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Ujike M, Suzuki T. Progress of research on coronaviruses and toroviruses in large domestic animals using reverse genetics systems. Vet J 2024; 305:106122. [PMID: 38641200 DOI: 10.1016/j.tvjl.2024.106122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/24/2024] [Accepted: 04/14/2024] [Indexed: 04/21/2024]
Abstract
The generation of genetically engineered recombinant viruses from modified DNA/RNA is commonly referred to as reverse genetics, which allows the introduction of desired mutations into the viral genome. Reverse genetics systems (RGSs) are powerful tools for studying fundamental viral processes, mechanisms of infection, pathogenesis and vaccine development. However, establishing RGS for coronaviruses (CoVs) and toroviruses (ToVs), which have the largest genomes among vertebrate RNA viruses, is laborious and hampered by technical constraints. Hence, little research has focused on animal CoVs and ToVs using RGSs, especially in large domestic animals such as pigs and cattle. In the last decade, however, studies of porcine CoVs and bovine ToVs using RGSs have been reported. In addition, the coronavirus disease-2019 pandemic has prompted the development of new and simple CoV RGSs, which will accelerate RGS-based research on animal CoVs and ToVs. In this review, we summarise the general characteristics of CoVs and ToVs, the RGSs available for CoVs and ToVs and the progress made in the last decade in RGS-based research on porcine CoVs and bovine ToVs.
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Affiliation(s)
- Makoto Ujike
- Laboratory of Veterinary Infectious Diseases, Faculty of Veterinary Medicine, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-8602, Japan; Research Center for Animal Life Science, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-8602, Japan.
| | - Tohru Suzuki
- Division of Zoonosis Research, Sapporo Research Station, National Institute of Animal Health, NARO, Sapporo, Hokkaido 062-0045, Japan
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2
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Moreno A, Canziani S, Lelli D, Castelli A, Bianchi A, Bertoletti I, Maccarinelli F, Carlomagno M, Paini M, Rossato M, Delledonne M, Giacomelli S, Cordedda A, Nicoloso S, Bellinello E, Campagnoli A, Trogu T. Molecular and Serological Detection of Bovine Coronaviruses in Marmots ( Marmota marmota) in the Alpine Region. Viruses 2024; 16:591. [PMID: 38675932 PMCID: PMC11054042 DOI: 10.3390/v16040591] [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: 03/11/2024] [Revised: 03/31/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
In this study, virological surveillance focused on coronaviruses in marmots in the Alpine region in 2022, captured as part of a population control reduction program in the Livigno area. Seventy-six faecal samples were randomly collected from marmots at the time of capture and release and tested for genome detection of pan-coronavirus, pan-pestivirus, canine distemper virus, and influenza A and D virus. Nine faecal samples were positive in the Pan-CoV RT-PCR, while all were negative for the other viruses. Pan-coronavirus positives were further identified using Illumina's complete genome sequencing, which showed the highest homology with Bovine Coronavirus previously detected in roe deer in the Alps. Blood samples (n.35) were collected randomly from animals at release and tested for bovine coronavirus (BCoV) antibodies using competitive ELISA and VNT. Serological analyses revealed that 8/35 sera were positive for BCoV antibodies in both serological tests. This study provides molecular and serological evidence of the presence of BCoV in an alpine marmot population due to a likely spillover event. Marmots share areas and pastures with roe deer and other wild ruminants, and environmental transmission is a concrete possibility.
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Affiliation(s)
- Ana Moreno
- Virology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Via A. Bianchi, 9, 25124 Brescia, Italy; (S.C.); (D.L.); (A.C.); (F.M.); (T.T.)
| | - Sabrina Canziani
- Virology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Via A. Bianchi, 9, 25124 Brescia, Italy; (S.C.); (D.L.); (A.C.); (F.M.); (T.T.)
| | - Davide Lelli
- Virology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Via A. Bianchi, 9, 25124 Brescia, Italy; (S.C.); (D.L.); (A.C.); (F.M.); (T.T.)
| | - Anna Castelli
- Virology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Via A. Bianchi, 9, 25124 Brescia, Italy; (S.C.); (D.L.); (A.C.); (F.M.); (T.T.)
| | - Alessandro Bianchi
- Sondrio Diagnostic Laboratory, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Via Bormio, 30, 23100 Sondrio, Italy; (A.B.); (I.B.)
| | - Irene Bertoletti
- Sondrio Diagnostic Laboratory, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Via Bormio, 30, 23100 Sondrio, Italy; (A.B.); (I.B.)
| | - Federica Maccarinelli
- Virology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Via A. Bianchi, 9, 25124 Brescia, Italy; (S.C.); (D.L.); (A.C.); (F.M.); (T.T.)
| | - Marco Carlomagno
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy; (M.C.); (M.P.); (M.R.); (M.D.)
| | - Matteo Paini
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy; (M.C.); (M.P.); (M.R.); (M.D.)
| | - Marzia Rossato
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy; (M.C.); (M.P.); (M.R.); (M.D.)
- Genartis s.r.l., Via IV Novembre 24, 37126 Verona, Italy
| | - Massimo Delledonne
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy; (M.C.); (M.P.); (M.R.); (M.D.)
- Genartis s.r.l., Via IV Novembre 24, 37126 Verona, Italy
| | - Stefano Giacomelli
- ATS della Montagna, Via Nazario Sauro, 36/38, 23100 Sondrio, Italy; (S.G.); (A.C.)
| | - Antonella Cordedda
- ATS della Montagna, Via Nazario Sauro, 36/38, 23100 Sondrio, Italy; (S.G.); (A.C.)
| | - Sandro Nicoloso
- Dimensione Ricerca Ecologie e Ambiente Italia Società Cooperativa, Via Enrico Bindi n. 14, 51100 Pistoia, Italy; (S.N.); (E.B.)
| | - Enrica Bellinello
- Dimensione Ricerca Ecologie e Ambiente Italia Società Cooperativa, Via Enrico Bindi n. 14, 51100 Pistoia, Italy; (S.N.); (E.B.)
| | | | - Tiziana Trogu
- Virology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Via A. Bianchi, 9, 25124 Brescia, Italy; (S.C.); (D.L.); (A.C.); (F.M.); (T.T.)
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3
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Zhu Q, Qi S, Guo D, Li C, Su M, Wang J, Li Z, Yang D, Sun H, Wang X, Wang M, Wu H, Yu S, Bai W, Zhang Y, Yang X, Jiang L, Liu J, Zhao Y, Xing X, Shi D, Feng L, Sun D. A survey of fecal virome and bacterial community of the diarrhea-affected cattle in northeast China reveals novel disease-associated ecological risk factors. mSystems 2024; 9:e0084223. [PMID: 38108282 PMCID: PMC10804951 DOI: 10.1128/msystems.00842-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/06/2023] [Indexed: 12/19/2023] Open
Abstract
Limited information on the virome and bacterial community hampers our ability to discern systemic ecological risk factors that cause cattle diarrhea, which has become a pressing issue in the control of disease. A total of 110 viruses, 1,011 bacterial genera, and 322 complete viral genomes were identified from 70 sequencing samples mixed with 1,120 fecal samples from 58 farms in northeast China. For the diarrheic samples, the identified virome and bacterial community varied in terms of composition, abundance, diversity, and geographic distribution in relation to different disease-associated ecological factors; the abundance of identified viruses and bacteria was significantly correlated with the host factors of clinical status, cattle type, and age, and with environmental factors such as aquaculture model and geographical location (P < 0.05); a significant interaction occurred between viruses and viruses, bacteria and bacteria, as well as between bacteria and viruses (P < 0.05). The abundance of SMB53, Butyrivibrio, Facklamia, Trichococcus, and Turicibacter was significantly correlated with the health status of cattle (P < 0.05). The proportion of BRV, BCoV, BKV, BToV, BoNoV, BoNeV, BoAstV, BEV, BoPV, and BVDV in 1,120 fecal samples varied from 1.61% to 12.05%. A series of significant correlations were observed between the prevalence of individual viruses and the disease-associated ecological factors. A genome-based phylogenetic analysis revealed high variability of 10 bovine enteric viruses. The bovine hungarovirus was initially identified in both dairy and beef cattle in China. This study elucidates the fecal virome and bacterial community signatures of cattle affected by diarrhea, and reveals novel disease-associated ecological risk factors, including cattle type, cattle age, aquaculture model, and geographical location.IMPORTANCEThe lack of data on the virome and bacterial community restricts our capability to recognize ecological risk factors for bovine diarrhea disease, thereby hindering our overall comprehension of the disease's cause. In this study, we found that, for the diarrheal samples, the identified virome and bacterial community varied in terms of composition, abundance, diversity, configuration, and geographic distribution in relation to different disease-associated ecological factors. A series of significant correlations were observed between the prevalence of individual viruses and the disease-associated ecological factors. Our study aims to uncover novel ecological risk factors of bovine diarrheal disease by examining the pathogenic microorganism-host-environment disease ecology, thereby providing a new perspective on the control of bovine diarrheal diseases.
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Affiliation(s)
- Qinghe Zhu
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Shanshan Qi
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Donghua Guo
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Chunqiu Li
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Mingjun Su
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jianfa Wang
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Zijian Li
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Dan Yang
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Haibo Sun
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Xiaoran Wang
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Meijiao Wang
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Haoyang Wu
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Shiping Yu
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Wenfei Bai
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yongchen Zhang
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Xu Yang
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Limin Jiang
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jiaying Liu
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yingying Zhao
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Xiaoxu Xing
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Da Shi
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Li Feng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Dongbo Sun
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
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4
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Singh G, Abbad A, Kleiner G, Srivastava K, Gleason C, Carreño JM, Simon V, Krammer F. The post-COVID-19 population has a high prevalence of cross-reactive antibodies to spikes from all Orthocoronavirinae genera. mBio 2024; 15:e0225023. [PMID: 38112467 PMCID: PMC10790767 DOI: 10.1128/mbio.02250-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 11/01/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE As demonstrated by severe acute respiratory syndrome coronavirus 2, coronaviruses pose a significant pandemic threat. Here, we show that coronavirus disease 2019 mRNA vaccination can induce significant levels of cross-reactive antibodies against diverse coronavirus spike proteins. While these antibodies are binding antibodies that likely have little neutralization capacity and while their contribution to cross-protection is unclear, it is possible that they may play a role in protection from progression to severe disease with novel coronaviruses.
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Affiliation(s)
- Gagandeep Singh
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Anass Abbad
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Giulio Kleiner
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Komal Srivastava
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Charles Gleason
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Lytras S, Wickenhagen A, Sugrue E, Stewart DG, Swingler S, Sims A, Jackson Ireland H, Davies EL, Ludlam EM, Li Z, Hughes J, Wilson SJ. Resurrection of 2'-5'-oligoadenylate synthetase 1 (OAS1) from the ancestor of modern horseshoe bats blocks SARS-CoV-2 replication. PLoS Biol 2023; 21:e3002398. [PMID: 38015855 PMCID: PMC10683996 DOI: 10.1371/journal.pbio.3002398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 10/20/2023] [Indexed: 11/30/2023] Open
Abstract
The prenylated form of the human 2'-5'-oligoadenylate synthetase 1 (OAS1) protein has been shown to potently inhibit the replication of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the virus responsible for the Coronavirus Disease 2019 (COVID-19) pandemic. However, the OAS1 orthologue in the horseshoe bats (superfamily Rhinolophoidea), the reservoir host of SARS-related coronaviruses (SARSr-CoVs), has lost the prenylation signal required for this antiviral activity. Herein, we used an ancestral state reconstruction approach to predict and reconstitute in vitro, the most likely OAS1 protein sequence expressed by the Rhinolophoidea common ancestor prior to its prenylation loss (RhinoCA OAS1). We exogenously expressed the ancient bat protein in vitro to show that, unlike its non-prenylated horseshoe bat descendants, RhinoCA OAS1 successfully blocks SARS-CoV-2 replication. Using protein structure predictions in combination with evolutionary hypothesis testing methods, we highlight sites under unique diversifying selection specific to OAS1's evolution in the Rhinolophoidea. These sites are located near the RNA-binding region and the C-terminal end of the protein where the prenylation signal would have been. Our results confirm that OAS1 prenylation loss at the base of the Rhinolophoidea clade ablated the ability of OAS1 to restrict SARSr-CoV replication and that subsequent evolution of the gene in these bats likely favoured an alternative function. These findings can advance our understanding of the tightly linked association between SARSr-CoVs and horseshoe bats.
