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Wang B, Cronin P, Mah MG, Yang XL, Su YCF. Genetic Diversity and Molecular Evolution of Hepatitis E Virus Within the Genus Chirohepevirus in Bats. Viruses 2025; 17:339. [PMID: 40143268 PMCID: PMC11945734 DOI: 10.3390/v17030339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2025] [Revised: 02/26/2025] [Accepted: 02/27/2025] [Indexed: 03/28/2025] Open
Abstract
Hepatitis E virus (HEV) is a major zoonotic pathogen causing hepatitis E, with strains identified in various animal species, including pigs, wild boar, rabbits, deer, camels, and rats. These variants are capable of crossing species barriers and infecting humans. HEV belongs to the family Hepeviridae, which has recently divided into two subfamilies: Orthohepevirinae and Parahepevirinae, and five genera: Paslahepevirus, Avihepevirus, Rocahepevirus, Chirohepevirus, and Piscihepevirus. Recent advances in high-throughput sequencing, particularly of bat viromes, have revealed numerous HEV-related viruses, raising concerns about their zoonotic potential. Bat-derived HEVs have been classified into the genus Chirohepevirus, which includes three distinct species. In this study, we analyzed 64 chirohepevirus sequences from 22 bat species across six bat families collected from nine countries. Twelve sequences represent complete or nearly complete viral genomes (>6410 nucleotides) containing the characteristic three HEV open reading frames (ORFs). These strains exhibited high sequence divergence (>25%) within their respective host genera or species. Phylogenetic analyses with maximum likelihood methods identified at least seven distinct subclades within Chirohepevirus, each potentially representing an independent species. Additionally, the close phylogenetic relationship between chirohepevirus strains and their bat hosts indicates a pattern of virus-host co-speciation. Our findings expand the known diversity within the family Hepeviridae and provide new insights into the evolution of bat-associated HEV. Continued surveillance of chirohepevirus will be essential for understanding its potential for zoonotic transmission and public health risks.
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Affiliation(s)
- Bo Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; (P.C.); (M.G.M.)
| | - Peter Cronin
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; (P.C.); (M.G.M.)
| | - Marcus G. Mah
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; (P.C.); (M.G.M.)
| | - Xing-Lou Yang
- Key Laboratory of Genetic Evolution & Animal Models, Yunnan International Joint Laboratory of Zoonotic Viruses, Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
| | - Yvonne C. F. Su
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; (P.C.); (M.G.M.)
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de Camargo LJ, Alves RS, dos Santos RN, Baumbach LF, Olegário JDC, Rabaioli V, Silva MDO, Witt AA, Godinho FM, Salvato RS, Weber MN, da Silva MS, Daudt C, Budaszewski RDF, Canal CW. Characterization of Three Novel Papillomavirus Genomes in Vampire Bats ( Desmodus rotundus). Animals (Basel) 2024; 14:3604. [PMID: 39765508 PMCID: PMC11672418 DOI: 10.3390/ani14243604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2024] [Revised: 12/11/2024] [Accepted: 12/12/2024] [Indexed: 01/11/2025] Open
Abstract
Bats are mammals with high biodiversity and wide geographical range. In Brazil, three haematophagous bat species are found. Desmodus rotundus is the most documented due to its role as a primary host of rabies virus in Latin America. Bats are known to harbor various emerging viruses causing severe human diseases. Beyond zoonotic viruses, these animals also harbor a diversity of non-zoonotic viruses. Papillomaviruses are circular double-stranded deoxyribonucleic acid (dsDNA) viruses that infect the epithelial and mucosal cells of many vertebrates, occasionally causing malignant lesions. High-throughput sequencing has enabled papillomaviruses discovery in different bat species. Here, 22 D. rotundus samples were collected through the rabies eradication program in Rio Grande do Sul. The DNA extracted from pooled intestines was amplified by the rolling-circle amplification (RCA) method and sequenced using the Illumina® MiSeq platform (San Diego, CA, USA).Analysis revealed three contigs corresponding to the Papillomaviridae family, representing three novel viruses named DrPV-1, DrPV-2, and DrPV-3. Phylogenetic analysis suggests DrPV-1 may constitute a new species within the Dyophipapillomavirus genus, while DrPV-2 and DrPV-3 may represent different types within the same species from a novel genus. This is the first description of a papillomavirus in the D. rotundus species, contributing to the characterization of PVs in the Chiropteran order.
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Affiliation(s)
- Laura Junqueira de Camargo
- Laboratório de Virologia Veterinária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91540-000, Brazil; (L.J.d.C.); (R.S.A.); (L.F.B.); (J.d.C.O.); (V.R.); (M.d.O.S.); (R.d.F.B.); (C.W.C.)
| | - Raquel Silva Alves
- Laboratório de Virologia Veterinária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91540-000, Brazil; (L.J.d.C.); (R.S.A.); (L.F.B.); (J.d.C.O.); (V.R.); (M.d.O.S.); (R.d.F.B.); (C.W.C.)
| | - Raíssa Nunes dos Santos
- Laboratório de Virologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 90035-003, Brazil;
| | - Letícia Ferreira Baumbach
- Laboratório de Virologia Veterinária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91540-000, Brazil; (L.J.d.C.); (R.S.A.); (L.F.B.); (J.d.C.O.); (V.R.); (M.d.O.S.); (R.d.F.B.); (C.W.C.)
| | - Juliana do Canto Olegário
- Laboratório de Virologia Veterinária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91540-000, Brazil; (L.J.d.C.); (R.S.A.); (L.F.B.); (J.d.C.O.); (V.R.); (M.d.O.S.); (R.d.F.B.); (C.W.C.)
| | - Vitória Rabaioli
- Laboratório de Virologia Veterinária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91540-000, Brazil; (L.J.d.C.); (R.S.A.); (L.F.B.); (J.d.C.O.); (V.R.); (M.d.O.S.); (R.d.F.B.); (C.W.C.)
| | - Matheus de Oliveira Silva
- Laboratório de Virologia Veterinária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91540-000, Brazil; (L.J.d.C.); (R.S.A.); (L.F.B.); (J.d.C.O.); (V.R.); (M.d.O.S.); (R.d.F.B.); (C.W.C.)
| | - André Alberto Witt
- Secretaria Estadual de Agricultura, Pecuária e Desenvolvimento Rural (SEAPDR), Rio Grande do Sul, Porto Alegre 90150-004, Brazil;
| | - Fernanda Marques Godinho
- Centro Estatual de Vigilância em Saúde (CEVS)—Centro de Desenvolvimento Científico e Tecnológico (CDCT), Rio Grande do Sul, Porto Alegre 90450-190, Brazil; (F.M.G.); (R.S.S.)
