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Cohen LE, Fagre AC, Chen B, Carlson CJ, Becker DJ. Coronavirus sampling and surveillance in bats from 1996-2019: a systematic review and meta-analysis. Nat Microbiol 2023; 8:1176-1186. [PMID: 37231088 PMCID: PMC10234814 DOI: 10.1038/s41564-023-01375-1] [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: 06/15/2022] [Accepted: 03/24/2023] [Indexed: 05/27/2023]
Abstract
The emergence of SARS-CoV-2 highlights a need for evidence-based strategies to monitor bat viruses. We performed a systematic review of coronavirus sampling (testing for RNA positivity) in bats globally. We identified 110 studies published between 2005 and 2020 that collectively reported positivity from 89,752 bat samples. We compiled 2,274 records of infection prevalence at the finest methodological, spatiotemporal and phylogenetic level of detail possible from public records into an open, static database named datacov, together with metadata on sampling and diagnostic methods. We found substantial heterogeneity in viral prevalence across studies, reflecting spatiotemporal variation in viral dynamics and methodological differences. Meta-analysis identified sample type and sampling design as the best predictors of prevalence, with virus detection maximized in rectal and faecal samples and by repeat sampling of the same site. Fewer than one in five studies collected and reported longitudinal data, and euthanasia did not improve virus detection. We show that bat sampling before the SARS-CoV-2 pandemic was concentrated in China, with research gaps in South Asia, the Americas and sub-Saharan Africa, and in subfamilies of phyllostomid bats. We propose that surveillance strategies should address these gaps to improve global health security and enable the origins of zoonotic coronaviruses to be identified.
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Affiliation(s)
- Lily E Cohen
- Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Anna C Fagre
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Binqi Chen
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC, USA
| | - Colin J Carlson
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC, USA
| | - Daniel J Becker
- Department of Biology, University of Oklahoma, Norman, OK, USA
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2
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Intestinal Tropism of a Betacoronavirus ( Merbecovirus) in Nathusius's Pipistrelle Bat ( Pipistrellus nathusii), Its Natural Host. J Virol 2023; 97:e0009923. [PMID: 36856426 PMCID: PMC10062147 DOI: 10.1128/jvi.00099-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
The emergence of several bat coronavirus-related disease outbreaks in human and domestic animals has fueled surveillance of coronaviruses in bats worldwide. However, little is known about how these viruses interact with their natural hosts. We demonstrate a Betacoronavirus (subgenus Merbecovirus), PN-βCoV, in the intestine of its natural host, Nathusius's Pipistrelle Bat (Pipistrellus nathusii), by combining molecular and microscopy techniques. Eighty-eight P. nathusii bat carcasses were tested for PN-βCoV RNA by RT-qPCR, of which 25 bats (28%) tested positive. PN-βCoV RNA was more often detected in samples of the intestinal tract than in other sample types. In addition, viral RNA loads were higher in intestinal samples compared to other sample types, both on average and in each individual bat. In one bat, we demonstrated Merbecovirus antigen and PN-βCoV RNA expression in intestinal epithelium and the underlying connective tissue using immunohistochemistry and in situ hybridization, respectively. These results indicate that PN-βCoV has a tropism for the intestinal epithelium of its natural host, Nathusius's Pipistrelle Bat, and imply that the fecal-oral route is a possible route of transmission. IMPORTANCE Virtually all mammal species circulate coronaviruses. Most of these viruses will infect one host species; however, coronaviruses are known to include species that can infect multiple hosts, for example the well-known virus that caused a pandemic, SARS-CoV-2. Chiroptera (bats) include over 1,400 different species, which are expected to harbor a great variety of coronaviruses. However, we know very little about how any of these coronaviruses interact with their bat hosts; for example, we do not know their modes of transmissions, or which cells they infect. Thus, we have a limited understanding of coronavirus infections in this important host group. The significance of our study is that we learned that a bat coronavirus that occurs in a common bat species in Europe has a tropism for the intestines. This implies the fecal-oral route is a likely transmission route.
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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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Woolaston K, Nay Z, Baker ML, Brockett C, Bruce M, Degeling C, Gilbert J, Jackson B, Johnson H, Peel A, Sahibzada S, Oskam C, Hewitt CL. An argument for pandemic risk management using a multidisciplinary One Health approach to governance: an Australian case study. Global Health 2022; 18:73. [PMID: 35883185 PMCID: PMC9321311 DOI: 10.1186/s12992-022-00850-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/19/2022] [Indexed: 11/22/2022] Open
Abstract
The emergence of SARS-CoV-2 and the subsequent COVID-19 pandemic has resulted in significant global impact. However, COVID-19 is just one of several high-impact infectious diseases that emerged from wildlife and are linked to the human relationship with nature. The rate of emergence of new zoonoses (diseases of animal origin) is increasing, driven by human-induced environmental changes that threaten biodiversity on a global scale. This increase is directly linked to environmental drivers including biodiversity loss, climate change and unsustainable resource extraction. Australia is a biodiversity hotspot and is subject to sustained and significant environmental change, increasing the risk of it being a location for pandemic origin. Moreover, the global integration of markets means that consumption trends in Australia contributes to the risk of disease spill-over in our regional neighbours in Asia-Pacific, and beyond. Despite the clear causal link between anthropogenic pressures on the environment and increasing pandemic risks, Australia’s response to the COVID-19 pandemic, like most of the world, has centred largely on public health strategies, with a clear focus on reactive management. Yet, the span of expertise and evidence relevant to the governance of pandemic risk management is much wider than public health and epidemiology. It involves animal/wildlife health, biosecurity, conservation sciences, social sciences, behavioural psychology, law, policy and economic analyses to name just a few. The authors are a team of multidisciplinary practitioners and researchers who have worked together to analyse, synthesise, and harmonise the links between pandemic risk management approaches and issues in different disciplines to provide a holistic overview of current practice, and conclude the need for reform in Australia. We discuss the adoption of a comprehensive and interdisciplinary ‘One Health’ approach to pandemic risk management in Australia. A key goal of the One Health approach is to be proactive in countering threats of emerging infectious diseases and zoonoses through a recognition of the interdependence between human, animal, and environmental health. Developing ways to implement a One Health approach to pandemic prevention would not only reduce the risk of future pandemics emerging in or entering Australia, but also provide a model for prevention strategies around the world.
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Affiliation(s)
- Katie Woolaston
- School of Law, Queensland University of Technology, Brisbane, Australia.
| | - Zoe Nay
- School of Law, Queensland University of Technology, Brisbane, Australia
| | - Michelle L Baker
- CSIRO, Health and Biosecurity Business Unit, Australian Centre for Disease Preparedness, Geelong, Australia
| | - Callum Brockett
- School of Law, Queensland University of Technology, Brisbane, Australia
| | - Mieghan Bruce
- Biosecurity and One Health Research Centre, Harry Butler Institute, Murdoch University, Western Australia, Australia
| | - Chris Degeling
- Australian Centre for Health Engagement Evidence and Values, School of Health and Society, University of Wollongong, New South Wales, Australia
| | - Joshua Gilbert
- Worimi agriculturalist and researcher, Policy Advisor at the Jumbunna Institute for Indigenous Education and Research, University of Technology Sydney, Australia and PhD Candidate at Charles Sturt University, Bathurst, Australia
| | - Bethany Jackson
- Biosecurity and One Health Research Centre, Harry Butler Institute, Murdoch University, Western Australia, Australia
| | - Hope Johnson
- School of Law, Queensland University of Technology, Brisbane, Australia
| | - Alison Peel
- Centre for Planetary Health and Food Security, Griffith University, Brisbane, Australia
| | - Shafi Sahibzada
- Biosecurity and One Health Research Centre, Harry Butler Institute, Murdoch University, Western Australia, Australia
| | - Charlotte Oskam
- Biosecurity and One Health Research Centre, Harry Butler Institute, Murdoch University, Western Australia, Australia
| | - Chad L Hewitt
- Biosecurity and One Health Research Centre, Harry Butler Institute, Murdoch University, Western Australia, Australia
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Cox-Witton K, Baker ML, Edson D, Peel AJ, Welbergen JA, Field H. Risk of SARS-CoV-2 transmission from humans to bats - An Australian assessment. One Health 2021; 13:100247. [PMID: 33969168 PMCID: PMC8092928 DOI: 10.1016/j.onehlt.2021.100247] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 12/18/2022] Open
Abstract
SARS-CoV-2, the cause of COVID-19, infected over 100 million people globally by February 2021. Reverse zoonotic transmission of SARS-CoV-2 from humans to other species has been documented in pet cats and dogs, big cats and gorillas in zoos, and farmed mink. As SARS-CoV-2 is closely related to known bat viruses, assessment of the potential risk of transmission of the virus from humans to bats, and its subsequent impacts on conservation and public health, is warranted. A qualitative risk assessment was conducted by a multi-disciplinary group to assess this risk in bats in the Australian context, with the aim of informing risk management strategies for human activities involving interactions with bats. The overall risk of SARS-CoV-2 establishing in an Australian bat population was assessed to be Low, however with a High level of uncertainty. The outcome of the assessment indicates that, for the Australian situation where the prevalence of COVID-19 in humans is very low, it is reasonable for research and rehabilitation of bats to continue, provided additional biosecurity measures are applied. Risk assessment is challenging for an emerging disease where information is lacking and the situation is changing rapidly; assessments should be revised if human prevalence or other important factors change significantly. The framework developed here, based on established animal disease risk assessment approaches adapted to assess reverse zoonotic transmission, has potential application to a range of wildlife species and situations.
