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Gong HY, Chen RX, Tan SM, Wang X, Chen JM, Zhang YL, Liao M. Viruses Identified in Shrews ( Soricidae) and Their Biomedical Significance. Viruses 2024; 16:1441. [PMID: 39339918 PMCID: PMC11437491 DOI: 10.3390/v16091441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Revised: 09/06/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
Shrews (Soricidae) are common small wild mammals. Some species of shrews, such as Asian house shrews (Suncus murinus), have a significant overlap in their habitats with humans and domestic animals. Currently, over 190 species of viruses in 32 families, including Adenoviridae, Arenaviridae, Arteriviridae, Astroviridae, Anelloviridae, Bornaviridae, Caliciviridae, Chuviridae, Coronaviridae, Filoviridae, Flaviviridae, Hantaviridae, Hepadnaviridae, Hepeviridae, Nairoviridae, Nodaviridae, Orthoherpesviridae, Orthomyxoviridae, Paramyxoviridae, Parvoviridae, Phenuiviridae, Picobirnaviridae, Picornaviridae, Polyomaviridae, Poxviridae, Rhabdoviridae, Sedoreoviridae, Spinareoviridae, and three unclassified families, have been identified in shrews. Diverse shrew viruses, such as Borna disease virus 1, Langya virus, and severe fever with thrombocytopenia syndrome virus, cause diseases in humans and/or domestic animals, posing significant threats to public health and animal health. This review compiled fundamental information about shrews and provided a comprehensive summary of the viruses that have been detected in shrews, with the aim of facilitating a deep understanding of shrews and the diversity, epidemiology, and risks of their viruses.
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Affiliation(s)
- Huan-Yu Gong
- School of Animal Science and Technology, Foshan University, Foshan 528225, China
| | - Rui-Xu Chen
- School of Animal Science and Technology, Foshan University, Foshan 528225, China
| | - Su-Mei Tan
- School of Animal Science and Technology, Foshan University, Foshan 528225, China
| | - Xiu Wang
- School of Animal Science and Technology, Foshan University, Foshan 528225, China
| | - Ji-Ming Chen
- School of Animal Science and Technology, Foshan University, Foshan 528225, China
| | - Yuan-Long Zhang
- Guangdong Center for Animal Disease Prevention and Control, Guangzhou 510230, China
| | - Ming Liao
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510230, China
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Omoga DCA, Tchouassi DP, Venter M, Ogola EO, Rotich G, Muthoni JN, Ondifu DO, Torto B, Junglen S, Sang R. Divergent Hantavirus in Somali Shrews ( Crocidura somalica) in the Semi-Arid North Rift, Kenya. Pathogens 2023; 12:pathogens12050685. [PMID: 37242355 DOI: 10.3390/pathogens12050685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/21/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Hantaviruses are zoonotic rodent-borne viruses that are known to infect humans and cause various symptoms of disease, including hemorrhagic fever with renal and cardiopulmonary syndromes. They have a segmented single-stranded, enveloped, negative-sense RNA genome and are widely distributed. This study aimed to investigate the circulation of rodent-borne hantaviruses in peridomestic rodents and shrews in two semi-arid ecologies within the Kenyan Rift Valley. The small mammals were trapped using baited folding Sherman traps set within and around houses, then they were sedated and euthanatized through cervical dislocation before collecting blood and tissue samples (liver, kidney, spleen, and lungs). Tissue samples were screened with pan-hantavirus PCR primers, targeting the large genome segment (L) encoding the RNA-dependent RNA polymerase (RdRp). Eleven of the small mammals captured were shrews (11/489, 2.5%) and 478 (97.5%) were rodents. A cytochrome b gene-based genetic assay for shrew identification confirmed the eleven shrews sampled to be Crocidura somalica. Hantavirus RNA was detected in three (3/11, 27%) shrews from Baringo County. The sequences showed 93-97% nucleotide and 96-99% amino acid identities among each other, as well as 74-76% nucleotide and 79-83% amino acid identities to other shrew-borne hantaviruses, such as Tanganya virus (TNGV). The detected viruses formed a monophyletic clade with shrew-borne hantaviruses from other parts of Africa. To our knowledge, this constitutes the first report published on the circulation of hantaviruses in shrews in Kenya.
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Affiliation(s)
- Dorcus C A Omoga
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
- Zoonotic arbo and Respiratory Virus Research Program, Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health, University of Pretoria, Gezina 0031, South Africa
| | - David P Tchouassi
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Marietjie Venter
- Zoonotic arbo and Respiratory Virus Research Program, Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health, University of Pretoria, Gezina 0031, South Africa
| | - Edwin O Ogola
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Gilbert Rotich
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Joseph N Muthoni
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Dickens O Ondifu
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Baldwyn Torto
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Sandra Junglen
- Institute of Virology, Charité Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Rosemary Sang
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
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3
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Kuhn JH, Bradfute SB, Calisher CH, Klempa B, Klingström J, Laenen L, Palacios G, Schmaljohn CS, Tischler ND, Maes P. Pending Reorganization of Hantaviridae to Include Only Completely Sequenced Viruses: A Call to Action. Viruses 2023; 15:660. [PMID: 36992369 PMCID: PMC10059669 DOI: 10.3390/v15030660] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 03/06/2023] Open
Abstract
The official classification of newly discovered or long-known unassigned viruses by the International Committee on Taxonomy of Viruses (ICTV) requires the deposition of coding-complete or -near-complete virus genome sequences in GenBank to fulfill a requirement of the taxonomic proposal (TaxoProp) process. However, this requirement is fairly new; thus, genomic sequence information is fragmented or absent for many already-classified viruses. As a result, taxon-wide modern phylogenetic analyses are often challenging, if not impossible. This problem is particularly eminent among viruses with segmented genomes, such as bunyavirals, which were frequently classified solely based on single-segment sequence information. To solve this issue for one bunyaviral family, Hantaviridae, we call on the community to provide additional sequence information for incompletely sequenced classified viruses by mid-June 2023. Such sequence information may be sufficient to prevent their possible declassification during the ongoing efforts to establish a coherent, consistent, and evolution-based hantavirid taxonomy.