| | - Richard Steiner Salvato
- Centro Estatual de Vigilância em Saúde (CEVS)—Centro de Desenvolvimento Científico e Tecnológico (CDCT), Rio Grande do Sul, Porto Alegre 90450-190, Brazil; (F.M.G.); (R.S.S.)
| | - Matheus Nunes Weber
- Laboratório de Imunologia e Biologia Molecular, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91540-000, Brazil
| | - Mariana Soares da Silva
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Novo Hamburgo 93525-075, Brazil;
| | - Cíntia Daudt
- Laboratório de Virologia Geral e Parasitologia (LABVIRPA), Universidade Federal do Acre (UFAC), Rio Branco 69920-900, Brazil;
| | - Renata da Fontoura Budaszewski
- Laboratório de Virologia Veterinária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91540-000, Brazil; (L.J.d.C.); (R.S.A.); (L.F.B.); (J.d.C.O.); (V.R.); (M.d.O.S.); (R.d.F.B.); (C.W.C.)
| | - Cláudio Wageck Canal
- Laboratório de Virologia Veterinária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91540-000, Brazil; (L.J.d.C.); (R.S.A.); (L.F.B.); (J.d.C.O.); (V.R.); (M.d.O.S.); (R.d.F.B.); (C.W.C.)
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3
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Waller SJ, Tortosa P, Thurley T, O’Donnell CFJ, Jackson R, Dennis G, Grimwood RM, Holmes EC, McInnes K, Geoghegan JL. Virome analysis of New Zealand's bats reveals cross-species viral transmission among the Coronaviridae. Virus Evol 2024; 10:veae008. [PMID: 38379777 PMCID: PMC10878368 DOI: 10.1093/ve/veae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 11/02/2023] [Accepted: 01/21/2024] [Indexed: 02/22/2024] Open
Abstract
The lesser short-tailed bat (Mystacina tuberculata) and the long-tailed bat (Chalinolobus tuberculatus) are Aotearoa New Zealand's only native extant terrestrial mammals and are believed to have migrated from Australia. Long-tailed bats arrived in New Zealand an estimated two million years ago and are closely related to other Australian bat species. Lesser short-tailed bats, in contrast, are the only extant species within the Mystacinidae and are estimated to have been living in isolation in New Zealand for the past 16-18 million years. Throughout this period of isolation, lesser short-tailed bats have become one of the most terrestrial bats in the world. Through a metatranscriptomic analysis of guano samples from eight locations across New Zealand, we aimed to characterise the viromes of New Zealand's bats and determine whether viruses have jumped between these species over the past two million years. High viral richness was observed among long-tailed bats with viruses spanning seven different viral families. In contrast, no bat-specific viruses were identified in lesser short-tailed bats. Both bat species harboured an abundance of likely dietary- and environment-associated viruses. We also identified alphacoronaviruses in long-tailed bat guano that had previously been identified in lesser short-tailed bats, suggesting that these viruses had jumped the species barrier after long-tailed bats migrated to New Zealand. Of note, an alphacoronavirus species discovered here possessed a complete genome of only 22,416 nucleotides with entire deletions or truncations of several non-structural proteins, thereby representing what may be the shortest genome within the Coronaviridae identified to date. Overall, this study has revealed a diverse range of novel viruses harboured by New Zealand's only native terrestrial mammals, in turn expanding our understanding of bat viral dynamics and evolution globally.
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Affiliation(s)
- Stephanie J Waller
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, Dunedin 9016, New Zealand
| | - Pablo Tortosa
- UMR PIMIT Processus Infectieux en Milieu Insulaire Tropical, Université de La Réunion, CNRS 9192, INSERM 1187, IRD 249, Plateforme de recherche CYROI, 2 rue Maxime Rivière, Ste Clotilde 97490, France
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Tertia Thurley
- Department of Conservation, New Zealand Government, P.O. Box 10420, Wellington 6143, New Zealand
| | - Colin F J O’Donnell
- Department of Conservation, New Zealand Government, P.O. Box 10420, Wellington 6143, New Zealand
| | - Rebecca Jackson
- Department of Conservation, New Zealand Government, P.O. Box 10420, Wellington 6143, New Zealand
| | - Gillian Dennis
- Department of Conservation, New Zealand Government, P.O. Box 10420, Wellington 6143, New Zealand
| | - Rebecca M Grimwood
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, Dunedin 9016, New Zealand
| | | | - Kate McInnes
- Department of Conservation, New Zealand Government, P.O. Box 10420, Wellington 6143, New Zealand
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, Dunedin 9016, New Zealand
- Institute of Environmental Science and Research, 34 Kenepuru Drive, Kenepuru, Porirua, Wellington 5022, New Zealand
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Westmead Hospital, Level 5, Block K, Westmead, Sydney, NSW 2006, Australia
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4
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Robson M, Chooi KM, Blouin AG, Knight S, MacDiarmid RM. A National Catalogue of Viruses Associated with Indigenous Species Reveals High-Throughput Sequencing as a Driver of Indigenous Virus Discovery. Viruses 2022; 14:v14112477. [PMID: 36366575 PMCID: PMC9693408 DOI: 10.3390/v14112477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022] Open
Abstract
Viruses are important constituents of ecosystems, with the capacity to alter host phenotype and performance. However, virus discovery cued by disease symptoms overlooks latent or beneficial viruses, which are best detected using targeted virus detection or discovered by non-targeted methods, e.g., high-throughput sequencing (HTS). To date, in 64 publications, 701 viruses have been described associated with indigenous species of Aotearoa New Zealand. Viruses were identified in indigenous birds (189 viruses), bats (13 viruses), starfish (4 viruses), insects (280 viruses), and plants (126 viruses). HTS gave rise to a 21.9-fold increase in virus discovery rate over the targeted methods, and 72.7-fold over symptom-based methods. The average number of viruses reported per publication has also increased proportionally over time. The use of HTS has driven the described national virome recently by 549 new-to-science viruses; all are indigenous. This report represents the first catalogue of viruses associated with indigenous species of a country. We provide evidence that the application of HTS to samples of Aotearoa New Zealand's unique fauna and flora has driven indigenous virus discovery, a key step in the process to understand the role of viruses in the biological diversity and ecology of the land, sea, and air environments of a country.