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Affiliation(s)
| | - Michelle L. Baker
- CSIRO, Health and Biosecurity Business Unit, Australian Centre for Disease Preparedness, Geelong, VIC 3220, Australia
| | - Dan Edson
- Australian Department of Agriculture, Water and the Environment, Canberra, ACT, 2601, Australia
| | - Alison J. Peel
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD, 4111, Australia
| | - Justin A. Welbergen
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753, Australia
- Australasian Bat Society Inc, Milsons Point NSW 1565, Australia
| | - Hume Field
- EcoHealth Alliance, New York, NY, USA
- The University of Queensland, St Lucia, QLD, 4072, Australia
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6
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Hoarau AOG, Goodman SM, Al Halabi D, Ramasindrazana B, Lagadec E, Le Minter G, Köster M, Dos Santos A, Schoeman MC, Gudo ES, Mavingui P, Lebarbenchon C. Investigation of astrovirus, coronavirus and paramyxovirus co-infections in bats in the western Indian Ocean. Virol J 2021; 18:205. [PMID: 34641936 PMCID: PMC8506490 DOI: 10.1186/s12985-021-01673-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/28/2021] [Indexed: 11/10/2022] Open
Abstract
Co-infections have a key role in virus transmission in wild reservoir hosts. We investigated the simultaneous presence of astroviruses, coronaviruses, and paramyxoviruses in bats from Madagascar, Mayotte, Mozambique, and Reunion Island. A total of 871 samples from 28 bat species representing 8 families were tested by polymerase chain reactions (PCRs) targeting the RNA-dependent RNA-polymerase genes. Overall, 2.4% of bats tested positive for the presence of at least two viruses, only on Madagascar and in Mozambique. Significant variation in the proportion of co-infections was detected among bat species, and some combinations of co-infection were more common than others. Our findings support that co-infections of the three targeted viruses occur in bats in the western Indian Ocean region, although further studies are needed to assess their epidemiological consequences.
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Affiliation(s)
- Axel O G Hoarau
- Processus Infectieux en Milieu Insulaire Tropical, INSERM 1187, CNRS 9192, IRD 249, Université de La Réunion, Sainte-Clotilde, La Réunion, France.
| | - Steven M Goodman
- Association Vahatra, Antananarivo, Madagascar.,Field Museum of Natural History, Chicago, USA
| | - Dana Al Halabi
- Processus Infectieux en Milieu Insulaire Tropical, INSERM 1187, CNRS 9192, IRD 249, Université de La Réunion, Sainte-Clotilde, La Réunion, France
| | - Beza Ramasindrazana
- Processus Infectieux en Milieu Insulaire Tropical, INSERM 1187, CNRS 9192, IRD 249, Université de La Réunion, Sainte-Clotilde, La Réunion, France.,Association Vahatra, Antananarivo, Madagascar.,Institut Pasteur de Madagascar, Antananarivo 101, BP 1274, Ambatofotsikely, Madagascar
| | - Erwan Lagadec
- Processus Infectieux en Milieu Insulaire Tropical, INSERM 1187, CNRS 9192, IRD 249, Université de La Réunion, Sainte-Clotilde, La Réunion, France
| | - Gildas Le Minter
- Processus Infectieux en Milieu Insulaire Tropical, INSERM 1187, CNRS 9192, IRD 249, Université de La Réunion, Sainte-Clotilde, La Réunion, France
| | - Marie Köster
- Processus Infectieux en Milieu Insulaire Tropical, INSERM 1187, CNRS 9192, IRD 249, Université de La Réunion, Sainte-Clotilde, La Réunion, France
| | | | - M Corrie Schoeman
- School of Life Sciences, University of Kwa-Zulu Natal, Kwa-Zulu Natal, South Africa
| | | | - Patrick Mavingui
- Processus Infectieux en Milieu Insulaire Tropical, INSERM 1187, CNRS 9192, IRD 249, Université de La Réunion, Sainte-Clotilde, La Réunion, France
| | - Camille Lebarbenchon
- Processus Infectieux en Milieu Insulaire Tropical, INSERM 1187, CNRS 9192, IRD 249, Université de La Réunion, Sainte-Clotilde, La Réunion, France
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7
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Do HQ, Nguyen VG, Chung CU, Jeon YS, Shin S, Jang KC, Pham LBH, Kong A, Kim CU, Park YH, Park BK, Chung HC. Genomic Characterization of a Novel Alphacoronavirus Isolated from Bats, Korea, 2020. Viruses 2021; 13:v13102041. [PMID: 34696471 PMCID: PMC8540747 DOI: 10.3390/v13102041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 12/19/2022] Open
Abstract
Coronavirus, an important zoonotic disease, raises concerns of future pandemics. The bat is considered a source of noticeable viruses resulting in human and livestock infections, especially the coronavirus. Therefore, surveillance and genetic analysis of coronaviruses in bats are essential in order to prevent the risk of future diseases. In this study, the genome of HCQD-2020, a novel alphacoronavirus detected in a bat (Eptesicus serotinus), was assembled and described using next-generation sequencing and bioinformatics analysis. The comparison of the whole-genome sequence and the conserved amino acid sequence of replicated proteins revealed that the new strain was distantly related with other known species in the Alphacoronavirus genus. Phylogenetic construction indicated that this strain formed a separated branch with other species, suggesting a new species of Alphacoronavirus. Additionally, in silico prediction also revealed the risk of cross-species infection of this strain, especially in the order Artiodactyla. In summary, this study provided the genetic characteristics of a possible new species belonging to Alphacoronavirus.
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Affiliation(s)
- Hai-Quynh Do
- Virology Lab, Department of Veterinary Medicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea;
| | - Van-Giap Nguyen
- Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi 100000, Vietnam;
| | - Chul-Un Chung
- Department of Life Science, Dongguk University, Gyeongju 38066, Korea;
- Correspondence: (C.-U.C.); (B.-K.P.); (H.-C.C.); Tel.: +82-2-880-1255 (C.-U.C., B.-K.P. & H.-C.C.); Fax: +82-2-885-0263 (C.-U.C., B.-K.P. & H.-C.C.)
| | - Yong-Shin Jeon
- Department of Life Science, Dongguk University, Gyeongju 38066, Korea;
| | - Sook Shin
- Noah Biotech Research Unit, Noah Biotech Co. Ltd, Suwon 16612, Korea; (S.S.); (K.-C.J.); (Y.-H.P.)
| | - Kuem-Chan Jang
- Noah Biotech Research Unit, Noah Biotech Co. Ltd, Suwon 16612, Korea; (S.S.); (K.-C.J.); (Y.-H.P.)
| | - Le Bich Hang Pham
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi 100000, Vietnam;
| | - Aeri Kong
- Department of Medical Science, University of California, Los Angeles, CA 90095, USA;
| | - Cheong-Ung Kim
- Department of Veterinary Medicine Microbology Lab, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea;
| | - Yong-Ho Park
- Noah Biotech Research Unit, Noah Biotech Co. Ltd, Suwon 16612, Korea; (S.S.); (K.-C.J.); (Y.-H.P.)
| | - Bong-Kyun Park
- Virology Lab, Department of Veterinary Medicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea;
- Correspondence: (C.-U.C.); (B.-K.P.); (H.-C.C.); Tel.: +82-2-880-1255 (C.-U.C., B.-K.P. & H.-C.C.); Fax: +82-2-885-0263 (C.-U.C., B.-K.P. & H.-C.C.)
| | - Hee-Chun Chung
- Virology Lab, Department of Veterinary Medicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea;
- Correspondence: (C.-U.C.); (B.-K.P.); (H.-C.C.); Tel.: +82-2-880-1255 (C.-U.C., B.-K.P. & H.-C.C.); Fax: +82-2-885-0263 (C.-U.C., B.-K.P. & H.-C.C.)