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Affiliation(s)
- Spyros Lytras
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Arthur Wickenhagen
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Elena Sugrue
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Douglas G. Stewart
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Simon Swingler
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Anna Sims
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Hollie Jackson Ireland
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Emma L. Davies
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Eliza M. Ludlam
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Zhuonan Li
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Joseph Hughes
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Sam J. Wilson
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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Llanco L, Retamozo K, Oviedo N, Manchego A, Lázaro C, Navarro-Mamani DA, Santos N, Rojas M. Co-Circulation of Multiple Coronavirus Genera and Subgenera during an Epizootic of Lethal Respiratory Disease in Newborn Alpacas ( Vicugna pacos) in Peru: First Report of Bat-like Coronaviruses in Alpacas. Animals (Basel) 2023; 13:2983. [PMID: 37760383 PMCID: PMC10525639 DOI: 10.3390/ani13182983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Coronaviruses (CoVs) infect a wide range of hosts, including humans, domestic animals, and wildlife, typically causing mild-to-severe respiratory or enteric disease. The main objective of this study was to identify CoV genera and subgenera detected in Peruvian alpacas. Lung lavage specimens were collected from 32 animals aged 1 to 6 weeks. CoVs were identified by using RT-PCR to amplify a pan-CoV conserved region of the RNA-dependent RNA polymerase-encoding gene. A nested PCR was performed to identify β-CoVs. Then, β-CoV-positive samples were subjected to RT-PCR using specific primers to identify the Embecovirus subgenus. Out of 32 analyzed samples, 30 (93.8%) tested positive for at least one CoV genus. β-, α-, or unclassified CoVs were identified in 24 (80%), 1 (3.3%), and 1 (3.3%) of the positive samples, respectively. A CoV genus could not be identified in two (6.7%) samples. A mixture of different CoV genera was detected in two (6.7%) samples: one was co-infected with β- and α-CoVs, and the other contained a β- and an unclassified CoV. A sequence analysis of the amplicons generated by the PCR identified 17 β-CoV strains belonging to the subgenus Embecovirus and two α-CoV strains belonging to Decacovirus. A phylogenetic analysis of two strains revealed a relationship with an unclassified Megaderma BatCoV strain. A subgenus could not be identified in nine β-CoV samples. Our data show a high prevalence and a high genetic diversity of CoV genera and subgenera that infect alpacas, in which the β-CoV subgenus Embecovirus predominated. Our data also suggest a new role for bats in the dissemination and transmission of uncommon CoVs to alpacas raised in rural Peru.
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Affiliation(s)
- Luis Llanco
- Escuela de Medicina Humana, Universidad Privada San Juan Bautista, Apartado, Chincha 15067, Peru;
| | - Karubya Retamozo
- Laboratório de Inmunología, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Apartado, Lima 03-5137, Peru; (K.R.); (N.O.); (A.M.)
| | - Noriko Oviedo
- Laboratório de Inmunología, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Apartado, Lima 03-5137, Peru; (K.R.); (N.O.); (A.M.)
| | - Alberto Manchego
- Laboratório de Inmunología, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Apartado, Lima 03-5137, Peru; (K.R.); (N.O.); (A.M.)
| | - César Lázaro
- Laboratório de Farmacología y Toxicología Veterinaria, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Apartado, Lima 03-5137, Peru;
| | - Dennis A. Navarro-Mamani
- Laboratório de Virología, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Apartado, Lima 03-5137, Peru;
| | - Norma Santos
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil;
| | - Miguel Rojas
- Laboratório de Inmunología, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Apartado, Lima 03-5137, Peru; (K.R.); (N.O.); (A.M.)
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7
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Wells HL, Bonavita CM, Navarrete-Macias I, Vilchez B, Rasmussen AL, Anthony SJ. The coronavirus recombination pathway. Cell Host Microbe 2023; 31:874-889. [PMID: 37321171 PMCID: PMC10265781 DOI: 10.1016/j.chom.2023.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 06/17/2023]
Abstract
Recombination is thought to be a mechanism that facilitates cross-species transmission in coronaviruses, thus acting as a driver of coronavirus spillover and emergence. Despite its significance, the mechanism of recombination is poorly understood, limiting our potential to estimate the risk of novel recombinant coronaviruses emerging in the future. As a tool for understanding recombination, here, we outline a framework of the recombination pathway for coronaviruses. We review existing literature on coronavirus recombination, including comparisons of naturally observed recombinant genomes as well as in vitro experiments, and place the findings into the recombination pathway framework. We highlight gaps in our understanding of coronavirus recombination illustrated by the framework and outline how further experimental research is critical for disentangling the molecular mechanism of recombination from external environmental pressures. Finally, we describe how an increased understanding of the mechanism of recombination can inform pandemic predictive intelligence, with a retrospective emphasis on SARS-CoV-2.
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Affiliation(s)
- Heather L Wells
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, USA; Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA.
| | - Cassandra M Bonavita
- Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA
| | - Isamara Navarrete-Macias
- Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA
| | - Blake Vilchez
- Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA
| | - Angela L Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Simon J Anthony
- Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA.
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8
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Lopes LR. Cervids ACE2 Residues that Bind the Spike Protein can Provide Susceptibility to SARS-CoV-2. ECOHEALTH 2023; 20:9-17. [PMID: 37106170 PMCID: PMC10139662 DOI: 10.1007/s10393-023-01632-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/18/2023] [Accepted: 03/01/2023] [Indexed: 06/11/2023]
Abstract
The susceptibility of the white-tailed deer (WTD; Odocoileus virginianus) to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted cervids as coronavirus reservoirs. This study aimed to evaluate the angiotensin-converting enzyme 2 (ACE2) residues which bind the spike protein of SARS-CoV-2 from 16 cervids to predict their potential susceptibility to SARS-CoV-2 infection. Eleven out of 16 species presented identical ACE2 key residues to WTD ACE2. Four cervids presented K31N, a variant associated with low SARS-CoV-2 susceptibility. Large herding of cervids with ACE2 key residues identical to that of the WTD can result in extensive reservoirs of SARS-CoV-2. Cervids as potential reservoirs could favor SARS-CoV-2 adaptation and the emergence of new coronavirus strains.
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Affiliation(s)
- Luciano Rodrigo Lopes
- Bioinformatics and Bio-Data Science Division, Health Informatics Department, Universidade Federal de São Paulo - UNIFESP, Rua Botucatu 862 - Prédio Leal Prado (térreo), São Paulo, SP, 04023-062, Brazil.
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9
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Geng HL, Meng XZ, Yan WL, Li XM, Jiang J, Ni HB, Liu WH. Prevalence of bovine coronavirus in cattle in China: A systematic review and meta-analysis. Microb Pathog 2023; 176:106009. [PMID: 36736543 DOI: 10.1016/j.micpath.2023.106009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/14/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023]
Abstract
Bovine coronavirus (BCoV) is one of the important pathogens that cause calf diarrhea (CD), winter dysentery (WD), and the bovine respiratory disease complex (BRDC), and spreads worldwide. An infection of BCoV in cattle can lead to death of young animals, stunted growth, reduced milk production, and milk quality, thus bringing serious economic losses to the bovine industry. Therefore, it is necessary to prevent and control the spread of BCoV. Here, a systematic review and meta-analysis was conducted to assess the prevalence of BCoV in cattle in China before 2022. A total of 57 articles regarding the prevalence of BCoV in cattle in China were collected from five databases (PubMed, ScienceDirect, CNKI, VIP, and Wan Fang). Based on the inclusion criteria, a total of 15,838 samples were included, and 6,136 were positive cases. The overall prevalence of BCoV was 30.8%, with the highest prevalence rate (60.5%) identified in South China and the lowest prevalence (15.6%) identified in Central China. We also analyzed other subgroup information, included sampling years, sample sources, detection methods, breeding methods, age, type of cattle, presence of diarrhea, and geographic and climatic factors. The results indicated that BCoV was widely prevalent in China. Among all subgroups, the sample sources, detection methods, breeding methods, and presence or absence of diarrheal might be potential risk factors responsible for BCoV prevalence. It is recommended to strengthen the detection of BCoV in cattle, in order to effectively control the spread of BCoV.
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Affiliation(s)
- Hong-Li Geng
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, PR China; College of Life Science, Changchun Sci-Tech University, Shuangyang, Jilin, PR China
| | - Xiang-Zhu Meng
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, PR China; College of Veterinary Medicine, Jilin Agricultural University, Changchun, Jilin, PR China
| | - Wei-Lan Yan
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Xiao-Man Li
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Jing Jiang
- College of Life Science, Changchun Sci-Tech University, Shuangyang, Jilin, PR China.
| | - Hong-Bo Ni
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, PR China.
| | - Wen-Hua Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, PR China.
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10
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Bandyopadhyay SS, Halder AK, Saha S, Chatterjee P, Nasipuri M, Basu S. Assessment of GO-Based Protein Interaction Affinities in the Large-Scale Human–Coronavirus Family Interactome. Vaccines (Basel) 2023; 11:vaccines11030549. [PMID: 36992133 DOI: 10.3390/vaccines11030549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/19/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
SARS-CoV-2 is a novel coronavirus that replicates itself via interacting with the host proteins. As a result, identifying virus and host protein-protein interactions could help researchers better understand the virus disease transmission behavior and identify possible COVID-19 drugs. The International Committee on Virus Taxonomy has determined that nCoV is genetically 89% compared to the SARS-CoV epidemic in 2003. This paper focuses on assessing the host–pathogen protein interaction affinity of the coronavirus family, having 44 different variants. In light of these considerations, a GO-semantic scoring function is provided based on Gene Ontology (GO) graphs for determining the binding affinity of any two proteins at the organism level. Based on the availability of the GO annotation of the proteins, 11 viral variants, viz., SARS-CoV-2, SARS, MERS, Bat coronavirus HKU3, Bat coronavirus Rp3/2004, Bat coronavirus HKU5, Murine coronavirus, Bovine coronavirus, Rat coronavirus, Bat coronavirus HKU4, Bat coronavirus 133/2005, are considered from 44 viral variants. The fuzzy scoring function of the entire host–pathogen network has been processed with ~180 million potential interactions generated from 19,281 host proteins and around 242 viral proteins. ~4.5 million potential level one host–pathogen interactions are computed based on the estimated interaction affinity threshold. The resulting host–pathogen interactome is also validated with state-of-the-art experimental networks. The study has also been extended further toward the drug-repurposing study by analyzing the FDA-listed COVID drugs.
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Affiliation(s)
- Soumyendu Sekhar Bandyopadhyay
- Department of Computer Science and Engineering, Jadavpur University, Kolkata 700032, India
- Department of Computer Science and Engineering, School of Engineering and Technology, Adamas University, Kolkata 700126, India
| | - Anup Kumar Halder
- Faculty of Mathematics and Information Sciences, Warsaw University of Technology, 00-662 Warsaw, Poland
| | - Sovan Saha
- Department of Computer Science and Engineering (Artificial Intelligence and Machine Learning), Techno Main Salt Lake, Sector V, Kolkata 700091, India
| | - Piyali Chatterjee
- Department of Computer Science and Engineering, Netaji Subhash Engineering College, Kolkata 700152, India
| | - Mita Nasipuri
- Department of Computer Science and Engineering, Jadavpur University, Kolkata 700032, India
| | - Subhadip Basu
- Department of Computer Science and Engineering, Jadavpur University, Kolkata 700032, India
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11
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Ji C, Feng Y, Sun R, Gu Q, Zhang Y, Ma J, Pan Z, Yao H. Development of a multienzyme isothermal rapid amplification and lateral flow dipstick combination assay for bovine coronavirus detection. Front Vet Sci 2023; 9:1059934. [PMID: 36686176 PMCID: PMC9845563 DOI: 10.3389/fvets.2022.1059934] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 12/08/2022] [Indexed: 01/06/2023] Open
Abstract
Bovine coronavirus (BCoV) is a major cause of infectious disease in cattle, causing huge economic losses to the beef and dairy industries worldwide. BCoV can infect humans and multiple other species of animals. A rapid, reliable, and simple test is needed to detect BCoV infection in suspected farms. In this study, we developed a novel multienzyme isothermal rapid amplification (MIRA) and lateral flow dipstick (LFD) combination assay, targeting a highly conserved region of the viral nucleocapsid (N) gene for BCoV detection. The MIRA-LFD assay was highly specific and sensitive, comparable to a published reverse transcription quantitative PCR (RT-qPCR) assay for BCoV detection. Compared with the published RT-qPCR assay, the κ value of the MIRA-LFD assay in the detection of 192 cattle clinical samples was 0.982. The MIRA-LFD assay did not require sophisticated instruments and the results could be observed with eyes. Our results showed that the MIRA-LFD assay was a useful diagnostic tool for rapid on-site detection of BCoV.
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12
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Hao Y, Wang Y, Wang M, Zhou L, Shi J, Cao J, Wang D. The origins of COVID-19 pandemic: A brief overview. Transbound Emerg Dis 2022; 69:3181-3197. [PMID: 36218169 PMCID: PMC9874793 DOI: 10.1111/tbed.14732] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/26/2022] [Accepted: 10/04/2022] [Indexed: 02/06/2023]
Abstract
The novel coronavirus disease (COVID-19) outbreak that emerged at the end of 2019 has now swept the world for more than 2 years, causing immeasurable damage to the lives and economies of the world. It has drawn so much attention to discovering how the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originated and entered the human body. The current argument revolves around two contradictory theories: a scenario of laboratory spillover events and human contact with zoonotic diseases. Here, we reviewed the transmission, pathogenesis, possible hosts, as well as the genome and protein structure of SARS-CoV-2, which play key roles in the COVID-19 pandemic. We believe the coronavirus was originally transmitted to human by animals rather than by a laboratory leak. However, there still needs more investigations to determine the source of the pandemic. Understanding how COVID-19 emerged is vital to developing global strategies for mitigating future outbreaks.