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Affiliation(s)
- Merlyn Robson
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland 1142, New Zealand
- Bio-Protection Research Centre, Lincoln University, P.O. Box 85084, Lincoln 7674, New Zealand
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand
| | - Kar Mun Chooi
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand
| | | | - Sarah Knight
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Robin Marion MacDiarmid
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland 1142, New Zealand
- Bio-Protection Research Centre, Lincoln University, P.O. Box 85084, Lincoln 7674, New Zealand
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand
- Correspondence:
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5
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French RK, Stone ZL, Parker KA, Holmes EC. Novel viral and microbial species in a translocated Toutouwai (Petroica longipes) population from Aotearoa/New Zealand. ONE HEALTH OUTLOOK 2022; 4:16. [PMID: 36224666 PMCID: PMC9558408 DOI: 10.1186/s42522-022-00072-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Translocation is a common tool in wildlife management and its implementation has resulted in many conservation successes. During translocations, any associated infectious agents are moved with their wildlife hosts. Accordingly, translocations can present a risk of infectious disease emergence, although they also provide an opportunity to restore natural infectious communities ('infectome') and mitigate the long-term risks of reduced natural resistance. METHODS We used metatranscriptomic sequencing to characterise the cloacal infectome of 41 toutouwai (North Island robin, Petroica longipes) that were translocated to establish a new population within the North Island of New Zealand. We also screened for pathogenic bacteria, fungi and parasites. RESULTS Although we did not detect any known avian diseases, which is a positive outcome for the translocated toutouwai population, we identified a number of novel viruses of interest, including a novel avian hepatovirus, as well as a divergent calici-like virus and four hepe-like viruses of which the host species is unknown. We also revealed a novel spirochete bacterium and a coccidian eukaryotic parasite. CONCLUSIONS The presumably non-pathogenic viruses and microbial species identified here support the idea that most microorganisms likely do not cause disease in their hosts, and that translocations could serve to help restore and maintain native infectious communities. We advise greater surveillance of infectious communities of both native and non-native wildlife before and after translocations to better understand the impact, positive or negative, that such movements may have on both host and infectome ecology.
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Affiliation(s)
- Rebecca K French
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia.
| | - Zoë L Stone
- Zoology and Ecology Group, School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Kevin A Parker
- Parker Conservation Ltd, 549 Rocks Road, Nelson, New Zealand
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia.
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Dunowska M, Perrott M, Biggs P. Identification of a novel polyomavirus from a marsupial host. Virus Evol 2022; 8:veac096. [PMID: 36381233 PMCID: PMC9662318 DOI: 10.1093/ve/veac096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/09/2022] [Accepted: 10/05/2022] [Indexed: 08/26/2023] Open
Abstract
We report the identification and analysis of a full sequence of a novel polyomavirus from a brushtail possum (Trichosurus vulpecula ) termed possum polyomavirus (PPyV). The sequence was obtained from the next-generation sequencing assembly during an investigation into the aetiological agent for a neurological disease of possums termed wobbly possum disease (WPD), but the virus was not aetiologically involved in WPD. The PPyV genome was 5,224 nt long with the organisation typical for polyomaviruses, including early (large and small T antigens) and late (Viral Protein 1 (VP1), VP2, and VP3) coding regions separated by the non-coding control region of 465 nt. PPyV clustered with betapolyomaviruses in the WUKI clade but showed less than 60 per cent identity to any of the members of this clade. We propose that PPyV is classified within a new species in the genus Betapolyomavirus . These data add to our limited knowledge of marsupial viruses and their evolution.
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Affiliation(s)
- Magdalena Dunowska
- School of Veterinary Science, Massey University, Palmerston North 4410, New Zealand
| | - Matthew Perrott
- School of Veterinary Science, Massey University, Palmerston North 4410, New Zealand
| | - Patrick Biggs
- School of Veterinary Science, Massey University, Palmerston North 4410, New Zealand
- School of Natural Sciences, Massey University, Palmerston North 4410, New Zealand
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Chirohepevirus from Bats: Insights into Hepatitis E Virus Diversity and Evolution. Viruses 2022; 14:v14050905. [PMID: 35632647 PMCID: PMC9146828 DOI: 10.3390/v14050905] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/22/2022] [Accepted: 04/25/2022] [Indexed: 02/06/2023] Open
Abstract
Homologs of the human hepatitis E virus (HEV) have been identified in more than a dozen animal species. Some of them have been evidenced to cross species barriers and infect humans. Zoonotic HEV infections cause chronic liver diseases as well as a broad range of extrahepatic manifestations, which increasingly become significant clinical problems. Bats comprise approximately one-fifth of all named mammal species and are unique in their distinct immune response to viral infection. Most importantly, they are natural reservoirs of several highly pathogenic viruses, which have induced severe human diseases. Since the first discovery of HEV-related viruses in bats in 2012, multiple genetically divergent HEV variants have been reported in a total of 12 bat species over the last decade, which markedly expanded the host range of the HEV family and shed light on the evolutionary origin of human HEV. Meanwhile, bat-borne HEV also raised critical public health concerns about its zoonotic potential. Bat HEV strains resemble genomic features but exhibit considerable heterogeneity. Due to the close evolutionary relationships, bat HEV altogether has been recently assigned to an independent genus, Chirohepevirus. This review focuses on the current state of bat HEV and provides novel insights into HEV genetic diversity and molecular evolution.
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Hayman DTS, Knox MA. Estimating the age of the subfamily Orthocoronavirinae using host divergence times as calibration ages at two internal nodes. Virology 2021; 563:20-27. [PMID: 34411808 PMCID: PMC8365511 DOI: 10.1016/j.virol.2021.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/11/2021] [Accepted: 08/11/2021] [Indexed: 12/04/2022]
Abstract
Viruses of the subfamily Orthocoronavirinae can cause mild to severe disease in people, including COVID-19, MERS and SARS. Their most common natural hosts are bat and bird species, which are mostly split across four virus genera. Molecular clock analyses of orthocoronaviruses suggested the most recent common ancestor of these viruses might have emerged either around 10,000 years ago or, using models accounting for selection, many millions of years. Here, we reassess the evolutionary history of these viruses. We present time-aware phylogenetic analyses of a RNA-dependent RNA polymerase locus from 123 orthocoronaviruses isolated from birds and bats, including those in New Zealand, which were geographically isolated from other bats around 35 million years ago. We used this age, as well as the age of the avian-mammals split, to calibrate the molecular clocks, under the assumption that these ages are applicable to the analyzed viruses. We found that the time to the most recent ancestor common for all orthocoronaviruses is likely 150 or more million years, supporting clock analyses that account for selection.
