR-HEV sequences were analyzed, of which 137 HEV-3 sequences were obtained from clinical specimens (from acute and chronic infection) by Sanger sequencing. Eight swine stool/liver samples were also analyzed. N- and C-terminal fragments were confirmed as being conserved, but they harbored differences between genotypes and were not proline-plentiful regions. The genuine PPR is the intermediate region between them. HEV-3 PPR contains a higher percentage (30.4%) of prolines than other genotypes. We describe for the first time: (1) the specific placement of HEV-3 PPR rearrangements in sites 1 to 14 of the PPR, noting that duplications are more frequently attached to sites 11 and 12 (AAs 74–79 and 113–118, respectively); (2) the cadence of repetitions follows a circular-like pattern of blocks A to J, with F, G, H, and I being the most frequent; (3) a previously unreported insertion homologous to apolipoprotein C1; and (4) the increase in frequency of potential N-glycosylation sites and differences in AAs composition related to duplications.
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Affiliation(s)
- Milagros Muñoz-Chimeno
- Hepatitis Unit, National Center of Microbiology, Carlos III Institute of Health, 28220 Madrid, Spain; (M.M.-C.); (A.C.); (M.A.G.-L.)
| | - Alejandro Cenalmor
- Hepatitis Unit, National Center of Microbiology, Carlos III Institute of Health, 28220 Madrid, Spain; (M.M.-C.); (A.C.); (M.A.G.-L.)
| | - Maira Alejandra Garcia-Lugo
- Hepatitis Unit, National Center of Microbiology, Carlos III Institute of Health, 28220 Madrid, Spain; (M.M.-C.); (A.C.); (M.A.G.-L.)
| | - Marta Hernandez
- Laboratorio de Biología Molecular y Microbiología, Instituto Tecnológico Agrario de Castilla y León (ITACyL), 47071 Valladolid, Spain;
- Microbiology Division, Faculty of Sciences, University of Burgos, 09001 Burgos, Spain;
| | | | - Ana Avellon
- Hepatitis Unit, National Center of Microbiology, Carlos III Institute of Health, 28220 Madrid, Spain; (M.M.-C.); (A.C.); (M.A.G.-L.)
- CIBER Epidemiology and Public Health, 28029 Madrid, Spain
- Correspondence:
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8
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Smith DB, Izopet J, Nicot F, Simmonds P, Jameel S, Meng XJ, Norder H, Okamoto H, van der Poel WH, Reuter G, Purdy MA. Update: proposed reference sequences for subtypes of hepatitis E virus (species Orthohepevirus A). J Gen Virol 2020; 101:692-698. [PMID: 32469300 PMCID: PMC7660235 DOI: 10.1099/jgv.0.001435] [Citation(s) in RCA: 221] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
In this recommendation, we update our 2016 table of reference sequences of subtypes of hepatitis E virus (HEV; species Orthohepevirus A, family Hepeviridae) for which complete genome sequences are available (Smith et al., 2016). This takes into account subsequent publications describing novel viruses and additional proposals for subtype names; there are now eight genotypes and 36 subtypes. Although it remains difficult to define strict criteria for distinguishing between virus subtypes, and is not within the remit of the International Committee on Taxonomy of Viruses (ICTV), the use of agreed reference sequences will bring clarity and stability to researchers, epidemiologists and clinicians working with HEV.