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Affiliation(s)
- Ying‐Jian Hao
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - Yu‐Lan Wang
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - Mei‐Yue Wang
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - Lan Zhou
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - Jian‐Yun Shi
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - Ji‐Min Cao
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - De‐Ping Wang
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
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13
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Pandemic origins and a One Health approach to preparedness and prevention: Solutions based on SARS-CoV-2 and other RNA viruses. Proc Natl Acad Sci U S A 2022; 119:e2202871119. [PMID: 36215506 PMCID: PMC9586299 DOI: 10.1073/pnas.2202871119] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
COVID-19 is the latest zoonotic RNA virus epidemic of concern. Learning how it began and spread will help to determine how to reduce the risk of future events. We review major RNA virus outbreaks since 1967 to identify common features and opportunities to prevent emergence, including ancestral viral origins in birds, bats, and other mammals; animal reservoirs and intermediate hosts; and pathways for zoonotic spillover and community spread, leading to local, regional, or international outbreaks. The increasing scientific evidence concerning the origins of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is most consistent with a zoonotic origin and a spillover pathway from wildlife to people via wildlife farming and the wildlife trade. We apply what we know about these outbreaks to identify relevant, feasible, and implementable interventions. We identify three primary targets for pandemic prevention and preparedness: first, smart surveillance coupled with epidemiological risk assessment across wildlife–livestock–human (One Health) spillover interfaces; second, research to enhance pandemic preparedness and expedite development of vaccines and therapeutics; and third, strategies to reduce underlying drivers of spillover risk and spread and reduce the influence of misinformation. For all three, continued efforts to improve and integrate biosafety and biosecurity with the implementation of a One Health approach are essential. We discuss new models to address the challenges of creating an inclusive and effective governance structure, with the necessary stable funding for cross-disciplinary collaborative research. Finally, we offer recommendations for feasible actions to close the knowledge gaps across the One Health continuum and improve preparedness and response in the future.
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14
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Abstract
The "Russian flu", which raged from 1889 to 1894, is considered as the first pandemic of the industrial era for which statistics have been collected. This planetary event started in Turkestan and hit the Russian Empire, before reaching all European countries, the United States of America, and the whole world. Contemporaries were surprised by its high contagiousness as evidenced by attack rates averaging 60% in urban populations, its rapid spread in successive waves circling the globe in a few months by rail and sea, and the tendency of the disease to relapse. Despite its low case-fatality rate (0.10%-0.28%), it is estimated to have caused one million deaths worldwide. On serological grounds, it is generally accepted that the causative agent of Russian influenza was Myxovirus influenzae, the virus identified for all influenza pandemics since the "Spanish flu" of 1918. In light of the Covid-19 pandemic, which has underscored the extraordinary epidemic potential of coronaviruses, this assumption has recently been questioned. Coronaviruses come from wild reservoirs (bats, rodents, birds, …). They induce respiratory symptoms mimicking influenza, possibly leading to respiratory distress with pneumonia. In addition to the Covid-19 pandemic, recent deadly and limited epidemics, such as SARS in 2002 and MERS in 2012, have occurred. Russian influenza presented as an influenza-like syndrome with clinical peculiarities (multivisceral and neurological involvement, skin rash, early iterative relapses), evoking some particularities of Covid-19. Four other coronaviruses circulating in the human population for decades (HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1) have been found to be responsible for 15 to 30% of seasonal colds. All of these viruses are of animal origin. Recently, phylogenetic studies have revealed the genetic proximity between a bovine coronavirus BCoV and the human virus HCoV-OC43, indicating that the latter emerged around 1890, at the time of the Russian flu, when an epizootic was raging among cattle throughout Europe. Could the current human virus be the attenuated remnant that appeared after the Russian flu in 1894? Was there a coronavirus pandemic before Covid-19 ?
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15
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Savard C, Provost C, Ariel O, Morin S, Fredrickson R, Gagnon CA, Broes A, Wang L. First report and genomic characterization of a bovine-like coronavirus causing enteric infection in an odd-toed non-ruminant species (Indonesian tapir, Acrocodia indica) during an outbreak of winter dysentery in a zoo. Transbound Emerg Dis 2022; 69:3056-3065. [PMID: 34427399 PMCID: PMC8943714 DOI: 10.1111/tbed.14300] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/16/2021] [Accepted: 08/22/2021] [Indexed: 02/05/2023]
Abstract
Bovine coronavirus (BCoV) is associated with three distinct clinical syndromes in cattle that is, neonatal diarrhoea, haemorrhagic diarrhoea in adults (the so-called winter dysentery syndrome, WD) and respiratory infections in cattle of different ages. In addition, bovine-like CoVs have been detected in various species including domestic and wild ruminants. However, bovine-like CoVs have not been reported so far in odd-toed ungulates. We describe an outbreak of WD associated with a bovine-like CoV affecting several captive wild ungulates, including Indonesian tapirs (Acrocodia indica) an odd-toed ungulate species (Perissodactyla) which, with even-toed ungulates species (Artiodactyla) form the clade Euungulata. Genomic characterization of the CoV revealed that it was closely related to BCoVs previously reported in America. This case illustrates the adaptability of bovine-like CoVs to new species and the necessity of continued surveillance of bovine-like CoVs in various species.
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Affiliation(s)
| | - Chantale Provost
- Molecular diagnostic laboratory, Centre de diagnostic vétérinaire de l’Université de Montréal (CDVUM), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, Canada
| | | | - Samuel Morin
- Bureau vétérinaire Iberville, Saint-Jean-sur-Richelieu, Québec, Canada
| | - Richard Fredrickson
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, Illinois, USA
| | - Carl A. Gagnon
- Molecular diagnostic laboratory, Centre de diagnostic vétérinaire de l’Université de Montréal (CDVUM), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, Canada
| | - André Broes
- Biovet Inc., Saint-Hyacinthe, Québec, Canada
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, Illinois, USA
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16
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Kim EM, Cho HC, Shin SU, Park J, Choi KS. Prevalence and genetic characterization of bovine coronavirus identified from diarrheic pre-weaned native Korean calves from 2019 to 2021. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 100:105263. [PMID: 35276339 DOI: 10.1016/j.meegid.2022.105263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/13/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Bovine coronavirus (BCoV) is associated with severe diarrhea in calves, winter dysentery in adult cattle, and respiratory diseases in cattle. However, there is currently limited information regarding its molecular characterization in the Republic of Korea (KOR). Therefore, this study investigated the prevalence of BCoV in diarrheic pre-weaned calves (aged ≤60 days) and compared BCoV genome sequences identified globally. A total of 846 fecal samples were collected from calves with diarrhea across 100 beef farms in the KOR. The samples were divided into three groups based on age as follows: 1-10 days (n = 490), 11-30 days (n = 277), and 31-60 days (n = 79). BCoV infection was detected in 50 calves by real-time RT-PCR analysis. The results showed that the prevalence of BCoV was associated with calf age (P = 0.028) and was significantly higher in calves aged 31-60 days (odds ratio: 2.69, 95% confidence interval: 1.24-5.85; P = 0.012) than in those aged 1-10 days. Our findings show that BCoV is an important etiological agent of diarrhea in calves aged 31-60 days. Fifteen full genome sequences (2019-2021 variants) of the spike, hemagglutinin/esterase, and nucleocapsid were obtained from the 50 BCoV-positive samples. Phylogenetic analysis of each gene revealed that BCoVs circulating worldwide might have no boundary between enteric and respiratory tropisms, demonstrating the presence of three BCoVs groups: the classical, Asia/USA, and European. Initially, Korean BCoVs were originated from the USA, but diverged since the 1980s and rapidly evolved independently, unlike in other Asian countries. In this study, Korean BCoVs are more recent BCoVs and present relatively high nucleotide substitution rates in all genes compared with other BCoVs. Our results showed that the 2019-2021 variants undergo continuous genetic evolution and that there are genetic differences among globally distributed BCoVs.
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Affiliation(s)
- Eun-Mi Kim
- Department of Animal Science and Biotechnology, College of Ecology and Environmental Science, Kyungpook National University, Sangju 37224, Republic of Korea
| | - Hyung-Chul Cho
- Department of Animal Science and Biotechnology, College of Ecology and Environmental Science, Kyungpook National University, Sangju 37224, Republic of Korea
| | - Seung-Uk Shin
- Department of Animal Science and Biotechnology, College of Ecology and Environmental Science, Kyungpook National University, Sangju 37224, Republic of Korea
| | - Jinho Park
- College of Veterinary Medicine, Jeonbuk National University, Iksan 54596, Republic of Korea
| | - Kyoung-Seong Choi
- Department of Animal Science and Biotechnology, College of Ecology and Environmental Science, Kyungpook National University, Sangju 37224, Republic of Korea.
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17
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Zhu Q, Li B, Sun D. Advances in Bovine Coronavirus Epidemiology. Viruses 2022; 14:v14051109. [PMID: 35632850 PMCID: PMC9147158 DOI: 10.3390/v14051109] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/02/2022] [Accepted: 05/19/2022] [Indexed: 11/16/2022] Open
Abstract
Bovine coronavirus (BCoV) is a causative agent of enteric and respiratory disease in cattle. BCoV has also been reported to cause a variety of animal diseases and is closely related to human coronaviruses, which has attracted extensive attention from both cattle farmers and researchers. However, there are few comprehensive epidemiological reviews, and key information regarding the effect of S-gene differences on tissue tendency and potential cross-species transmission remain unclear. In this review, we summarize BCoV epidemiology, including the transmission, infection-associated factors, co-infection, pathogenicity, genetic evolution, and potential cross-species transmission. Furthermore, the potential two-receptor binding motif system for BCoV entry and the association between BCoV and SARS-CoV-2 are also discussed in this review. Our aim is to provide valuable information for the prevention and treatment of BCoV infection throughout the world.
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Affiliation(s)
- Qinghe Zhu
- Heilongjiang Provincial Key Laboratory of the Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China;
| | - Bin Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
- Correspondence: (B.L.); (D.S.); Tel.: +86-045-9681-9121 (D.S.)
| | - Dongbo Sun
- Heilongjiang Provincial Key Laboratory of the Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China;
- Correspondence: (B.L.); (D.S.); Tel.: +86-045-9681-9121 (D.S.)
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18
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Maroli N, Bhasuran B, Natarajan J, Kolandaivel P. The potential role of procyanidin as a therapeutic agent against SARS-CoV-2: a text mining, molecular docking and molecular dynamics simulation approach. J Biomol Struct Dyn 2022; 40:1230-1245. [PMID: 32960159 PMCID: PMC7544928 DOI: 10.1080/07391102.2020.1823887] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 09/10/2020] [Indexed: 02/07/2023]
Abstract
A novel coronavirus (SARS-CoV-2) has caused a major outbreak in human all over the world. There are several proteins interplay during the entry and replication of this virus in human. Here, we have used text mining and named entity recognition method to identify co-occurrence of the important COVID 19 genes/proteins in the interaction network based on the frequency of the interaction. Network analysis revealed a set of genes/proteins, highly dense genes/protein clusters and sub-networks of Angiotensin-converting enzyme 2 (ACE2), Helicase, spike (S) protein (trimeric), membrane (M) protein, envelop (E) protein, and the nucleocapsid (N) protein. The isolated proteins are screened against procyanidin-a flavonoid from plants using molecular docking. Further, molecular dynamics simulation of critical proteins such as ACE2, Mpro and spike proteins are performed to elucidate the inhibition mechanism. The strong network of hydrogen bonds and hydrophobic interactions along with van der Waals interactions inhibit receptors, which are essential to the entry and replication of the SARS-CoV-2. The binding energy which largely arises from van der Waals interactions is calculated (ACE2=-50.21 ± 6.3, Mpro=-89.50 ± 6.32 and spike=-23.06 ± 4.39) through molecular mechanics Poisson-Boltzmann surface area also confirm the affinity of procyanidin towards the critical receptors. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nikhil Maroli
- Computational Biology Division, DRDO Center for Life Sciences, Bharathiar University Campus, Coimbatore, Tamil Nadu, India
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, Karnataka, India
| | - Balu Bhasuran
- Computational Biology Division, DRDO Center for Life Sciences, Bharathiar University Campus, Coimbatore, Tamil Nadu, India
| | - Jeyakumar Natarajan
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India
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19
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Kong F, Wang Q, Kenney SP, Jung K, Vlasova AN, Saif LJ. Porcine Deltacoronaviruses: Origin, Evolution, Cross-Species Transmission and Zoonotic Potential. Pathogens 2022; 11:79. [PMID: 35056027 PMCID: PMC8778258 DOI: 10.3390/pathogens11010079] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/30/2021] [Accepted: 01/04/2022] [Indexed: 01/27/2023] Open
Abstract
Porcine deltacoronavirus (PDCoV) is an emerging enteropathogenic coronavirus of swine that causes acute diarrhoea, vomiting, dehydration and mortality in seronegative neonatal piglets. PDCoV was first reported in Hong Kong in 2012 and its etiological features were first characterized in the United States in 2014. Currently, PDCoV is a concern due to its broad host range, including humans. Chickens, turkey poults, and gnotobiotic calves can be experimentally infected by PDCoV. Therefore, as discussed in this review, a comprehensive understanding of the origin, evolution, cross-species transmission and zoonotic potential of epidemic PDCoV strains is urgently needed.
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Affiliation(s)
- Fanzhi Kong
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China;
| | - Qiuhong Wang
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; (S.P.K.); (K.J.); (A.N.V.); (L.J.S.)
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Scott P. Kenney
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; (S.P.K.); (K.J.); (A.N.V.); (L.J.S.)
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Kwonil Jung
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; (S.P.K.); (K.J.); (A.N.V.); (L.J.S.)
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Anastasia N. Vlasova
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; (S.P.K.); (K.J.); (A.N.V.); (L.J.S.)