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Affiliation(s)
- David T S Hayman
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, New Zealand.
| | - Matthew A Knox
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, New Zealand
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9
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The virome of German bats: comparing virus discovery approaches. Sci Rep 2021; 11:7430. [PMID: 33795699 PMCID: PMC8016945 DOI: 10.1038/s41598-021-86435-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/15/2021] [Indexed: 12/14/2022] Open
Abstract
Bats are known to be reservoirs of several highly pathogenic viruses. Hence, the interest in bat virus discovery has been increasing rapidly over the last decade. So far, most studies have focused on a single type of virus detection method, either PCR, virus isolation or virome sequencing. Here we present a comprehensive approach in virus discovery, using all three discovery methods on samples from the same bats. By family-specific PCR screening we found sequences of paramyxoviruses, adenoviruses, herpesviruses and one coronavirus. By cell culture we isolated a novel bat adenovirus and bat orthoreovirus. Virome sequencing revealed viral sequences of ten different virus families and orders: three bat nairoviruses, three phenuiviruses, one orbivirus, one rotavirus, one orthoreovirus, one mononegavirus, five parvoviruses, seven picornaviruses, three retroviruses, one totivirus and two thymoviruses were discovered. Of all viruses identified by family-specific PCR in the original samples, none was found by metagenomic sequencing. Vice versa, none of the viruses found by the metagenomic virome approach was detected by family-specific PCRs targeting the same family. The discrepancy of detected viruses by different detection approaches suggests that a combined approach using different detection methods is necessary for virus discovery studies.
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10
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Koba R, Suzuki S, Sato G, Sato S, Suzuki K, Maruyama S, Tohya Y. Identification and characterization of a novel bat polyomavirus in Japan. Virus Genes 2020; 56:772-776. [PMID: 32816186 PMCID: PMC7439235 DOI: 10.1007/s11262-020-01789-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/13/2020] [Indexed: 11/28/2022]
Abstract
A novel polyomavirus (PyV) was identified in the intestinal contents of Japanese eastern bent-wing bats (Miniopterus fuliginosus) via metagenomic analysis. We subsequently sequenced the full genome of the virus, which has been tentatively named Miniopterus fuliginosus polyomavirus (MfPyV). The nucleotide sequence identity of the genome with those of other bat PyVs was less than 80%. Phylogenetic analysis revealed that MfPyV belonged to the same cluster as PyVs detected in Miniopterus schreibersii. This study has identified the presence of a novel PyV in Japanese bats and provided genetic information about the virus.
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Affiliation(s)
- Ryota Koba
- Laboratory of Veterinary Microbiology, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Satori Suzuki
- Laboratory of Veterinary Microbiology, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Go Sato
- Laboratory of Veterinary Microbiology, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Shingo Sato
- Laboratory of Veterinary Public Health, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Kazuo Suzuki
- Hikiiwa Park Center, 1629 Inari-cho, Tanabe, Wakayama, 646-0051, Japan
| | - Soichi Maruyama
- Laboratory of Veterinary Public Health, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Yukinobu Tohya
- Laboratory of Veterinary Microbiology, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan.
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11
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Extensive Genetic Diversity of Polyomaviruses in Sympatric Bat Communities: Host Switching versus Coevolution. J Virol 2020; 94:JVI.02101-19. [PMID: 32075934 DOI: 10.1128/jvi.02101-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 02/11/2020] [Indexed: 01/17/2023] Open
Abstract
Polyomaviruses (PyVs) are small DNA viruses carried by diverse vertebrates. The evolutionary relationships of viruses and hosts remain largely unclear due to very limited surveillance in sympatric communities. In order to investigate whether PyVs can transmit among different mammalian species and to identify host-switching events in the field, we conducted a systematic study of a large collection of bats (n = 1,083) from 29 sympatric communities across China which contained multiple species with frequent contact. PyVs were detected in 21 bat communities, with 192 PyVs identified in 186 bats from 15 species within 6 families representing at least 28 newly described PyVs. Surveillance results and phylogenetic analyses surprisingly revealed three interfamily PyV host-switching events in these sympatric bat communities: two distinct PyVs were identified in two bat species in restricted geographical locations, while another PyV clustered phylogenetically with PyVs carried by bats from a different host family. Virus-host relationships of all discovered PyVs were also evaluated, and no additional host-switching events were found. PyVs were identified in different horseshoe bat species in sympatric communities without observation of host-switching events, showed high genomic identities, and clustered with each other. This suggested that even for PyVs with high genomic identities in closely related host species, the potential for host switching is low. In summary, our findings revealed that PyV host switching in sympatric bat communities can occur but is limited and that host switching of bat-borne PyVs is relatively rare on the predominantly evolutionary background of codivergence with their hosts.IMPORTANCE Since the discovery of murine polyomavirus in the 1950s, polyomaviruses (PyVs) have been considered highly host restricted in mammals. Sympatric bat communities commonly contain several different bat species in an ecological niche facilitating viral transmission, and they therefore represent a model to identify host-switching events of PyVs. In this study, we screened PyVs in a large number of bats in sympatric communities from diverse habitats across China. We provide evidence that cross-species bat-borne PyV transmission exists, though is limited, and that host-switching events appear relatively rare during the evolutionary history of these viruses. PyVs with close genomic identities were also identified in different bat species without host-switching events. Based on these findings, we propose an evolutionary scheme for bat-borne PyVs in which limited host-switching events occur on the background of codivergence and lineage duplication, generating the viral genetic diversity in bats.
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Diversity and Evolution of Viral Pathogen Community in Cave Nectar Bats ( Eonycteris spelaea). Viruses 2019; 11:v11030250. [PMID: 30871070 PMCID: PMC6466414 DOI: 10.3390/v11030250] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/07/2019] [Accepted: 03/07/2019] [Indexed: 12/12/2022] Open
Abstract
Bats are unique mammals, exhibit distinctive life history traits and have unique immunological approaches to suppression of viral diseases upon infection. High-throughput next-generation sequencing has been used in characterizing the virome of different bat species. The cave nectar bat, Eonycteris spelaea, has a broad geographical range across Southeast Asia, India and southern China, however, little is known about their involvement in virus transmission. Here we investigate the diversity and abundance of viral communities from a colony of Eonycteris spelaea residing in Singapore. Our results detected 47 and 22 different virus families from bat fecal and urine samples, respectively. Among these, we identify a large number of virus families including Adenoviridae, Flaviviridae, Reoviridae, Papillomaviridae, Paramyxoviridae, Parvoviridae, Picornaviridae, and Polyomaviridae. In most cases, viral sequences from Eonycteris spelaea are genetically related to a group of bat viruses from other bat genera (e.g., Eidolon, Miniopterus, Rhinolophus and Rousettus). The results of this study improve our knowledge of the host range, spread and evolution of several important viral pathogens. More significantly, our findings provide a baseline to study the temporal patterns of virus shedding and how they correlate with bat phenological trends.