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Affiliation(s)
- Donald B. Smith
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,*Correspondence: Donald B. Smith,
| | | | | | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Shahid Jameel
- The Wellcome Trust/DBT India Alliance, Hyderabad, India
| | - Xiang-Jin Meng
- College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Heléne Norder
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 41345 Gothenburg, Sweden
| | - Hiroaki Okamoto
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Tochigi-ken, Japan
| | - Wim H.M. van der Poel
- Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands
| | - Gábor Reuter
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Michael A. Purdy
- Centers for Disease Control and Prevention, National Center for HIV/Hepatitis/STD/TB Prevention, Division of Viral Hepatitis, Atlanta, Georgia, USA
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9
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García N, Hernández M, Gutierrez-Boada M, Valero A, Navarro A, Muñoz-Chimeno M, Fernández-Manzano A, Escobar FM, Martínez I, Bárcena C, González S, Avellón A, Eiros JM, Fongaro G, Domínguez L, Goyache J, Rodríguez-Lázaro D. Occurrence of Hepatitis E Virus in Pigs and Pork Cuts and Organs at the Time of Slaughter, Spain, 2017. Front Microbiol 2020; 10:2990. [PMID: 32047480 PMCID: PMC6997137 DOI: 10.3389/fmicb.2019.02990] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/10/2019] [Indexed: 12/13/2022] Open
Abstract
Zoonotic hepatitis E, mainly caused by hepatitis E virus (HEV) genotype (gt) 3, is a foodborne disease that has emerged in Europe in recent decades. The main animal reservoir for genotype 3 is domestic pigs. Pig liver and liver derivates are considered the major risk products, and studies focused on the presence of HEV in pig muscles are scarce. The objective of the present study was to evaluate the presence of HEV in different organs and tissues of 45 apparently healthy pigs from nine Spanish slaughterhouses (50% national production) that could enter into the food supply chain. Anti-HEV antibodies were evaluated in serum by an ELISA test. Ten samples from each animal were analyzed for the presence of HEV RNA by reverse transcription real-time PCR (RT-qPCR). The overall seroprevalence obtained was 73.3% (33/45). From the 450 samples analyzed, a total of 26 RT-qPCR positive samples were identified in the liver (7/45), feces (6/45), kidney (5/45), heart (4/45), serum (3/45), and diaphragm (1/45). This is the first report on detection of HEV RNA in kidney and heart samples of naturally infected pigs. HEV RNA detection was negative for rib, bacon, lean ham, and loin samples. These findings indicate that pig meat could be considered as a low risk material for foodborne HEV infection.
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Affiliation(s)
- Nerea García
- VISAVET Health Surveillance Centre, Universidad Complutense Madrid, Madrid, Spain
| | - Marta Hernández
- Division of Microbiology, Department of Biotechnology and Food Science, Universidad de Burgos, Burgos, Spain
| | - Maialen Gutierrez-Boada
- Division of Microbiology, Department of Biotechnology and Food Science, Universidad de Burgos, Burgos, Spain
| | - Antonio Valero
- Department of Food Science and Technology, University of Córdoba, Córdoba, Spain
| | - Alejandro Navarro
- VISAVET Health Surveillance Centre, Universidad Complutense Madrid, Madrid, Spain
| | - Milagros Muñoz-Chimeno
- Laboratorio de Referencia e Investigación en Hepatitis Víricas, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Franco Matías Escobar
- Departamento de Microbiología e Inmunología, Universidad Nacional de Río Cuarto, Córdoba, Argentina
| | - Irene Martínez
- VISAVET Health Surveillance Centre, Universidad Complutense Madrid, Madrid, Spain
| | - Carmen Bárcena
- VISAVET Health Surveillance Centre, Universidad Complutense Madrid, Madrid, Spain
| | - Sergio González
- VISAVET Health Surveillance Centre, Universidad Complutense Madrid, Madrid, Spain
| | - Ana Avellón
- Laboratorio de Referencia e Investigación en Hepatitis Víricas, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Jose M. Eiros
- Department of Microbiology, Hospital Universitario Rio Hortega, Valladolid, Spain
| | - Gislaine Fongaro
- Laboratory of Applied Virology, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Lucas Domínguez
- VISAVET Health Surveillance Centre, Universidad Complutense Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary, Universidad Complutense Madrid, Madrid, Spain