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Linda J. Saif
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; (S.P.K.); (K.J.); (A.N.V.); (L.J.S.)
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
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20
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Pratelli A, Tempesta M, Elia G, Martella V, Decaro N, Buonavoglia C. The knotty biology of canine coronavirus: A worrying model of coronaviruses' danger. Res Vet Sci 2021; 144:190-195. [PMID: 34838321 PMCID: PMC8605815 DOI: 10.1016/j.rvsc.2021.11.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 12/20/2022]
Abstract
Severe clinical diseases associated to αCoronavirus (αCoV) infections were recently demonstrated for the first time in humans and a closely related but distinct canine CoV (CCoV) variant was identified in the nasopharyngeal swabs of children with pneumonia hospitalized in Malaysia, in 2017-2018. The complete genome sequence analysis demonstrated that the isolated strain, CCoV-HuPn-2018, was a novel canine-feline-like recombinant virus with a unique nucleoprotein. The occurrence of three human epidemics/pandemic caused by CoVs in the recent years and the detection of CCoV-HuPn-2018, raises questions about the ability of these viruses to overcome species barriers from their reservoirs jumping to humans. Interestingly, in this perspective, it is interesting to consider the report concerning new CCoV strains with a potential dual recombinant origin through partial S-gene exchange with porcine transmissible gastroenteritis virus (TGEV) identified in pups died with acute gastroenteritis in 2009. The significance of the ability of CCoVs to evolve is still unclear, but several questions arisen on the biology of these viruses, focusing important epidemiological outcomes in the field, in terms of both virus evolution and prophylaxis. The new CCoV-Hupn-2018 should lead researchers to pay more attention to the mechanisms of recombination among CoVs, rather than to the onset of variants as a result of mutations, suggesting a continuous monitoring of these viruses and in particular of SARS-CoV-2.
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Affiliation(s)
- Annamaria Pratelli
- Department of Veterinary Medicine, University Aldo Moro of Bari, Strada per Casamassima Km 3, 70010 Valenzano, BA, Italy.
| | - Maria Tempesta
- Department of Veterinary Medicine, University Aldo Moro of Bari, Strada per Casamassima Km 3, 70010 Valenzano, BA, Italy
| | - Gabriella Elia
- Department of Veterinary Medicine, University Aldo Moro of Bari, Strada per Casamassima Km 3, 70010 Valenzano, BA, Italy
| | - Vito Martella
- Department of Veterinary Medicine, University Aldo Moro of Bari, Strada per Casamassima Km 3, 70010 Valenzano, BA, Italy
| | - Nicola Decaro
- Department of Veterinary Medicine, University Aldo Moro of Bari, Strada per Casamassima Km 3, 70010 Valenzano, BA, Italy
| | - Canio Buonavoglia
- Department of Veterinary Medicine, University Aldo Moro of Bari, Strada per Casamassima Km 3, 70010 Valenzano, BA, Italy
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21
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Zhu Q, Su M, Li Z, Wang X, Qi S, Zhao F, Li L, Guo D, Feng L, Li B, Sun D. Epidemiological survey and genetic diversity of bovine coronavirus in Northeast China. Virus Res 2021; 308:198632. [PMID: 34793872 DOI: 10.1016/j.virusres.2021.198632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/31/2021] [Accepted: 11/01/2021] [Indexed: 10/19/2022]
Abstract
In 2020, to trace the prevalence and evolution of bovine coronavirus (BCoV) in China, a total of 1383 samples (1016 fecal samples and 367 nasal swab samples) were collected from 1016 cattle exhibiting diarrhea symptoms on dairy farms and beef cattle farms in Heilongjiang Province, Northeast China. All samples were subjected to reverse transcription-polymerase chain reaction (RT-PCR) detection of the BCoV N gene, followed by an analysis of its epidemiology and genetic evolution. The results indicated that of the 1016 diarrhea-affected cattle, 15.45% (157/1016) were positive for BCoV, in which positive rates of the fecal and nasal swab samples were 12.20% (124/1016) and 21.53% (79/367), respectively. Of the 367 cattle whose nasal swab samples were collected, the BCoV positive rate of the corresponding fecal samples was 15.26% (56/367). BCoV infection was significantly associated with age, farming pattern, cattle type, farm latitude, sample type, and clinical symptom (p < 0.05). Of the 203 BCoV-positive samples, 20 spike (S) genes were successfully sequenced. The 20 identified BCoV strains shared nucleotide homologies of 97.7-100.0%, and their N-terminal domain of S1 subunit (S1-NTD: residues 15-298) differed genetically from the reference strains of South Korea and Europe. The 20 identified BCoV strains were clustered in the Asia-North America group (GII group) in the global strain-based phylogenetic tree and formed three clades in the Chinese strain-based phylogenetic tree. The HLJ/HH-10/2020 strain was clustered into the Europe group (GI group) in the S1-NTD-based phylogenetic tree, exhibiting N146/I, D148/G, and L154/F mutations that affect the S protein structure. Of the identified BCoV strains, one potential recombination event occurred between the HLJ/HH-20/2020 and HLJ/HH-10/2020 strains, which led to the generation of the recombinant BCV-AKS-01 strain. A selective pressure analysis on the S protein revealed one positively selected site (Asn509) among the 20 identified BCoV strains located inside the putative receptor binding domain (residues 326-540). These data provide a greater understanding of the epidemiology and evolution of BCoV in China.
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Affiliation(s)
- Qinghe Zhu
- Laboratory for the Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China; Branch of Animal Husbandry and Veterinary of Heilongjiang Academy of Agricultural Sciences, Qiqihar 161000, China
| | - Mingjun Su
- Laboratory for the Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China
| | - Zijian Li
- Laboratory for the Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China
| | - Xiaoran Wang
- Laboratory for the Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China
| | - Shanshan Qi
- Laboratory for the Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China
| | - Feiyu Zhao
- Laboratory for the Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China
| | - Lu Li
- Laboratory for the Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China
| | - Donghua Guo
- Laboratory for the Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China
| | - Li Feng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Bin Li
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Dongbo Sun
- Laboratory for the Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China.
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22
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Liu X, Wu Q, Zhang Z. Global Diversification and Distribution of Coronaviruses With Furin Cleavage Sites. Front Microbiol 2021; 12:649314. [PMID: 34690939 PMCID: PMC8529245 DOI: 10.3389/fmicb.2021.649314] [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: 01/04/2021] [Accepted: 09/14/2021] [Indexed: 12/24/2022] Open
Abstract
Knowledge about coronaviruses (CoVs) with furin cleavage sites is extremely limited, although these sites mediate the hydrolysis of glycoproteins in plasma membranes required for MERS-CoV or SARS-CoV-2 to enter cells and infect humans. Thus, we have examined the global epidemiology and evolutionary history of SARS-CoV-2 and 248 other CoVs with 86 diversified furin cleavage sites that have been detected in 24 animal hosts in 28 countries since 1954. Besides MERS-CoV and SARS-CoV-2, two of five other CoVs known to infect humans (HCoV-OC43 and HCoV-HKU1) also have furin cleavage sites. In addition, human enteric coronavirus (HECV-4408) has a furin cleavage site and has been detected in humans (first in Germany in 1988), probably via spillover events from bovine sources. In conclusion, the presence of furin cleavage sites might explain the polytropic nature of SARS-CoV-2- and SARS-CoV-2-like CoVs, which would be helpful for ending the COVID-19 pandemic and preventing outbreaks of novel CoVs.
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Affiliation(s)
- Xiaotong Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Qunfu Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Zhigang Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
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23
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Parkhe P, Verma S. Evolution, Interspecies Transmission, and Zoonotic Significance of Animal Coronaviruses. Front Vet Sci 2021; 8:719834. [PMID: 34738021 PMCID: PMC8560429 DOI: 10.3389/fvets.2021.719834] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/07/2021] [Indexed: 12/18/2022] Open
Abstract
Coronaviruses are single-stranded RNA viruses that affect humans and a wide variety of animal species, including livestock, wild animals, birds, and pets. These viruses have an affinity for different tissues, such as those of the respiratory and gastrointestinal tract of most mammals and birds and the hepatic and nervous tissues of rodents and porcine. As coronaviruses target different host cell receptors and show divergence in the sequences and motifs of their structural and accessory proteins, they are classified into groups, which may explain the evolutionary relationship between them. The interspecies transmission, zoonotic potential, and ability to mutate at a higher rate and emerge into variants of concern highlight their importance in the medical and veterinary fields. The contribution of various factors that result in their evolution will provide better insight and may help to understand the complexity of coronaviruses in the face of pandemics. In this review, important aspects of coronaviruses infecting livestock, birds, and pets, in particular, their structure and genome organization having a bearing on evolutionary and zoonotic outcomes, have been discussed.
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Affiliation(s)
| | - Subhash Verma
- Department of Veterinary Microbiology, DGCN College of Veterinary and Animal Sciences, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, India
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24
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Jacob Machado D, Scott R, Guirales S, Janies DA. Fundamental evolution of all Orthocoronavirinae including three deadly lineages descendent from Chiroptera-hosted coronaviruses: SARS-CoV, MERS-CoV and SARS-CoV-2. Cladistics 2021; 37:461-488. [PMID: 34570933 PMCID: PMC8239696 DOI: 10.1111/cla.12454] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2021] [Indexed: 12/14/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in humans in 2002. Despite reports showing Chiroptera as the original animal reservoir of SARS-CoV, many argue that Carnivora-hosted viruses are the most likely origin. The emergence of the Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 also involves Chiroptera-hosted lineages. However, factors such as the lack of comprehensive phylogenies hamper our understanding of host shifts once MERS-CoV emerged in humans and Artiodactyla. Since 2019, the origin of SARS-CoV-2, causative agent of coronavirus disease 2019 (COVID-19), added to this episodic history of zoonotic transmission events. Here we introduce a phylogenetic analysis of 2006 unique and complete genomes of different lineages of Orthocoronavirinae. We used gene annotations to align orthologous sequences for total evidence analysis under the parsimony optimality criterion. Deltacoronavirus and Gammacoronavirus were set as outgroups to understand spillovers of Alphacoronavirus and Betacoronavirus among ten orders of animals. We corroborated that Chiroptera-hosted viruses are the sister group of SARS-CoV, SARS-CoV-2 and MERS-related viruses. Other zoonotic events were qualified and quantified to provide a comprehensive picture of the risk of coronavirus emergence among humans. Finally, we used a 250 SARS-CoV-2 genomes dataset to elucidate the phylogenetic relationship between SARS-CoV-2 and Chiroptera-hosted coronaviruses.
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Affiliation(s)
- Denis Jacob Machado
- Department of Bioinformatics and GenomicsUniversity of North Carolina at Charlotte9331 Robert D. Snyder RdCharlotteNC28223USA
| | - Rachel Scott
- Department of Bioinformatics and GenomicsUniversity of North Carolina at Charlotte9331 Robert D. Snyder RdCharlotteNC28223USA
| | - Sayal Guirales
- Department of Bioinformatics and GenomicsUniversity of North Carolina at Charlotte9331 Robert D. Snyder RdCharlotteNC28223USA
| | - Daniel A. Janies
- Department of Bioinformatics and GenomicsUniversity of North Carolina at Charlotte9331 Robert D. Snyder RdCharlotteNC28223USA
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25
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Islam A, Ferdous J, Islam S, Sayeed MA, Dutta Choudhury S, Saha O, Hassan MM, Shirin T. Evolutionary Dynamics and Epidemiology of Endemic and Emerging Coronaviruses in Humans, Domestic Animals, and Wildlife. Viruses 2021; 13:1908. [PMID: 34696338 PMCID: PMC8537103 DOI: 10.3390/v13101908] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/12/2021] [Accepted: 09/17/2021] [Indexed: 12/21/2022] Open
Abstract
Diverse coronavirus (CoV) strains can infect both humans and animals and produce various diseases. CoVs have caused three epidemics and pandemics in the last two decades, and caused a severe impact on public health and the global economy. Therefore, it is of utmost importance to understand the emergence and evolution of endemic and emerging CoV diversity in humans and animals. For diverse bird species, the Infectious Bronchitis Virus is a significant one, whereas feline enteric and canine coronavirus, recombined to produce feline infectious peritonitis virus, infects wild cats. Bovine and canine CoVs have ancestral relationships, while porcine CoVs, especially SADS-CoV, can cross species barriers. Bats are considered as the natural host of diverse strains of alpha and beta coronaviruses. Though MERS-CoV is significant for both camels and humans, humans are nonetheless affected more severely. MERS-CoV cases have been reported mainly in the Arabic peninsula since 2012. To date, seven CoV strains have infected humans, all descended from animals. The severe acute respiratory syndrome coronaviruses (SARS-CoV and SARS-CoV-2) are presumed to be originated in Rhinolopoid bats that severely infect humans with spillover to multiple domestic and wild animals. Emerging alpha and delta variants of SARS-CoV-2 were detected in pets and wild animals. Still, the intermediate hosts and all susceptible animal species remain unknown. SARS-CoV-2 might not be the last CoV to cross the species barrier. Hence, we recommend developing a universal CoV vaccine for humans so that any future outbreak can be prevented effectively. Furthermore, a One Health approach coronavirus surveillance should be implemented at human-animal interfaces to detect novel coronaviruses before emerging to humans and to prevent future epidemics and pandemics.