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Detection of adenovirus, papillomavirus and parvovirus in Brazilian bats of the species Artibeus lituratus and Sturnira lilium. Arch Virol 2019; 164:1015-1025. [PMID: 30740637 PMCID: PMC7086806 DOI: 10.1007/s00705-018-04129-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 11/27/2018] [Indexed: 01/21/2023]
Abstract
Bats play a significant role in maintaining their ecosystems through pollination, dispersal of seeds, and control of insect populations, but they are also known to host many microorganisms and have been described as natural reservoirs for viruses with zoonotic potential. The diversity of viruses in these animals remains largely unknown, however, because studies are limited by species, location, virus target, or sample type. Therefore, the aim of this study was to detect fragments of viral genomes in bat samples. We performed high-throughput sequencing analysis and specific PCR and RT-PCR on pools of anal and oropharyngeal swabs from Artibeus lituratus and Sturnira lilium collected in southern Brazil. As a result, a member of the family Adenoviridae related to human adenovirus C was detected in anal swabs from S. lilium. In addition, we detected a papillomavirus in an anal swab from A. lituratus. Our analyses also allowed the detection of adenoviruses and parvoviruses in oropharyngeal swabs collected from A. lituratus. These results increase our knowledge about viral diversity and illustrate the importance of conducting virus surveillance in bats.
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14
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Viruses in bats and potential spillover to animals and humans. Curr Opin Virol 2019; 34:79-89. [PMID: 30665189 PMCID: PMC7102861 DOI: 10.1016/j.coviro.2018.12.007] [Citation(s) in RCA: 178] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 12/17/2018] [Accepted: 12/17/2018] [Indexed: 12/17/2022]
Abstract
Bats are a very important source of emerging viruses. Bat coronavirus, filovirus, paramyxovirus and reovirus are known zoonotic viruses. Many of the emergent bat viruses are highly lethal in livestock and humans. Past incidents and viral genetic features predict bat coronaviruses as the highest risk.
In the last two decades, several high impact zoonotic disease outbreaks have been linked to bat-borne viruses. These include SARS coronavirus, Hendra virus and Nipah virus. In addition, it has been suspected that ebolaviruses and MERS coronavirus are also linked to bats. It is being increasingly accepted that bats are potential reservoirs of a large number of known and unknown viruses, many of which could spillover into animal and human populations. However, our knowledge into basic bat biology and immunology is very limited and we have little understanding of major factors contributing to the risk of bat virus spillover events. Here we provide a brief review of the latest findings in bat viruses and their potential risk of cross-species transmission.
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Bat Caliciviruses and Human Noroviruses Are Antigenically Similar and Have Overlapping Histo-Blood Group Antigen Binding Profiles. mBio 2018; 9:mBio.00869-18. [PMID: 29789360 PMCID: PMC5964351 DOI: 10.1128/mbio.00869-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Emerging zoonotic viral diseases remain a challenge to global public health. Recent surveillance studies have implicated bats as potential reservoirs for a number of viral pathogens, including coronaviruses and Ebola viruses. Caliciviridae represent a major viral family contributing to emerging diseases in both human and animal populations and have been recently identified in bats. In this study, we blended metagenomics, phylogenetics, homology modeling, and in vitro assays to characterize two novel bat calicivirus (BtCalV) capsid sequences, corresponding to strain BtCalV/A10/USA/2009, identified in Perimyotis subflavus near Little Orleans, MD, and bat norovirus. We observed that bat norovirus formed virus-like particles and had epitopes and receptor-binding patterns similar to those of human noroviruses. To determine whether these observations stretch across multiple bat caliciviruses, we characterized a novel bat calicivirus, BtCalV/A10/USA/2009. Phylogenetic analysis revealed that BtCalV/A10/USA/2009 likely represents a novel Caliciviridae genus and is most closely related to "recoviruses." Homology modeling revealed that the capsid sequences of BtCalV/A10/USA/2009 and bat norovirus resembled human norovirus capsid sequences and retained host ligand binding within the receptor-binding domains similar to that seen with human noroviruses. Both caliciviruses bound histo-blood group antigens in patterns that overlapped those seen with human and animal noroviruses. Taken together, our results indicate the potential for bat caliciviruses to bind histo-blood group antigens and overcome a significant barrier to cross-species transmission. Additionally, we have shown that bat norovirus maintains antigenic epitopes similar to those seen with human noroviruses, providing further evidence of evolutionary descent. Our results reiterate the importance of surveillance of wild-animal populations, especially of bats, for novel viral pathogens.IMPORTANCE Caliciviruses are rapidly evolving viruses that cause pandemic outbreaks associated with significant morbidity and mortality globally. The animal reservoirs for human caliciviruses are unknown; bats represent critical reservoir species for several emerging and zoonotic diseases. Recent reports have identified several bat caliciviruses but have not characterized biological functions associated with disease risk, including their potential emergence in other mammalian populations. In this report, we identified a novel bat calicivirus that is most closely related to nonhuman primate caliciviruses. Using this new bat calicivirus and a second norovirus-like bat calicivirus capsid gene sequence, we generated virus-like particles that have host carbohydrate ligand binding patterns similar to those of human and animal noroviruses and that share antigens with human noroviruses. The similarities to human noroviruses with respect to binding patterns and antigenic epitopes illustrate the potential for bat caliciviruses to emerge in other species and the importance of pathogen surveillance in wild-animal populations.