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Affiliation(s)
- Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Steven B. Bradfute
- Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | | | - Boris Klempa
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, 84505 Bratislava, Slovakia
| | - Jonas Klingström
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
| | - Lies Laenen
- Zoonotic Infectious Diseases Unit, KU Leuven, Rega Institute, 3000 Leuven, Belgium
- Belgium Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Gustavo Palacios
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Connie S. Schmaljohn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Nicole D. Tischler
- Laboratorio de Virología Molecular, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago 8581151, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago 7510157, Chile
| | - Piet Maes
- Zoonotic Infectious Diseases Unit, KU Leuven, Rega Institute, 3000 Leuven, Belgium
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Kiwira Virus, a Newfound Hantavirus Discovered in Free-tailed Bats (Molossidae) in East and Central Africa. Viruses 2022; 14:v14112368. [PMID: 36366466 PMCID: PMC9693593 DOI: 10.3390/v14112368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/13/2022] [Accepted: 10/25/2022] [Indexed: 01/31/2023] Open
Abstract
A novel hantavirus, named Kiwira virus, was molecularly detected in six Angolan free-tailed bats (Mops condylurus, family Molossidae) captured in Tanzania and in one free-tailed bat in the Democratic Republic of Congo. Hantavirus RNA was found in different organs, with the highest loads in the spleen. Nucleotide sequences of large parts of the genomic S and L segments were determined by in-solution hybridisation capture and high throughput sequencing. Phylogenetic analyses placed Kiwira virus into the genus Mobatvirus of the family Hantaviridae, with the bat-infecting Quezon virus and Robina virus as closest relatives. The detection of several infected individuals in two African countries, including animals with systemic hantavirus infection, provides evidence of active replication and a stable circulation of Kiwira virus in M. condylurus bats and points to this species as a natural host. Since the M. condylurus home range covers large regions of Sub-Saharan Africa and the species is known to roost inside and around human dwellings, a potential spillover of the Kiwira virus to humans must be considered.
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Ogola JG, Alburkat H, Masika M, Korhonen E, Uusitalo R, Nyaga P, Anzala O, Vapalahti O, Sironen T, Forbes KM. Seroevidence of Zoonotic Viruses in Rodents and Humans in Kibera Informal Settlement, Nairobi, Kenya. Vector Borne Zoonotic Dis 2021; 21:973-978. [DOI: 10.1089/vbz.2021.0046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Joseph Ganda Ogola
- Department of Medical Microbiology, KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Hussein Alburkat
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Moses Masika
- Department of Medical Microbiology, KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Essi Korhonen
- Department of Virology, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Ruut Uusitalo
- Department of Virology, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
| | - Philip Nyaga
- Department of Pathology, Microbiology and Parasitology, University of Nairobi, Nairobi, Kenya
| | - Omu Anzala
- Department of Medical Microbiology, KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Olli Vapalahti
- Department of Virology, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Tarja Sironen
- Department of Virology, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Kristian M. Forbes
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
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Těšíková J, Krásová J, Goüy de Bellocq J. Multiple Mammarenaviruses Circulating in Angolan Rodents. Viruses 2021; 13:982. [PMID: 34070551 PMCID: PMC8227972 DOI: 10.3390/v13060982] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 12/14/2022] Open
Abstract
Rodents are a speciose group of mammals with strong zoonotic potential. Some parts of Africa are still underexplored for the occurrence of rodent-borne pathogens, despite this high potential. Angola is at the convergence of three major biogeographical regions of sub-Saharan Africa, each harbouring a specific rodent community. This rodent-rich area is, therefore, strategic for studying the diversity and evolution of rodent-borne viruses. In this study we examined 290 small mammals, almost all rodents, for the presence of mammarenavirus and hantavirus RNA. While no hantavirus was detected, we found three rodent species positive for distinct mammarenaviruses with a particularly high prevalence in Namaqua rock rats (Micaelamys namaquensis). We characterised four complete virus genomes, which showed typical mammarenavirus organisation. Phylogenetic and genetic distance analyses revealed: (i) the presence of a significantly divergent strain of Luna virus in Angolan representatives of the ubiquitous Natal multimammate mouse (Mastomys natalensis), (ii) a novel Okahandja-related virus associated with the Angolan lineage of Micaelamys namaquensis for which we propose the name Bitu virus (BITV) and (iii) the occurrence of a novel Mobala-like mammarenavirus in the grey-bellied pygmy mouse (Mus triton) for which we propose the name Kwanza virus (KWAV). This high virus diversity in a limited host sample size and in a relatively small geographical area supports the idea that Angola is a hotspot for mammarenavirus diversity.
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Affiliation(s)
- Jana Těšíková
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic; (J.K.); (J.G.B.)
- Department of Botany and Zoology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Jarmila Krásová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic; (J.K.); (J.G.B.)
- Department of Zoology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Joëlle Goüy de Bellocq
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic; (J.K.); (J.G.B.)
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic
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Abstract
Identifying the animal reservoirs from which zoonotic viruses will likely emerge is central to understanding the determinants of disease emergence. Accordingly, there has been an increase in studies attempting zoonotic “risk assessment.” Herein, we demonstrate that the virological data on which these analyses are conducted are incomplete, biased, and rapidly changing with ongoing virus discovery. Together, these shortcomings suggest that attempts to assess zoonotic risk using available virological data are likely to be inaccurate and largely only identify those host taxa that have been studied most extensively. We suggest that virus surveillance at the human–animal interface may be more productive. Determining which organisms harbour viruses that could potentially infect humans is of great topical interest. This Essay demonstrates that the data on which such zoonotic risk assessments are conducted are incomplete, biased, and rapidly changing with ongoing virus discovery.
