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Downie DL, Rao P, David-Ferdon C, Courtney S, Lee JS, Kugley S, MacDonald PDM, Barnes K, Fisher S, Andreadis JL, Chaitram J, Mauldin MR, Salerno RM, Schiffer J, Gundlapalli AV. Literature Review of Pathogen Agnostic Molecular Testing of Clinical Specimens From Difficult-to-Diagnose Patients: Implications for Public Health. Health Secur 2024; 22:93-107. [PMID: 38608237 PMCID: PMC11044852 DOI: 10.1089/hs.2023.0100] [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: 05/22/2023] [Revised: 08/15/2023] [Accepted: 08/15/2023] [Indexed: 04/14/2024] Open
Abstract
To better identify emerging or reemerging pathogens in patients with difficult-to-diagnose infections, it is important to improve access to advanced molecular testing methods. This is particularly relevant for cases where conventional microbiologic testing has been unable to detect the pathogen and the patient's specimens test negative. To assess the availability and utility of such testing for human clinical specimens, a literature review of published biomedical literature was conducted. From a corpus of more than 4,000 articles, a set of 34 reports was reviewed in detail for data on where the testing was being performed, types of clinical specimens tested, pathogen agnostic techniques and methods used, and results in terms of potential pathogens identified. This review assessed the frequency of advanced molecular testing, such as metagenomic next generation sequencing that has been applied to clinical specimens for supporting clinicians in caring for difficult-to-diagnose patients. Specimen types tested were from cerebrospinal fluid, respiratory secretions, and other body tissues and fluids. Publications included case reports and series, and there were several that involved clinical trials, surveillance studies, research programs, or outbreak situations. Testing identified both known human pathogens (sometimes in new sites) and previously unknown human pathogens. During this review, there were no apparent coordinated efforts identified to develop regional or national reports on emerging or reemerging pathogens. Therefore, development of a coordinated sentinel surveillance system that applies advanced molecular methods to clinical specimens which are negative by conventional microbiological diagnostic testing would provide a foundation for systematic characterization of emerging and underdiagnosed pathogens and contribute to national biodefense strategy goals.
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Affiliation(s)
- Diane L. Downie
- Diane L. Downie, PhD, MPH, is Deputy Associate Director for Science, Office of Readiness and Response; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Preetika Rao
- Preetika Rao, MPH, is a Health Scientist; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Corinne David-Ferdon
- Corinne David-Ferdon, PhD, is Associate Director of Science, Office of Public Health Data, Surveillance, and Technology; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Sean Courtney
- Sean Courtney, PhD, is a Health Scientist, at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Justin S. Lee
- Justin Lee, DVM, PhD, is a Health Scientist, Division of Global Health Protection; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Shannon Kugley
- Shannon Kugley, MLIS, is a Research Public Health Analyst; in Social, Statistical, and Environmental Sciences, RTI International, Research Triangle Park, NC
| | - Pia D. M. MacDonald
- Pia D. M. MacDonald, PhD, MPH, is a Senior Infectious Disease Epidemiologist; in Social, Statistical, and Environmental Sciences, RTI International, Research Triangle Park, NC
| | - Keegan Barnes
- Keegan Barnes is a Public Health Analyst; in Social, Statistical, and Environmental Sciences, RTI International, Research Triangle Park, NC
| | - Shelby Fisher
- Shelby Fisher, MPH, is an Epidemiologist; in Social, Statistical, and Environmental Sciences, RTI International, Research Triangle Park, NC
| | - Joanne L. Andreadis
- Joanne L. Andreadis, PhD, is Associate Director for Science, at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Jasmine Chaitram
- Jasmine Chaitram, MPH, is Branch Chief, at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Matthew R. Mauldin
- Matthew R. Mauldin, PhD, is Health Scientists, Office of Readiness and Response; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Reynolds M. Salerno
- Reynolds M. Salerno, PhD, is Director, Division of Laboratory Systems; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Jarad Schiffer
- Jarad Schiffer, MS, is Health Scientists, Office of Readiness and Response; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Adi V. Gundlapalli
- Adi V. Gundlapalli, MD, PhD, is a Senior Advisor, Data Readiness and Response, Office of Public Health Data, Surveillance, and Technology; at the US Centers for Disease Control and Prevention, Atlanta, GA
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Huang X, Hou J, Le X, Hou Y, Yang L, Li Q, Wang B, Xia X. Diversity of astroviruses in wild animals in Yunnan province, China. Virol J 2024; 21:51. [PMID: 38414022 PMCID: PMC10900740 DOI: 10.1186/s12985-024-02314-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/08/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Astroviruses (AstVs) are single-stranded RNA viruses that have been detected in a wide range of mammals and birds. They are associated with numerous interspecies transmissions and viral recombination events, posing a threat to human and animal health. METHODS We collected 1,333 samples from wild animals, including bats, rodents, wild boars, and birds, from various states and cities in the Yunnan Province, China, between 2020 and 2023 to investigate the presence of AstVs. AstVs were detected using a polymerase chain reaction targeting the RdRp gene. Finally, the Molecular Evolutionary Genetics Analysis software was used to construct the phylogenetic tree. RESULTS The overall positivity rate for AstVs was 7.12% in four species, indicating their widespread occurrence in the region. High genetic diversity among AstVs was observed in different animal species, suggesting the potential for interspecies transmission, particularly among rodents and birds. Additionally, we identified a novel AstV strain and, for the first time, provided information on the presence of bastroviruses in Yunnan, China. CONCLUSIONS The widespread distribution and high genetic diversity of AstVs, along with the observed potential for interspecies transmission, highlight the importance of further investigation and surveillance in the region. The findings emphasize the need for increased attention to AstVs and their potential impact on human and animal health in Yunnan and other regions.
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Affiliation(s)
- Xingyu Huang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 650500, Kunming, Yunnan, P.R. China
| | - Junjie Hou
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 650500, Kunming, Yunnan, P.R. China
| | - Xiang Le
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 650500, Kunming, Yunnan, P.R. China
| | - Yutong Hou
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 650500, Kunming, Yunnan, P.R. China
| | - Lingsi Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 650500, Kunming, Yunnan, P.R. China
| | - Qian Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 650500, Kunming, Yunnan, P.R. China
| | - Binghui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 650500, Kunming, Yunnan, P.R. China.
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 650500, Kunming, Yunnan, P.R. China.