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Simmonds P, Williams S, Harvala H. Understanding the outcomes of COVID-19 - does the current model of an acute respiratory infection really fit? J Gen Virol 2021; 102:001545. [PMID: 33331810 PMCID: PMC8222868 DOI: 10.1099/jgv.0.001545] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 12/01/2020] [Indexed: 12/11/2022] Open
Abstract
Although coronavirus disease 2019 (COVID-19) is regarded as an acute, resolving infection followed by the development of protective immunity, recent systematic literature review documents evidence for often highly prolonged shedding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in respiratory and faecal samples, periodic recurrence of PCR positivity in a substantial proportion of individuals and increasingly documented instances of reinfection associated with a lack of protective immunity. This pattern of infection is quite distinct from the acute/resolving nature of other human pathogenic respiratory viruses, such as influenza A virus and respiratory syncytial virus. Prolonged shedding of SARS-CoV-2 furthermore occurs irrespective of disease severity or development of virus-neutralizing antibodies. SARS-CoV-2 possesses an intensely structured RNA genome, an attribute shared with other human and veterinary coronaviruses and with other mammalian RNA viruses such as hepatitis C virus. These are capable of long-term persistence, possibly through poorly understood RNA structure-mediated effects on innate and adaptive host immune responses. The assumption that resolution of COVID-19 and the appearance of anti-SARS-CoV-2 IgG antibodies represents virus clearance and protection from reinfection, implicit for example in the susceptible-infected-recovered (SIR) model used for epidemic prediction, should be rigorously re-evaluated.
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Affiliation(s)
- Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sarah Williams
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Heli Harvala
- National Microbiology Services, NHS Blood and Transplant, London, UK
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9
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Comparison of Selected Characteristics of SARS-CoV-2, SARS-CoV, and HCoV-NL63. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11041497] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The global pandemic known as coronavirus disease 2019 (COVID-19) was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This review article presents the taxonomy of SARS-CoV-2 coronaviruses, which have been classified as the seventh known human pathogenic coronavirus. The etiology of COVID-19 is also briefly discussed. Selected characteristics of SARS-CoV-2, SARS-CoV, and HCoV-NL63 are compared in the article. The angiotensin converting enzyme-2 (ACE-2) has been identified as the receptor for the SARS-CoV-2 viral entry. ACE2 is well-known as a counter-regulator of the renin-angiotensin system (RAAS) and plays a key role in the cardiovascular system. In the therapy of patients with COVID-19, there has been a concern about the use of RAAS inhibitors. As a result, it is hypothesized that ACE inhibitors do not directly affect ACE2 activity in clinical use. Coronaviruses are zoonotic RNA viruses. Identification of the primary causative agent of the SARS-CoV-2 is essential. Sequencing showed that the genome of the Bat CoVRaTG13 virus found in bats matches the genome of up to (96.2%) of SARS-CoV-2 virus. Sufficient knowledge of the molecular and biological mechanisms along with reliable information related to SARS-CoV-2 gives hope for a quick solution to epidemiological questions and therapeutic processes.
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10
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Biodiversity loss and COVID-19 pandemic: The role of bats in the origin and the spreading of the disease. Biochem Biophys Res Commun 2021; 538:2-13. [PMID: 33092787 PMCID: PMC7566801 DOI: 10.1016/j.bbrc.2020.10.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 10/14/2020] [Indexed: 12/15/2022]
Abstract
The loss of biodiversity in the ecosystems has created the general conditions that have favored and, in fact, made possible, the insurgence of the COVID-19 pandemic. A lot of factors have contributed to it: deforestation, changes in forest habitats, poorly regulated agricultural surfaces, mismanaged urban growth. They have altered the composition of wildlife communities, greatly increased the contacts of humans with wildlife, and altered niches that harbor pathogens, increasing their chances to come in contact with humans. Among the wildlife, bats have adapted easily to anthropized environments such as houses, barns, cultivated fields, orchards, where they found the suitable ecosystem to prosper. Bats are major hosts for αCoV and βCoV: evolution has shaped their peculiar physiology and their immune system in a way that makes them resistant to viral pathogens that would instead successfully attack other species, including humans. In time, the coronaviruses that bats host as reservoirs have undergone recombination and other modifications that have increased their ability for inter-species transmission: one modification of particular importance has been the development of the ability to use ACE2 as a receptor in host cells. This particular development in CoVs has been responsible for the serious outbreaks in the last two decades, and for the present COVID-19 pandemic.
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11
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Thompson CW, Phelps KL, Allard MW, Cook JA, Dunnum JL, Ferguson AW, Gelang M, Khan FAA, Paul DL, Reeder DM, Simmons NB, Vanhove MPM, Webala PW, Weksler M, Kilpatrick CW. Preserve a Voucher Specimen! The Critical Need for Integrating Natural History Collections in Infectious Disease Studies. mBio 2021; 12:e02698-20. [PMID: 33436435 PMCID: PMC7844540 DOI: 10.1128/mbio.02698-20] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Despite being nearly 10 months into the COVID-19 (coronavirus disease 2019) pandemic, the definitive animal host for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the causal agent of COVID-19, remains unknown. Unfortunately, similar problems exist for other betacoronaviruses, and no vouchered specimens exist to corroborate host species identification for most of these pathogens. This most basic information is critical to the full understanding and mitigation of emerging zoonotic diseases. To overcome this hurdle, we recommend that host-pathogen researchers adopt vouchering practices and collaborate with natural history collections to permanently archive microbiological samples and host specimens. Vouchered specimens and associated samples provide both repeatability and extension to host-pathogen studies, and using them mobilizes a large workforce (i.e., biodiversity scientists) to assist in pandemic preparedness. We review several well-known examples that successfully integrate host-pathogen research with natural history collections (e.g., yellow fever, hantaviruses, helminths). However, vouchering remains an underutilized practice in such studies. Using an online survey, we assessed vouchering practices used by microbiologists (e.g., bacteriologists, parasitologists, virologists) in host-pathogen research. A much greater number of respondents permanently archive microbiological samples than archive host specimens, and less than half of respondents voucher host specimens from which microbiological samples were lethally collected. To foster collaborations between microbiologists and natural history collections, we provide recommendations for integrating vouchering techniques and archiving of microbiological samples into host-pathogen studies. This integrative approach exemplifies the premise underlying One Health initiatives, providing critical infrastructure for addressing related issues ranging from public health to global climate change and the biodiversity crisis.
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Affiliation(s)
- Cody W Thompson
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
- Museum of Zoology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Marc W Allard
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, College Park, Maryland, USA
| | - Joseph A Cook
- Museum of Southwestern Biology, Biology Department, University of New Mexico, Albuquerque, New Mexico, USA
| | - Jonathan L Dunnum
- Museum of Southwestern Biology, Biology Department, University of New Mexico, Albuquerque, New Mexico, USA
| | - Adam W Ferguson
- Gantz Family Collections Center, Field Museum of Natural History, Chicago, Illinois, USA
| | - Magnus Gelang
- Gothenburg Natural History Museum, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | | | - Deborah L Paul
- Florida State University, Tallahassee, Florida, USA
- Species File Group, University of Illinois, Urbana-Champaign, Illinois, USA
| | | | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Maarten P M Vanhove
- Hasselt University, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Diepenbeek, Belgium
| | - Paul W Webala
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok, Kenya
| | - Marcelo Weksler
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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12
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Boardman WSJ, Baker ML, Boyd V, Crameri G, Peck GR, Reardon T, Smith IG, Caraguel CGB, Prowse TAA. Serological evidence of exposure to a coronavirus antigenically related to severe acute respiratory syndrome virus (SARS-CoV-1) in the Grey-headed flying fox (Pteropus poliocephalus). Transbound Emerg Dis 2020; 68:2628-2632. [PMID: 33142031 DOI: 10.1111/tbed.13908] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/29/2020] [Accepted: 10/29/2020] [Indexed: 12/25/2022]
Abstract
Many infectious pathogens can be transmitted by highly mobile species, like bats that can act as reservoir hosts for viruses such as henipaviruses, lyssaviruses and coronaviruses. In this study, we investigated the seroepidemiology of protein antigens to Severe acute respiratory syndrome virus (SARS-CoV-1) and Middle eastern respiratory syndrome virus (MERS-CoV) in Grey-headed flying foxes (Pteropus poliocephalus) in Adelaide, Australia sampled between September 2015 and February 2018. A total of 301 serum samples were collected and evaluated using a multiplex Luminex binding assay, and median fluorescence intensity thresholds were determined using finite-mixture modelling. We found evidence of antibodies reactive to SARS-CoV-1 or a related antigen with 42.5% (CI: 34.3%-51.2%) seroprevalence but insufficient evidence of reactivity to MERS-CoV antigen. This study provides evidence that the Grey-headed flying foxes sampled in Adelaide have been exposed to a SARS-like coronavirus.