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Affiliation(s)
- Michelle Wille
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia
- * E-mail:
| | - Jemma L. Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia
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8
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Kikuchi F, Aoki K, Ohdachi SD, Tsuchiya K, Motokawa M, Jogahara T, Sơn NT, Bawm S, Lin KS, Thwe TL, Gamage CD, Ranorosoa MC, Omar H, Maryanto I, Suzuki H, Tanaka-Taya K, Morikawa S, Mizutani T, Suzuki M, Yanagihara R, Arai S. Genetic Diversity and Phylogeography of Thottapalayam thottimvirus ( Hantaviridae) in Asian House Shrew ( Suncus murinus) in Eurasia. Front Cell Infect Microbiol 2020; 10:438. [PMID: 32974220 PMCID: PMC7481397 DOI: 10.3389/fcimb.2020.00438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/16/2020] [Indexed: 11/27/2022] Open
Abstract
Murid and cricetid rodents were previously believed to be the principal reservoir hosts of hantaviruses. Recently, however, multiple newfound hantaviruses have been discovered in shrews, moles, and bats, suggesting a complex evolutionary history. Little is known about the genetic diversity and geographic distribution of the prototype shrew-borne hantavirus, Thottapalayam thottimvirus (TPMV), carried by the Asian house shrew (Suncus murinus), which is widespread in Asia, Africa, and the Middle East. Comparison of TPMV genomic sequences from two Asian house shrews captured in Myanmar and Pakistan with TPMV strains in GenBank revealed that the Myanmar TPMV strain (H2763) was closely related to the prototype TPMV strain (VRC66412) from India. In the L-segment tree, on the other hand, the Pakistan TPMV strain (PK3629) appeared to be the most divergent, followed by TPMV strains from Nepal, then the Indian-Myanmar strains, and finally TPMV strains from China. The Myanmar strain of TPMV showed sequence similarity of 79.3-96.1% at the nucleotide level, but the deduced amino acid sequences showed a high degree of conservation of more than 94% with TPMV strains from Nepal, India, Pakistan, and China. Cophylogenetic analysis of host cytochrome b and TPMV strains suggested that the Pakistan TPMV strain was mismatched. Phylogenetic trees, based on host cytochrome b and cytochrome c oxidase subunit I genes of mitochondrial DNA, and on host recombination activating gene 1 of nuclear DNA, suggested that the Asian house shrew and Asian highland shrew (Suncus montanus) comprised a species complex. Overall, the geographic-specific clustering of TPMV strains in Asian countries suggested local host-specific adaptation. Additional in-depth studies are warranted to ascertain if TPMV originated in Asian house shrews on the Indian subcontinent.
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Affiliation(s)
- Fuka Kikuchi
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Chemistry, Faculty of Science, Tokyo University of Science, Tokyo, Japan
- Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Keita Aoki
- Department of Chemistry, Faculty of Science, Tokyo University of Science, Tokyo, Japan
| | - Satoshi D. Ohdachi
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | | | | | - Takamichi Jogahara
- Faculty of Law, Economics and Management, Okinawa University, Naha, Japan
| | - Nguyễn Trường Sơn
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Saw Bawm
- Department of Pharmacology and Parasitology, University of Veterinary Science, Nay Pyi Taw, Myanmar
| | - Kyaw San Lin
- Department of Aquaculture and Aquatic Disease, University of Veterinary Science, Nay Pyi Taw, Myanmar
| | - Thida Lay Thwe
- Department of Zoology, Yangon University of Distance Education, Yangon, Myanmar
| | - Chandika D. Gamage
- Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka
| | - Marie Claudine Ranorosoa
- Mention Foresterie et Environnement, Ecole Supérieur des Sciences Agronomiques, Université d'Antananarivo, Antananarivo, Madagascar
| | - Hasmahzaiti Omar
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Ibnu Maryanto
- Research Centre for Biology, Indonesian Institute of Sciences (LIPI), Bogor, Indonesia
| | - Hitoshi Suzuki
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan
| | - Keiko Tanaka-Taya
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shigeru Morikawa
- Department of Microbiology, Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Japan
| | - Tetsuya Mizutani
- Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Motoi Suzuki
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Richard Yanagihara
- Pacific Center for Emerging Infectious Diseases Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Satoru Arai
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
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Li N, Li A, Liu Y, Wu W, Li C, Yu D, Zhu Y, Li J, Li D, Wang S, Liang M. Genetic diversity and evolution of Hantaan virus in China and its neighbors. PLoS Negl Trop Dis 2020; 14:e0008090. [PMID: 32817670 PMCID: PMC7462299 DOI: 10.1371/journal.pntd.0008090] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 09/01/2020] [Accepted: 07/08/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Hantaan virus (HTNV; family Hantaviridae, order Bunyavirales) causes hemorrhagic fever with renal syndrome (HFRS), which has raised serious concerns in Eurasia, especially in China, Russia, and South Korea. Previous studies reported genetic diversity and phylogenetic features of HTNV in different parts of China, but the analyses from the holistic perspective are rare. METHODOLOGY AND PRINCIPAL FINDINGS To better understand HTNV genetic diversity and gene evolution, we analyzed all available complete sequences derived from the small (S) and medium (M) segments with bioinformatic tools. Eleven phylogenetic groups were defined and showed geographic clustering; 42 significant amino acid variant sites were found, and 19 of them were located in immune epitopes; nine recombinant events and eight reassortments with highly divergent sequences were found and analyzed. We found that sequences from Guizhou showed high genetic divergence, contributing to multiple lineages of the phylogenetic tree and also to the recombination and reassortment events. Bayesian stochastic search variable selection analysis revealed that Heilongjiang, Shaanxi, and Guizhou played important roles in HTNV evolution and migration; the virus may originate from Zhejiang Province in the eastern part of China; and the virus population size expanded from the 1980s to 1990s. CONCLUSIONS/SIGNIFICANCE These findings revealed the original and evolutionary features of HTNV, which will help to illustrate hantavirus epidemic trends, thus aiding in disease control and prevention.