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A metagenomic viral discovery approach identifies potential zoonotic and novel mammalian viruses in Neoromicia bats within South Africa. PLoS One 2018; 13:e0194527. [PMID: 29579103 PMCID: PMC5868816 DOI: 10.1371/journal.pone.0194527] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/05/2018] [Indexed: 01/02/2023] Open
Abstract
Species within the Neoromicia bat genus are abundant and widely distributed in Africa. It is common for these insectivorous bats to roost in anthropogenic structures in urban regions. Additionally, Neoromicia capensis have previously been identified as potential hosts for Middle East respiratory syndrome (MERS)-related coronaviruses. This study aimed to ascertain the gastrointestinal virome of these bats, as viruses excreted in fecal material or which may be replicating in rectal or intestinal tissues have the greatest opportunities of coming into contact with other hosts. Samples were collected in five regions of South Africa over eight years. Initial virome composition was determined by viral metagenomic sequencing by pooling samples and enriching for viral particles. Libraries were sequenced on the Illumina MiSeq and NextSeq500 platforms, producing a combined 37 million reads. Bioinformatics analysis of the high throughput sequencing data detected the full genome of a novel species of the Circoviridae family, and also identified sequence data from the Adenoviridae, Coronaviridae, Herpesviridae, Parvoviridae, Papillomaviridae, Phenuiviridae, and Picornaviridae families. Metagenomic sequencing data was insufficient to determine the viral diversity of certain families due to the fragmented coverage of genomes and lack of suitable sequencing depth, as some viruses were detected from the analysis of reads-data only. Follow up conventional PCR assays targeting conserved gene regions for the Adenoviridae, Coronaviridae, and Herpesviridae families were used to confirm metagenomic data and generate additional sequences to determine genetic diversity. The complete coding genome of a MERS-related coronavirus was recovered with additional amplicon sequencing on the MiSeq platform. The new genome shared 97.2% overall nucleotide identity to a previous Neoromicia-associated MERS-related virus, also from South Africa. Conventional PCR analysis detected diverse adenovirus and herpesvirus sequences that were widespread throughout Neoromicia populations in South Africa. Furthermore, similar adenovirus sequences were detected within these populations throughout several years. With the exception of the coronaviruses, the study represents the first report of sequence data from several viral families within a Southern African insectivorous bat genus; highlighting the need for continued investigations in this regard.
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López-Baucells A, Rocha R, Fernández-Llamazares Á. When bats go viral: negative framings in virological research imperil bat conservation. Mamm Rev 2017. [DOI: 10.1111/mam.12110] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Adrià López-Baucells
- Centre for Ecology, Evolution and Environmental Changes; University of Lisbon; C2 Building 1749-016 Lisbon Portugal
- Museum of Natural Sciences of Granollers; c/Palaudàries 102-Jardins Antoni Jonch Cuspinera 08402 Granollers Catalonia Spain
| | - Ricardo Rocha
- Conservation Science Group; University of Cambridge; Downing St. CB23EJ Cambridge UK
- Metapopulation Research Centre; Department of Biosciences; University of Helsinki; Viikinkaari 1 00790 Helsinki Finland
| | - Álvaro Fernández-Llamazares
- Metapopulation Research Centre; Department of Biosciences; University of Helsinki; Viikinkaari 1 00790 Helsinki Finland
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18
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Qi D, Shan T, Liu Z, Deng X, Zhang Z, Bi W, Owens JR, Feng F, Zheng L, Huang F, Delwart E, Hou R, Zhang W. A novel polyomavirus from the nasal cavity of a giant panda (Ailuropoda melanoleuca). Virol J 2017; 14:207. [PMID: 29078783 PMCID: PMC5658932 DOI: 10.1186/s12985-017-0867-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 10/11/2017] [Indexed: 02/07/2023] Open
Abstract
Background Polyomaviruses infect a wide variety of mammalian and avian hosts with a broad spectrum of outcomes including asymptomatic infection, acute systemic disease, and tumor induction. Methods Viral metagenomics and general PCR methods were used to detected viral nucleic acid in the samples from a diseased and healthy giant pandas. Results A novel polyomavirus, the giant panda polyomavirus 1 (GPPyV1) from the nasal cavity of a dead giant panda (Ailuropoda melanoleuca) was characterized. The GPPyV1 genome is 5144 bp in size and reveals five putative open-reading frames coding for the classic small and large T antigens in the early region, and the VP1, VP2 and VP3 capsid proteins in the late region. Phylogenetic analyses of the large T antigen of the GPPyV1 indicated GPPyV1 belonged to a putative new species within genus Deltapolyomavirus, clustering with four human polyomavirus species. The GPPyV1 VP1 and VP2 clustered with genus Alphapolyomavirus. Our epidemiologic study indicated that this novel polyomavirus was also detected in nasal swabs and fecal samples collected from captive healthy giant pandas. Conclusion A novel polyomavirus was detected in giant pandas and its complete genome was characterized, which may cause latency infection in giant pandas.
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Affiliation(s)
- Dunwu Qi
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, 610081, China.,Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Zhijian Liu
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, California, 94118, USA
| | - Zhihe Zhang
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, 610081, China
| | - Wenlei Bi
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, 610081, China
| | - Jacob Robert Owens
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, 610081, China
| | - Feifei Feng
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, 610081, China
| | - Lisong Zheng
- Liziping Nature Reserve, YaAn, Sichuan Province, Sichuan, 625499, China
| | - Feng Huang
- Liziping Nature Reserve, YaAn, Sichuan Province, Sichuan, 625499, China
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, California, 94118, USA
| | - Rong Hou
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, 610081, China.
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China.
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Carr M, Gonzalez G, Sasaki M, Dool SE, Ito K, Ishii A, Hang'ombe BM, Mweene AS, Teeling EC, Hall WW, Orba Y, Sawa H. Identification of the same polyomavirus species in different African horseshoe bat species is indicative of short-range host-switching events. J Gen Virol 2017; 98:2771-2785. [PMID: 28984241 DOI: 10.1099/jgv.0.000935] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Polyomaviruses (PyVs) are considered to be highly host-specific in different mammalian species, with no well-supported evidence for host-switching events. We examined the species diversity and host specificity of PyVs in horseshoe bats (Rhinolophus spp.), a broadly distributed and highly speciose mammalian genus. We annotated six PyV genomes, comprising four new PyV species, based on pairwise identity within the large T antigen (LTAg) coding region. Phylogenetic comparisons revealed two instances of highly related PyV species, one in each of the Alphapolyomavirus and Betapolyomavirus genera, present in different horseshoe bat host species (Rhinolophus blasii and R. simulator), suggestive of short-range host-switching events. The two pairs of Rhinolophus PyVs in different horseshoe bat host species were 99.9 and 88.8 % identical with each other over their respective LTAg coding sequences and thus constitute the same virus species. To corroborate the species identification of the bat hosts, we analysed mitochondrial cytb and a large nuclear intron dataset derived from six independent and neutrally evolving loci for bat taxa of interest. Bayesian estimates of the ages of the most recent common ancestors suggested that the near-identical and more distantly related PyV species diverged approximately 9.1E4 (5E3-2.8E5) and 9.9E6 (4E6-18E6) years before the present, respectively, in contrast to the divergence times of the bat host species: 12.4E6 (10.4E6-15.4E6). Our findings provide evidence that short-range host-switching of PyVs is possible in horseshoe bats, suggesting that PyV transmission between closely related mammalian species can occur.