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Roev GV, Borisova NI, Chistyakova NV, Vyhodtseva AV, Akimkin VG, Khafizov KF. Bastroviruses ( Astroviridae): genetic diversity and potential impact on human and animal health. Vopr Virusol 2023; 68:505-512. [PMID: 38156566 DOI: 10.36233/0507-4088-192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Indexed: 12/30/2023]
Abstract
INTRODUCTION Bastroviruses were discovered in the Netherlands in 2016 in human stool samples and show partial genetic similarities to astroviruses and hepatitis E viruses. Their association with disease onset has not yet been established. MATERIALS AND METHODS Metagenomic sequencing of fecal samples of Nyctalus noctula bats collected in the Russian Federation in 2023 was performed. Two almost complete genomes of bastroviruses were assembled. The zoonotic potential of these viruses was assessed using machine learning methods, their recombination was studied, and phylogenetic trees were constructed. RESULTS A nearly complete bastrovirus genome was de novo assembled in one of the samples, and it was used to assemble another genome in another sample. The zoonotic potential of the virus from one of these samples was estimated as high. The existence of recombination between structural and non-structural polyproteins was demonstrated. CONCLUSION Two bastrovirus genomes were assembled, phylogenetic and recombination analyses were performed, and the zoonotic potential was evaluated.
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Affiliation(s)
- G V Roev
- Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
- Moscow Institute of Physics and Technology (National Research University)
| | - N I Borisova
- Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
| | - N V Chistyakova
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences
| | - A V Vyhodtseva
- Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
| | - V G Akimkin
- Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
| | - K F Khafizov
- Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
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Van Brussel K, Mahar JE, Hall J, Bender H, Ortiz-Baez AS, Chang WS, Holmes EC, Rose K. Gammaretroviruses, novel viruses and pathogenic bacteria in Australian bats with neurological signs, pneumonia and skin lesions. Virology 2023; 586:43-55. [PMID: 37487325 DOI: 10.1016/j.virol.2023.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/25/2023] [Accepted: 07/12/2023] [Indexed: 07/26/2023]
Abstract
More than 70 bat species are found in mainland Australia. While most studies of bat viromes focus on sampling seemingly healthy individuals, little is known about the viruses and bacteria associated with diseased bats. We performed traditional diagnostic techniques and metatranscriptomic sequencing on tissue samples from 43 Australian bats, comprising three flying fox (Pteropodidae) and two microbat species experiencing a range of disease syndromes, including mass mortality, neurological signs, pneumonia and skin lesions. Of note, we identified the recently discovered Hervey pteropid gammaretrovirus in a bat with lymphoid leukemia, with evidence of replication consistent with an exogenous virus. The possible association of Hervey pteropid gammaretrovirus with lymphoid leukemia clearly merits additional investigation. One novel picornavirus and at least three new astroviruses and bat pegiviruses were also identified in a variety of tissue types, as well as a number of likely bacterial pathogens or opportunistic infections, most notably Pseudomonas aeruginosa.
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Affiliation(s)
- Kate Van Brussel
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, NSW, 2006, Australia
| | - Jackie E Mahar
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, NSW, 2006, Australia
| | - Jane Hall
- Australian Registry of Wildlife Health, Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | - Hannah Bender
- Australian Registry of Wildlife Health, Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | - Ayda Susana Ortiz-Baez
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, NSW, 2006, Australia
| | - Wei-Shan Chang
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, NSW, 2006, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, NSW, 2006, Australia.
| | - Karrie Rose
- Australian Registry of Wildlife Health, Taronga Conservation Society Australia, Mosman, New South Wales, Australia.
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Jones BD, Kaufman EJ, Peel AJ. Viral Co-Infection in Bats: A Systematic Review. Viruses 2023; 15:1860. [PMID: 37766267 PMCID: PMC10535902 DOI: 10.3390/v15091860] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Co-infection is an underappreciated phenomenon in contemporary disease ecology despite its ubiquity and importance in nature. Viruses, and other co-infecting agents, can interact in ways that shape host and agent communities, influence infection dynamics, and drive evolutionary selective pressures. Bats are host to many viruses of zoonotic potential and have drawn increasing attention in their role as wildlife reservoirs for human spillover. However, the role of co-infection in driving viral transmission dynamics within bats is unknown. Here, we systematically review peer-reviewed literature reporting viral co-infections in bats. We show that viral co-infection is common in bats but is often only reported as an incidental finding. Biases identified in our study database related to virus and host species were pre-existing in virus studies of bats generally. Studies largely speculated on the role co-infection plays in viral recombination and few investigated potential drivers or impacts of co-infection. Our results demonstrate that current knowledge of co-infection in bats is an ad hoc by-product of viral discovery efforts, and that future targeted co-infection studies will improve our understanding of the role it plays. Adding to the broader context of co-infection studies in other wildlife species, we anticipate our review will inform future co-infection study design and reporting in bats. Consideration of detection strategy, including potential viral targets, and appropriate analysis methodology will provide more robust results and facilitate further investigation of the role of viral co-infection in bat reservoirs.
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Affiliation(s)
- Brent D. Jones
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD 4111, Australia
- School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
| | | | - Alison J. Peel
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD 4111, Australia
- School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
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Isolation and Characterization of Distinct Rotavirus A in Bat and Rodent Hosts. J Virol 2023; 97:e0145522. [PMID: 36633410 PMCID: PMC9888233 DOI: 10.1128/jvi.01455-22] [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] [Indexed: 01/13/2023] Open
Abstract
Rotavirus A (RVA) causes diarrheal disease in humans and various animals. Recent studies have identified bat and rodent RVAs with evidence of zoonotic transmission and genome reassortment. However, the virological properties of bat and rodent RVAs with currently identified genotypes still need to be better clarified. Here, we performed virus isolation-based screening for RVA in animal specimens and isolated RVAs (representative strains: 16-06 and MpR12) from Egyptian fruit bat and Natal multimammate mouse collected in Zambia. Whole-genome sequencing and phylogenetic analysis revealed that the genotypes of bat RVA 16-06 were identical to that of RVA BATp39 strain from the Kenyan fruit bat, which has not yet been characterized. Moreover, all segments of rodent RVA MpR12 were highly divergent and assigned to novel genotypes, but RVA MpR12 was phylogenetically closer to bat RVAs than to other rodent RVAs, indicating a unique evolutionary history. We further investigated the virological properties of the isolated RVAs. In brief, we found that 16-06 entered cells by binding to sialic acids on the cell surface, while MpR12 entered in a sialic acid-independent manner. Experimental inoculation of suckling mice with 16-06 and MpR12 revealed that these RVAs are causative agents of diarrhea. Moreover, 16-06 and MpR12 demonstrated an ability to infect and replicate in a 3D-reconstructed primary human intestinal epithelium with comparable efficiency to the human RVA. Taken together, our results detail the unique genetic and virological features of bat and rodent RVAs and demonstrate the need for further investigation of their zoonotic potential. IMPORTANCE Recent advances in nucleotide sequence detection methods have enabled the detection of RVA genomes from various animals. These studies have discovered multiple divergent RVAs and have resulted in proposals for the genetic classification of novel genotypes. However, most of these RVAs have been identified via dsRNA viral genomes and not from infectious viruses, and their virological properties, such as cell/host tropisms, transmissibility, and pathogenicity, are unclear and remain to be clarified. Here, we successfully isolated RVAs with novel genome constellations from three bats and one rodent in Zambia. In addition to whole-genome sequencing, the isolated RVAs were characterized by glycan-binding affinity, pathogenicity in mice, and infectivity to the human gut using a 3D culture of primary intestinal epithelium. Our study reveals the first virological properties of bat and rodent RVAs with high genetic diversity and unique evolutional history and provides basic knowledge to begin estimating the potential of zoonotic transmission.