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Affiliation(s)
- Naizhe Li
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Aqian Li
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yang Liu
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wei Wu
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Chuan Li
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dongyang Yu
- Department of Microbiology, Anhui Medical University, Hefei, China
| | - Yu Zhu
- Department of Microbiology, Anhui Medical University, Hefei, China
| | - Jiandong Li
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dexin Li
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shiwen Wang
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- China CDC-WIV Joint Research Center for Emerging Diseases and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, P. R. China
- * E-mail: (SW); (ML)
| | - Mifang Liang
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- China CDC-WIV Joint Research Center for Emerging Diseases and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, P. R. China
- * E-mail: (SW); (ML)
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10
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Kang HJ, Gu SH, Yashina LN, Cook JA, Yanagihara R. Highly Divergent Genetic Variants of Soricid-Borne Altai Virus ( Hantaviridae) in Eurasia Suggest Ancient Host-Switching Events. Viruses 2019; 11:E857. [PMID: 31540127 PMCID: PMC6783933 DOI: 10.3390/v11090857] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/08/2019] [Accepted: 09/12/2019] [Indexed: 12/31/2022] Open
Abstract
With the recent discovery of genetically distinct hantaviruses (family Hantaviridae) in shrews (order Eulipotyphla, family Soricidae), the once-conventional view that rodents (order Rodentia) served as the primordial reservoir hosts now appears improbable. The newly identified soricid-borne hantaviruses generally demonstrate well-resolved lineages organized according to host taxa and geographic origin. However, beginning in 2007, we detected sequences that did not conform to the prototypic hantaviruses associated with their soricid host species and/or geographic locations. That is, Eurasian common shrews (Sorexaraneus), captured in Hungary and Russia, were found to harbor hantaviruses belonging to two separate and highly divergent lineages. We have since accumulated additional examples of these highly distinctive hantavirus sequences in the Laxmann's shrew (Sorexcaecutiens), flat-skulled shrew (Sorexroboratus) and Eurasian least shrew (Sorexminutissimus), captured at the same time and in the same location in the Sakha Republic in Far Eastern Russia. Pair-wise alignment and phylogenetic analysis of partial and full-length S-, M- and/or L-segment sequences indicate that a distinct hantavirus species related to Altai virus (ALTV), first reported in a Eurasian common shrew from Western Siberia, was being maintained in these closely related syntopic soricine shrew species. These findings suggest that genetic variants of ALTV might have resulted from ancient host-switching events with subsequent diversification within the Soricini tribe in Eurasia.
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Affiliation(s)
- Hae Ji Kang
- John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA.
| | - Se Hun Gu
- John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA.
| | - Liudmila N Yashina
- State Research Center of Virology and Biotechnology, "Vector", Koltsovo 630559, Russia.
| | - Joseph A Cook
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA.
| | - Richard Yanagihara
- John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA.
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11
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Meheretu Y, Stanley WT, Craig EW, Goüy de Bellocq J, Bryja J, Leirs H, Pahlmann M, Günther S. Tigray Orthohantavirus Infects Two Related Rodent Species Adapted to Different Elevations in Ethiopia. Vector Borne Zoonotic Dis 2019; 19:950-953. [PMID: 31355714 PMCID: PMC6882452 DOI: 10.1089/vbz.2019.2452] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Orthohantaviruses are RNA viruses that some members are known to cause severe zoonotic diseases in humans. Orthohantaviruses are hosted by rodents, soricomorphs (shrews and moles), and bats. Only two orthohantaviruses associated with murid rodents are known in Africa, Sangassou orthohantavirus (SANGV) in two species of African wood mice (Hylomyscus), and Tigray orthohantavirus (TIGV) in the Ethiopian white-footed rat (Stenocephalemys albipes). In this article, we report evidence that, like SANGV, two strains of TIGV occur in two genetically related rodent species, S. albipes and S. sp. A, occupying different elevational zones in the same mountain. Investigating the other members of the genus Stenocephalemys for TIGV could reveal the real diversity of TIGV in the genus.
