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Poonsin P, Wiwatvisawakorn V, Chansaenroj J, Poovorawan Y, Piewbang C, Techangamsuwan S. Canine respiratory coronavirus in Thailand undergoes mutation and evidences a potential putative parent for genetic recombination. Microbiol Spectr 2023; 11:e0226823. [PMID: 37707446 PMCID: PMC10581155 DOI: 10.1128/spectrum.02268-23] [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: 06/06/2023] [Accepted: 07/27/2023] [Indexed: 09/15/2023] Open
Abstract
Canine respiratory coronavirus (CRCoV) is associated with canine infectious respiratory disease complex. Although its detection has been reported worldwide, the genomic characteristics and evolutionary patterns of this virus remain poorly defined. In this study, 21 CRCoV sequences obtained from dogs in Thailand during two episodes (2013-2015, group A; 2021-2022, group B) were characterized and analyzed. The genomic characteristics of Thai CRCoVs changed from 2013 to 2022 and showed a distinct phylogenetic cluster. Phylogenetic analysis of the spike (S) genes divided the analyzed CRCoV strains into five clades. The full-length genome characterization revealed that all Thai CRCoVs possessed a nonsense mutation within the nonstructural gene located between the S and envelope genes, leading to a truncated putative nonstructural protein. Group B Thai CRCoV strains represented the signature nonsynonymous mutations in the S gene that was not identified in group A Thai CRCoVs, suggesting the ongoing evolutionary process of Thai CRCoVs. Although no evidence of recombination of Thai CRCoV strains was found, our analysis identified one Thai CRCoV strain as a potential parent virus for a CRCoV strain found in the United States. Selective pressure analysis of the hypervariable S region indicated that the CRCoV had undergone purifying selection during evolution. Evolutionary analysis suggested that the CRCoV was emerged in 1992 and was first introduced in Thailand in 2004, sharing a common ancestor with Korean CRCoV strains. These findings regarding the genetic characterization and evolutionary analysis of CRCoVs add to the understanding of CRCoVs. IMPORTANCE Knowledge of genomic characterization of the CRCoV is still limited and its evolution remains poorly investigated. We, therefore, investigated the full-length genome of CRCoV in Thailand for the first time and analyzed the evolutionary dynamic of CRCoV. Genomic characterization of Thai CRCoV strains revealed that they possess unique genome structures and have undergone nonsynonymous mutations, which have not been reported in previously described CRCoV strains. Our work suggests that the Thai CRCoVs were not undergone mutation through genetic recombination for their evolution. However, one Thai CRCoV strain PP158_THA_2015 was found to be a potential parent virus for the CRCoV strains found in the United States. This study provides an understanding of the genomic characterization and highlights the signature mutations and ongoing evolutionary process of CRCoV that could be crucial for monitoring in the future.
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Affiliation(s)
- Panida Poonsin
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | | | - Jira Chansaenroj
- Department of Pediatrics, Faculty of Medicine, Center of Excellence in Clinical Virology, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Department of Pediatrics, Faculty of Medicine, Center of Excellence in Clinical Virology, Chulalongkorn University, Bangkok, Thailand
| | - Chutchai Piewbang
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Somporn Techangamsuwan
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
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Stummer M, Frisch V, Glitz F, Hinney B, Spergser J, Krücken J, Diekmann I, Dimmel K, Riedel C, Cavalleri JMV, Rümenapf T, Joachim A, Lyrakis M, Auer A. Presence of Equine and Bovine Coronaviruses, Endoparasites, and Bacteria in Fecal Samples of Horses with Colic. Pathogens 2023; 12:1043. [PMID: 37624003 PMCID: PMC10458731 DOI: 10.3390/pathogens12081043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/26/2023] Open
Abstract
Acute abdominal pain (colic) is one of the major equine health threats worldwide and often necessitates intensive veterinary medical care and surgical intervention. Equine coronavirus (ECoV) infections can cause colic in horses but are rarely considered as a differential diagnosis. To determine the frequency of otherwise undetected ECoV infections in horses with acute colic, fresh fecal samples of 105 horses with acute colic and 36 healthy control horses were screened for viruses belonging to the Betacoronavirus 1 species by RT-PCR as well as for gastrointestinal helminths and bacteria commonly associated with colic. Horses with colic excreted significantly fewer strongyle eggs than horses without colic. The prevalence of anaerobic, spore-forming, gram-positive bacteria (Clostridium perfringens and Clostridioides difficile) was significantly higher in the feces of horses with colic. Six horses with colic (5.7%) and one horse from the control group (2.8%) tested positive for Betacoronaviruses. Coronavirus-positive samples were sequenced to classify the virus by molecular phylogeny (N gene). Interestingly, in three out of six coronavirus-positive horses with colic, sequences closely related to bovine coronaviruses (BCoV) were found. The pathogenic potential of BCoV in horses remains unclear and warrants further investigation.