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Affiliation(s)
- Michael Carr
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan.,National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - Gabriel Gonzalez
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Michihito Sasaki
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Serena E Dool
- Zoological Institute and Museum, University of Greifswald, Anklamer Street 20, D-17489 Greifswald, Germany
| | - Kimihito Ito
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Akihiro Ishii
- Hokudai Center for Zoonosis Control in Zambia, Research Center for Zoonosis Control, Hokkaido University, Lusaka, Zambia
| | - Bernard M Hang'ombe
- Department of Para-clinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Aaron S Mweene
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - William W Hall
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan.,Global Virus Network, Baltimore, MD 21201, USA
| | - Yasuko Orba
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Hirofumi Sawa
- Global Virus Network, Baltimore, MD 21201, USA.,Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan.,Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia.,Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
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20
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Viral metagenomics of six bat species in close contact with humans in southern China. Arch Virol 2017; 163:73-88. [PMID: 28983731 PMCID: PMC7086785 DOI: 10.1007/s00705-017-3570-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 09/14/2017] [Indexed: 01/28/2023]
Abstract
Accumulating studies have shown that bats could harbor various important pathogenic viruses that could be transmitted to humans and other animals. Extensive metagenomic studies of different organs/tissues from bats have revealed a large number of novel or divergent viruses. To elucidate viral diversity and epidemiological and phylogenetic characteristics, six pooled fecal samples from bats were generated (based on bat species and geographic regions characteristic for virome analysis). These contained 500 fecal samples from six bat species, collected in four geographic regions. Metagenomic analysis revealed a plethora of divergent viruses originally found in bats. Multiple contigs from influenza A virus and coronaviruses in bats shared high identity with those from humans, suggesting possible cross-species transmission, whereas a number of contigs, whose sequences were taxonomically classifiable within Alphapapillomavirus, Betaretrovirus, Alpharetrovirus, Varicellovirus, Cyprinivirus, Chlorovirus and Cucumovirus had low identity to viruses in existing databases, which indicated possible evolution of novel viral species. None of the established caliciviruses and picornaviruses were found in the 500 fecal specimens. Papillomaviruses with high amino acid identity were found in Scotophilus kuhlii and Rhinolophus blythi, challenging the hypotheses regarding the strict host specificity and co-evolution of papillomaviruses. Phylogenetic analysis showed that four bat rotavirus A strains might be tentative G3 strains, according to the Rotavirus Classification Working Group classification.
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Ricci A, Allende A, Bolton D, Chemaly M, Davies R, Fernandez Escamez PS, Herman L, Koutsoumanis K, Lindqvist R, Nørrung B, Robertson L, Ru G, Sanaa M, Simmons M, Skandamis P, Snary E, Speybroeck N, Ter Kuile B, Threlfall J, Wahlström H, Di Bartolo I, Johne R, Pavio N, Rutjes S, van der Poel W, Vasickova P, Hempen M, Messens W, Rizzi V, Latronico F, Girones R. Public health risks associated with hepatitis E virus (HEV) as a food-borne pathogen. EFSA J 2017; 15:e04886. [PMID: 32625551 PMCID: PMC7010180 DOI: 10.2903/j.efsa.2017.4886] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Hepatitis E virus (HEV) is an important infection in humans in EU/EEA countries, and over the last 10 years more than 21,000 acute clinical cases with 28 fatalities have been notified with an overall 10-fold increase in reported HEV cases; the majority (80%) of cases were reported from France, Germany and the UK. However, as infection in humans is not notifiable in all Member States, and surveillance differs between countries, the number of reported cases is not comparable and the true number of cases would probably be higher. Food-borne transmission of HEV appears to be a major route in Europe; pigs and wild boars are the main source of HEV. Outbreaks and sporadic cases have been identified in immune-competent persons as well as in recognised risk groups such as those with pre-existing liver damage, immunosuppressive illness or receiving immunosuppressive treatments. The opinion reviews current methods for the detection, identification, characterisation and tracing of HEV in food-producing animals and foods, reviews literature on HEV reservoirs and food-borne pathways, examines information on the epidemiology of HEV and its occurrence and persistence in foods, and investigates possible control measures along the food chain. Presently, the only efficient control option for HEV infection from consumption of meat, liver and products derived from animal reservoirs is sufficient heat treatment. The development of validated quantitative and qualitative detection methods, including infectivity assays and consensus molecular typing protocols, is required for the development of quantitative microbial risk assessments and efficient control measures. More research on the epidemiology and control of HEV in pig herds is required in order to minimise the proportion of pigs that remain viraemic or carry high levels of virus in intestinal contents at the time of slaughter. Consumption of raw pig, wild boar and deer meat products should be avoided.
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22
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Carr M, Gonzalez G, Sasaki M, Ito K, Ishii A, Hang’ombe BM, Mweene AS, Orba Y, Sawa H. Discovery of African bat polyomaviruses and infrequent recombination in the large T antigen in the Polyomaviridae. J Gen Virol 2017; 98:726-738. [DOI: 10.1099/jgv.0.000737] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Michael Carr
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - Gabriel Gonzalez
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Michihito Sasaki
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Kimihito Ito
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Akihiro Ishii
- Hokudai Center for Zoonosis Control in Zambia, Research Center for Zoonosis Control, Hokkaido University, Lusaka, Zambia
| | - Bernard M Hang’ombe
- Department of Para-clinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Aaron S Mweene
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Yasuko Orba
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Hirofumi Sawa
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
- Global Virus Network, Baltimore, Maryland 21201, USA
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
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23
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Yinda CK, Rector A, Zeller M, Conceição-Neto N, Heylen E, Maes P, Ghogomu SM, Van Ranst M, Matthijnssens J. A single bat species in Cameroon harbors multiple highly divergent papillomaviruses in stool identified by metagenomics analysis. ACTA ACUST UNITED AC 2016; 6:74-80. [PMID: 32289018 PMCID: PMC7103942 DOI: 10.1016/j.virep.2016.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 08/18/2016] [Accepted: 08/18/2016] [Indexed: 01/28/2023]
Abstract
A number of PVs have been described in bats but to the best of our knowledge not from feces. Using a previously described NetoVIR protocol, Eidolon helvum pooled fecal samples (Eh) were treated and sequenced by Illumina next generation sequencing technology. Two complete genomes of novel PVs (EhPV2 and EhPV3) and 3 partial sequences (BATPV61, BATPV890a and BATPV890b) were obtained and analysis showed that the EhPV2 and EhPV3 major capsid proteins cluster with and share 60-64% nucleotide identity with that of Rousettus aegyptiacus PV1, thus representing new species of PVs within the genus Psipapillomavirus. The other PVs clustered in different branches of our phylogenetic tree and may potentially represent novel species and/or genera. This points to the vast diversity of PVs in bats and in Eidolon helvum bats in particular, therefore adding support to the current concept that PV evolution is more complex than merely strict PV-host co-evolution.