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Affiliation(s)
- Ariful Islam
- EcoHealth Alliance, New York, NY 10001-2320, USA; (J.F.); (S.I.); (M.A.S.); (S.D.C.)
- Centre for Integrative Ecology, School of Life and Environmental Science, Deakin University, Burwood, VIC 3216, Australia
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Jinnat Ferdous
- EcoHealth Alliance, New York, NY 10001-2320, USA; (J.F.); (S.I.); (M.A.S.); (S.D.C.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
- School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia
| | - Shariful Islam
- EcoHealth Alliance, New York, NY 10001-2320, USA; (J.F.); (S.I.); (M.A.S.); (S.D.C.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Md. Abu Sayeed
- EcoHealth Alliance, New York, NY 10001-2320, USA; (J.F.); (S.I.); (M.A.S.); (S.D.C.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Shusmita Dutta Choudhury
- EcoHealth Alliance, New York, NY 10001-2320, USA; (J.F.); (S.I.); (M.A.S.); (S.D.C.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Otun Saha
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh;
| | - Mohammad Mahmudul Hassan
- Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram 4225, Bangladesh;
| | - Tahmina Shirin
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
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26
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King A. Down on the farm: Farm coronaviruses are a large reservoir for new spillover events into humans. EMBO Rep 2021; 22:e53701. [PMID: 34402184 DOI: 10.15252/embr.202153701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/05/2021] [Indexed: 11/09/2022] Open
Abstract
Until COVID-19, coronaviruses were largely overlooked by virologists. Yet, their abundance in mammalian species could cause new spillover events into humans.
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27
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Brüssow H, Brüssow L. Clinical evidence that the pandemic from 1889 to 1891 commonly called the Russian flu might have been an earlier coronavirus pandemic. Microb Biotechnol 2021; 14:1860-1870. [PMID: 34254725 PMCID: PMC8441924 DOI: 10.1111/1751-7915.13889] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 06/27/2021] [Indexed: 01/10/2023] Open
Abstract
Contemporary medical reports from Britain and Germany on patients suffering from a pandemic infection between 1889 and 1891, which was historically referred to as the Russian flu, share a number of characteristics with COVID-19. Most notable are aspects of multisystem affections comprising respiratory, gastrointestinal and neurological symptoms including loss of taste and smell perception; a protracted recovery resembling long covid and pathology observations of thrombosis in multiple organs, inflammation and rheumatic affections. As in COVID-19 and unlike in influenza, mortality was seen in elderly subjects while children were only weakly affected. Contemporary reports noted trans-species infection between pet animals or horses and humans, which would concur with a cross-infection by a broad host range bovine coronavirus dated by molecular clock arguments to an about 1890 cross-species infection event.
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Affiliation(s)
- Harald Brüssow
- Department of BiosystemsLaboratory of Gene TechnologyKU LeuvenLeuvenBelgium
| | - Lutz Brüssow
- Internal Medicine, Angiology and Gastroenterology SpecialistNeussGermany
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28
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Islam MS, Hasib FMY, Nath C, Ara J, Nu MS, Fazal MA, Chowdhury S. Coronavirus disease 2019 and its potential animal reservoirs: A review. INTERNATIONAL JOURNAL OF ONE HEALTH 2021. [DOI: 10.14202/ijoh.2021.171-181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In the 21st century, the world has been plagued by coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a virus of the family Coronaviridae epidemiologically suspected to be linked to a wet market in Wuhan, China. The involvement of wildlife and wet markets with the previous outbreaks simultaneously has been brought into sharp focus. Although scientists are yet to ascertain the host range and zoonotic potential of SARS-CoV-2 rigorously, information about its two ancestors, SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV), is a footprint for research on COVID-19. A 96% genetic similarity with bat coronaviruses and SARS-CoV-2 indicates that the bat might be a potential reservoir of SARS-CoV-2 just like SARS-CoV and MERS-CoV, where civets and dromedary camels are considered the potential intermediate host, respectively. Perceiving the genetic similarity between pangolin coronavirus and SARS-CoV-2, many scientists also have given the scheme that the pangolin might be the intermediate host. The involvement of SARS-CoV-2 with other animals, such as mink, snake, and turtle has also been highlighted in different research articles based on the interaction between the key amino acids of S protein in the receptor-binding domain and angiotensin-converting enzyme II (ACE2). This study highlights the potential animal reservoirs of SARS-CoV-2 and the role of wildlife in the COVID-19 pandemic. Although different causes, such as recurring viral genome recombination, wide genetic assortment, and irksome food habits, have been blamed for this emergence, basic research studies and literature reviews indicate an enormous consortium between humans and animals for the COVID-19 pandemic.
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Affiliation(s)
- Md. Sirazul Islam
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - F. M. Yasir Hasib
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Chandan Nath
- Department of Microbiology and Veterinary Public Health, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Jahan Ara
- One Health Institute, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Mong Sing Nu
- Department of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Md. Abul Fazal
- Department of Microbiology and Veterinary Public Health, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Sharmin Chowdhury
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
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29
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Lin CN, Chan KR, Ooi EE, Chiou MT, Hoang M, Hsueh PR, Ooi PT. Animal Coronavirus Diseases: Parallels with COVID-19 in Humans. Viruses 2021; 13:1507. [PMID: 34452372 PMCID: PMC8402828 DOI: 10.3390/v13081507] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 07/26/2021] [Accepted: 07/29/2021] [Indexed: 12/11/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel coronavirus in humans, has expanded globally over the past year. COVID-19 remains an important subject of intensive research owing to its huge impact on economic and public health globally. Based on historical archives, the first coronavirus-related disease recorded was possibly animal-related, a case of feline infectious peritonitis described as early as 1912. Despite over a century of documented coronaviruses in animals, the global animal industry still suffers from outbreaks. Knowledge and experience handling animal coronaviruses provide a valuable tool to complement our understanding of the ongoing COVID-19 pandemic. In this review, we present an overview of coronaviruses, clinical signs, COVID-19 in animals, genome organization and recombination, immunopathogenesis, transmission, viral shedding, diagnosis, treatment, and prevention. By drawing parallels between COVID-19 in animals and humans, we provide perspectives on the pathophysiological mechanisms by which coronaviruses cause diseases in both animals and humans, providing a critical basis for the development of effective vaccines and therapeutics against these deadly viruses.
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Affiliation(s)
- Chao-Nan Lin
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan;
- Animal Disease Diagnostic Center, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan
| | - Kuan Rong Chan
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore 169857, Singapore; (K.R.C.); (E.E.O.)
| | - Eng Eong Ooi
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore 169857, Singapore; (K.R.C.); (E.E.O.)
- Viral Research and Experimental Medicine Centre (ViREMiCS), SingHealth Duke-NUS Academic Medical Centre, Singapore 169856, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549, Singapore
| | - Ming-Tang Chiou
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan;
- Animal Disease Diagnostic Center, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan
| | - Minh Hoang
- Department of Anatomy and Histology, College of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi 100000, Vietnam;
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine and Internal Medicine, China Medical University Hospital, School of Medicine, China Medical University, Taichung 404332, Taiwan
- Departments of Laboratory Medicine and Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei 10051, Taiwan
| | - Peck Toung Ooi
- Faculty of Veterinary Medicine, Universiti Putra Malaysia, UPM, Serdang 43400, Selangor, Malaysia
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30
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Abstract
Causal Organism COVID-19 is a disease caused by the novel coronavirus (SARS-CoV-2). Positive-sense ssRNA viruses are about 30 kb long. Coronaviruses have a broad spectrum of action and affect multiple organisms. Origin of Disease The disease outbreak has been initiated in Wuhan, China, in December 2019. The disease has been originated from the wet animal market of Wuhan City, where a large number of peoples have come in contact with animals. It is known to infect the neurological, respiratory, enteric, and hepatic systems. SARSCoV-2 is highly infectious, and its outbreak is worldwide (national and international level) and becomes pandemic. Control Presently, the number of cases continues to rise at a global level, and it is clear that these viruses pose a significant threat to public health. Consequently, extensive treatments, vaccines, and drugs have been developed by researchers to control the transmission of infection. This led to the isolation of patients that were administered a variety of treatments. Special attention and guidelines have been given by various government organizations to protect or reduce transmission between children, healthcare providers, and old-aged peoples.
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Carvalho T, Krammer F, Iwasaki A. The first 12 months of COVID-19: a timeline of immunological insights. Nat Rev Immunol 2021; 21:245-256. [PMID: 33723416 PMCID: PMC7958099 DOI: 10.1038/s41577-021-00522-1] [Citation(s) in RCA: 261] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2021] [Indexed: 12/15/2022]
Abstract
Since the initial reports of a cluster of pneumonia cases of unidentified origin in Wuhan, China, in December 2019, the novel coronavirus that causes this disease - severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) - has spread throughout the world, igniting the twenty-first century's deadliest pandemic. Over the past 12 months, a dizzying array of information has emerged from numerous laboratories, covering everything from the putative origin of SARS-CoV-2 to the development of numerous candidate vaccines. Many immunologists quickly pivoted from their existing research to focus on coronavirus disease 2019 (COVID-19) and, owing to this unprecedented convergence of efforts on one viral infection, a remarkable body of work has been produced and disseminated, through both preprint servers and peer-reviewed journals. Here, we take readers through the timeline of key discoveries during the first year of the pandemic, which showcases the extraordinary leaps in our understanding of the immune response to SARS-CoV-2 and highlights gaps in our knowledge as well as areas for future investigations.
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Affiliation(s)
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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Vlasova AN, Saif LJ. Bovine Coronavirus and the Associated Diseases. Front Vet Sci 2021; 8:643220. [PMID: 33869323 PMCID: PMC8044316 DOI: 10.3389/fvets.2021.643220] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/08/2021] [Indexed: 12/17/2022] Open
Abstract
Coronaviruses (CoVs) possess the largest and most complex RNA genome (up to 32 kb) that encodes for 16 non-structural proteins regulating RNA synthesis and modification. Coronaviruses are known to infect a wide range of mammalian and avian species causing remarkably diverse disease syndromes. Variable tissue tropism and the ability to easily cross interspecies barriers are the well-known characteristics of certain CoVs. The 21st century epidemics of severe acute respiratory CoV (SARS-CoV), Middle East respiratory CoV and the ongoing SARS-CoV-2 pandemic further highlight these characteristics and emphasize the relevance of CoVs to the global public health. Bovine CoVs (BCoVs) are betacoronaviruses associated with neonatal calf diarrhea, and with winter dysentery and shipping fever in older cattle. Of interest, no distinct genetic or antigenic markers have been identified in BCoVs associated with these distinct clinical syndromes. In contrast, like other CoVs, BCoVs exist as quasispecies. Besides cattle, BCoVs and bovine-like CoVs were identified in various domestic and wild ruminant species (water buffalo, sheep, goat, dromedary camel, llama, alpaca, deer, wild cattle, antelopes, giraffes, and wild goats), dogs and humans. Surprisingly, bovine-like CoVs also cannot be reliably distinguished from BCoVs using comparative genomics. Additionally, there are historical examples of zoonotic transmission of BCoVs. This article will discuss BCoV pathogenesis, epidemiology, interspecies transmission, immune responses, vaccines, and diagnostics.
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Affiliation(s)
- Anastasia N Vlasova
- Center for Food Animal Health Research, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH, United States
| | - Linda J Saif
- Center for Food Animal Health Research, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH, United States
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Vlasova AN, Kenney SP, Jung K, Wang Q, Saif LJ. Deltacoronavirus Evolution and Transmission: Current Scenario and Evolutionary Perspectives. Front Vet Sci 2021; 7:626785. [PMID: 33681316 PMCID: PMC7928354 DOI: 10.3389/fvets.2020.626785] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/31/2020] [Indexed: 11/19/2022] Open
Abstract
Deltacoronavirus (DCoV)–the only coronavirus that can infect multiple species of mammals and birds–was initially identified in several avian and mammalian species, including pigs, in China in 2009–2011. Porcine DCoV has since spread worldwide and is associated with multiple outbreaks of diarrheal disease of variable severity in farmed pigs. In contrast, avian DCoV is being reported in wild birds in different countries without any evidence of disease. The DCoV transboundary nature and the recent discovery of its remarkably broad reactivity with its cellular receptor–aminopeptidase N (APN)–from different species emphasize its epidemiological relevance and necessitate additional research. Further, the ability of porcine DCoV to infect and cause disease in chicks and turkey poults and gnotobiotic calves is suggestive of its increased potential for interspecies transmission or of its avian origin. Whether, porcine DCoVs were initially acquired by one or several mammalian species from birds and whether avian and porcine DCoVs continue co-evolving with frequent spillover events remain to be major unanswered questions. In this review, we will discuss the current information on the prevalence, genetic diversity, and pathogenic potential of porcine and avian DCoVs. We will also analyze the existing evidence of the ongoing interspecies transmission of DCoVs that may provide novel insights into their complex evolution.