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Affiliation(s)
- Moritz Stummer
- Institute of Virology, University of Veterinary Medicine, 1210 Vienna, Austria (K.D.); (T.R.)
| | - Vicky Frisch
- Clinical Unit of Equine Internal Medicine, University of Veterinary Medicine, 1210 Vienna, Austria; (V.F.); (J.-M.V.C.)
| | | | - Barbara Hinney
- Institute of Parasitology, University of Veterinary Medicine, 1210 Vienna, Austria; (B.H.); (A.J.)
| | - Joachim Spergser
- Institute of Microbiology, University of Veterinary Medicine, 1210 Vienna, Austria;
| | - Jürgen Krücken
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany; (J.K.); (I.D.)
| | - Irina Diekmann
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany; (J.K.); (I.D.)
| | - Katharina Dimmel
- Institute of Virology, University of Veterinary Medicine, 1210 Vienna, Austria (K.D.); (T.R.)
| | - Christiane Riedel
- CIRI-Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, 46 allée d’Italie, 69364 Lyon, France;
| | | | - Till Rümenapf
- Institute of Virology, University of Veterinary Medicine, 1210 Vienna, Austria (K.D.); (T.R.)
| | - Anja Joachim
- Institute of Parasitology, University of Veterinary Medicine, 1210 Vienna, Austria; (B.H.); (A.J.)
| | - Manolis Lyrakis
- Platform for Bioinformatics and Biostatistics, Department of Biomedical Sciences, University of Veterinary Medicine, 1210 Vienna, Austria;
| | - Angelika Auer
- Institute of Virology, University of Veterinary Medicine, 1210 Vienna, Austria (K.D.); (T.R.)
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Jevšnik Virant M, Černe D, Petrovec M, Paller T, Toplak I. Genetic Characterisation and Comparison of Three Human Coronaviruses (HKU1, OC43, 229E) from Patients and Bovine Coronavirus (BCoV) from Cattle with Respiratory Disease in Slovenia. Viruses 2021; 13:v13040676. [PMID: 33920821 PMCID: PMC8071153 DOI: 10.3390/v13040676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 11/16/2022] Open
Abstract
Coronaviruses (CoV) are widely distributed pathogens of human and animals and can cause mild or severe respiratory and gastrointestinal disease. Antigenic and genetic similarity of some CoVs within the Betacoronavirus genus is evident. Therefore, for the first time in Slovenia, we investigated the genetic diversity of partial 390-nucleotides of RNA-dependent-RNA polymerase gene (RdRp) for 66 human (HCoV) and 24 bovine CoV (BCoV) positive samples, collected between 2010 and 2016 from human patients and cattle with respiratory disease. The characterized CoV strains belong to four different clusters, in three separate human clusters HCoV-HKU1 (n = 34), HCoV-OC43 (n = 31) and HCoV 229E (n = 1) and bovine grouping only as BCoVs (n = 24). BCoVs from cattle and HCoV-OC43 were genetically the most closely related and share 96.4-97.1% nucleotide and 96.9-98.5% amino acid identity.
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Affiliation(s)
- Monika Jevšnik Virant
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia; (M.J.V.); (M.P.)
| | - Danijela Černe
- Virology Unit, Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1115 Ljubljana, Slovenia;
| | - Miroslav Petrovec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia; (M.J.V.); (M.P.)