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Dezordi FZ, Coutinho GB, Dias YJM, Wallau GL. Ancient origin of Jingchuvirales derived glycoproteins integrated in arthropod genomes. Genet Mol Biol 2023; 46:e20220218. [PMID: 37036390 PMCID: PMC10084718 DOI: 10.1590/1678-4685-gmb-2022-0218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 02/11/2023] [Indexed: 04/11/2023] Open
Abstract
Endogenous virus elements (EVEs) are viral-derived sequences integrated into their host genomes. EVEs of the Jingchuvirales order were detected in a wide range of insect genomes covering several distantly related families. Moreover, Jingchuvirales-derived glycoproteins were recently associated by our group with the origin of a putative new retrovirus based on a glycoprotein captured by a mosquito retrotransposon. But, except for mosquitoes, there is a lack of a more detailed understanding of the endogenization mechanism, timing, and frequency per Jingchuvirales viral lineages. Here we screened Jingchuvirales glycoprotein-derived EVEs (Jg-EVEs) in eukaryotic genomes. We found six distinct endogenization events of Jg-EVEs, that belong to two out of five known Jingchuvirales families (Chuviridae and Natareviridae). For seven arthropod families bearing Jg-EVEs there is no register of bona fide circulating chuvirus infection. Hence, our results show that Jingchuvirales viruses infected or still infect these host families. Although we found abundant evidence of LTR-Gypsy retrotransposons fragments associated with the glycoprotein in Hymenoptera and other insect orders, our results show that the widespread distribution of Jingchuvirales glycoproteins in extant Arhtropods is a result of multiple ancient endogenization events and that these virus fossils are being vertically inherited in Arthropods genomes for millions of years.
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Affiliation(s)
- Filipe Zimmer Dezordi
- Fundação Oswaldo Cruz (FIOCRUZ), Instituto Aggeu Magalhães (IAM), Departamento de Entomologia, Recife, PE, Brazil
- Fundação Oswaldo Cruz (FIOCRUZ), Instituto Aggeu Magalhães (IAM), Núcleo de Bioinformática, Recife, PE, Brazil
| | - Gutembergmann Batista Coutinho
- Fundação Oswaldo Cruz (FIOCRUZ), Instituto Aggeu Magalhães (IAM), Departamento de Entomologia, Recife, PE, Brazil
- Universidade Federal de Pernambuco, Centro de Biociências, Recife, PE, Brazil
| | - Yago José Mariz Dias
- Fundação Oswaldo Cruz (FIOCRUZ), Instituto Aggeu Magalhães (IAM), Departamento de Entomologia, Recife, PE, Brazil
- Fundação Oswaldo Cruz (FIOCRUZ), Instituto Aggeu Magalhães (IAM), Núcleo de Bioinformática, Recife, PE, Brazil
- Universidade Federal de Pernambuco, Centro de Biociências, Recife, PE, Brazil
| | - Gabriel Luz Wallau
- Fundação Oswaldo Cruz (FIOCRUZ), Instituto Aggeu Magalhães (IAM), Departamento de Entomologia, Recife, PE, Brazil
- Fundação Oswaldo Cruz (FIOCRUZ), Instituto Aggeu Magalhães (IAM), Núcleo de Bioinformática, Recife, PE, Brazil
- WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, Department of Arbovirology, Hamburg, Germany
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8
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Passive epidemiological surveillance in wildlife in Costa Rica identifies pathogens of zoonotic and conservation importance. PLoS One 2022; 17:e0262063. [PMID: 36155648 PMCID: PMC9512195 DOI: 10.1371/journal.pone.0262063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 09/11/2022] [Indexed: 12/27/2022] Open
Abstract
Epidemiological surveillance systems for pathogens in wild species have been proposed as a preventive measure for epidemic events. These systems can minimize the detrimental effects of an outbreak, but most importantly, passive surveillance systems are the best adapted to countries with limited resources. Therefore, this research aimed to evaluate the technical and infrastructural feasibility of establishing this type of scheme in Costa Rica by implementing a pilot program targeting the detection of pathogens of zoonotic and conservation importance in wildlife. Between 2018 and 2020, 85 carcasses of free-ranging vertebrates were admitted for post-mortem and microbiology analysis. However, we encountered obstacles mainly related to the initial identification of cases and limited local logistics capacity. Nevertheless, this epidemiological surveillance scheme allowed us to estimate the general state of health of the country’s wildlife by establishing the causes of death according to pathological findings. For instance, 60% (51/85) of the deaths were not directly associated with an infectious agent. Though in 37.6% (32/85) of these cases an infectious agent associated or not with disease was detected. In 27.1% (23/85) of the cases, death was directly related to infectious agents. Furthermore, 12.9% (11/85), the cause of death was not determined. Likewise, this wildlife health monitoring program allowed the detection of relevant pathogens such as Canine Distemper Virus, Klebsiella pneumoniae, Angiostrongylus spp., Baylisascaris spp., among others. Our research demonstrated that this passive surveillance scheme is cost-effective and feasible in countries with limited resources. This passive surveillance can be adapted to the infrastructure dedicated to monitoring diseases in productive animals according to the scope and objectives of monitoring wildlife specific to each region. The information generated from the experience of the initial establishment of a WHMP is critical to meeting the challenges involved in developing this type of scheme in regions with limited resources and established as hotspots for emerging infectious diseases.
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Van Brussel K, Mahar JE, Ortiz-Baez AS, Carrai M, Spielman D, Boardman WSJ, Baker ML, Beatty JA, Geoghegan JL, Barrs VR, Holmes EC. Faecal virome of the Australian grey-headed flying fox from urban/suburban environments contains novel coronaviruses, retroviruses and sapoviruses. Virology 2022; 576:42-51. [PMID: 36150229 DOI: 10.1016/j.virol.2022.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/02/2022] [Accepted: 09/04/2022] [Indexed: 01/04/2023]
Abstract
Bats are important reservoirs for viruses of public health and veterinary concern. Virus studies in Australian bats usually target the families Paramyxoviridae, Coronaviridae and Rhabdoviridae, with little known about their overall virome composition. We used metatranscriptomic sequencing to characterise the faecal virome of grey-headed flying foxes from three colonies in urban/suburban locations from two Australian states. We identified viruses from three mammalian-infecting (Coronaviridae, Caliciviridae, Retroviridae) and one possible mammalian-infecting (Birnaviridae) family. Of particular interest were a novel bat betacoronavirus (subgenus Nobecovirus) and a novel bat sapovirus (Caliciviridae), the first identified in Australian bats, as well as a potentially exogenous retrovirus. The novel betacoronavirus was detected in two sampling locations 1375 km apart and falls in a viral lineage likely with a long association with bats. This study highlights the utility of unbiased sequencing of faecal samples for identifying novel viruses and revealing broad-scale patterns of virus ecology and evolution.