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Affiliation(s)
- Anastasia N Vlasova
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH, United States
| | - Scott P Kenney
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH, United States
| | - Kwonil Jung
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH, United States
| | - Qiuhong Wang
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH, United States
| | - Linda J Saif
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH, United States
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Jacob Machado D, White RA, Kofsky J, Janies DA. Fundamentals of genomic epidemiology, lessons learned from the coronavirus disease 2019 (COVID-19) pandemic, and new directions. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2021; 1:e60. [PMID: 36168505 PMCID: PMC9495640 DOI: 10.1017/ash.2021.222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 04/19/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic was one of the significant causes of death worldwide in 2020. The disease is caused by severe acute coronavirus syndrome (SARS) coronavirus 2 (SARS-CoV-2), an RNA virus of the subfamily Orthocoronavirinae related to 2 other clinically relevant coronaviruses, SARS-CoV and MERS-CoV. Like other coronaviruses and several other viruses, SARS-CoV-2 originated in bats. However, unlike other coronaviruses, SARS-CoV-2 resulted in a devastating pandemic. The SARS-CoV-2 pandemic rages on due to viral evolution that leads to more transmissible and immune evasive variants. Technology such as genomic sequencing has driven the shift from syndromic to molecular epidemiology and promises better understanding of variants. The COVID-19 pandemic has exposed critical impediments that must be addressed to develop the science of pandemics. Much of the progress is being applied in the developed world. However, barriers to the use of molecular epidemiology in low- and middle-income countries (LMICs) remain, including lack of logistics for equipment and reagents and lack of training in analysis. We review the molecular epidemiology literature to understand its origins from the SARS epidemic (2002-2003) through influenza events and the current COVID-19 pandemic. We advocate for improved genomic surveillance of SARS-CoV and understanding the pathogen diversity in potential zoonotic hosts. This work will require training in phylogenetic and high-performance computing to improve analyses of the origin and spread of pathogens. The overarching goals are to understand and abate zoonosis risk through interdisciplinary collaboration and lowering logistical barriers.
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Affiliation(s)
- Denis Jacob Machado
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
- Author for correspondence: Denis Jacob Machado, PhD, Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, BINF 224, Charlotte, NC28223. E-mail:
| | - Richard Allen White
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
- University of North Carolina at Charlotte, North Carolina Research Campus (NCRC), Kannapolis, North Carolina
| | - Janice Kofsky
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
| | - Daniel A. Janies
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
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Tiwari R, Dhama K, Sharun K, Iqbal Yatoo M, Malik YS, Singh R, Michalak I, Sah R, Bonilla-Aldana DK, Rodriguez-Morales AJ. COVID-19: animals, veterinary and zoonotic links. Vet Q 2020; 40:169-182. [PMID: 32393111 PMCID: PMC7755411 DOI: 10.1080/01652176.2020.1766725] [Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/05/2020] [Accepted: 05/05/2020] [Indexed: 12/13/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), has spread over 210 countries and territories beyond China shortly. On February 29, 2020, the World Health Organization (WHO) denoted it in a high-risk category, and on March 11, 2020, this virus was designated pandemic, after its declaration being a Public Health International Emergency on January 30, 2020. World over high efforts are being made to counter and contain this virus. The COVID-19 outbreak once again proves the potential of the animal-human interface to act as the primary source of emerging zoonotic diseases. Even though the circumstantial evidence suggests the possibility of an initial zoonotic emergence, it is too early to confirm the role of intermediate hosts such as snakes, pangolins, turtles, and other wild animals in the origin of SARS-CoV-2, in addition to bats, the natural hosts of multiple coronaviruses such as SARS-CoV and MERS-CoV. The lessons learned from past episodes of MERS-CoV and SARS-CoV are being exploited to retort this virus. Best efforts are being taken up by worldwide nations to implement effective diagnosis, strict vigilance, heightened surveillance, and monitoring, along with adopting appropriate preventive and control strategies. Identifying the possible zoonotic emergence and the exact mechanism responsible for its initial transmission will help us to design and implement appropriate preventive barriers against the further transmission of SARS-CoV-2. This review discusses in brief about the COVID-19/SARS-CoV-2 with a particular focus on the role of animals, the veterinary and associated zoonotic links along with prevention and control strategies based on One-health approaches.
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Affiliation(s)
- Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, UP Pt. Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU), Mathura, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Khan Sharun
- Division of Surgery, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Mohd. Iqbal Yatoo
- Sher-E, Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, India
| | - Yashpal Singh Malik
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Rajendra Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Izabela Michalak
- Faculty of Chemistry, Department of Advanced Material Technologies, Wrocław University of Science and Technology, Wrocław, Poland
| | - Ranjit Sah
- Department of Microbiology, Tribhuvan University Teaching Hospital, Institute of Medicine, Kathmandu, Nepal
| | - D. Katterine Bonilla-Aldana
- Semillero de Zoonosis, Grupo de Investigación BIOECOS, Fundación Universitaria Autónoma de las Américas, Sede Pereira, Pereira, Risaralda, Colombia
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia
| | - Alfonso J Rodriguez-Morales
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia
- Grupo de Investigacion Biomedicina, Faculty of Medicine, Fundacion Universitaria Autonoma de las Americas, Pereira, Risaralda, Colombia
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Application of a Photocatalyst as an Inactivator of Bovine Coronavirus. Viruses 2020; 12:v12121372. [PMID: 33266175 PMCID: PMC7761435 DOI: 10.3390/v12121372] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/26/2020] [Accepted: 11/29/2020] [Indexed: 02/06/2023] Open
Abstract
Bovine coronavirus (BCoV), a major causative pathogen of bovine enteric and respiratory diseases and a zoonotic pathogen transmissible between animals and humans, has led to severe economic losses in numerous countries. BCoV belongs to the genus Betacoronavirus, which is a model of a pathogen that is threatening human health and includes severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2, and Middle East respiratory syndrome coronavirus. This study aimed to determine whether photocatalytic material effectively reduces CoVs in the environment. Using the film adhesion method of photocatalytic materials, we assessed its antiviral activity and the effect of visible light irradiation according to methods defined by the International Organization for Standardization. Consequently, photocatalytic material was found to have antiviral activity, reducing the viral loads by 2.7 log TCID50 (tissue culture infective dose 50)/0.1 mL (500 lux), 2.8 log TCID50/0.1 mL (1000 lux), and 2.4 log TCID50/0.1 mL (3000 lux). Hence, this photocatalytic material might be applicable not only to reducing CoVs in the cattle breeding environment but also perhaps in other indoor spaces, such as offices and hospital rooms. To our knowledge, this study is the first to evaluate the antiviral activity of a photocatalytic material against CoV.
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Amoroso MG, Lucifora G, Degli Uberti B, Serra F, De Luca G, Borriello G, De Domenico A, Brandi S, Cuomo MC, Bove F, Riccardi MG, Galiero G, Fusco G. Fatal Interstitial Pneumonia Associated with Bovine Coronavirus in Cows from Southern Italy. Viruses 2020; 12:v12111331. [PMID: 33228210 PMCID: PMC7699522 DOI: 10.3390/v12111331] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 12/13/2022] Open
Abstract
An outbreak of winter dysentery, complicated by severe respiratory syndrome, occurred in January 2020 in a high production dairy cow herd located in a hilly area of the Calabria region. Of the 52 animals belonging to the farm, 5 (9.6%) died with severe respiratory distress, death occurring 3–4 days after the appearance of the respiratory signs (caught and gasping breath). Microbiological analysis revealed absence of pathogenic bacteria whilst Real-time PCR identified the presence of RNA from Bovine Coronavirus (BCoV) in several organs: lungs, small intestine (jejunum), mediastinal lymph nodes, liver and placenta. BCoV was therefore hypothesized to play a role in the lethal pulmonary infection. Like the other CoVs, BCoV is able to cause different syndromes. Its role in calf diarrhea and in mild respiratory disease is well known: we report instead the involvement of this virus in a severe and fatal respiratory disorder, with symptoms and disease evolution resembling those of Severe Acute Respiratory Syndromes (SARS).
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Affiliation(s)
- Maria Grazia Amoroso
- Unit of Virology, Department of Animal Health, Experimental Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (B.D.U.); (F.S.); (G.D.L.); (S.B.); (G.F.)
- Correspondence:
| | - Giuseppe Lucifora
- Section of Vibo Valentia, Experimental Zooprophylactic Institute of Southern Italy, Contrada Piano di Bruno, 89852 Mileto, Italy;
| | - Barbara Degli Uberti
- Unit of Virology, Department of Animal Health, Experimental Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (B.D.U.); (F.S.); (G.D.L.); (S.B.); (G.F.)
| | - Francesco Serra
- Unit of Virology, Department of Animal Health, Experimental Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (B.D.U.); (F.S.); (G.D.L.); (S.B.); (G.F.)
| | - Giovanna De Luca
- Unit of Virology, Department of Animal Health, Experimental Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (B.D.U.); (F.S.); (G.D.L.); (S.B.); (G.F.)
| | - Giorgia Borriello
- Department of Animal Health, Experimental Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (G.B.); (M.C.C.); (F.B.); (M.G.R.); (G.G.)
| | - Alessandro De Domenico
- Freelance Veterinary, Ordine dei Veterinari di Vibo Valentia, 89900 Vibo Valentia, Italy;
| | - Sergio Brandi
- Unit of Virology, Department of Animal Health, Experimental Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (B.D.U.); (F.S.); (G.D.L.); (S.B.); (G.F.)
| | - Maria Concetta Cuomo
- Department of Animal Health, Experimental Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (G.B.); (M.C.C.); (F.B.); (M.G.R.); (G.G.)
| | - Francesca Bove
- Department of Animal Health, Experimental Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (G.B.); (M.C.C.); (F.B.); (M.G.R.); (G.G.)
| | - Marita Georgia Riccardi
- Department of Animal Health, Experimental Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (G.B.); (M.C.C.); (F.B.); (M.G.R.); (G.G.)
| | - Giorgio Galiero
- Department of Animal Health, Experimental Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (G.B.); (M.C.C.); (F.B.); (M.G.R.); (G.G.)
| | - Giovanna Fusco
- Unit of Virology, Department of Animal Health, Experimental Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (B.D.U.); (F.S.); (G.D.L.); (S.B.); (G.F.)
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Bovine Coronavirus: Variability, Evolution, and Dispersal Patterns of a No Longer Neglected Betacoronavirus. Viruses 2020; 12:v12111285. [PMID: 33182765 PMCID: PMC7697035 DOI: 10.3390/v12111285] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 12/13/2022] Open
Abstract
Bovine coronavirus (BoCV) is an important pathogen of cattle, causing severe enteric disease and playing a role in the bovine respiratory disease complex. Similar to other coronaviruses, a remarkable variability characterizes both its genome and biology. Despite their potential relevance, different aspects of the evolution of BoCV remain elusive. The present study reconstructs the history and evolution of BoCV using a phylodynamic approach based on complete genome and spike protein sequences. The results demonstrate high mutation and recombination rates affecting different parts of the viral genome. In the spike gene, this variability undergoes significant selective pressures—particularly episodic pressure—located mainly on the protein surface, suggesting an immune-induced selective pressure. The occurrence of compensatory mutations was also identified. On the contrary, no strong evidence in favor of host and/or tissue tropism affecting viral evolution has been proven. The well-known plasticity is thus ascribable to the innate broad viral tropism rather than mid- or long-term adaptation. The evaluation of the geographic spreading pattern clearly evidenced two clusters: a European cluster and an American–Asian cluster. While a relatively dense and quick migration network was identified in the former, the latter was dominated by the primary role of the United States (US) as a viral exportation source. Since the viral spreading pattern strongly mirrored the cattle trade, the need for more intense monitoring and preventive measures cannot be underestimated as well as the need to enforce the vaccination of young animals before international trade, to reduce not only the clinical impact but also the transferal and mixing of BoCV strains.
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Zhang M, Hill JE, Alexander TW, Huang Y. The nasal viromes of cattle on arrival at western Canadian feedlots and their relationship to development of bovine respiratory disease. Transbound Emerg Dis 2020; 68:2209-2218. [PMID: 33031627 DOI: 10.1111/tbed.13873] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/03/2020] [Indexed: 01/08/2023]
Abstract
Bovine respiratory disease (BRD) has a complex pathogenesis and aetiology, being the costliest disease affecting the cattle industry in North America. In this study, we applied Nanopore-based viral metagenomic sequencing to explore the nasal virome of cattle upon arrival at feedlot and related the findings to the development of BRD. Deep nasal swabs (DNS) from 310 cattle for which BRD outcomes were known (155 cattle developed BRD within 40 days and 155 remained healthy) were included. The most prevalent virus in on-arrival samples was bovine coronavirus (BCV) (45.2%, 140/310), followed by bovine rhinitis virus B (BRBV) (21.9%, 68/310), enterovirus E (EVE) (19.6%, 60/310), bovine parainfluenza virus 3 (BPIV3) (10.3%, 32/310), ungulate tetraparvovirus 1 (UTPV1) (9.7%, 30/310) and influenza D virus (7.1%, 22/310). No relationship was found between BRD development and the number of viruses detected, the presence of any specific individual virus or combination of viruses. Bovine kobuvirus (BKV) was detected in 2.6% of animals (8/310), being the first report of this virus in Canada. Results of this study demonstrate the diversity of viruses in bovine DNS collected upon arrival at feedlot and highlights the need for further research into prediction of BRD development in the context of mixed infections.