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Affiliation(s)
- Yonas Meheretu
- Department of Biology and Institute of Mountain Research and Development, Mekelle University, Mekelle Ethiopia
| | | | - Evan W Craig
- Field Museum of Natural History, Chicago, Illinois.,Environmental Studies, Antioch University New England, Keene, New Hampshire
| | - Joëlle Goüy de Bellocq
- Department of Population Biology, Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
| | - Josef Bryja
- Department of Population Biology, Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
| | - Herwig Leirs
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | - Meike Pahlmann
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Stephan Günther
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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12
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Igbokwe J, Nicolas V, Oyeyiola A, Obadare A, Adesina AS, Awodiran MO, Van Houtte N, Fichet-Calvet E, Verheyen E, Olayemi A. Molecular taxonomy of Crocidura species (Eulipotyphla: Soricidae) in a key biogeographical region for African shrews, Nigeria. C R Biol 2019; 342:108-117. [PMID: 31056422 DOI: 10.1016/j.crvi.2019.03.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 12/20/2022]
Abstract
The taxonomy of African shrew species is still unresolved due to their conserved morphology. This also affects knowledge concerning their geographic distribution. In Nigeria, using mitochondrial Cytochrome b gene sequences, we carried out a survey for shrews from the genus Crocidura across various ecological zones to determine taxa that are present and also to assess their phylogeographic structure. Our analyses include 183 specimens collected with Sherman traps from 19 localities around the country. We detected six taxa: Crocidura olivieri lineages II, III and IV, C. hildegardeae, C. jouvenetae, and C. foxi. Among these, C. hildegardeae and C. jouvenetae are reported in Nigeria for the first time. Phylogenetic comparison of our genetic sequences to those generated from other parts of Africa demonstrate that all species in our study, as currently defined, are in need of taxonomic revision. Geographically, Nigeria seems to represent the easternmost boundary for C. olivieri lineage II and C. jouvenetae, and the western distribution limit of C. olivieri lineage IV and C. hildegardeae. The Niger River appears to be the most significant topographical barrier restricting these taxa. This information is vital to preserving the diversity but also managing the epidemiological potential of these small mammals.
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Affiliation(s)
- Joseph Igbokwe
- Department of Zoology, Obafemi Awolowo University, HO 220005 Ile Ife, Nigeria.
| | - Violaine Nicolas
- Institut de Systématique, Évolution, Biodiversité, ISYEB, UMR 7205 CNRS, MNHN, UPMC, EPHE, Muséum National d'Histoire Naturelle, Sorbonne Universités, 57 rue Cuvier, CP 51, Sorbonne, France.
| | - Akinlabi Oyeyiola
- Natural History Museum, Obafemi Awolowo University, HO 220005 Ile Ife, Nigeria.
| | - Adeoba Obadare
- Natural History Museum, Obafemi Awolowo University, HO 220005 Ile Ife, Nigeria.
| | - Adetunji Samuel Adesina
- Department of Biochemistry and Molecular Biology, Obafemi Awolowo University, HO 220005, Ile Ife, Nigeria.
| | | | - Natalie Van Houtte
- Biology Department, University of Antwerpen, Evolutionary Ecology Group, Universiteitsplein 1, B-2610 Wilrijk, Belgium.
| | - Elisabeth Fichet-Calvet
- Bernhard-Nocht Institute of Tropical Medicine, Bernhard-Nocht-Straße 74, 20359 Hamburg, Germany.
| | - Erik Verheyen
- Biology Department, University of Antwerpen, Evolutionary Ecology Group, Universiteitsplein 1, B-2610 Wilrijk, Belgium; Royal Belgian Institute of Natural Sciences, Operational Direction Taxonomy and Phylogeny, Molecular Laboratory, Vautierstraat 29, 1000 Brussels, Belgium.
| | - Ayodeji Olayemi
- Natural History Museum, Obafemi Awolowo University, HO 220005 Ile Ife, Nigeria.
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13
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Arai S, Kikuchi F, Bawm S, Sơn NT, Lin KS, Tú VT, Aoki K, Tsuchiya K, Tanaka-Taya K, Morikawa S, Oishi K, Yanagihara R. Molecular Phylogeny of Mobatviruses ( Hantaviridae) in Myanmar and Vietnam. Viruses 2019; 11:E228. [PMID: 30866403 PMCID: PMC6466252 DOI: 10.3390/v11030228] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 12/11/2022] Open
Abstract
The discovery of highly divergent lineages of hantaviruses (family Hantaviridae) in shrews, moles, and bats of multiple species raises the possibility that non-rodent hosts may have played a significant role in their evolutionary history. To further investigate this prospect, total RNA was extracted from RNAlater®-preserved lung tissues of 277 bats (representing five families, 14 genera and 40 species), captured in Myanmar and Vietnam during 2013⁻2016. Hantavirus RNA was detected in two of 15 black-bearded tomb bats (Taphozous melanopogon) and two of 26 Pomona roundleaf bats (Hipposideros pomona) in Myanmar, and in three of six ashy leaf-nosed bats (Hipposideros cineraceus) in Vietnam. Pair-wise alignment and comparison of coding regions of the S, M, and L segments of hantaviruses from Taphozous and Hipposideros bats revealed high nucleotide and amino acid sequence similarities to prototype Láibīn virus (LAIV) and Xuân Sơn virus (XSV), respectively. Phylogenetic analyses, generated by maximum-likelihood and Bayesian methods, showed a geographic clustering of LAIV strains from China and Myanmar, but not of XSV strains from China and Vietnam. These findings confirm that the black-bearded tomb bat is the natural reservoir of LAIV, and that more than one species of Hipposideros bats can host XSV.
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Affiliation(s)
- Satoru Arai
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan.
| | - Fuka Kikuchi
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan.
- Department of Chemistry, Faculty of Science, Tokyo University of Science, Tokyo 162-8601, Japan.
| | - Saw Bawm
- Department of Pharmacology and Parasitology, University of Veterinary Science, Yezin, Nay Pyi Taw 15013, Myanmar.
| | - Nguyễn Trường Sơn
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
| | - Kyaw San Lin
- Department of Aquaculture and Aquatic Disease, University of Veterinary Science, Yezin, Nay Pyi Taw 15013, Myanmar.
| | - Vương Tân Tú
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
| | - Keita Aoki
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan.
- Department of Liberal Arts, Faculty of Science, Tokyo University of Science, Tokyo 162-8601, Japan.
| | - Kimiyuki Tsuchiya
- Laboratory of Bioresources, Applied Biology Co., Ltd., Tokyo 107-0062, Japan.
| | - Keiko Tanaka-Taya
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan.
| | - Shigeru Morikawa
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo 162-8640, Japan.
| | - Kazunori Oishi
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan.
| | - Richard Yanagihara
- Pacific Center for Emerging Infectious Diseases Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA.