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Affiliation(s)
| | - Michelle L Baker
- Australian Centre for Disease Preparedness, Geelong, Vic, Australia
| | - Victoria Boyd
- Australian Centre for Disease Preparedness, Geelong, Vic, Australia
| | - Gary Crameri
- Australian Centre for Disease Preparedness, Geelong, Vic, Australia
| | - Grantley R Peck
- Australian Centre for Disease Preparedness, Geelong, Vic, Australia
| | | | - Ian G Smith
- The University of Adelaide, Adelaide, SA, Australia.,Zoos South Australia, Adelaide, SA, Australia
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13
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Kumar D, Chauhan G, Kalra S, Kumar B, Gill MS. A perspective on potential target proteins of COVID-19: Comparison with SARS-CoV for designing new small molecules. Bioorg Chem 2020; 104:104326. [PMID: 33142431 PMCID: PMC7524440 DOI: 10.1016/j.bioorg.2020.104326] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/25/2020] [Accepted: 09/26/2020] [Indexed: 02/08/2023]
Abstract
SARS-CoV-2 (COVID-19) epidemic has created an unprecedented medical and economic crisis all over the world. SARS-CoV-2 is found to have more contagious character as compared to MERS-CoV and is spreading in a very fast manner all around the globe. It has affected over 31 million people all over the world till date. This virus shares around 80% of genome similarity with SARS-CoV. In this perspective, we have explored three major targets namely; SARS-CoV-2 spike (S) protein, RNA dependent RNA polymerase, and 3CL or Mpro Protease for the inhibition of SARS-CoV-2. These targets have attracted attention of the medicinal chemists working on computer-aided drug design in developing new small molecules that might inhibit these targets for combating COVID-19 disease. Moreover, we have compared the similarity of these target proteins with earlier reported coronavirus (SARS-CoV). We have observed that both the coronaviruses share around 80% similarity in their amino acid sequence. The key amino acid interactions which can play a crucial role in designing new small molecule inhibitors against COVID-19 have been reported in this perspective. Authors believe that this study will help the medicinal chemists to understand the key amino acids essential for interactions at the active site of target proteins in SARS-CoV-2, based on their similarity with earlier reported viruses. In this review, we have also described the lead molecules under various clinical trials for their efficacy against COVID-19.
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Affiliation(s)
- Devendra Kumar
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Ghal Kalan, G.T Road, Moga, Punjab 142001, India
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501 Sur, 64849 Monterrey, Nuevo León, Mexico
| | - Sourav Kalra
- Department of Pharmaceutical Technology (Process Chemistry), National Institute of Pharmaceutical Education and Research, SAS Nagar, Sector 67, Mohali, Punjab 160062, India
| | - Bhupinder Kumar
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Ghal Kalan, G.T Road, Moga, Punjab 142001, India.
| | - Manjinder Singh Gill
- Department of Pharmaceutical Technology (Process Chemistry), National Institute of Pharmaceutical Education and Research, SAS Nagar, Sector 67, Mohali, Punjab 160062, India.
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14
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Simmonds P. Pervasive RNA Secondary Structure in the Genomes of SARS-CoV-2 and Other Coronaviruses. mBio 2020; 11:e01661-20. [PMID: 33127861 PMCID: PMC7642675 DOI: 10.1128/mbio.01661-20] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/12/2020] [Indexed: 12/25/2022] Open
Abstract
The ultimate outcome of the coronavirus disease 2019 (COVID-19) pandemic is unknown and is dependent on a complex interplay of its pathogenicity, transmissibility, and population immunity. In the current study, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was investigated for the presence of large-scale internal RNA base pairing in its genome. This property, termed genome-scale ordered RNA structure (GORS) has been previously associated with host persistence in other positive-strand RNA viruses, potentially through its shielding effect on viral RNA recognition in the cell. Genomes of SARS-CoV-2 were remarkably structured, with minimum folding energy differences (MFEDs) of 15%, substantially greater than previously examined viruses such as hepatitis C virus (HCV) (MFED of 7 to 9%). High MFED values were shared with all coronavirus genomes analyzed and created by several hundred consecutive energetically favored stem-loops throughout the genome. In contrast to replication-associated RNA structure, GORS was poorly conserved in the positions and identities of base pairing with other sarbecoviruses-even similarly positioned stem-loops in SARS-CoV-2 and SARS-CoV rarely shared homologous pairings, indicative of more rapid evolutionary change in RNA structure than in the underlying coding sequences. Sites predicted to be base paired in SARS-CoV-2 showed less sequence diversity than unpaired sites, suggesting that disruption of RNA structure by mutation imposes a fitness cost on the virus that is potentially restrictive to its longer evolution. Although functionally uncharacterized, GORS in SARS-CoV-2 and other coronaviruses represents important elements in their cellular interactions that may contribute to their persistence and transmissibility.IMPORTANCE The detection and characterization of large-scale RNA secondary structure in the genome of SARS-CoV-2 indicate an extraordinary and unsuspected degree of genome structural organization; this could be effectively visualized through a newly developed contour plotting method that displays positions, structural features, and conservation of RNA secondary structure between related viruses. Such RNA structure imposes a substantial evolutionary cost; paired sites showed greater restriction in diversity and represent a substantial additional constraint in reconstructing its molecular epidemiology. Its biological relevance arises from previously documented associations between possession of structured genomes and persistence, as documented for HCV and several other RNA viruses infecting humans and mammals. Shared properties potentially conferred by large-scale structure in SARS-CoV-2 include increasing evidence for prolonged infections and induced immune dysfunction that prevents development of protective immunity. The findings provide an additional element to cellular interactions that potentially influences the natural history of SARS-CoV-2, its pathogenicity, and its transmission.
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Affiliation(s)
- P Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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15
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Vallejo BM, Ong RAC. Policy responses and government science advice for the COVID 19 pandemic in the Philippines: January to April 2020. PROGRESS IN DISASTER SCIENCE 2020; 7:100115. [PMID: 34173440 PMCID: PMC7299863 DOI: 10.1016/j.pdisas.2020.100115] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/14/2020] [Accepted: 06/15/2020] [Indexed: 05/05/2023]
Abstract
In this paper we examine two policy questions about the COVID 19 pandemic in the Philippines. These are science informed policy questions that will have to take into consideration a large degree of uncertainties in outcomes. The first question is on when to lift the Enhanced Community Quarantine (ECQ) as informed by epidemiological modelling. The second deals on how the Philippines can respond to a future pandemic crisis. We review the Philippine government's responses and introduce the complicating scientific, social, and political contexts for both questions and address proposals for strengthening the science advisory structures. We propose a permanent science advisory body for emergencies with the widest source of expertise as needed.
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Affiliation(s)
- Benjamin M Vallejo
- Institute of Environmental Science and Meteorology, University of the Philippines Diliman, Philippines
- Science and Society Program, University of the Philippines Diliman, Philippines
- International Network for Government Science Advice-Asia, Kuala Lumpur, Malaysia
| | - Rodrigo Angelo C Ong
- Institute of Environmental Science and Meteorology, University of the Philippines Diliman, Philippines
- Science and Society Program, University of the Philippines Diliman, Philippines
- College of Medicine, University of the Philippines Manila, Philippines
- International Network for Government Science Advice-Asia, Kuala Lumpur, Malaysia
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16
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Lo VT, Yoon SW, Noh JY, Kim Y, Choi YG, Jeong DG, Kim HK. Long-term surveillance of bat coronaviruses in Korea: Diversity and distribution pattern. Transbound Emerg Dis 2020; 67:2839-2848. [PMID: 32473082 PMCID: PMC7300860 DOI: 10.1111/tbed.13653] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 05/22/2020] [Accepted: 05/23/2020] [Indexed: 12/13/2022]
Abstract
Bats harbour diverse coronaviruses (CoVs), some of which are associated with zoonotic infections, as well as inter‐species transmission. In this study, a total of 512 bat faecal samples from the bat habitats at different geographical locations in South Korea were investigated between 2016 and 2019. Seventy‐eight samples were positive for coronaviruses (15.2%), comprising 68 alphacoronaviruses (13.3%) and 10 betacoronaviruses (2.0%). The positive rates tended to increase during the awakening (April) period. Notably, betacoronaviruses were only found in the site where Rhinolophus ferrumequinum was the major species of bats, and were related to SARS‐ and MERS‐related CoVs identified in China and South Korea, respectively. No betacoronaviruses were closely related to SARS‐CoV‐2 in this study. Alphacoronaviruses were detected in the sites where Hypsugo alaschanicus, Miniopterus fuliginosus, Miniopterus schreibersii, Rhinolophus ferrumequinum, Myotis bombinus, Myotis macrodactylus and Myotis petax were found to be the major bat species. Furthermore, alphacoronaviruses had higher genetic diversity than betacoronaviruses and had a wider distribution in Korea. Considering that different bat species are co‐roosting in crowded conditions in the same habitat, the diverse coronaviruses in Korean bats are likely to undergo cross‐species transmission events due to the richness in host species. Therefore, continuous monitoring should be performed, especially at the awakening time of the hibernating bats in the habitats where diverse bat species co‐roost, to better understand the evolution of coronaviruses in bats.