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Affiliation(s)
- Claude Kwe Yinda
- KULeuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, Leuven, Belgium
- KULeuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium
| | - Annabel Rector
- KULeuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium
| | - Mark Zeller
- KULeuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Nádia Conceição-Neto
- KULeuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, Leuven, Belgium
- KULeuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium
| | - Elisabeth Heylen
- KULeuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Piet Maes
- KULeuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium
| | - Stephen Mbigha Ghogomu
- University of Buea, Department of Biochemistry and Molecular Biology, Biotechnology Unit, Molecular and Cell Biology Laboratory, Buea, Cameroon
| | - Marc Van Ranst
- KULeuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium
| | - Jelle Matthijnssens
- KULeuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, Leuven, Belgium
- Corresponding author.
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Genetic Characterization of Providence Virus Isolated from Bat Guano in Hungary. GENOME ANNOUNCEMENTS 2016; 4:4/3/e00403-16. [PMID: 27198029 PMCID: PMC4888983 DOI: 10.1128/genomea.00403-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
We report the complete genome sequence and genetic characterization of a novel strain of Providence virus, detected in Barbastella barbastellus bat guano, collected in Hungary in 2014. Our data may facilitate the understanding of the evolutionary processes of this unique viral family of Carmotetraviridae.
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Kemenesi G, Gellért Á, Dallos B, Görföl T, Boldogh S, Estók P, Marton S, Oldal M, Martella V, Bányai K, Jakab F. Sequencing and molecular modeling identifies candidate members of Caliciviridae family in bats. INFECTION GENETICS AND EVOLUTION 2016; 41:227-232. [PMID: 27085289 PMCID: PMC7172268 DOI: 10.1016/j.meegid.2016.04.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 04/05/2016] [Accepted: 04/06/2016] [Indexed: 12/20/2022]
Abstract
Emerging viral diseases represent an ongoing challenge for globalized world and bats constitute an immense, partially explored, reservoir of potentially zoonotic viruses. Caliciviruses are important human and animal pathogens and, as observed for human noroviruses, they may impact on human health on a global scale. By screening fecal samples of bats in Hungary, calicivirus RNA was identified in the samples of Myotis daubentonii and Eptesicus serotinus bats. In order to characterize more in detail the bat caliciviruses, large portions of the genome sequence of the viruses were determined. Phylogenetic analyses and molecular modeling identified firmly the two viruses as candidate members within the Caliciviridae family, with one calicivirus strain resembling members of the Sapovirus genus and the other bat calicivirus being more related to porcine caliciviruses of the proposed genus Valovirus. This data serves the effort for detecting reservoir hosts for potential emerging viruses and recognize important evolutionary relationships. Two novel bat caliciviruses were genetically characterized. Mature viral capsids were molecularly modeled. Bat caliciviruses are highly heterogeneous genetically. The two novel viruses are genetically related to valoviruses and sapoviruses. New sequences were most closely related to Chinese sequences.
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Affiliation(s)
- Gábor Kemenesi
- Virological Research Group, János Szentágothai Research Center, University of Pécs, Pécs, Hungary; Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Ákos Gellért
- Department of Applied Genomics, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Bianka Dallos
- Virological Research Group, János Szentágothai Research Center, University of Pécs, Pécs, Hungary; Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Tamás Görföl
- Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary; Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | | | - Péter Estók
- Department of Zoology, Eszterházy Károly College, Eger, Hungary
| | - Szilvia Marton
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Miklós Oldal
- Virological Research Group, János Szentágothai Research Center, University of Pécs, Pécs, Hungary; Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Vito Martella
- Dipartimento di Medicina Veterinaria, Universitá Aldo Moro di Bari, Valenzano, Italy
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Ferenc Jakab
- Virological Research Group, János Szentágothai Research Center, University of Pécs, Pécs, Hungary; Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary.
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Nouri S, Salem N, Nigg JC, Falk BW. Diverse Array of New Viral Sequences Identified in Worldwide Populations of the Asian Citrus Psyllid (Diaphorina citri) Using Viral Metagenomics. J Virol 2015; 90:2434-45. [PMID: 26676774 PMCID: PMC4810699 DOI: 10.1128/jvi.02793-15] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 12/08/2015] [Indexed: 12/26/2022] Open
Abstract
UNLABELLED The Asian citrus psyllid, Diaphorina citri, is the natural vector of the causal agent of Huanglongbing (HLB), or citrus greening disease. Together; HLB and D. citri represent a major threat to world citrus production. As there is no cure for HLB, insect vector management is considered one strategy to help control the disease, and D. citri viruses might be useful. In this study, we used a metagenomic approach to analyze viral sequences associated with the global population of D. citri. By sequencing small RNAs and the transcriptome coupled with bioinformatics analysis, we showed that the virus-like sequences of D. citri are diverse. We identified novel viral sequences belonging to the picornavirus superfamily, the Reoviridae, Parvoviridae, and Bunyaviridae families, and an unclassified positive-sense single-stranded RNA virus. Moreover, a Wolbachia prophage-related sequence was identified. This is the first comprehensive survey to assess the viral community from worldwide populations of an agricultural insect pest. Our results provide valuable information on new putative viruses, some of which may have the potential to be used as biocontrol agents. IMPORTANCE Insects have the most species of all animals, and are hosts to, and vectors of, a great variety of known and unknown viruses. Some of these most likely have the potential to be important fundamental and/or practical resources. In this study, we used high-throughput next-generation sequencing (NGS) technology and bioinformatics analysis to identify putative viruses associated with Diaphorina citri, the Asian citrus psyllid. D. citri is the vector of the bacterium causing Huanglongbing (HLB), currently the most serious threat to citrus worldwide. Here, we report several novel viral sequences associated with D. citri.
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Affiliation(s)
- Shahideh Nouri
- Department of Plant Pathology, University of California, Davis, California, USA
| | - Nidá Salem
- Department of Plant Protection, The University of Jordan, Amman, Jordan
| | - Jared C Nigg
- Department of Plant Pathology, University of California, Davis, California, USA
| | - Bryce W Falk
- Department of Plant Pathology, University of California, Davis, California, USA
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