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Affiliation(s)
- Maodong Zhang
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Janet E Hill
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Trevor W Alexander
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Yanyun Huang
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada.,Prairie Diagnostic Services Inc, Saskatoon, SK, Canada
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40
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Luo X, Zhou GZ, Zhang Y, Peng LH, Zou LP, Yang YS. Coronaviruses and gastrointestinal diseases. Mil Med Res 2020; 7:49. [PMID: 33054860 PMCID: PMC7556584 DOI: 10.1186/s40779-020-00279-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/02/2020] [Indexed: 02/07/2023] Open
Abstract
The effects of coronaviruses on the respiratory system are of great concern, but their effects on the digestive system receive much less attention. Coronaviruses that infect mammals have shown gastrointestinal pathogenicity and caused symptoms such as diarrhea and vomiting. Available data have shown that human coronaviruses, including the newly emerged SARS-CoV-2, mainly infect the respiratory system and cause symptoms such as cough and fever, while they may generate gastrointestinal symptoms. However, there is little about the relation between coronavirus and digestive system. This review specifically addresses the effects of mammalian and human coronaviruses, including SARS-CoV-2, on the digestive tract, helping to cope with the new virus infection-induced disease, COVID-19.
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Affiliation(s)
- Xi Luo
- Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China.,Department of Pediatrics, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Guan-Zhou Zhou
- Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Yan Zhang
- Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Li-Hua Peng
- Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Li-Ping Zou
- Department of Pediatrics, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Yun-Sheng Yang
- Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China.
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An emerging novel bovine coronavirus with a 4-amino-acid insertion in the receptor-binding domain of the hemagglutinin-esterase gene. Arch Virol 2020; 165:3011-3015. [PMID: 33025200 PMCID: PMC7538171 DOI: 10.1007/s00705-020-04840-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 09/08/2020] [Indexed: 12/28/2022]
Abstract
The hemagglutinin-esterase (HE) protein of betacoronavirus lineage A is a secondary receptor in the infection process and is involved in the emergence of new betacoronavirus genotypes with altered host specificity and tissue tropism. We previously reported a novel recombinant bovine coronavirus (BCoV) strain that was circulating in dairy cattle in China, but this virus was not successfully isolated, and the genetic characteristics of BCoV are still largely unknown. In this study, 20 diarrheic faecal samples were collected from a farm in Liaoning province that had an outbreak of calf diarrhea (≤ 3 months of age) in November 2018, and all of the samples tested positive for BCoV by RT-PCR. In addition, a BCoV strain with a recombinant HE (designated as SWUN/A1/2018) and another BCoV strain with a recombinant HE containing an insertion (designated as SWUN/A10/2018) were successfully isolated in cell culture (TCID50: 104.25/mL and 104.73/mL, respectively). Unexpectedly, we identified the emergence of a novel BCoV variant characterized by a 12-nt bovine gene insertion in the receptor-binding domain in a natural recombinant HE gene, suggesting a novel evolutionary pattern in BCoV.
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Dhama K, Khan S, Tiwari R, Sircar S, Bhat S, Malik YS, Singh KP, Chaicumpa W, Bonilla-Aldana DK, Rodriguez-Morales AJ. Coronavirus Disease 2019-COVID-19. Clin Microbiol Rev 2020. [PMID: 32580969 DOI: 10.1128/cmr.00028-20/asset/32473ce7-130a–42a6-b589-0dd2f00518eb/assets/graphic/cmr.00028-20-f0007.jpeg] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
SUMMARYIn recent decades, several new diseases have emerged in different geographical areas, with pathogens including Ebola virus, Zika virus, Nipah virus, and coronaviruses (CoVs). Recently, a new type of viral infection emerged in Wuhan City, China, and initial genomic sequencing data of this virus do not match with previously sequenced CoVs, suggesting a novel CoV strain (2019-nCoV), which has now been termed severe acute respiratory syndrome CoV-2 (SARS-CoV-2). Although coronavirus disease 2019 (COVID-19) is suspected to originate from an animal host (zoonotic origin) followed by human-to-human transmission, the possibility of other routes should not be ruled out. Compared to diseases caused by previously known human CoVs, COVID-19 shows less severe pathogenesis but higher transmission competence, as is evident from the continuously increasing number of confirmed cases globally. Compared to other emerging viruses, such as Ebola virus, avian H7N9, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV-2 has shown relatively low pathogenicity and moderate transmissibility. Codon usage studies suggest that this novel virus has been transferred from an animal source, such as bats. Early diagnosis by real-time PCR and next-generation sequencing has facilitated the identification of the pathogen at an early stage. Since no antiviral drug or vaccine exists to treat or prevent SARS-CoV-2, potential therapeutic strategies that are currently being evaluated predominantly stem from previous experience with treating SARS-CoV, MERS-CoV, and other emerging viral diseases. In this review, we address epidemiological, diagnostic, clinical, and therapeutic aspects, including perspectives of vaccines and preventive measures that have already been globally recommended to counter this pandemic virus.
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Affiliation(s)
- Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Sharun Khan
- Division of Surgery, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, Uttar Pradesh Pandit Deen Dayal Upadhyaya Pashu Chikitsa Vigyan Vishwavidyalaya Evam Go Anusandhan Sansthan (DUVASU), Mathura, India
| | - Shubhankar Sircar
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Sudipta Bhat
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Yashpal Singh Malik
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Karam Pal Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Wanpen Chaicumpa
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - D Katterine Bonilla-Aldana
- Semillero de Zoonosis, Grupo de Investigación BIOECOS, Fundación Universitaria Autónoma de las Américas, Sede Pereira, Pereira, Risaralda, Colombia
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia
- Latin American Network of Coronavirus Disease 2019-COVID-19 Research (LANCOVID-19), Pereira, Risaralda, Colombia
| | - Alfonso J Rodriguez-Morales
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia
- Latin American Network of Coronavirus Disease 2019-COVID-19 Research (LANCOVID-19), Pereira, Risaralda, Colombia
- Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Americas, Pereira, Risaralda, Colombia
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Dhama K, Khan S, Tiwari R, Sircar S, Bhat S, Malik YS, Singh KP, Chaicumpa W, Bonilla-Aldana DK, Rodriguez-Morales AJ. Coronavirus Disease 2019-COVID-19. Clin Microbiol Rev 2020. [PMID: 32580969 DOI: 10.20944/preprints202003.0001.v1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
SUMMARYIn recent decades, several new diseases have emerged in different geographical areas, with pathogens including Ebola virus, Zika virus, Nipah virus, and coronaviruses (CoVs). Recently, a new type of viral infection emerged in Wuhan City, China, and initial genomic sequencing data of this virus do not match with previously sequenced CoVs, suggesting a novel CoV strain (2019-nCoV), which has now been termed severe acute respiratory syndrome CoV-2 (SARS-CoV-2). Although coronavirus disease 2019 (COVID-19) is suspected to originate from an animal host (zoonotic origin) followed by human-to-human transmission, the possibility of other routes should not be ruled out. Compared to diseases caused by previously known human CoVs, COVID-19 shows less severe pathogenesis but higher transmission competence, as is evident from the continuously increasing number of confirmed cases globally. Compared to other emerging viruses, such as Ebola virus, avian H7N9, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV-2 has shown relatively low pathogenicity and moderate transmissibility. Codon usage studies suggest that this novel virus has been transferred from an animal source, such as bats. Early diagnosis by real-time PCR and next-generation sequencing has facilitated the identification of the pathogen at an early stage. Since no antiviral drug or vaccine exists to treat or prevent SARS-CoV-2, potential therapeutic strategies that are currently being evaluated predominantly stem from previous experience with treating SARS-CoV, MERS-CoV, and other emerging viral diseases. In this review, we address epidemiological, diagnostic, clinical, and therapeutic aspects, including perspectives of vaccines and preventive measures that have already been globally recommended to counter this pandemic virus.
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Affiliation(s)
- Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Sharun Khan
- Division of Surgery, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, Uttar Pradesh Pandit Deen Dayal Upadhyaya Pashu Chikitsa Vigyan Vishwavidyalaya Evam Go Anusandhan Sansthan (DUVASU), Mathura, India
| | - Shubhankar Sircar
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Sudipta Bhat
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Yashpal Singh Malik
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Karam Pal Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Wanpen Chaicumpa
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - D Katterine Bonilla-Aldana
- Semillero de Zoonosis, Grupo de Investigación BIOECOS, Fundación Universitaria Autónoma de las Américas, Sede Pereira, Pereira, Risaralda, Colombia
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia
- Latin American Network of Coronavirus Disease 2019-COVID-19 Research (LANCOVID-19), Pereira, Risaralda, Colombia
| | - Alfonso J Rodriguez-Morales
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia
- Latin American Network of Coronavirus Disease 2019-COVID-19 Research (LANCOVID-19), Pereira, Risaralda, Colombia
- Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Americas, Pereira, Risaralda, Colombia
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Dhama K, Khan S, Tiwari R, Sircar S, Bhat S, Malik YS, Singh KP, Chaicumpa W, Bonilla-Aldana DK, Rodriguez-Morales AJ. Coronavirus Disease 2019-COVID-19. Clin Microbiol Rev 2020; 33:e00028-20. [PMID: 32580969 PMCID: PMC7405836 DOI: 10.1128/cmr.00028-20] [Citation(s) in RCA: 537] [Impact Index Per Article: 134.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
SUMMARYIn recent decades, several new diseases have emerged in different geographical areas, with pathogens including Ebola virus, Zika virus, Nipah virus, and coronaviruses (CoVs). Recently, a new type of viral infection emerged in Wuhan City, China, and initial genomic sequencing data of this virus do not match with previously sequenced CoVs, suggesting a novel CoV strain (2019-nCoV), which has now been termed severe acute respiratory syndrome CoV-2 (SARS-CoV-2). Although coronavirus disease 2019 (COVID-19) is suspected to originate from an animal host (zoonotic origin) followed by human-to-human transmission, the possibility of other routes should not be ruled out. Compared to diseases caused by previously known human CoVs, COVID-19 shows less severe pathogenesis but higher transmission competence, as is evident from the continuously increasing number of confirmed cases globally. Compared to other emerging viruses, such as Ebola virus, avian H7N9, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV-2 has shown relatively low pathogenicity and moderate transmissibility. Codon usage studies suggest that this novel virus has been transferred from an animal source, such as bats. Early diagnosis by real-time PCR and next-generation sequencing has facilitated the identification of the pathogen at an early stage. Since no antiviral drug or vaccine exists to treat or prevent SARS-CoV-2, potential therapeutic strategies that are currently being evaluated predominantly stem from previous experience with treating SARS-CoV, MERS-CoV, and other emerging viral diseases. In this review, we address epidemiological, diagnostic, clinical, and therapeutic aspects, including perspectives of vaccines and preventive measures that have already been globally recommended to counter this pandemic virus.
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Affiliation(s)
- Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Sharun Khan
- Division of Surgery, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, Uttar Pradesh Pandit Deen Dayal Upadhyaya Pashu Chikitsa Vigyan Vishwavidyalaya Evam Go Anusandhan Sansthan (DUVASU), Mathura, India
| | - Shubhankar Sircar
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Sudipta Bhat
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Yashpal Singh Malik
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Karam Pal Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Wanpen Chaicumpa
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - D Katterine Bonilla-Aldana
- Semillero de Zoonosis, Grupo de Investigación BIOECOS, Fundación Universitaria Autónoma de las Américas, Sede Pereira, Pereira, Risaralda, Colombia
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia
- Latin American Network of Coronavirus Disease 2019-COVID-19 Research (LANCOVID-19), Pereira, Risaralda, Colombia
| | - Alfonso J Rodriguez-Morales
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia
- Latin American Network of Coronavirus Disease 2019-COVID-19 Research (LANCOVID-19), Pereira, Risaralda, Colombia
- Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Americas, Pereira, Risaralda, Colombia
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45
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Zhang G, Li B, Yoo D, Qin T, Zhang X, Jia Y, Cui S. Animal coronaviruses and SARS-CoV-2. Transbound Emerg Dis 2020; 68:1097-1110. [PMID: 32799433 PMCID: PMC7461065 DOI: 10.1111/tbed.13791] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/27/2020] [Accepted: 08/10/2020] [Indexed: 01/08/2023]
Abstract
COVID-19 is a highly contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It has rapidly spread to 216 countries and territories since first outbreak in December of 2019, posing a substantial economic losses and extraordinary threats to the public health worldwide. Although bats have been suggested as the natural host of SARS-CoV-2, transmission chains of this virus, role of animals during cross-species transmission, and future concerns remain unclear. Diverse animal coronaviruses have extensively been studied since the discovery of avian coronavirus in 1930s. The current article comprehensively reviews and discusses the current understanding about animal coronaviruses and SARS-CoV-2 for their emergence, transmission, zoonotic potential, alteration of tissue/host tropism, evolution, status of vaccines and surveillance. This study aims at providing guidance for control of COVID-19 and preventative strategies for possible future outbreaks of zoonotic coronavirus via cross-species transmission.