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Affiliation(s)
- Kate Van Brussel
- Sydney Institute for Infectious Diseases, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, NSW, 2006, Australia
| | - Jackie E Mahar
- Sydney Institute for Infectious Diseases, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, NSW, 2006, Australia
| | - Ayda Susana Ortiz-Baez
- Sydney Institute for Infectious Diseases, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, NSW, 2006, Australia
| | - Maura Carrai
- Jockey Club College of Veterinary Medicine & Life Sciences, City University of Hong Kong, Kowloon Tong, People's Republic of China
| | - Derek Spielman
- School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW, 2006, Australia
| | - Wayne S J Boardman
- School of Animal and Veterinary Sciences, Faculty of Science, Engineering and Technology, University of Adelaide, Adelaide, SA, 5371, Australia
| | - Michelle L Baker
- CSIRO Australian Centre for Disease Preparedness, Health and Biosecurity Business Unit, Geelong, VIC, 3220, Australia
| | - Julia A Beatty
- Jockey Club College of Veterinary Medicine & Life Sciences, City University of Hong Kong, Kowloon Tong, People's Republic of China
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin 9010, New Zealand; Institute of Environmental Science and Research, Wellington, 5022, New Zealand
| | - Vanessa R Barrs
- Jockey Club College of Veterinary Medicine & Life Sciences, City University of Hong Kong, Kowloon Tong, People's Republic of China; Centre for Animal Health and Welfare, City University of Hong Kong, Kowloon Tong, People's Republic of China.
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, NSW, 2006, Australia.
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10
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Montecino-Latorre D, Goldstein T, Kelly TR, Wolking DJ, Kindunda A, Kongo G, Bel-Nono SO, Kazwala RR, Suu-Ire RD, Barker CM, Johnson CK, Mazet JAK. Seasonal shedding of coronavirus by straw-colored fruit bats at urban roosts in Africa. PLoS One 2022; 17:e0274490. [PMID: 36107832 PMCID: PMC9477308 DOI: 10.1371/journal.pone.0274490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/29/2022] [Indexed: 11/19/2022] Open
Abstract
The straw-colored fruit bat (Eidolon helvum) is a pteropodid whose conservation is crucial for maintaining functional connectivity of plant populations in tropical Africa. Land conversion has pushed this species to adapt to roosting in urban centers across its range. These colonies often host millions of individuals, creating intensive human-bat contact interfaces that could facilitate the spillover of coronaviruses shed by these bats. A better understanding of coronavirus dynamics in these roosts is needed to identify peak times of exposure risk in order to propose evidence-based management that supports safe human-bat coexistence, as well as the conservation of this chiropteran. We studied the temporal patterns of coronavirus shedding in E. helvum, by testing thousands of longitudinally-collected fecal samples from two spatially distant urban roosts in Ghana and Tanzania. Shedding of coronaviruses peaked during the second part of pup weaning in both roosts. Assuming that coronavirus shedding is directly related to spillover risk, our results indicate that exposure mitigation should target reducing contact between people and E. helvum roosts during the pup “weaning” period. This recommendation can be applied across the many highly-populated urban sites occupied by E. helvum across Africa.
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Affiliation(s)
- Diego Montecino-Latorre
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
- * E-mail: (JAKM); (DML)
| | - Tracey Goldstein
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Terra R. Kelly
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - David J. Wolking
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Adam Kindunda
- College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Godphrey Kongo
- College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | | | - Rudovick R. Kazwala
- College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Richard D. Suu-Ire
- School of Veterinary Medicine, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Christopher M. Barker
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Christine Kreuder Johnson
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Jonna A. K. Mazet
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
- * E-mail: (JAKM); (DML)
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11
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Virus Diversity, Abundance, and Evolution in Three Different Bat Colonies in Switzerland. Viruses 2022; 14:v14091911. [PMID: 36146717 PMCID: PMC9505930 DOI: 10.3390/v14091911] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/08/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Bats are increasingly recognized as reservoirs for many different viruses that threaten public health, such as Hendravirus, Ebolavirus, Nipahvirus, and SARS- and MERS-coronavirus. To assess spillover risk, viromes of bats from different parts of the world have been investigated in the past. As opposed to most of these prior studies, which determined the bat virome at a single time point, the current work was performed to monitor changes over time. Specifically, fecal samples of three endemic Swiss bat colonies consisting of three different bat species were collected over three years and analyzed using next-generation sequencing. Furthermore, single nucleotide variants of selected DNA and RNA viruses were analyzed to investigate virus genome evolution. In total, sequences of 22 different virus families were found, of which 13 are known to infect vertebrates. Most interestingly, in a Vespertilio murinus colony, sequences from a MERS-related beta-coronavirus were consistently detected over three consecutive years, which allowed us to investigate viral genome evolution in a natural reservoir host.
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12
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Chitcharoen S, Sivapornnukul P, Payungporn S. Revolutionized virome research using systems microbiology approaches. Exp Biol Med (Maywood) 2022; 247:1135-1147. [PMID: 35723062 PMCID: PMC9335507 DOI: 10.1177/15353702221102895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Currently, both pathogenic and commensal viruses are continuously being discovered and acknowledged as ubiquitous components of microbial communities. The advancements of systems microbiological approaches have changed the face of virome research. Here, we focus on viral metagenomic approach to study virus community and their interactions with other microbial members as well as their hosts. This review also summarizes challenges, limitations, and benefits of the current virome approaches. Potentially, the studies of virome can be further applied in various biological and clinical fields.
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Affiliation(s)
- Suwalak Chitcharoen
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand,Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pavaret Sivapornnukul
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sunchai Payungporn
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Sunchai Payungporn.
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13
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Zeng J, Yang Z, Guo W, Wang X, Yang S, Shen Q, Wang H, Zhang W. Identification and genome characterization of novel parechovirus sequences from Hipposideros armiger in China. Virol J 2022; 19:80. [PMID: 35570277 PMCID: PMC9107582 DOI: 10.1186/s12985-022-01806-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 05/04/2022] [Indexed: 11/13/2022] Open
Abstract
Background Bats were identified as a natural reservoir of emerging and re-emerging infectious pathogens threatening human health and life. Methods This study collected 21 fecal samples of Hipposideros armiger in Mengla County of Xishuangbanna Prefecture Yunnan Province to combine one pool for viral metagenomic sequencing. Results Two nearly complete genomes of parechoviruses, BPeV11 and BPeV20, were sequenced. Genome analysis revealed that BPeV11 and BPeV20 follow a 3-3-4 genome layout: 5′ UTR-VP0-VP3-VP1-2A-2B-2C-3A-3B-3C-3D-3′ UTR. The prevalence of BPev11 and BPev20 by Nested-PCR showed that 1 of 21 fecal samples was positive. Based on amino acid identity comparison and phylogenetic analysis of P1, 2C, and 3D, BPeV11 and BPeV20 were closely related to but distinct from FPeVs. Conclusion It was probably proposed to be a novel species in the genus Parechovirus of the family Picornaviridae. The isolation of BPev11 and BPev20 from H. armiger in China is the first complete genome of parechovirus isolations from bat feces of the genus Hipposideros. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-022-01806-1.