| | - Joaquín Goyache
- VISAVET Health Surveillance Centre, Universidad Complutense Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary, Universidad Complutense Madrid, Madrid, Spain
| | - David Rodríguez-Lázaro
- Division of Microbiology, Department of Biotechnology and Food Science, Universidad de Burgos, Burgos, Spain
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10
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Hepatitis E Virus Shows More Genomic Alterations in Cell Culture than In Vivo. Pathogens 2019; 8:pathogens8040255. [PMID: 31766624 PMCID: PMC6963849 DOI: 10.3390/pathogens8040255] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/12/2019] [Accepted: 11/18/2019] [Indexed: 12/16/2022] Open
Abstract
Hepatitis E Virus (HEV) mutations following ribavirin treatment have been associated with treatment non-response and viral persistence, but spontaneous occurring genomic variations have been less well characterized. We here set out to study the HEV genome composition in 2 patient sample types and 2 infection models. Near full HEV genome Sanger sequences of serum- and feces-derived HEV from two chronic HEV genotype 3 (gt3) patients were obtained. In addition, viruses were sequenced after in vitro or in vivo expansion on A549 cells or a humanized mouse model, respectively. We show that HEV acquired 19 nucleotide mutations, of which 7 nonsynonymous amino acids changes located in Open Reading Frame 1 (ORF1), ORF2, and ORF3 coding regions, after prolonged in vitro culture. In vivo passage resulted in selection of 8 nucleotide mutations with 2 altered amino acids in the X domain and Poly-proline region of ORF1. Intra-patient comparison of feces- and serum-derived HEV gt3 of two patients showed 7 and 2 nucleotide mutations with 2 and 0 amino acid changes, respectively. Overall, the number of genomic alterations was up to 1.25× per 1000 nucleotides or amino acids in in vivo samples, and up to 2.84× after in vitro expansion of the same clinical HEV strain. In vitro replication of a clinical HEV strain is therefore associated with more mutations, compared to the minor HEV genomic alterations seen after passage of the same strain in an immune deficient humanized mouse; as well as in feces and blood of 2 immunosuppressed chronically infected HEV patients. These data suggest that HEV infected humanized mice more closely reflect the HEV biology seen in solid organ transplant recipients.
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11
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Hepatitis E virus infections in Europe. J Clin Virol 2019; 120:20-26. [DOI: 10.1016/j.jcv.2019.09.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 09/06/2019] [Indexed: 12/11/2022]
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12
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Lhomme S, Gallian P, Dimeglio C, Assal A, Abravanel F, Tiberghien P, Izopet J. Viral load and clinical manifestations of hepatitis E virus genotype 3 infections. J Viral Hepat 2019; 26:1139-1142. [PMID: 31099059 DOI: 10.1111/jvh.13128] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 05/01/2019] [Indexed: 12/27/2022]
Abstract
A fraction of plasma donations undergoes hepatitis E virus (HEV) RNA screening since late 2014 in France. The aim of this study was to determine the frequency of HEV RNA as well as the viral load and the evolution of genotype distribution over a 3-year period (2015-2017) in asymptomatic blood donors in comparison with symptomatic patients routinely diagnosed. The overall detection rate of HEV RNA in plasma donations was 0.10% during the 3-year period, with a median viral load of 717 IU/mL (range: <60-168 000 IU/mL) in the 189 samples found HEV RNA positive. One hundred and twenty samples (64.4%) were successfully HEV genotyped. Most strains were HEV3f (n = 54; 44.3%) and HEV3c (n = 46; 37.7%). The genotype distribution was not different throughout the 3-year period and we found no association between the genotype and where the blood donors lived (P = 0.96). The HEV genotype distributions in infected blood donors and symptomatic patients were similar. However, the symptomatic patients had a higher viral load (median 282 000 IU/mL; range: <60-136 000 000 IU/mL; P < 0.01) than the blood donors. Overall, asymptomatic blood donors and patients with symptomatic hepatitis E had similar genotype distributions but the blood donors had lower viral loads.