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Affiliation(s)
- Guangzhi Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Technology of Beijing, Ministry of Agriculture, Beijing, China
| | - Bin Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, China
| | - Dongwan Yoo
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Tong Qin
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Technology of Beijing, Ministry of Agriculture, Beijing, China
| | - Xiaodong Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis and Department of Public Health, Jilin University, Changchun, China
| | - Yaxiong Jia
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shangjin Cui
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Technology of Beijing, Ministry of Agriculture, Beijing, China
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46
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Dhama K, Patel SK, Sharun K, Pathak M, Tiwari R, Yatoo MI, Malik YS, Sah R, Rabaan AA, Panwar PK, Singh KP, Michalak I, Chaicumpa W, Martinez-Pulgarin DF, Bonilla-Aldana DK, Rodriguez-Morales AJ. SARS-CoV-2 jumping the species barrier: Zoonotic lessons from SARS, MERS and recent advances to combat this pandemic virus. Travel Med Infect Dis 2020; 37:101830. [PMID: 32755673 PMCID: PMC7396141 DOI: 10.1016/j.tmaid.2020.101830] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 07/26/2020] [Accepted: 07/27/2020] [Indexed: 12/17/2022]
Abstract
Coronavirus Disease 2019 (COVID-19), caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome - Coronavirus-2) of the family Coronaviridae, appeared in China in December 2019. This disease was declared as posing Public Health International Emergency by World Health Organization on January 30, 2020, attained the status of a very high-risk category on February 29, and now having a pandemic status (March 11). COVID-19 has presently spread to more than 215 countries/territories while killing nearly 0.75 million humans out of cumulative confirmed infected asymptomatic or symptomatic cases accounting to almost 20.5 million as of August 12, 2020, within a short period of just a few months. Researchers worldwide are pacing with high efforts to counter the spread of this virus and to design effective vaccines and therapeutics/drugs. Few of the studies have shown the potential of the animal-human interface and zoonotic links in the origin of SARS-CoV-2. Exploring the possible zoonosis and revealing the factors responsible for its initial transmission from animals to humans will pave ways to design and implement effective preventive and control strategies to counter the COVID-19. The present review presents a comprehensive overview of COVID-19 and SARS-CoV-2, with emphasis on the role of animals and their jumping the cross-species barriers, experiences learned from SARS- and MERS-CoVs, zoonotic links, and spillover events, transmission to humans and rapid spread, and highlights the new advances in diagnosis, vaccine and therapies, preventive and control measures, one health concept along with recent research developments to counter this pandemic disease.
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Affiliation(s)
- Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, 243 122, Bareilly, Uttar Pradesh, India.
| | - Shailesh Kumar Patel
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, 243 122, Bareilly, Uttar Pradesh, India
| | - Khan Sharun
- Division of Surgery, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243 122, Uttar Pradesh, India
| | - Mamta Pathak
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, 243 122, Bareilly, Uttar Pradesh, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, UP Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU), Mathura, India
| | - Mohd Iqbal Yatoo
- Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, 190025, Srinagar, Jammu and Kashmir, India
| | - Yashpal Singh Malik
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243 122, Uttar Pradesh, India
| | - Ranjit Sah
- Department of Microbiology, Tribhuvan University Teaching Hospital, Institute of Medicine, Kathmandu, Nepal
| | - Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
| | | | - Karam Pal Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, 243 122, Bareilly, Uttar Pradesh, India
| | - Izabela Michalak
- Faculty of Chemistry, Department of Advanced Material Technologies, Wrocław University of Science and Technology, Wrocław, 50-370, Poland
| | - Wanpen Chaicumpa
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Dayron F Martinez-Pulgarin
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia
| | - D Katterine Bonilla-Aldana
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia; Semillero de Investigación en Zoonosis (SIZOO), Grupo de Investigación BIOECOS, Fundación Universitaria Autónoma de Las Américas, Sede Pereira, Pereira, Risaralda, Colombia
| | - Alfonso J Rodriguez-Morales
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia; Grupo de Investigacion Biomedicina, Faculty of Medicine, Fundacion Universitaria Autonoma de Las Americas, Pereira, Risaralda, Colombia; School of Medicine, Universidad Privada Franz Tamayo (UNIFRANZ), Cochabamba, Bolivia.
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47
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Domańska-Blicharz K, Woźniakowski G, Konopka B, Niemczuk K, Welz M, Rola J, Socha W, Orłowska A, Antas M, Śmietanka K, Cuvelier-Mizak B. Animal Coronaviruses in the Light of COVID-19. J Vet Res 2020; 64:333-345. [PMID: 32984621 PMCID: PMC7497757 DOI: 10.2478/jvetres-2020-0050] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 07/20/2020] [Indexed: 12/24/2022] Open
Abstract
Coronaviruses are extremely susceptible to genetic changes due to the characteristic features of the genome structure, life cycle and environmental pressure. Their remarkable variability means that they can infect many different species of animals and cause different disease symptoms. Moreover, in some situations, coronaviruses might be transmitted across species. Although they are commonly found in farm, companion and wild animals, causing clinical and sometimes serious signs resulting in significant economic losses, not all of them have been classified by the World Organization for Animal Health (OIE) as hazardous and included on the list of notifiable diseases. Currently, only three diseases caused by coronaviruses are on the OIE list of notifiable terrestrial and aquatic animal diseases. However, none of these three entails any administrative measures. The emergence of the SARS-CoV-2 infections that have caused the COVID-19 pandemic in humans has proved that the occurrence and variability of coronaviruses is highly underestimated in the animal reservoir and reminded us of the critical importance of the One Health approach. Therefore, domestic and wild animals should be intensively monitored, both to broaden our knowledge of the viruses circulating among them and to understand the mechanisms of the emergence of viruses of relevance to animal and human health.
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Affiliation(s)
| | - Grzegorz Woźniakowski
- Department of Swine Diseases, National Veterinary Research Institute, 24-100Puławy, Poland
| | | | - Krzysztof Niemczuk
- Director General, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Mirosław Welz
- General Veterinary Inspectorate, 00-930Warsaw, Poland
| | - Jerzy Rola
- Department of Virology, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Wojciech Socha
- Department of Virology, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Anna Orłowska
- Department of Virology, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Marta Antas
- Department of Swine Diseases, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Krzysztof Śmietanka
- Department of Poultry Diseases, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Beata Cuvelier-Mizak
- Department of Veterinary Pharmacy, National Veterinary Research Institute, 24-100Puławy, Poland
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48
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Comparative Pathogenesis of Bovine and Porcine Respiratory Coronaviruses in the Animal Host Species and SARS-CoV-2 in Humans. J Clin Microbiol 2020; 58:JCM.01355-20. [PMID: 32522830 PMCID: PMC7383540 DOI: 10.1128/jcm.01355-20] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Discovery of bats with severe acute respiratory syndrome (SARS)-related coronaviruses (CoVs) raised the specter of potential future outbreaks of zoonotic SARS-CoV-like disease in humans, which largely went unheeded. Nevertheless, the novel SARS-CoV-2 of bat ancestral origin emerged to infect humans in Wuhan, China, in late 2019 and then became a global pandemic. Less than 5 months after its emergence, millions of people worldwide have been infected asymptomatically or symptomatically and at least 360,000 have died. Coronavirus disease 2019 (COVID-19) in severely affected patients includes atypical pneumonia characterized by a dry cough, persistent fever, and progressive dyspnea and hypoxia, sometimes accompanied by diarrhea and often followed by multiple organ failure, especially of the respiratory and cardiovascular systems. In this minireview, we focus on two endemic respiratory CoV infections of livestock: bovine coronavirus (BCoV) and porcine respiratory coronavirus (PRCV). Both animal respiratory CoVs share some common features with SARS-CoV and SARS-CoV-2. BCoV has a broad host range including wild ruminants and a zoonotic potential. BCoV also has a dual tropism for the respiratory and gastrointestinal tracts. These aspects, their interspecies transmission, and certain factors that impact disease severity in cattle parallel related facets of SARS-CoV or SARS-CoV-2 in humans. PRCV has a tissue tropism for the upper and lower respiratory tracts and a cellular tropism for type 1 and 2 pneumocytes in lung but is generally a mild infection unless complicated by other exacerbating factors, such as bacterial or viral coinfections and immunosuppression (corticosteroids).
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49
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Nutho B, Mahalapbutr P, Hengphasatporn K, Pattaranggoon NC, Simanon N, Shigeta Y, Hannongbua S, Rungrotmongkol T. Why Are Lopinavir and Ritonavir Effective against the Newly Emerged Coronavirus 2019? Atomistic Insights into the Inhibitory Mechanisms. Biochemistry 2020; 59:1769-1779. [PMID: 32293875 PMCID: PMC7184878 DOI: 10.1021/acs.biochem.0c00160] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/08/2020] [Indexed: 12/12/2022]
Abstract
Since the emergence of a novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported from Wuhan, China, neither a specific vaccine nor an antiviral drug against SARS-CoV-2 has become available. However, a combination of two HIV-1 protease inhibitors, lopinavir and ritonavir, has been found to be effective against SARS-CoV, and both drugs could bind well to the SARS-CoV 3C-like protease (SARS-CoV 3CLpro). In this work, molecular complexation between each inhibitor and SARS-CoV-2 3CLpro was studied using all-atom molecular dynamics simulations, free energy calculations, and pair interaction energy analyses based on MM/PB(GB)SA and FMO-MP2/PCM/6-31G* methods. Both anti-HIV drugs interacted well with the residues at the active site of SARS-CoV-2 3CLpro. Ritonavir showed a somewhat higher number atomic contacts, a somewhat higher binding efficiency, and a somewhat higher number of key binding residues compared to lopinavir, which correspond with the slightly lower water accessibility at the 3CLpro active site. In addition, only ritonavir could interact with the oxyanion hole residues N142 and G143 via the formation of two hydrogen bonds. The interactions in terms of electrostatics, dispersion, and charge transfer played an important role in the drug binding. The obtained results demonstrated how repurposed anti-HIV drugs could be used to combat COVID-19.
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Affiliation(s)
- Bodee Nutho
- Center of Excellence in Computational Chemistry
(CECC), Department of Chemistry, Faculty of Science, Chulalongkorn
University, Bangkok 10330, Thailand
| | - Panupong Mahalapbutr
- Structural and Computational Biology Research Unit,
Department of Biochemistry, Faculty of Science, Chulalongkorn
University, Bangkok 10330, Thailand
| | - Kowit Hengphasatporn
- Center for Computational Sciences,
University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki
305-8577, Japan
| | | | - Nattapon Simanon
- Program in Bioinformatics and Computational Biology,
Graduate School, Chulalongkorn University, Bangkok 10330,
Thailand
| | - Yasuteru Shigeta
- Center for Computational Sciences,
University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki
305-8577, Japan
| | - Supot Hannongbua
- Center of Excellence in Computational Chemistry
(CECC), Department of Chemistry, Faculty of Science, Chulalongkorn
University, Bangkok 10330, Thailand
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Research Unit,
Department of Biochemistry, Faculty of Science, Chulalongkorn
University, Bangkok 10330, Thailand
- Program in Bioinformatics and Computational Biology,
Graduate School, Chulalongkorn University, Bangkok 10330,
Thailand
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Suzuki T, Otake Y, Uchimoto S, Hasebe A, Goto Y. Genomic Characterization and Phylogenetic Classification of Bovine Coronaviruses Through Whole Genome Sequence Analysis. Viruses 2020; 12:v12020183. [PMID: 32041103 PMCID: PMC7077292 DOI: 10.3390/v12020183] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 01/31/2020] [Accepted: 02/04/2020] [Indexed: 01/18/2023] Open
Abstract
Bovine coronavirus (BCoV) is zoonotically transmissible among species, since BCoV-like viruses have been detected in wild ruminants and humans. BCoV causing enteric and respiratory disease is widespread in cattle farms worldwide; however, limited information is available regarding the molecular characterization of BCoV because of its large genome size, despite its significant economic impact. This study aimed to better understand the genomic characterization and evolutionary dynamics of BCoV via comparative sequence and phylogenetic analyses through whole genome sequence analysis using 67 BCoV isolates collected throughout Japan from 2006 to 2017. On comparing the genomic sequences of the 67 BCoVs, genetic variations were detected in 5 of 10 open reading frames (ORFs) in the BCoV genome. Phylogenetic analysis using whole genomes from the 67 Japanese BCoV isolates in addition to those from 16 reference BCoV strains, revealed the existence of two major genotypes (classical and US wild ruminant genotypes). All Japanese BCoV isolates originated from the US wild ruminant genotype, and they tended to form the same clusters based on the year and farm of collection, not the disease type. Phylogenetic trees on hemagglutinin-esterase protein (HE), spike glycoprotein (S), nucleocapsid protein (N) genes and ORF1 revealed clusters similar to that on whole genome, suggesting that the evolution of BCoVs may be closely associated with variations in these genes. Furthermore, phylogenetic analysis of BCoV S genes including those of European and Asian BCoVs and human enteric coronavirus along with the Japanese BCoVs revealed that BCoVs differentiated into two major types (European and American types). Moreover, the European and American types were divided into eleven and three genotypes, respectively. Our analysis also demonstrated that BCoVs with different genotypes periodically emerged and predominantly circulated within the country. These findings provide useful information to elucidate the detailed molecular characterization of BCoVs, which have spread worldwide. Further genomic analyses of BCoV are essential to deepen the understanding of the evolution of this virus.
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Affiliation(s)
- Tohru Suzuki
- Division of Viral Disease and Epidemiology, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 3050856, Japan
- Correspondence: ; Tel.: +81-29-838-7914
| | - Yoshihiro Otake
- Central Tochigi Prefectural Livestock Health and Hygiene Center, Utsunomiya, Tochigi 3210905, Japan;
| | - Satoko Uchimoto
- Shiga Prefectural Livestock Health and Hygiene Center, Omihachiman, Shiga 5230813, Japan;
| | - Ayako Hasebe
- Central Gifu Prefectural Livestock Health and Hygiene Center, Gifu 5011112, Japan;
| | - Yusuke Goto
- Central Iwate Prefectural Livestock Health and Hygiene Center, Takizawa, Iwate 0200605, Japan;
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