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14
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Tian J, Sun J, Li D, Wang N, Wang L, Zhang C, Meng X, Ji X, Suchard MA, Zhang X, Lai A, Su S, Veit M. Emerging viruses: Cross-species transmission of Coronaviruses, Filoviruses, Henipaviruses and Rotaviruses from bats. Cell Rep 2022; 39:110969. [PMID: 35679864 PMCID: PMC9148931 DOI: 10.1016/j.celrep.2022.110969] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 04/10/2022] [Accepted: 05/25/2022] [Indexed: 11/25/2022] Open
Abstract
Emerging infectious diseases, especially if caused by bat-borne viruses, significantly affect public health and the global economy. There is an urgent need to understand the mechanism of interspecies transmission, particularly to humans. Viral genetics; host factors, including polymorphisms in the receptors; and ecological, environmental, and population dynamics are major parameters to consider. Here, we describe the taxonomy, geographic distribution, and unique traits of bats associated with their importance as virus reservoirs. Then, we summarize the origin, intermediate hosts, and the current understanding of interspecies transmission of Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2, Nipah, Hendra, Ebola, Marburg virus, and rotaviruses. Finally, the molecular interactions of viral surface proteins with host cell receptors are examined, and a comparison of these interactions in humans, intermediate hosts, and bats is conducted. This uncovers adaptive mutations in virus spike protein that facilitate cross-species transmission and risk factors associated with the emergence of novel viruses from bats.
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15
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Du H, Zhang L, Zhang X, Yun F, Chang Y, Tuersun A, Aisaiti K, Ma Z. Metagenome-Assembled Viral Genomes Analysis Reveals Diversity and Infectivity of the RNA Virome of Gerbillinae Species. Viruses 2022; 14:356. [PMID: 35215951 PMCID: PMC8874536 DOI: 10.3390/v14020356] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/04/2022] [Accepted: 02/06/2022] [Indexed: 11/21/2022] Open
Abstract
Rodents are a known reservoir for extensive zoonotic viruses, and also possess a propensity to roost in human habitation. Therefore, it is necessary to identify and catalogue the potentially emerging zoonotic viruses that are carried by rodents. Here, viral metagenomic sequencing was used for zoonotic virus detection and virome characterization on 32 Great gerbils of Rhombomys opimus, Meriones meridianus, and Meiiones Unguiculataus species in Xinjiang, Northwest China. In total, 1848 viral genomes that are potentially pathogenic to rodents and humans, as well as to other wildlife, were identified namely Retro-, Flavi-, Pneumo-, Picobirna-, Nairo-, Arena-, Hepe-, Phenui-, Rhabdo-, Calici-, Reo-, Corona-, Orthomyxo-, Peribunya-, and Picornaviridae families. In addition, a new genotype of rodent Hepacivirus was identified in heart and lung homogenates of seven viscera pools and phylogenetic analysis revealed the closest relationship to rodent Hepacivirus isolate RtMm-HCV/IM2014 that was previously reported to infect rodents from Inner Mongolia, China. Moreover, nine new genotype viral sequences that corresponded to Picobirnaviruses (PBVs), which have a bi-segmented genome and belong to the family Picobirnaviridae, comprising of three segment I and six segment II sequences, were identified in intestines and liver of seven viscera pools. In the two phylogenetic trees that were constructed using ORF1 and ORF2 of segment I, the three segment I sequences were clustered into distinct clades. Additionally, phylogenetic analysis showed that PBV sequences were distributed in the whole tree that was constructed using the RNA-dependent RNA polymerase (RdRp) gene of segment II with high diversity, sharing 68.42-82.67% nucleotide identities with other genogroup I and genogroup II PBV strains based on the partial RdRp gene. By RNA sequencing, we found a high degree of biodiversity of Retro-, Flavi-, Pneumo-, and Picobirnaridae families and other zoonotic viruses in gerbils, indicating that zoonotic viruses are a common presence in gerbils from Xinjiang, China. Therefore, further research is needed to determine the zoonotic potential of these viruses that are carried by other rodent species from different ecosystems and wildlife in general.
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Affiliation(s)
| | | | | | | | | | | | | | - Zhenghai Ma
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China; (H.D.); (L.Z.); (X.Z.); (F.Y.); (Y.C.); (A.T.); (K.A.)
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16
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Jingchuvirales: a new taxonomical framework for a rapidly expanding order of unusual monjiviricete viruses broadly distributed among arthropod subphyla. Appl Environ Microbiol 2022; 88:e0195421. [PMID: 35108077 DOI: 10.1128/aem.01954-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Technical advances in metagenomics and metatranscriptomics have dramatically accelerated virus discovery in recent years. "Chuviruses" were first described in 2015 as obscure negative-sense RNA viruses of diverse arthropods. Although "chuviruses" first appeared to be members of the negarnaviricot order Mononegavirales in phylogenetic analyses using RNA-directed RNA polymerase sequences, further characterization revealed unusual gene orders in genomes that are non-segmented, segmented, and/or possibly circular. Consequently, a separate order, Jingchuvirales was established to include a monospecific family Chuviridae. Recently, it has become apparent that jingchuvirals are broadly distributed and are therefore likely of ecologic and economic importance. Here we describe recent and ongoing efforts to create the necessary taxonomic framework to accommodate the expected flood of novel viruses belonging to the order.