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Affiliation(s)
- Sebastien Lhomme
- Laboratoire de Virologie, CHU Purpan, Toulouse, France.,INSERM, UMR1043, Toulouse, France.,Université Paul Sabatier, Toulouse, France
| | - Pierre Gallian
- Etablissement Français du Sang (EFS), La Plaine St Denis, France.,Unité des Virus Emergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207, IHU Méditerranée Infection), Marseille, France
| | | | - Azzedine Assal
- Etablissement Français du Sang (EFS), Aquitaine Limousin, Bordeaux, France
| | - Florence Abravanel
- Laboratoire de Virologie, CHU Purpan, Toulouse, France.,INSERM, UMR1043, Toulouse, France.,Université Paul Sabatier, Toulouse, France
| | - Pierre Tiberghien
- Etablissement Français du Sang (EFS), La Plaine St Denis, France.,Inserm, Etablissement Français du Sang, UMR 1098, Université de Franche-Comté, Besançon, France
| | - Jacques Izopet
- Laboratoire de Virologie, CHU Purpan, Toulouse, France.,INSERM, UMR1043, Toulouse, France.,Université Paul Sabatier, Toulouse, France
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13
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Caballero-Gómez J, Jiménez-Ruiz S, Lopez-Lopez P, Vicente J, Risalde MA, Cano-Terriza D, Frias M, Barasona JA, Rivero A, García-Bocanegra I, Rivero-Juarez A. Emergent subtype of hepatitis E virus genotype 3 in wild boar in Spain. Transbound Emerg Dis 2019; 66:1803-1808. [PMID: 31127865 DOI: 10.1111/tbed.13251] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 05/21/2019] [Accepted: 05/22/2019] [Indexed: 12/27/2022]
Abstract
Wild boar (Sus scrofa) is considered as the main wildlife reservoir of zoonotic hepatitis E virus (HEV) genotypes. The aim of this study was to evaluate the circulation of HEV in free-ranging wild boar in the Doñana National Park (DNP), Spain. Blood samples were collected from 99 wild boar in the DNP during 2015. Sera were analysed in parallel using indirect ELISA and real-time RT-PCR. A total of 57 of the 99 tested animals (57.6%; 95%CI: 47.8%-67.3%) had anti-HEV antibodies, indicating that this virus is widespread in wild boar in the DNP. HEV RNA was detected in one animal and phylogenetic analysis showed that the sequence isolated belonged to subtype 3r. The results suggest a potential risk of zoonotic transmission of this novel HEV-3 subtype, which could be of public health concern. Further studies are required to assess the role of wild boar in the epidemiology of HEV-3r and to determine the infectivity of this emergent HEV subtype in other species, including humans.
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Affiliation(s)
- Javier Caballero-Gómez
- Animal Health Department, University of Cordoba, Cordoba, Spain.,Infectious Diseases Unit and Clinical Virology and Zoonoses Unit, Maimonides Institute for Biomedical Research, Reina Sofia Hospital, University of Cordoba, Cordoba, Spain
| | - Saul Jiménez-Ruiz
- Animal Health Department, University of Cordoba, Cordoba, Spain.,Health & Biotechnology (SaBio) Group, Spanish Wildlife Research Institute (IREC; CSIC-UCLM-JCCCM), Ciudad Real, Spain
| | - Pedro Lopez-Lopez
- Infectious Diseases Unit and Clinical Virology and Zoonoses Unit, Maimonides Institute for Biomedical Research, Reina Sofia Hospital, University of Cordoba, Cordoba, Spain
| | - Joaquin Vicente
- Health & Biotechnology (SaBio) Group, Spanish Wildlife Research Institute (IREC; CSIC-UCLM-JCCCM), Ciudad Real, Spain
| | - Maria A Risalde
- Animal Pathology Department, University of Cordoba, Cordoba, Spain
| | | | - Mario Frias
- Infectious Diseases Unit and Clinical Virology and Zoonoses Unit, Maimonides Institute for Biomedical Research, Reina Sofia Hospital, University of Cordoba, Cordoba, Spain
| | - Jose A Barasona
- Health & Biotechnology (SaBio) Group, Spanish Wildlife Research Institute (IREC; CSIC-UCLM-JCCCM), Ciudad Real, Spain.,VISAVET Center and Animal Health Department, Veterinary School, Complutense University of Madrid, Madrid, Spain
| | - Antonio Rivero
- Infectious Diseases Unit and Clinical Virology and Zoonoses Unit, Maimonides Institute for Biomedical Research, Reina Sofia Hospital, University of Cordoba, Cordoba, Spain
| | | | - Antonio Rivero-Juarez
- Infectious Diseases Unit and Clinical Virology and Zoonoses Unit, Maimonides Institute for Biomedical Research, Reina Sofia Hospital, University of Cordoba, Cordoba, Spain