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Affiliation(s)
- Van Thi Lo
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea.,Bio-Analytical Science Division, Korea University of Science and Technology (UST), Daejeon, Korea
| | - Sun-Woo Yoon
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea.,Bio-Analytical Science Division, Korea University of Science and Technology (UST), Daejeon, Korea
| | - Ji Yeong Noh
- Department of Microbiology, College of Natural Sciences, Chungbuk National University, Cheongju, Korea
| | - Youngji Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Yong Gun Choi
- The Korean Institute of Biospeleology, Daejeon, Korea
| | - Dae Gwin Jeong
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea.,Bio-Analytical Science Division, Korea University of Science and Technology (UST), Daejeon, Korea
| | - Hye Kwon Kim
- Department of Microbiology, College of Natural Sciences, Chungbuk National University, Cheongju, Korea
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17
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Joffrin L, Goodman SM, Wilkinson DA, Ramasindrazana B, Lagadec E, Gomard Y, Le Minter G, Dos Santos A, Corrie Schoeman M, Sookhareea R, Tortosa P, Julienne S, Gudo ES, Mavingui P, Lebarbenchon C. Bat coronavirus phylogeography in the Western Indian Ocean. Sci Rep 2020; 10:6873. [PMID: 32327721 PMCID: PMC7181612 DOI: 10.1038/s41598-020-63799-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/31/2020] [Indexed: 12/28/2022] Open
Abstract
Bats provide key ecosystem services such as crop pest regulation, pollination, seed dispersal, and soil fertilization. Bats are also major hosts for biological agents responsible for zoonoses, such as coronaviruses (CoVs). The islands of the Western Indian Ocean are identified as a major biodiversity hotspot, with more than 50 bat species. In this study, we tested 1,013 bats belonging to 36 species from Mozambique, Madagascar, Mauritius, Mayotte, Reunion Island and Seychelles, based on molecular screening and partial sequencing of the RNA-dependent RNA polymerase gene. In total, 88 bats (8.7%) tested positive for coronaviruses, with higher prevalence in Mozambican bats (20.5% ± 4.9%) as compared to those sampled on islands (4.5% ± 1.5%). Phylogenetic analyses revealed a large diversity of α- and β-CoVs and a strong signal of co-evolution between CoVs and their bat host species, with limited evidence for host-switching, except for bat species sharing day roost sites. These results highlight that strong variation between islands does exist and is associated with the composition of the bat species community on each island. Future studies should investigate whether CoVs detected in these bats have a potential for spillover in other hosts.
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Affiliation(s)
- Léa Joffrin
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France.
| | - Steven M Goodman
- Association Vahatra, Antananarivo, Madagascar
- Field Museum of Natural History, Chicago, USA
| | - David A Wilkinson
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Beza Ramasindrazana
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
- Association Vahatra, Antananarivo, Madagascar
- Beza Ramasindrazana, Institut Pasteur de Madagascar, BP 1274, Ambatofotsikely, Antananarivo, 101, Madagascar
| | - Erwan Lagadec
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Yann Gomard
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Gildas Le Minter
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | | | - M Corrie Schoeman
- School of Life Sciences, University of Kwa-Zulu Natal, Kwa-Zulu Natal, South Africa
| | | | - Pablo Tortosa
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Simon Julienne
- Seychelles Ministry of Health, Victoria, Mahe, Seychelles
| | | | - Patrick Mavingui
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Camille Lebarbenchon
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France.
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18
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Valitutto MT, Aung O, Tun KYN, Vodzak ME, Zimmerman D, Yu JH, Win YT, Maw MT, Thein WZ, Win HH, Dhanota J, Ontiveros V, Smith B, Tremeau-Brevard A, Goldstein T, Johnson CK, Murray S, Mazet J. Detection of novel coronaviruses in bats in Myanmar. PLoS One 2020; 15:e0230802. [PMID: 32271768 PMCID: PMC7144984 DOI: 10.1371/journal.pone.0230802] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/09/2020] [Indexed: 12/25/2022] Open
Abstract
The recent emergence of bat-borne zoonotic viruses warrants vigilant surveillance in their natural hosts. Of particular concern is the family of coronaviruses, which includes the causative agents of severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and most recently, Coronavirus Disease 2019 (COVID-19), an epidemic of acute respiratory illness originating from Wuhan, China in December 2019. Viral detection, discovery, and surveillance activities were undertaken in Myanmar to identify viruses in animals at high risk contact interfaces with people. Free-ranging bats were captured, and rectal and oral swabs and guano samples collected for coronaviral screening using broadly reactive consensus conventional polymerase chain reaction. Sequences from positives were compared to known coronaviruses. Three novel alphacoronaviruses, three novel betacoronaviruses, and one known alphacoronavirus previously identified in other southeast Asian countries were detected for the first time in bats in Myanmar. Ongoing land use change remains a prominent driver of zoonotic disease emergence in Myanmar, bringing humans into ever closer contact with wildlife, and justifying continued surveillance and vigilance at broad scales.
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Affiliation(s)
- Marc T. Valitutto
- Global Health Program, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, District of Columbia, United States of America
| | - Ohnmar Aung
- Global Health Program, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, District of Columbia, United States of America
| | - Kyaw Yan Naing Tun
- Global Health Program, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, District of Columbia, United States of America
| | - Megan E. Vodzak
- Global Health Program, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, District of Columbia, United States of America
| | - Dawn Zimmerman
- Global Health Program, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, District of Columbia, United States of America
| | - Jennifer H. Yu
- Global Health Program, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, District of Columbia, United States of America
| | - Ye Tun Win
- Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock and Irrigation, Naypyitaw, Myanmar
| | - Min Thein Maw
- Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock and Irrigation, Naypyitaw, Myanmar
| | - Wai Zin Thein
- Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock and Irrigation, Naypyitaw, Myanmar
| | - Htay Htay Win
- Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock and Irrigation, Naypyitaw, Myanmar
| | - Jasjeet Dhanota
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Victoria Ontiveros
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Brett Smith
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Alexandre Tremeau-Brevard
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Tracey Goldstein
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Christine K. Johnson
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Suzan Murray
- Global Health Program, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, District of Columbia, United States of America
| | - Jonna Mazet
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
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19
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Sheahan TP, Frieman MB. The continued epidemic threat of SARS-CoV-2 and implications for the future of global public health. Curr Opin Virol 2020; 40:37-40. [PMID: 32569751 PMCID: PMC7269927 DOI: 10.1016/j.coviro.2020.05.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/11/2020] [Accepted: 05/27/2020] [Indexed: 11/17/2022]
Abstract
A new coronavirus (CoV) called SARS-CoV-2 emerged in Wuhan, China in December 2019 as the etiological agent of a viral pneumonia called COVID-19. The global spread of SARS-CoV-2 has been so extensive that the WHO declared COVID-19 a pandemic on March 11, 2020. Below, we discuss the emergence of SARS-CoV-2 and provide the historical context, which strongly suggests emerging CoVs provide an immediate threat to global public health and will continue to do so in the future.
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Affiliation(s)
- Timothy P Sheahan
- University of North Carolina at Chapel Hill, Gillings School of Global Public Health, Chapel Hill, NC, United States
| | - Matthew B Frieman
- Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, MD, United States.
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20
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Prada D, Boyd V, Baker ML, O’Dea M, Jackson B. Viral Diversity of Microbats within the South West Botanical Province of Western Australia. Viruses 2019; 11:E1157. [PMID: 31847282 PMCID: PMC6950384 DOI: 10.3390/v11121157] [Citation(s) in RCA: 15] [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: 11/26/2019] [Revised: 12/06/2019] [Accepted: 12/06/2019] [Indexed: 12/30/2022] Open
Abstract
Bats are known reservoirs of a wide variety of viruses that rarely result in overt clinical disease in the bat host. However, anthropogenic influences on the landscape and climate can change species assemblages and interactions, as well as undermine host-resilience. The cumulative result is a disturbance of bat-pathogen dynamics, which facilitate spillover events to sympatric species, and may threaten bat communities already facing synergistic stressors through ecological change. Therefore, characterisation of viral pathogens in bat communities provides important basal information to monitor and predict the emergence of diseases relevant to conservation and public health. This study used targeted molecular techniques, serological assays and next generation sequencing to characterise adenoviruses, coronaviruses and paramyxoviruses from 11 species of insectivorous bats within the South West Botanical Province of Western Australia. Phylogenetic analysis indicated complex ecological interactions including virus-host associations, cross-species infections, and multiple viral strains circulating concurrently within selected bat populations. Additionally, we describe the entire coding sequences for five alphacoronaviruses (representing four putative new species), and one novel adenovirus. Results indicate that viral burden (both prevalence and richness) is not homogeneous among species, with Chalinolobus gouldii identified as a key epidemiological element within the studied communities.