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17
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Ayolabi CI, Olusola BA, Lawal AA, Chibuike AD, Nzekwue BN. Detection of novel paramyxoviruses in Chaerephon bat species in Nigeria and phylogenetics of paramyxoviruses co-evolution with bats in Africa. Zoonoses Public Health 2021; 69:117-135. [PMID: 34817117 DOI: 10.1111/zph.12900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 09/28/2021] [Accepted: 10/28/2021] [Indexed: 11/28/2022]
Abstract
Bat paramyxoviruses (PmV) are a diverse group of viruses and include zoonotic viruses such as henipaviruses. Members of this group in other continents have been associated with severe respiratory and neurological infections in animals and humans. Furthermore, despite the richness of diverse bat species that can transmit this virus in African countries like Nigeria, there is very scanty information as to the presence and co-evolution of paramyxoviruses in bats. There is a need for continuous surveillance of zoonotic viruses and their biological reservoirs as this will help in the prevention and management of pathogens' spillovers. This study detected novel paramyxoviruses in Chaerephon nigeriae bat species found in Badagry, Lagos. Phylogenetic analyses of paramyxovirus sequences' co-evolution with frugivorous and insectivorous bats circulating in African countries were also performed using sequences of African origin available in the Database of Bat-Associated Viruses (DBatVir: http://www.mgc.ac.cn/DBatVir/). Oral swabs (n = 18) and blood samples (n = 32) were collected from C. nigeriae bats in Badagry, Lagos. The L gene of bat paramyxovirus was detected in all oral swabs using PCR techniques. Six of the amplicons were successfully sequenced. Estimated phylogenies placed the sequences in close relationship with those isolated from insectivorous bats. Phylogenetic analyses of previously sequenced isolates in the African region showed the likelihood of different co-evolution mechanisms of paramyxoviruses with frugivorous bats compared with insectivorous bats. This may be due to codon usage bias of the L gene. Spatial distribution of paramyxoviruses in African countries showed limited ongoing surveillance of this virus in the continent, especially in southern and northern countries. Extensive surveillance of paramyxoviruses with possible zoonotic potentials among bat species in the continent is recommended. This will provide further insights into co-evolution as well as prevent possible spillover into the human population.
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18
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He W, Gao Y, Wen Y, Ke X, Ou Z, Li Y, He H, Chen Q. Detection of Virus-Related Sequences Associated With Potential Etiologies of Hepatitis in Liver Tissue Samples From Rats, Mice, Shrews, and Bats. Front Microbiol 2021; 12:653873. [PMID: 34177835 PMCID: PMC8221242 DOI: 10.3389/fmicb.2021.653873] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/10/2021] [Indexed: 01/08/2023] Open
Abstract
Hepatitis is a major global health concern. However, the etiology of 10-20% hepatitis cases remains unclear. Some hepatitis-associated viruses, like the hepatitis E virus, are zoonotic pathogens. Rats, shrews, and bats are reservoirs for many zoonotic pathogens. Therefore, understanding the virome in the liver of these animals is important for the investigation of the etiologies of hepatitis and monitoring the emerging zoonotic viruses. In this study, viral metagenomics and PCR methods were used to investigate viral communities in rats, mice, house shrews, and bats livers. Viral metagenomic analysis showed a diverse set of sequences in liver samples, comprising: sequences related to herpesviruses, orthomyxoviruses, anelloviruses, hepeviruses, hepadnaviruses, flaviviruses, parvoviruses, and picornaviruses. Using PCR methods, we first detected hepatovirus sequences in Hipposideros larvatus (3.85%). We also reported the first detection of Zika virus-related sequences in rats and house shrews. Sequences related to influenza A virus and herpesviruses were detected in liver. Higher detection rates of pegivirus sequences were found in liver tissue and serum samples from rats (7.85% and 15.79%, respectively) than from house shrews. Torque teno virus sequences had higher detection rates in the serum samples of rats and house shrews (52.72% and 5.26%, respectively) than in the liver. Near-full length genomes of pegivirus and torque teno virus were amplified. This study is the first to compare the viral communities in the liver of bats, rats, mice, and house shrews. Its findings expand our understanding of the virome in the liver of these animals and provide an insight into hepatitis-related viruses.
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Affiliation(s)
- Wenqiao He
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
| | - Yuhan Gao
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
| | - Yuqi Wen
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
| | - Xuemei Ke
- Xiamen Center for Disease Control and Prevention, Xiamen, China
| | - Zejin Ou
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
| | - Yongzhi Li
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
| | - Huan He
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
| | - Qing Chen
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
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Lazov CM, Belsham GJ, Bøtner A, Rasmussen TB. Full-Genome Sequences of Alphacoronaviruses and Astroviruses from Myotis and Pipistrelle Bats in Denmark. Viruses 2021; 13:1073. [PMID: 34199948 PMCID: PMC8229204 DOI: 10.3390/v13061073] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/28/2021] [Accepted: 06/02/2021] [Indexed: 12/16/2022] Open
Abstract
Bat species worldwide are receiving increased attention for the discovery of emerging viruses, cross-species transmission, and zoonoses, as well as for characterizing virus infections specific to bats. In a previous study, we investigated the presence of coronaviruses in faecal samples from bats at different locations in Denmark, and made phylogenies based on short, partial ORF1b sequences. In this study, selected samples containing bat coronaviruses from three different bat species were analysed, using a non-targeted approach of next-generation sequencing. From the resulting metagenomics data, we assembled full-genome sequences of seven distinct alphacoronaviruses, three astroviruses, and a polyomavirus, as well as partial genome sequences of rotavirus H and caliciviruses, from the different bat species. Comparisons to published sequences indicate that the bat alphacoronaviruses belong to three different subgenera-i.e., Pedacovirus, Nyctacovirus, and Myotacovirus-that the astroviruses may be new species in the genus Mamastrovirus, and that the polyomavirus could also be a new species, but unassigned to a genus. Furthermore, several viruses of invertebrates-including two Rhopalosiphum padi (aphid) viruses and a Kadipiro virus-present in the faecal material were assembled. Interestingly, this is the first detection in Europe of a Kadipiro virus.
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Affiliation(s)
- Christina M. Lazov
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kongens Lyngby, Denmark;
| | - Graham J. Belsham
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (G.J.B.); (A.B.)
| | - Anette Bøtner
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (G.J.B.); (A.B.)
| | - Thomas Bruun Rasmussen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, 2300 Copenhagen, Denmark
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20
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Darcissac E, Donato D, de Thoisy B, Lacoste V, Lavergne A. Paramyxovirus circulation in bat species from French Guiana. INFECTION GENETICS AND EVOLUTION 2021; 90:104769. [PMID: 33588065 DOI: 10.1016/j.meegid.2021.104769] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/08/2021] [Accepted: 02/10/2021] [Indexed: 12/24/2022]
Abstract
Bats are recognized as reservoirs of numerous viruses. Among them, paramyxoviruses, for example, Hendra and Nipah viruses, are highly pathogenic to humans. Nothing is known regarding the circulation of this viral family in bats from French Guiana. To search for the presence of paramyxoviruses in this territory, 103 bats of seven different species were sampled and screened using a molecular approach. Four distinct paramyxovirus sequences were detected from three bat species (Desmodus rotundus, Carollia perspicillata, and Pteronotus alitonus) at high prevalence rates. In D. rotundus, two types of paramyxovirus co-circulate, with most of the bats co-infected. The phylogenetic analysis of these sequences revealed that three of them were closely related to previously characterized sequences from D. rotundus, C. perspicillata, and P. parnellii from Brazil and Costa Rica. The fourth sequence, identified in D. rotundus, was closely related to the one detected in P. alitonus in French Guiana and to previously described sequences detected in P. parnellii in Costa Rica. All paramyxovirus sequences detected in this study are close to the Jeilongvirus genus. Altogether, our results and those of previous studies indicate a wide geographical distribution of these paramyxoviruses (from Central to South America) and suggest potential cross-species transmissions of paramyxoviruses between two different bat families: Mormoopidae (P. alitonus) and Phyllostomidae (D. rotundus). In addition, their closeness to paramyxoviruses identified in rodents emphasizes the need to investigate the role of these animals as potential reservoirs or incidental hosts. Finally, the high prevalence rates of some paramyxoviruses in certain bat species, associated with the presence of large bat colonies and, in some cases, their potential proximity with humans are all parameters that can contribute to the risk of cross-species transmission between bat species and to the emergence of new paramyxoviruses in humans, a risk that deserves further investigation.