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14
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Rivero-Juarez A, Jarilla-Fernandez M, Frias M, Madrigal-Sanchez E, López-López P, Andújar-Troncoso G, Machuca I, Camacho A, Muñoz-Valbuena P, Rivero A. Hepatitis E virus in Spanish donors and the necessity for screening. J Viral Hepat 2019; 26:603-608. [PMID: 30661278 DOI: 10.1111/jvh.13064] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/31/2018] [Accepted: 12/18/2018] [Indexed: 12/27/2022]
Abstract
Hepatitis E virus (HEV) represents a major health problem worldwide. As the course of HEV cases is often subclinical, asymptomatic infections could represent an important source of viral spread and infection via routes such as blood donations. Before universal screening for HEV in blood donations can be implemented, studies evaluating the incidence of infection are needed to establish the potential risk of viral transmission. This is a prospective longitudinal study that included blood donors recruited at the Hospital de Ciudad Real Transfusion Service between October 2017 and January 2018. Pools of eight donations were tested for HEV viremia by PCR. Positive pools were individually evaluated following the same procedure. Positive samples were tested for anti-HEV IgG and IgM. Recipients of blood transfusions obtained from HEV-positive donors were retrospectively evaluated. The prevalence of HEV was calculated. A total of 11 313 healthy donors were analysed during the study period. Four blood donations from four different donors were HEV RNA-reactive. The prevalence of HEV infection was 0.035% (95% CI: 0.01%-0.09%), which meant a ratio of one positive donation per 2828 donations. All donors were negative for anti-HEV IgM at the time of the donation. Five patients received transfusions from HEV-positive blood donations, none of them showed an increase in alanine aminotransferase levels after transfusion. In conclusion, our study found a high prevalence of HEV infection in blood donors from south-central Spain. In view of the prevalence, Spanish blood banks should carefully consider including screening for HEV.
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Affiliation(s)
- Antonio Rivero-Juarez
- Infectious Diseases Unit, Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía de Córdoba, Universidad de Córdoba, Cordoba, Spain
| | | | - Mario Frias
- Infectious Diseases Unit, Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía de Córdoba, Universidad de Córdoba, Cordoba, Spain
| | | | - Pedro López-López
- Infectious Diseases Unit, Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía de Córdoba, Universidad de Córdoba, Cordoba, Spain
| | | | - Isabel Machuca
- Infectious Diseases Unit, Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía de Córdoba, Universidad de Córdoba, Cordoba, Spain
| | - Angela Camacho
- Infectious Diseases Unit, Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía de Córdoba, Universidad de Córdoba, Cordoba, Spain
| | | | - Antonio Rivero
- Infectious Diseases Unit, Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía de Córdoba, Universidad de Córdoba, Cordoba, Spain
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15
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García-Bocanegra I, Rivero A, Caballero-Gómez J, López-López P, Cano-Terriza D, Frías M, Jiménez-Ruiz S, Risalde MA, Gómez-Villamandos JC, Rivero-Juarez A. Hepatitis E virus infection in equines in Spain. Transbound Emerg Dis 2018; 66:66-71. [PMID: 30047239 DOI: 10.1111/tbed.12962] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 06/27/2018] [Accepted: 06/28/2018] [Indexed: 12/27/2022]
Abstract
Hepatitis E (HE) is an important emerging disease in European countries. To analyse the role of equids as potential reservoirs for HE virus (HEV), we determined the prevalence of HEV infection in 861 equines from 464 herds in Spain. HEV RNA in serum was detected in 0.4% (3/692) of horses, 1.2% (1/86) of donkeys and 3.6% (3/83) of mules. Phylogenetic analysis identified the zoonotic genotype 3 as being closely related to viral human and swine strains. In this first report on HEV in equids in Europe, we confirm the susceptibility of horses, donkeys and mules to HEV infection. The low prevalence detected indicates that equids may be considered spillover hosts rather than true reservoirs.