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Affiliation(s)
- Diana Prada
- School of Veterinary Medicine, Murdoch University, Perth, WA 6150, Australia; (M.O.); (B.J.)
| | - Victoria Boyd
- Health and Biosecurity Business Unit, Australian Animal Health Laboratories, CSIRO, Geelong, VIC 3220, Australia; (V.B.); (M.L.B.)
| | - Michelle L. Baker
- Health and Biosecurity Business Unit, Australian Animal Health Laboratories, CSIRO, Geelong, VIC 3220, Australia; (V.B.); (M.L.B.)
| | - Mark O’Dea
- School of Veterinary Medicine, Murdoch University, Perth, WA 6150, Australia; (M.O.); (B.J.)
| | - Bethany Jackson
- School of Veterinary Medicine, Murdoch University, Perth, WA 6150, Australia; (M.O.); (B.J.)
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21
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Wong ACP, Li X, Lau SKP, Woo PCY. Global Epidemiology of Bat Coronaviruses. Viruses 2019; 11:v11020174. [PMID: 30791586 PMCID: PMC6409556 DOI: 10.3390/v11020174] [Citation(s) in RCA: 201] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/12/2019] [Accepted: 02/18/2019] [Indexed: 12/22/2022] Open
Abstract
Bats are a unique group of mammals of the order Chiroptera. They are highly diversified and are the group of mammals with the second largest number of species. Such highly diversified cell types and receptors facilitate them to be potential hosts of a large variety of viruses. Bats are the only group of mammals capable of sustained flight, which enables them to disseminate the viruses they harbor and enhance the chance of interspecies transmission. This article aims at reviewing the various aspects of the global epidemiology of bat coronaviruses (CoVs). Before the SARS epidemic, bats were not known to be hosts for CoVs. In the last 15 years, bats have been found to be hosts of >30 CoVs with complete genomes sequenced, and many more if those without genome sequences are included. Among the four CoV genera, only alphaCoVs and betaCoVs have been found in bats. As a whole, both alphaCoVs and betaCoVs have been detected from bats in Asia, Europe, Africa, North and South America and Australasia; but alphaCoVs seem to be more widespread than betaCoVs, and their detection rate is also higher. For betaCoVs, only those from subgenera Sarbecovirus, Merbecovirus, Nobecovirus and Hibecovirus have been detected in bats. Most notably, horseshoe bats are the reservoir of SARS-CoV, and several betaCoVs from subgenus Merbecovirus are closely related to MERS-CoV. In addition to the interactions among various bat species themselves, bat⁻animal and bat⁻human interactions, such as the presence of live bats in wildlife wet markets and restaurants in Southern China, are important for interspecies transmission of CoVs and may lead to devastating global outbreaks.
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Affiliation(s)
- Antonio C P Wong
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong.
| | - Xin Li
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong.
| | - Susanna K P Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong.
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong.
- Research Centre of Infection and Immunology, The University of Hong Kong, Pokfulam, Hong Kong.
- Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong.
- Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong.
| | - Patrick C Y Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong.
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong.
- Research Centre of Infection and Immunology, The University of Hong Kong, Pokfulam, Hong Kong.
- Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong.
- Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong.
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Peel AJ, Field HE, Aravena MR, Edson D, McCallum H, Plowright RK, Prada D. Coronaviruses and Australian bats: a review in the midst of a pandemic. AUST J ZOOL 2019. [DOI: 10.1071/zo20046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Australia’s 81 bat species play vital ecological and economic roles via suppression of insect pests and maintenance of native forests through pollination and seed dispersal. Bats also host a wide diversity of coronaviruses globally, including several viral species that are closely related to SARS-CoV-2 and other emergent human respiratory coronaviruses. Although there are hundreds of studies of bat coronaviruses globally, there are only three studies of bat coronaviruses in Australian bat species, and no systematic studies of drivers of shedding. These limited studies have identified two betacoronaviruses and seven alphacoronaviruses, but less than half of Australian species are included in these studies and further research is therefore needed. There is no current evidence of spillover of coronaviruses from bats to humans in Australia, either directly or indirectly via intermediate hosts. The limited available data are inadequate to determine whether this lack of evidence indicates that spillover does not occur or occurs but is undetected. Conversely, multiple international agencies have flagged the potential transmission of human coronaviruses (including SARS CoV-2) from humans to bats, and the consequent threat to bat conservation and human health. Australia has a long history of bat research across a broad range of ecological and associated disciplines, as well as expertise in viral spillover from bats. This strong foundation is an ideal platform for developing integrative approaches to understanding bat health and sustainable protection of human health.
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Virus survey in populations of two subspecies of bent-winged bats (Miniopterus orianae bassanii and oceanensis) in south-eastern Australia reveals a high prevalence of diverse herpesviruses. PLoS One 2018; 13:e0197625. [PMID: 29795610 PMCID: PMC5967723 DOI: 10.1371/journal.pone.0197625] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/05/2018] [Indexed: 01/03/2023] Open
Abstract
While bats are often viewed as carriers of infectious disease agents, little research has been conducted on the effects these potential pathogens may have on the bat populations themselves. The southern bent-winged bat (Miniopterus orianae bassanii) is a critically endangered subspecies endemic to south-eastern Australia. Population numbers of this bat have been declining for the past 50 years, but the reasons for this are unclear. As part of a larger study to determine if disease could be a contributing factor to this decline, 351 southern bent-winged bats from four locations were captured, and oral swabs were collected and tested for the presence of potentially pathogenic viruses. Results were compared with those obtained from 116 eastern bent-winged bats (Miniopterus orianae oceanensis) from three different locations. The eastern bent-winged bat is a related but more common and widespread subspecies whose geographical range overlaps partly with southern bent-winged bats. Herpesviruses were detected in bent-winged bats from all seven locations. At least six novel herpesviruses (five betaherpesviruses and one gammaherpesvirus) were identified. The prevalence of herpesvirus infection was higher in eastern bent-winged bats (44%, 51/116), compared to southern bent-winged bats (27%, 95/351), although this varied across the locations and sampling periods. Adenoviruses and a range of different RNA viruses (lyssaviruses, filoviruses, coronaviruses and henipaviruses) were also tested for but not detected. The detected herpesviruses did not appear to be associated with obvious ill health, and may thus not be playing a role in the population decline of the southern bent-winged bat. The detection of multiple novel herpesviruses at a high prevalence of infection is consistent with our understanding of bats as hosts to a rich diversity of viruses.
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Leopardi S, Holmes EC, Gastaldelli M, Tassoni L, Priori P, Scaravelli D, Zamperin G, De Benedictis P. Interplay between co-divergence and cross-species transmission in the evolutionary history of bat coronaviruses. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2018; 58:279-289. [PMID: 29355607 PMCID: PMC7106311 DOI: 10.1016/j.meegid.2018.01.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 01/10/2018] [Accepted: 01/12/2018] [Indexed: 01/01/2023]
Abstract
Coronaviruses (CoVs) have been documented in almost every species of bat sampled. Bat CoVs exhibit both extensive genetic diversity and a broad geographic range, indicative of a long-standing host association. Despite this, the respective roles of long-term virus-host co-divergence and cross-species transmission (host-jumping) in the evolution of bat coronaviruses are unclear. Using a phylogenetic approach we provide evidence that CoV diversity in bats is shaped by both species richness and their geographical distribution, and that CoVs exhibit clustering at the level of bat genera, with these genus-specific clusters largely associated with distinct CoV species. Co-phylogenetic analyses revealed that cross-species transmission has been more common than co-divergence across coronavirus evolution as a whole, and that cross-species transmission events were more likely between sympatric bat hosts. Notably, however, an analysis of the CoV RNA polymerase phylogeny suggested that many such host-jumps likely resulted in short-term spill-over infections, with little evidence for sustained onward transmission in new co-roosting host species.
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Affiliation(s)
- Stefania Leopardi
- National Reference Centre, OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Universita' 10, Legnaro, Padova 35020, Italy.