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Affiliation(s)
- Edith Darcissac
- Laboratoire des Interaction Virus Hôtes, Institut Pasteur de la Guyane, Cayenne, French Guiana.
| | - Damien Donato
- Laboratoire des Interaction Virus Hôtes, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Benoît de Thoisy
- Laboratoire des Interaction Virus Hôtes, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Vincent Lacoste
- Laboratoire des Interaction Virus Hôtes, Institut Pasteur de la Guyane, Cayenne, French Guiana; Département de Virologie, Institut Pasteur, Paris, France
| | - Anne Lavergne
- Laboratoire des Interaction Virus Hôtes, Institut Pasteur de la Guyane, Cayenne, French Guiana.
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At Least Seven Distinct Rotavirus Genotype Constellations in Bats with Evidence of Reassortment and Zoonotic Transmissions. mBio 2021; 12:mBio.02755-20. [PMID: 33468689 PMCID: PMC7845630 DOI: 10.1128/mbio.02755-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The increased research on bat coronaviruses after severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) allowed the very rapid identification of SARS-CoV-2. This is an excellent example of the importance of knowing viruses harbored by wildlife in general, and bats in particular, for global preparedness against emerging viral pathogens. Bats host many viruses pathogenic to humans, and increasing evidence suggests that rotavirus A (RVA) also belongs to this list. Rotaviruses cause diarrheal disease in many mammals and birds, and their segmented genomes allow them to reassort and increase their genetic diversity. Eighteen out of 2,142 bat fecal samples (0.8%) collected from Europe, Central America, and Africa were PCR-positive for RVA, and 11 of those were fully characterized using viral metagenomics. Upon contrasting their genomes with publicly available data, at least 7 distinct bat RVA genotype constellations (GCs) were identified, which included evidence of reassortments and 6 novel genotypes. Some of these constellations are spread across the world, whereas others appear to be geographically restricted. Our analyses also suggest that several unusual human and equine RVA strains might be of bat RVA origin, based on their phylogenetic clustering, despite various levels of nucleotide sequence identities between them. Although SA11 is one of the most widely used reference strains for RVA research and forms the backbone of a reverse genetics system, its origin remained enigmatic. Remarkably, the majority of the genotypes of SA11-like strains were shared with Gabonese bat RVAs, suggesting a potential common origin. Overall, our findings suggest an underexplored genetic diversity of RVAs in bats, which is likely only the tip of the iceberg. Increasing contact between humans and bat wildlife will further increase the zoonosis risk, which warrants closer attention to these viruses.
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Komoto S, Tacharoenmuang R, Guntapong R, Upachai S, Singchai P, Ide T, Fukuda S, Hatazawa R, Sutthiwarakom K, Kongjorn S, Onvimala N, Luechakham T, Sriwanthana B, Murata T, Uppapong B, Taniguchi K. Genomic characterization of a novel G3P[10] rotavirus strain from a diarrheic child in Thailand: Evidence for bat-to-human zoonotic transmission. INFECTION GENETICS AND EVOLUTION 2021; 87:104667. [DOI: 10.1016/j.meegid.2020.104667] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/18/2020] [Accepted: 12/02/2020] [Indexed: 02/04/2023]
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AL-Eitan LN, Tarkhan AH, Alghamdi MA, Marston DA, Wu G, McElhinney LM, Brown IH, Fooks AR. Bat-Borne Coronaviruses in Jordan and Saudi Arabia: A Threat to Public Health? Viruses 2020; 12:E1413. [PMID: 33316899 PMCID: PMC7764733 DOI: 10.3390/v12121413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/30/2020] [Accepted: 12/03/2020] [Indexed: 11/22/2022] Open
Abstract
Emerging infectious diseases are of great concern to public health, as highlighted by the ongoing coronavirus disease 2019 (COVID-19) pandemic. Such diseases are of particular danger during mass gathering and mass influx events, as large crowds of people in close proximity to each other creates optimal opportunities for disease transmission. The Hashemite Kingdom of Jordan and the Kingdom of Saudi Arabia are two countries that have witnessed mass gatherings due to the arrival of Syrian refugees and the annual Hajj season. The mass migration of people not only brings exotic diseases to these regions but also brings new diseases back to their own countries, e.g., the outbreak of MERS in South Korea. Many emerging pathogens originate in bats, and more than 30 bat species have been identified in these two countries. Some of those bat species are known to carry viruses that cause deadly diseases in other parts of the world, such as the rabies virus and coronaviruses. However, little is known about bats and the pathogens they carry in Jordan and Saudi Arabia. Here, the importance of enhanced surveillance of bat-borne infections in Jordan and Saudi Arabia is emphasized, promoting the awareness of bat-borne diseases among the general public and building up infrastructure and capability to fill the gaps in public health preparedness to prevent future pandemics.
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Affiliation(s)
- Laith N. AL-Eitan
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan;
| | - Amneh H. Tarkhan
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan;
| | - Mansour A. Alghamdi
- Department of Anatomy, College of Medicine, King Khalid University, Abha 61421, Saudi Arabia;
- Genomics and Personalized Medicine Unit, College of Medicine, King Khalid University, Abha 61421, Saudi Arabia
| | - Denise A. Marston
- Department of Virology, Animal and Plant Health Agency (APHA, Weybridge), Surrey KT15 3NB, UK; (D.A.M.); (G.W.); (L.M.M.); (I.H.B.); (A.R.F.)
| | - Guanghui Wu
- Department of Virology, Animal and Plant Health Agency (APHA, Weybridge), Surrey KT15 3NB, UK; (D.A.M.); (G.W.); (L.M.M.); (I.H.B.); (A.R.F.)
| | - Lorraine M. McElhinney
- Department of Virology, Animal and Plant Health Agency (APHA, Weybridge), Surrey KT15 3NB, UK; (D.A.M.); (G.W.); (L.M.M.); (I.H.B.); (A.R.F.)
| | - Ian H. Brown
- Department of Virology, Animal and Plant Health Agency (APHA, Weybridge), Surrey KT15 3NB, UK; (D.A.M.); (G.W.); (L.M.M.); (I.H.B.); (A.R.F.)
| | - Anthony R. Fooks
- Department of Virology, Animal and Plant Health Agency (APHA, Weybridge), Surrey KT15 3NB, UK; (D.A.M.); (G.W.); (L.M.M.); (I.H.B.); (A.R.F.)