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Affiliation(s)
| | - Antonio Rivero
- Infectious Diseases Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Cordoba, Spain
| | | | - Pedro López-López
- Infectious Diseases Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Cordoba, Spain
| | | | - Mario Frías
- Infectious Diseases Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Cordoba, Spain
| | | | - Maria A Risalde
- Infectious Diseases Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Cordoba, Spain
| | | | - Antonio Rivero-Juarez
- Infectious Diseases Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Cordoba, Spain
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16
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Nicot F, Jeanne N, Roulet A, Lefebvre C, Carcenac R, Manno M, Dubois M, Kamar N, Lhomme S, Abravanel F, Izopet J. Diversity of hepatitis E virus genotype 3. Rev Med Virol 2018; 28:e1987. [PMID: 29939461 DOI: 10.1002/rmv.1987] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/12/2018] [Accepted: 05/21/2018] [Indexed: 12/27/2022]
Abstract
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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Affiliation(s)
- Florence Nicot
- Centre National de Référence du virus de l'hépatite E, Laboratoire de Virologie, Hôpital Purpan, CHU de Toulouse, Toulouse, France
| | - Nicolas Jeanne
- Centre National de Référence du virus de l'hépatite E, Laboratoire de Virologie, Hôpital Purpan, CHU de Toulouse, Toulouse, France
| | - Alain Roulet
- Plateforme Génomique, Centre INRA Occitanie-Toulouse, Castanet-Tolosan, France
| | - Caroline Lefebvre
- Centre National de Référence du virus de l'hépatite E, Laboratoire de Virologie, Hôpital Purpan, CHU de Toulouse, Toulouse, France
| | - Romain Carcenac
- Centre National de Référence du virus de l'hépatite E, Laboratoire de Virologie, Hôpital Purpan, CHU de Toulouse, Toulouse, France
| | - Maxime Manno
- Plateforme Génomique, Centre INRA Occitanie-Toulouse, Castanet-Tolosan, France
| | - Martine Dubois
- Centre National de Référence du virus de l'hépatite E, Laboratoire de Virologie, Hôpital Purpan, CHU de Toulouse, Toulouse, France
| | - Nassim Kamar
- Center of Pathophysiology, Toulouse Purpan, INSERM, U1043, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France.,Service de néphrologie, Dialyse et Transplantation d'Organe, Hôpital Rangueil, CHU de Toulouse, Toulouse, France
| | - Sébastien Lhomme
- Centre National de Référence du virus de l'hépatite E, Laboratoire de Virologie, Hôpital Purpan, CHU de Toulouse, Toulouse, France.,Center of Pathophysiology, Toulouse Purpan, INSERM, U1043, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Florence Abravanel
- Centre National de Référence du virus de l'hépatite E, Laboratoire de Virologie, Hôpital Purpan, CHU de Toulouse, Toulouse, France.,Center of Pathophysiology, Toulouse Purpan, INSERM, U1043, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Jacques Izopet
- Centre National de Référence du virus de l'hépatite E, Laboratoire de Virologie, Hôpital Purpan, CHU de Toulouse, Toulouse, France.,Center of Pathophysiology, Toulouse Purpan, INSERM, U1043, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
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