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14
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First serological evidence of hantavirus among febrile patients in Mozambique. Int J Infect Dis 2017; 61:51-55. [DOI: 10.1016/j.ijid.2017.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 12/26/2022] Open
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15
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Těšíková J, Bryjová A, Bryja J, Lavrenchenko LA, Goüy de Bellocq J. Hantavirus Strains in East Africa Related to Western African Hantaviruses. Vector Borne Zoonotic Dis 2017; 17:278-280. [DOI: 10.1089/vbz.2016.2022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jana Těšíková
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Anna Bryjová
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Josef Bryja
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | | | - Joëlle Goüy de Bellocq
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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16
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Goüy de Bellocq J, Těšíková J, Meheretu Y, Čížková D, Bryjová A, Leirs H, Bryja J. Complete genome characterisation and phylogenetic position of Tigray hantavirus from the Ethiopian white-footed mouse, Stenocephalemys albipes. INFECTION GENETICS AND EVOLUTION 2016; 45:242-245. [PMID: 27619058 DOI: 10.1016/j.meegid.2016.09.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/08/2016] [Accepted: 09/08/2016] [Indexed: 11/16/2022]
Abstract
Hantaviruses, well-known human pathogens, have only recently been identified on the African continent. Tigray virus (TIGV) was found in Ethiopia in 2012 in a Murinae species, Stenocephalemys albipes, but the genetic data obtained at that time were too limited to correctly assess its phylogenetic position within the hantavirus tree. We used high throughput sequencing to determine the complete genome of TIGV, which showed a typical hantavirus organisation. The large (L), medium (M), and small (S) genome segments were found to be 6532, 3594 and 1908 nucleotides long, respectively, and the 5' and 3' termini for all three segments were predicted to form the panhandle-like structure typical for bunyaviruses. Nucleotide-based phylogenetic analyses revealed that all three coding segments cluster in the phylogroup III sensu Guo et al. (2013). However, while TIGV S segment is basal to the Murinae-associated hantaviruses, the M and L segments are basal to the Soricomorpha-associated hantaviruses. TIGV is the first Murinae-borne hantavirus showing this inconsistent segmental clustering in the hantavirus phylogenetic tree. We finally propose non-exclusive scenarios that could explain the original phylogenetic position of TIGV.
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Affiliation(s)
- Joëlle Goüy de Bellocq
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic; University of Antwerp, Evolutionary Ecology Group, Antwerp, Belgium.
| | - Jana Těšíková
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Yonas Meheretu
- Mekelle University, Department of Biology, Mekelle, Ethiopia
| | - Dagmar Čížková
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
| | - Anna Bryjová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
| | - Herwig Leirs
- University of Antwerp, Evolutionary Ecology Group, Antwerp, Belgium
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
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17
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Heinemann P, Tia M, Alabi A, Anon JC, Auste B, Essbauer S, Gnionsahe A, Kigninlman H, Klempa B, Kraef C, Kruger N, Leendertz FH, Ndhatz-Sanogo M, Schaumburg F, Witkowski PT, Akoua-Koffi CG, Kruger DH. Human Infections by Non-Rodent-Associated Hantaviruses in Africa. J Infect Dis 2016; 214:1507-1511. [PMID: 27601619 DOI: 10.1093/infdis/jiw401] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 08/22/2016] [Indexed: 12/24/2022] Open
Abstract
Various hantaviruses have been discovered in unconventional hosts (shrews and bats) in Africa. Up to now, it was unknown whether these viruses pose a threat for human health. In this study, using newly established serological assays, we demonstrated evidence of shrew-borne hantavirus infections in humans from Côte d'Ivoire and Gabon.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Boris Klempa
- Charité Medical School.,Biomedical Research Center, Bratislava, Slovakia
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18
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Molecular phylogeny of a genetically divergent hantavirus harbored by the Geoffroy's rousette (Rousettus amplexicaudatus), a frugivorous bat species in the Philippines. INFECTION GENETICS AND EVOLUTION 2016; 45:26-32. [PMID: 27516187 DOI: 10.1016/j.meegid.2016.08.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 07/11/2016] [Accepted: 08/08/2016] [Indexed: 11/21/2022]
Abstract
The recent discovery of genetically distinct hantaviruses in multiple species of shrews and moles (order Eulipotyphla, families Soricidae and Talpidae) prompted a further exploration of their host diversification and geographic distribution by analyzing lung tissues from 376 fruit bats representing six genera (order Chiroptera, suborder Yinpterochiroptera, family Pteropodidae), collected in the Republic of the Philippines during 2008 to 2013. Hantavirus RNA was detected by RT-PCR in one of 15 Geoffroy's rousettes (Rousettus amplexicaudatus), captured in Quezon Memorial National Park on Luzon Island in 2009. Phylogenetic analyses of the S, M and L segments, using maximum-likelihood and Bayesian methods, showed that the newfound hantavirus, designated Quezon virus (QZNV), shared a common ancestry with hantaviruses hosted by insectivorous bats, in keeping with their evolutionary relationships and suggests that ancestral bats may have served as the early or original mammalian hosts of primordial hantaviruses. As the first hantavirus detected in a megabat or flying fox species, QZNV extends our knowledge about the reservoir host range.