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Michele Gastaldelli
- National Reference Centre, OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Universita' 10, Legnaro, Padova 35020, Italy
| | - Luca Tassoni
- National Reference Centre, OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Universita' 10, Legnaro, Padova 35020, Italy
| | | | | | - Gianpiero Zamperin
- National Reference Centre, OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Universita' 10, Legnaro, Padova 35020, Italy
| | - Paola De Benedictis
- National Reference Centre, OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Universita' 10, Legnaro, Padova 35020, Italy
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25
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Abstract
The four endemic human coronaviruses HCoV-229E, -NL63, -OC43, and -HKU1 contribute a considerable share of upper and lower respiratory tract infections in adults and children. While their clinical representation resembles that of many other agents of the common cold, their evolutionary histories, and host associations could provide important insights into the natural history of past human pandemics. For two of these viruses, we have strong evidence suggesting an origin in major livestock species while primordial associations for all four viruses may have existed with bats and rodents. HCoV-NL63 and -229E may originate from bat reservoirs as assumed for many other coronaviruses, but HCoV-OC43 and -HKU1 seem more likely to have speciated from rodent-associated viruses. HCoV-OC43 is thought to have emerged from ancestors in domestic animals such as cattle or swine. The bovine coronavirus has been suggested to be a possible ancestor, from which HCoV-OC43 may have emerged in the context of a pandemic recorded historically at the end of the 19th century. New data suggest that HCoV-229E may actually be transferred from dromedary camels similar to Middle East respiratory syndrome (MERS) coronavirus. This scenario provides important ecological parallels to the present prepandemic pattern of host associations of the MERS coronavirus.
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Affiliation(s)
- Victor M Corman
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany; German Center for Infection Research (DZIF), Berlin, Germany
| | - Doreen Muth
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany; German Center for Infection Research (DZIF), Berlin, Germany
| | - Daniela Niemeyer
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Christian Drosten
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany; German Center for Infection Research (DZIF), Berlin, Germany.
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Circulation of Alphacoronavirus, Betacoronavirus and Paramyxovirus in Hipposideros bat species in Zimbabwe. INFECTION GENETICS AND EVOLUTION 2018; 58:253-257. [PMID: 29331670 PMCID: PMC7106086 DOI: 10.1016/j.meegid.2018.01.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 01/08/2018] [Accepted: 01/09/2018] [Indexed: 12/19/2022]
Abstract
Bats carry a great diversity of zoonotic viruses with a high-impact on human health and livestock. Since the emergence of new coronaviruses and paramyxoviruses in humans (e.g. Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Nipah virus), numerous studies clearly established that bats can maintain some of these viruses. Improving our understanding on the role of bats in the epidemiology of the pathogens they harbour is necessary to prevent cross-species spill over along the wild/domestic/human gradient. In this study, we screened bat faecal samples for the presence of Coronavirus and Paramyxovirus in two caves frequently visited by local people to collect manure and/or to hunt bats in Zimbabwe. We amplified partial RNA-dependent RNA polymerase genes of Alpha and Betacoronavirus together with the partial polymerase gene of Paramyxovirus. Identified coronaviruses were related to pathogenic human strains and the paramyxovirus belonged to the recently described Jeilongvirus genus. Our results highlighted the importance of monitoring virus circulation in wildlife, especially bats, in the context of intense human-wildlife interfaces in order to strengthen prevention measures among local populations and to implement sentinel surveillance in sites with high zoonotic diseases transmission potential. Coronavirus and Paramyxovirus circulate in Hipposideros bat species in Zimbabwe. Importance of widening viral screening in under-investigated countries Sentinel surveillance in sites with high zoonotic transmission potential
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27
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Lee S, Jo SD, Son K, An I, Jeong J, Wang SJ, Kim Y, Jheong W, Oem JK. Genetic Characteristics of Coronaviruses from Korean Bats in 2016. MICROBIAL ECOLOGY 2018; 75:174-182. [PMID: 28725945 PMCID: PMC7079938 DOI: 10.1007/s00248-017-1033-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 07/04/2017] [Indexed: 05/31/2023]
Abstract
Bats have increasingly been recognized as the natural reservoir of severe acute respiratory syndrome (SARS), coronavirus, and other coronaviruses found in mammals. However, little research has been conducted on bat coronaviruses in South Korea. In this study, bat samples (332 oral swabs, 245 fecal samples, 38 urine samples, and 57 bat carcasses) were collected at 33 natural bat habitat sites in South Korea. RT-PCR and sequencing were performed for specific coronavirus genes to identify the bat coronaviruses in different bat samples. Coronaviruses were detected in 2.7% (18/672) of the samples: 13 oral swabs from one species of the family Rhinolophidae, and four fecal samples and one carcass (intestine) from three species of the family Vespertiliodae. To determine the genetic relationships of the 18 sequences obtained in this study and previously known coronaviruses, the nucleotide sequences of a 392-nt region of the RNA-dependent RNA polymerase (RdRp) gene were analyzed phylogenetically. Thirteen sequences belonging to SARS-like betacoronaviruses showed the highest nucleotide identity (97.1-99.7%) with Bat-CoV-JTMC15 reported in China. The other five sequences were most similar to MERS-like betacoronaviruses. Four nucleotide sequences displayed the highest identity (94.1-95.1%) with Bat-CoV-HKU5 from Hong Kong. The one sequence from a carcass showed the highest nucleotide identity (99%) with Bat-CoV-SC2013 from China. These results suggest that careful surveillance of coronaviruses from bats should be continued, because animal and human infections may result from the genetic variants present in bat coronavirus reservoirs.
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Affiliation(s)
- Saemi Lee
- Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea
| | - Seong-Deok Jo
- Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea
| | - Kidong Son
- Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea
| | - Injung An
- Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea
| | - Jipseol Jeong
- Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea
| | - Seung-Jun Wang
- Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea
| | - Yongkwan Kim
- Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea
| | - Weonhwa Jheong
- Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea
| | - Jae-Ku Oem
- Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea.
- Department of Veterinary Infectious Diseases, College of Veterinary Medicine, Chonbuk National University, Iksan, Republic of Korea.
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Discovery of a Highly Divergent Coronavirus in the Asian House Shrew from China Illuminates the Origin of the Alphacoronaviruses. J Virol 2017. [PMID: 28637760 DOI: 10.1128/jvi.00764-17] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although shrews are one of the largest groups of mammals, little is known about their role in the evolution and transmission of viral pathogens, including coronaviruses (CoVs). We captured 266 Asian house shrews (Suncus murinus) in Jiangxi and Zhejiang Provinces, China, during 2013 to 2015. CoV RNA was detected in 24 Asian house shrews, with an overall prevalence of 9.02%. Complete viral genome sequences were successfully recovered from the RNA-positive samples. The newly discovered shrew CoV fell into four lineages reflecting their geographic origins, indicative of largely allopatric evolution. Notably, these viruses were most closely related to alphacoronaviruses but sufficiently divergent that they should be considered a novel member of the genus Alphacoronavirus, which we denote Wénchéng shrew virus (WESV). Phylogenetic analysis revealed that WESV was a highly divergent member of the alphacoronaviruses and, more dramatically, that the S gene of WESV fell in a cluster that was genetically distinct from that of known coronaviruses. The divergent position of WESV suggests that coronaviruses have a long association with Asian house shrews. In addition, the genome of WESV contains a distinct NS7 gene that exhibits no sequence similarity to genes of any known viruses. Together, these data suggest that shrews are natural reservoirs for coronaviruses and may have played an important and long-term role in CoV evolution.IMPORTANCE The subfamily Coronavirinae contains several notorious human and animal pathogens, including severe acute respiratory syndrome coronavirus, Middle East respiratory syndrome coronavirus, and porcine epidemic diarrhea virus. Because of their genetic diversity and phylogenetic relationships, it has been proposed that the alphacoronaviruses likely have their ultimate ancestry in the viruses residing in bats. Here, we describe a novel alphacoronavirus (Wénchéng shrew virus [WESV]) that was sampled from Asian house shrews in China. Notably, WESV is a highly divergent member of the alphacoronaviruses and possesses an S gene that is genetically distinct from those of all known coronaviruses. In addition, the genome of WESV contains a distinct NS7 gene that exhibits no sequence similarity to those of any known viruses. Together, these data suggest that shrews are important and longstanding hosts for coronaviruses that merit additional research and surveillance.