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Santiago-Rodriguez TM, Hollister EB. Potential Applications of Human Viral Metagenomics and Reference Materials: Considerations for Current and Future Viruses. Appl Environ Microbiol 2020; 86:e01794-20. [PMID: 32917759 PMCID: PMC7642086 DOI: 10.1128/aem.01794-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Viruses are ubiquitous particles comprising genetic material that can infect bacteria, archaea, and fungi, as well as human and other animal cells. Given that determining virus composition and function in association with states of human health and disease is of increasing interest, we anticipate that the field of viral metagenomics will continue to expand and be applied in a variety of areas ranging from surveillance to discovery and will rely heavily upon the continued development of reference materials and databases. Information regarding viral composition and function readily translates into biological and clinical applications, including the rapid sequence identification of pathogenic viruses in various sample types. However, viral metagenomic approaches often lack appropriate standards and reference materials to enable cross-study comparisons and assess potential biases which can be introduced at the various stages of collection, storage, processing, and sequence analysis. In addition, implementation of appropriate viral reference materials can aid in the benchmarking of current and development of novel assays for virus identification, discovery, and surveillance. As the field of viral metagenomics expands and standardizes, results will continue to translate into diverse applications.
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Islam A, Hossain ME, Rostal MK, Ferdous J, Islam A, Hasan R, Miah M, Rahman M, Rahman MZ, Daszak P, Epstein JH. Epidemiology and Molecular Characterization of Rotavirus A in Fruit Bats in Bangladesh. ECOHEALTH 2020; 17:398-405. [PMID: 32876756 PMCID: PMC7464061 DOI: 10.1007/s10393-020-01488-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 07/07/2020] [Accepted: 07/28/2020] [Indexed: 05/06/2023]
Abstract
Rotavirus A (RVA) is the primary cause of acute dehydrating diarrhea in human and numerous animal species. Animal-to-human interspecies transmission is one of the evolutionary mechanisms driving rotavirus strain diversity in humans. We screened fresh feces from 416 bats (201 Pteropus medius, 165 Rousettus leschenaultii and 50 Taphozous melanopogon) for RVA using rRT-PCR. We detected a prevalence of 7% (95% CI 3.5-10.8) and 2% (95% CI 0.4-5.2) in P. medius and R. leschenaultii, respectively. We did not detect RVA in the insectivorous bat (T. melanopogon). We identified RVA strains similar to the human strains of G1 and G8 based on sequence-based genotyping, which underscores the importance of including wildlife species in surveillance for zoonotic pathogens to understand pathogen transmission and evolution better.
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Affiliation(s)
- Ariful Islam
- EcoHealth Alliance, 460 West 34th Street, Suite 17, New York, NY, 10001, USA
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Mohammad Enayet Hossain
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Melinda K Rostal
- EcoHealth Alliance, 460 West 34th Street, Suite 17, New York, NY, 10001, USA
| | - Jinnat Ferdous
- EcoHealth Alliance, 460 West 34th Street, Suite 17, New York, NY, 10001, USA
- Institute of Epidemiology, Disease Control and Research (IEDCR), Mohakhali, Dhaka, 1212, Bangladesh
| | - Ausraful Islam
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Rashedul Hasan
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mojnu Miah
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mustafizur Rahman
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mohammed Ziaur Rahman
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Peter Daszak
- EcoHealth Alliance, 460 West 34th Street, Suite 17, New York, NY, 10001, USA
| | - Jonathan H Epstein
- EcoHealth Alliance, 460 West 34th Street, Suite 17, New York, NY, 10001, USA.
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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: 2.8] [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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Algahtani H, Shirah B, Chtourou E, Abuhawi O, Abdelghaffar N, Alshehri M. Feral dog bite causing paralytic rabies: Difficult diagnosis and failure of prevention. SAUDI JOURNAL FOR HEALTH SCIENCES 2020. [DOI: 10.4103/sjhs.sjhs_106_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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A Duarte M, F Silva JM, R Brito C, S Teixeira D, L Melo F, M Ribeiro B, Nagata T, S Campos F. Faecal Virome Analysis of Wild Animals from Brazil. Viruses 2019; 11:E803. [PMID: 31480274 PMCID: PMC6784175 DOI: 10.3390/v11090803] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/27/2019] [Accepted: 08/28/2019] [Indexed: 12/15/2022] Open
Abstract
The Brazilian Cerrado fauna shows very wide diversity and can be a potential viral reservoir. Therefore, the animal's susceptibility to some virus can serve as early warning signs of potential human virus diseases. Moreover, the wild animal virome of this biome is unknown. Based on this scenario, high-throughput sequencing contributes a robust tool for the identification of known and unknown virus species in this environment. In the present study, faeces samples from cerrado birds (Psittacara leucophthalmus, Amazona aestiva, and Sicalis flaveola) and mammals (Didelphis albiventris, Sapajus libidinosus, and Galictis cuja) were collected at the Veterinary Hospital, University of Brasília. Viral nucleic acid was extracted, submitted to random amplification, and sequenced by Illumina HiSeq platform. The reads were de novo assembled, and the identities of the contigs were evaluated by Blastn and tblastx searches. Most viral contigs analyzed were closely related to bacteriophages. Novel archaeal viruses of the Smacoviridae family were detected. Moreover, sequences of members of Adenoviridae, Anelloviridae, Circoviridae, Caliciviridae, and Parvoviridae families were identified. Complete and nearly complete genomes of known anelloviruses, circoviruses, and parvoviruses were obtained, as well as putative novel species. We demonstrate that the metagenomics approach applied in this work was effective for identification of known and putative new viruses in faeces samples from Brazilian Cerrado fauna.
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Affiliation(s)
- Matheus A Duarte
- Faculdade de Agronomia e Veterinária, Universidade de Brasília, Brasília-DF 70.910-900, Brazil
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília-DF 70.910-900, Brazil
| | - João M F Silva
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília-DF 70.910-900, Brazil
| | - Clara R Brito
- Faculdade de Agronomia e Veterinária, Universidade de Brasília, Brasília-DF 70.910-900, Brazil
| | - Danilo S Teixeira
- Núcleo de Atendimento e Pesquisa de Animais Silvestres, Universidade Estadual de Santa Cruz, Ilhéus-BA 45.662-900, Brazil
| | - Fernando L Melo
- Departamento de Fitopatologia, Instituto de Biologia, Universidade de Brasília, Brasília-DF 70.910-900, Brazil
| | - Bergmann M Ribeiro
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília-DF 70.910-900, Brazil
| | - Tatsuya Nagata
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília-DF 70.910-900, Brazil
| | - Fabrício S Campos
- Laboratório de Bioinformática e Biotecnologia, Campus de Gurupi, Universidade Federal do Tocantins, Tocantins-TO 77.410-570, Brazil.
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