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19
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Kang HJ, Gu SH, Cook JA, Yanagihara R. Dahonggou Creek virus, a divergent lineage of hantavirus harbored by the long-tailed mole (Scaptonyx fusicaudus). Trop Med Health 2016; 44:16. [PMID: 27433135 PMCID: PMC4940846 DOI: 10.1186/s41182-016-0017-6] [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: 02/28/2016] [Accepted: 05/13/2016] [Indexed: 01/12/2023] Open
Abstract
Novel hantaviruses, recently detected in moles (order Eulipotyphla, family Talpidae) from Europe, Asia, and North America would predict a broader host range and wider ecological diversity. Employing RT-PCR, archival frozen tissues from the Chinese shrew mole (Uropsilus soricipes), broad-footed mole (Scapanus latimanus), coast mole (Scapanus orarius), Townsend’s mole (Scapanus townsendii), and long-tailed mole (Scaptonyx fusicaudus) were analyzed for hantavirus RNA. Following multiple attempts, a previously unrecognized hantavirus, designated Dahonggou Creek virus (DHCV), was detected in a long-tailed mole, captured in Shimian County, Sichuan Province, People’s Republic of China, in August 1989. Analyses of a 1058-nucleotide region of the RNA-dependent RNA polymerase-encoding L segment indicated that DHCV was genetically distinct from other rodent-, shrew-, mole-, and bat-borne hantaviruses. Phylogenetic trees, using maximum likelihood and Bayesian methods, showed that DHCV represented a divergent lineage comprising crocidurine and myosoricine shrew-borne hantaviruses. Although efforts to obtain the S- and M-genomic segments failed, the L-segment sequence analysis, reported here, expands the genetic database of non-rodent-borne hantaviruses. Also, by further mining natural history collections of archival specimens, the genetic diversity of hantaviruses will elucidate their evolutionary origins.
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Affiliation(s)
- Hae Ji Kang
- Pacific Center for Emerging Infectious Diseases Research, Departments of Pediatrics and Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI USA
| | - Se Hun Gu
- Pacific Center for Emerging Infectious Diseases Research, Departments of Pediatrics and Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI USA
| | - Joseph A Cook
- Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, NM USA
| | - Richard Yanagihara
- Pacific Center for Emerging Infectious Diseases Research, Departments of Pediatrics and Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI USA
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20
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Möncke-Buchner E, Szczepek M, Bokelmann M, Heinemann P, Raftery MJ, Krüger DH, Reuter M. Sin Nombre hantavirus nucleocapsid protein exhibits a metal-dependent DNA-specific endonucleolytic activity. Virology 2016; 496:67-76. [PMID: 27261891 DOI: 10.1016/j.virol.2016.05.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/10/2016] [Accepted: 05/12/2016] [Indexed: 01/09/2023]
Abstract
We demonstrate that the nucleocapsid protein of Sin Nombre hantavirus (SNV-N) has a DNA-specific endonuclease activity. Upon incubation of SNV-N with DNA in the presence of magnesium or manganese, we observed DNA digestion in sequence-unspecific manner. In contrast, RNA was not affected under the same conditions. Moreover, pre-treatment of SNV-N with RNase before DNA cleavage increased the endonucleolytic activity. Structure-based protein fold prediction using known structures from the PDB database revealed that Asp residues in positions 88 and 103 of SNV-N show sequence similarity with the active site of the restriction endonuclease HindIII. Crystal structure of HindIII predicts that residues Asp93 and Asp108 are essential for coordination of the metal ions required for HindIII DNA cleavage. Therefore, we hypothesized that homologous residues in SNV-N, Asp88 and Asp103, may have a similar function. Replacing Asp88 and Asp103 by alanine led to an SNV-N protein almost completely abrogated for endonuclease activity.
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Affiliation(s)
- Elisabeth Möncke-Buchner
- Institute of Medical Virology, Helmut-Ruska-Haus, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Michal Szczepek
- Institute of Medical Physics and Biophysics, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Marcel Bokelmann
- Institute of Medical Virology, Helmut-Ruska-Haus, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Patrick Heinemann
- Institute of Medical Virology, Helmut-Ruska-Haus, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Martin J Raftery
- Institute of Medical Virology, Helmut-Ruska-Haus, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Detlev H Krüger
- Institute of Medical Virology, Helmut-Ruska-Haus, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Monika Reuter
- Institute of Medical Virology, Helmut-Ruska-Haus, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
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21
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Gu SH, Arai S, Yu HT, Lim BK, Kang HJ, Yanagihara R. Genetic variants of Cao Bang hantavirus in the Chinese mole shrew (Anourosorex squamipes) and Taiwanese mole shrew (Anourosorex yamashinai). INFECTION GENETICS AND EVOLUTION 2016; 40:113-118. [PMID: 26921799 DOI: 10.1016/j.meegid.2016.01.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 01/09/2016] [Accepted: 01/30/2016] [Indexed: 01/03/2023]
Abstract
To determine the genetic diversity and geographic distribution of Cao Bang virus (CBNV) and to ascertain the existence of CBNV-related hantaviruses, natural history collections of archival tissues from Chinese mole shrews (Anourosorex squamipes) and Taiwanese mole shrews (Anourosorex yamashinai), captured in Guizho Province, People's Republic of China, and in Nantou County, Taiwan, in 2006 and 1989, respectively, were analyzed for hantavirus RNA by RT-PCR. Pair-wise alignment and comparison of the S-, M- and L-segment sequences indicated CBNV in two of five Chinese mole shrews and a previously unrecognized hantavirus, named Xinyi virus (XYIV), in seven of 15 Taiwanese mole shrews. XYIV was closely related to CBNV in Vietnam and China, as well as to Lianghe virus (LHEV), recently reported as a distinct hantavirus species in Chinese mole shrews from Yunnan Province in China. Phylogenetic analyses, using maximum-likelihood and Bayesian methods, showed that XYIV shared a common ancestry with CBNV and LHEV, in keeping with the evolutionary relationship between Anourosorex mole shrews. Until such time that tissue culture isolates of CBNV, LHEV and XYIV can be fully analyzed, XYIV and LHEV should be regarded as genetic variants, or genotypes, of CBNV.