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Lin XD, Wang W, Hao ZY, Wang ZX, Guo WP, Guan XQ, Wang MR, Wang HW, Zhou RH, Li MH, Tang GP, Wu J, Holmes EC, Zhang YZ. Extensive diversity of coronaviruses in bats from China. Virology 2017; 507:1-10. [PMID: 28384506 PMCID: PMC7111643 DOI: 10.1016/j.virol.2017.03.019] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 03/27/2017] [Accepted: 03/28/2017] [Indexed: 01/04/2023]
Abstract
To help reveal the diversity and evolution of bat coronaviruses we collected 1067 bats from 21 species in China. A total of 73 coronaviruses (32 alphacoronaviruses and 41 betacoronaviruses) were identified in these bats, with an overall prevalence of 6.84%. All newly-identified betacoronaviruses were SARS-related Rhinolophus bat coronaviruses (SARSr-Rh-BatCoV). Importantly, with the exception of the S gene, the genome sequences of the SARSr-Rh-BatCoVs sampled in Guizhou province were closely related to SARS-related human coronavirus. Additionally, the newly-identified alphacoronaviruses exhibited high genetic diversity and some may represent novel species. Our phylogenetic analyses also provided insights into the transmission of these viruses among bat species, revealing a general clustering by geographic location rather than by bat species. Inter-species transmission among bats from the same genus was also commonplace in both the alphacoronaviruses and betacoronaviruses. Overall, these data suggest that high contact rates among specific bat species enable the acquisition and spread of coronaviruses. 32 alpha-CoVs and 41 beta-CoVs were identified in bats sampled from China. SARSr-Rh-BatCoVs from Guizhou province were closely related to SARS-CoV. Some of the newly identified CoVs may be novel species in the genus Alphacoronavirus. High contact rates among some bat species enable the acquisition and spread of CoVs.
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Affiliation(s)
- Xian-Dan Lin
- 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; Wenzhou Center for Disease Control and Prevention, Wenzhou, Zhejiang Province, China
| | - Wen Wang
- 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
| | - Zong-Yu Hao
- Henan Center for Disease Control and Prevention, Zhengzhou, Henan Province, China
| | - Zhao-Xiao Wang
- Guizhou Center for Disease Control and Prevention, Guiyang, Guizhou Province, China
| | - Wen-Ping Guo
- 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
| | - Xiao-Qing Guan
- 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
| | - Miao-Ruo Wang
- Longquan Center for Disease Control and Prevention, Longquan, Zhejiang Province, China
| | - Hong-Wei Wang
- Neixiang Center for Disease Control and Prevention, Neixiang, Henan Province, China
| | - Run-Hong Zhou
- 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
| | - Ming-Hui Li
- 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
| | - Guang-Peng Tang
- Guizhou Center for Disease Control and Prevention, Guiyang, Guizhou Province, China
| | - Jun Wu
- Jiyuan Center for Disease Control and Prevention, Jiyuan, Henan Province, China
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - 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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30
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Smith C. Persistent or long-term coronavirus infection in Australian bats. MICROBIOLOGY AUSTRALIA 2017. [DOI: 10.1071/ma17004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
When the World Health Organization declared the end of the global outbreak of severe acute respiratory syndrome (SARS) on the 5 July 2003, more than 8000 cases with over 800 fatalities had been reported in 32 countries worldwide and financial costs to the global economy were close to $US40 billion1,2. Coronaviruses were identified as being responsible for the outbreaks of both SARS and Middle East respiratory syndrome (MERS, the latter in 2013). Subsequently, bats (order Chiroptera) were identified as the natural hosts for a large number of novel and genetically diverse coronaviruses, including the likely ancestors to SARS-like and MERS-like coronaviruses3–8.
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31
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Martínez Gómez JM, Periasamy P, Dutertre CA, Irving AT, Ng JHJ, Crameri G, Baker ML, Ginhoux F, Wang LF, Alonso S. Phenotypic and functional characterization of the major lymphocyte populations in the fruit-eating bat Pteropus alecto. Sci Rep 2016; 6:37796. [PMID: 27883085 PMCID: PMC5121612 DOI: 10.1038/srep37796] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 11/02/2016] [Indexed: 12/11/2022] Open
Abstract
The unique ability of bats to act as reservoir for viruses that are highly pathogenic to humans suggests unique properties and functional characteristics of their immune system. However, the lack of bat specific reagents, in particular antibodies, has limited our knowledge of bat's immunity. Using cross-reactive antibodies, we report the phenotypic and functional characterization of T cell subsets, B and NK cells in the fruit-eating bat Pteropus alecto. Our findings indicate the predominance of CD8+ T cells in the spleen from wild-caught bats that may reflect either the presence of viruses in this organ or predominance of this cell subset at steady state. Instead majority of T cells in circulation, lymph nodes and bone marrow (BM) were CD4+ subsets. Interestingly, 40% of spleen T cells expressed constitutively IL-17, IL-22 and TGF-β mRNA, which may indicate a strong bias towards the Th17 and regulatory T cell subsets. Furthermore, the unexpected high number of T cells in bats BM could suggest an important role in T cell development. Finally, mitogenic stimulation induced proliferation and production of effector molecules by bats immune cells. This work contributes to a better understanding of bat's immunity, opening up new perspectives of therapeutic interventions for humans.
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Affiliation(s)
- Julia María Martínez Gómez
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Immunology programme, Life Sciences Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Pravin Periasamy
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Immunology programme, Life Sciences Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Charles-Antoine Dutertre
- Programme in Emerging Infectious Disease, Duke-NUS Medical School, Singapore
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (ASTAR), Singapore
| | - Aaron Trent Irving
- Programme in Emerging Infectious Disease, Duke-NUS Medical School, Singapore
| | - Justin Han Jia Ng
- Programme in Emerging Infectious Disease, Duke-NUS Medical School, Singapore
| | - Gary Crameri
- CSIRO, Health and Biosecurity Business Unit, Australian Animal Health Laboratory, Geelong, Australia
| | - Michelle L. Baker
- CSIRO, Health and Biosecurity Business Unit, Australian Animal Health Laboratory, Geelong, Australia
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (ASTAR), Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Disease, Duke-NUS Medical School, Singapore
| | - Sylvie Alonso
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Immunology programme, Life Sciences Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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McMichael L, Edson D, Mayer D, McLaughlin A, Goldspink L, Vidgen ME, Kopp S, Meers J, Field H. Temporal Variation in Physiological Biomarkers in Black Flying-Foxes (Pteropus alecto), Australia. ECOHEALTH 2016; 13:49-59. [PMID: 27026357 PMCID: PMC7087910 DOI: 10.1007/s10393-016-1113-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 02/11/2016] [Accepted: 02/23/2016] [Indexed: 06/05/2023]
Abstract
Bats of the genus Pteropus (Pteropodidae) are recognised as the natural host of multiple emerging pathogenic viruses of animal and human health significance, including henipaviruses, lyssaviruses and ebolaviruses. Some studies have suggested that physiological and ecological factors may be associated with Hendra virus infection in flying-foxes in Australia; however, it is essential to understand the normal range and seasonal variability of physiological biomarkers before seeking physiological associations with infection status. We aimed to measure a suite of physiological biomarkers in P. alecto over time to identify any seasonal fluctuations and to examine possible associations with life-cycle and environmental stressors. We sampled 839 adult P. alecto in the Australian state of Queensland over a 12-month period. The adjusted population means of every assessed hematologic and biochemical parameter were within the reported reference range on every sampling occasion. However, within this range, we identified significant temporal variation in these parameters, in urinary parameters and body condition, which primarily reflected the normal annual life cycle. We found no evident effect of remarkable physiological demands or nutritional stress, and no indication of clinical disease driving any parameter values outside the normal species reference range. Our findings identify underlying temporal physiological changes at the population level that inform epidemiological studies and assessment of putative physiological risk factors driving Hendra virus infection in P. alecto. More broadly, the findings add to the knowledge of Pteropus populations in terms of their relative resistance and resilience to emerging infectious disease.
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Affiliation(s)
- Lee McMichael
- School of Veterinary Science, University of Queensland, Gatton, QLD, 4343, Australia.
- Biosecurity Queensland, Department of Agriculture and Fisheries, Brisbane, QLD, 4108, Australia.
| | - Daniel Edson
- Biosecurity Queensland, Department of Agriculture and Fisheries, Brisbane, QLD, 4108, Australia
- Department of Agriculture and Water Resources, Canberra, ACT, 2601, Australia
| | - David Mayer
- Department of Agriculture and Fisheries, Brisbane, QLD, 4103, Australia
| | - Amanda McLaughlin
- Biosecurity Queensland, Department of Agriculture and Fisheries, Brisbane, QLD, 4108, Australia
| | - Lauren Goldspink
- Biosecurity Queensland, Department of Agriculture and Fisheries, Brisbane, QLD, 4108, Australia
| | - Miranda E Vidgen
- School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia
| | - Steven Kopp
- School of Veterinary Science, University of Queensland, Gatton, QLD, 4343, Australia
| | - Joanne Meers
- School of Veterinary Science, University of Queensland, Gatton, QLD, 4343, Australia
| | - Hume Field
- Ecohealth Alliance, New York, NY, 10001, USA
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