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Affiliation(s)
- Se Hun Gu
- Departments of Pediatrics and Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Satoru Arai
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hon-Tsen Yu
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Burton K Lim
- Department of Natural History, Royal Ontario Museum, Toronto, Canada
| | - Hae Ji Kang
- Departments of Pediatrics and Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Richard Yanagihara
- Departments of Pediatrics and Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA.
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22
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Gu SH, Kumar M, Sikorska B, Hejduk J, Markowski J, Markowski M, Liberski PP, Yanagihara R. Isolation and partial characterization of a highly divergent lineage of hantavirus from the European mole (Talpa europaea). Sci Rep 2016; 6:21119. [PMID: 26892544 PMCID: PMC4759689 DOI: 10.1038/srep21119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 01/18/2016] [Indexed: 12/21/2022] Open
Abstract
Genetically distinct hantaviruses have been identified in five species of fossorial moles (order Eulipotyphla, family Talpidae) from Eurasia and North America. Here, we report the isolation and partial characterization of a highly divergent hantavirus, named Nova virus (NVAV), from lung tissue of a European mole (Talpa europaea), captured in central Poland in August 2013. Typical hantavirus-like particles, measuring 80-120 nm in diameter, were found in NVAV-infected Vero E6 cells by transmission electron microscopy. Whole-genome sequences of the isolate, designated NVAV strain Te34, were identical to that amplified from the original lung tissue, and phylogenetic analysis of the full-length L, M and S segments, using maximum-likelihood and Bayesian methods, showed that NVAV was most closely related to hantaviruses harbored by insectivorous bats, consistent with an ancient evolutionary origin. Infant Swiss Webster mice, inoculated with NVAV by the intraperitoneal route, developed weight loss and hyperactivity, beginning at 16 days, followed by hind-limb paralysis and death. High NVAV RNA copies were detected in lung, liver, kidney, spleen and brain by quantitative real-time RT-PCR. Neuropathological examination showed astrocytic and microglial activation and neuronal loss. The first mole-borne hantavirus isolate will facilitate long-overdue studies on its infectivity and pathogenic potential in humans.
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Affiliation(s)
- Se Hun Gu
- Departments of Pediatrics and Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Mukesh Kumar
- Departments of Pediatrics and Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Beata Sikorska
- Department of Molecular Pathology and Neuropathology, Faculty of Medicine, Medical University of Łódź, 92-216 Łódź, Poland
| | - Janusz Hejduk
- Department of Biodiversity Studies, Didactics and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, 90-237 Łódź, Poland
| | - Janusz Markowski
- Department of Biodiversity Studies, Didactics and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, 90-237 Łódź, Poland
| | - Marcin Markowski
- Department of Experimental Zoology and Evolutionary Biology, Faculty of Biology and Environmental Protection, University of Łódź, 90-237 Łódź, Poland
| | - Paweł P Liberski
- Department of Molecular Pathology and Neuropathology, Faculty of Medicine, Medical University of Łódź, 92-216 Łódź, Poland
| | - Richard Yanagihara
- Departments of Pediatrics and Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
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23
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Holmes EC, Zhang YZ. The evolution and emergence of hantaviruses. Curr Opin Virol 2015; 10:27-33. [PMID: 25562117 DOI: 10.1016/j.coviro.2014.12.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 11/25/2014] [Accepted: 12/17/2014] [Indexed: 12/20/2022]
Abstract
Hantaviruses are a major class of zoonotic pathogens and cause a variety of severe diseases in humans. For most of the last 50 years rodents have been considered to be the primary hosts of hantaviruses, with hantavirus evolution thought to reflect a process of virus-rodent co-divergence over a time-scale of millions of years, with occasional spill-over into humans. However, recent discoveries have revealed that hantaviruses infect a more diverse range of mammalian hosts, particularly Chiroptera (bats) and Soricomorpha (moles and shrews), and that cross-species transmission at multiple scales has played an important role in hantavirus evolution. As a consequence, the evolution and emergence of hantaviruses is more complex than previously anticipated, and may serve as a realistic model for other viral groups.
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Affiliation(s)
- Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia; State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China.
| | - Yong-Zhen Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
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24
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Bennett SN, Gu SH, Kang HJ, Arai S, Yanagihara R. Reconstructing the evolutionary origins and phylogeography of hantaviruses. Trends Microbiol 2014; 22:473-82. [PMID: 24852723 DOI: 10.1016/j.tim.2014.04.008] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 04/17/2014] [Accepted: 04/17/2014] [Indexed: 11/29/2022]
Abstract
Rodents have long been recognized as the principal reservoirs of hantaviruses. However, with the discovery of genetically distinct and phylogenetically divergent lineages of hantaviruses in multiple species of shrews, moles, and insectivorous bats from widely separated geographic regions, a far more complex landscape of hantavirus host distribution, evolution, and phylogeography is emerging. Detailed phylogenetic analyses, based on partial and full-length genomes of previously described rodent-borne hantaviruses and newly detected non-rodent-borne hantaviruses, indicate an Asian origin and support the emerging concept that ancestral non-rodent mammals may have served as the hosts of primordial hantaviruses.
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Affiliation(s)
- Shannon N Bennett
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawai'i at Mānoa, Honolulu, HI, USA; Department of Microbiology, California Academy of Sciences, San Francisco, CA, USA
| | - Se Hun Gu
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Hae Ji Kang
- Division of Respiratory Viruses, Korea National Institute of Health, Cheongwon-gun, Chungcheongbuk-do, Korea
| | - Satoru Arai
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Richard Yanagihara
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawai'i at Mānoa, Honolulu, HI, USA; Department of Pediatrics, John A. Burns School of Medicine, University of Hawai'i at Mānoa, Honolulu, HI, USA.
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