| | - Tomislav Paller
- National Veterinary Institute, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1115 Ljubljana, Slovenia;
| | - Ivan Toplak
- Virology Unit, Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1115 Ljubljana, Slovenia;
- Correspondence:
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de Mira Fernandes A, Brandão PE, dos Santos Lima M, de Souza Nunes Martins M, da Silva TG, da Silva Cardoso Pinto V, de Paula LT, Vicente MES, Okuda LH, Pituco EM. Genetic diversity of BCoV in Brazilian cattle herds. Vet Med Sci 2018; 4:183-189. [PMID: 29687958 PMCID: PMC6090412 DOI: 10.1002/vms3.102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Bovine coronavirus (BCoV) is one of the main aetiological agents of gastroenteritis in calves, causing significant economic damage to livestock. This study aims to characterise BCoV genetically on the basis of the N gene. A total of 114 faecal samples from beef and dairy calves with or without clinical symptoms of diarrhoea from five Brazilian states (São Paulo, Minas Gerais, Santa Catarina, Mato Grosso and Bahia) were evaluated between 2008 and 2015 by technique of Semi-nested RT-PCR for gene N and genealogical analysis. Of the 114 samples analysed, 14.91% (17/114) were positive. BCoV was detected in 22.72% (10/44) of the animals with diarrhoea and in 10% (7/70) of asymptomatic animals. BCoV was identified in calves from rural properties located in all of the regions sampled. Genealogical analysis showed that the Brazilian sequences of BCoV for the gene which codes for the N protein can be broken down into two distinct clusters, and the samples from this study were closely linked to Asian strains. These results contribute to the molecular characterization of BCoV in Brazil and are the first report of the circulation of BCoV in the states of Santa Catarina and Bahia.
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Affiliation(s)
- Adeline de Mira Fernandes
- Laboratory of Bovine VirusesCenter of Research and Development of Animal HealthBiological Institute of São PauloSão PauloBrazil
| | - Paulo E. Brandão
- Department of Preventative Veterinary Medicine and Animal HealthFaculty of Veterinary and Zootechnical MedicineUniversity of São PauloSão PauloBrazil
| | - Michele dos Santos Lima
- Laboratory of Bovine VirusesCenter of Research and Development of Animal HealthBiological Institute of São PauloSão PauloBrazil
| | - Maira de Souza Nunes Martins
- Laboratory of Bovine VirusesCenter of Research and Development of Animal HealthBiological Institute of São PauloSão PauloBrazil
| | - Thais G. da Silva
- Laboratory of Bovine VirusesCenter of Research and Development of Animal HealthBiological Institute of São PauloSão PauloBrazil
| | - Vivian da Silva Cardoso Pinto
- Laboratory of Bovine VirusesCenter of Research and Development of Animal HealthBiological Institute of São PauloSão PauloBrazil
| | - Larissa T. de Paula
- Laboratory of Bovine VirusesCenter of Research and Development of Animal HealthBiological Institute of São PauloSão PauloBrazil
| | - Marta Elisabete S. Vicente
- Laboratory of Bovine VirusesCenter of Research and Development of Animal HealthBiological Institute of São PauloSão PauloBrazil
| | - Liria H. Okuda
- Laboratory of Bovine VirusesCenter of Research and Development of Animal HealthBiological Institute of São PauloSão PauloBrazil
| | - Edviges M. Pituco
- Laboratory of Bovine VirusesCenter of Research and Development of Animal HealthBiological Institute of São PauloSão PauloBrazil
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Bok M, Miño S, Rodriguez D, Badaracco A, Nuñes I, Souza SP, Bilbao G, Louge Uriarte E, Galarza R, Vega C, Odeon A, Saif LJ, Parreño V. Molecular and antigenic characterization of bovine Coronavirus circulating in Argentinean cattle during 1994-2010. Vet Microbiol 2015; 181:221-9. [PMID: 26520931 PMCID: PMC7185509 DOI: 10.1016/j.vetmic.2015.10.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 08/28/2015] [Accepted: 10/13/2015] [Indexed: 12/11/2022]
Abstract
Detection rate of BCoV was statistically higher in dairy than in beef calves. Argentinean strains are distant from the Mebus strain included in local vaccines. In vitro cross-protection between Arg95 field strain and Mebus reference strain.
Bovine coronavirus (BCoV) is an important viral pathogen associated with neonatal calf diarrhea. Our aim was to investigate the incidence of BCoV in diarrhea outbreaks in beef and dairy herds from Argentina during 1994–2010. A total of 5.365 fecal samples from diarrheic calves were screened for BCoV diagnosis by ELISA. The virus was detected in 1.71% (92/5365) of the samples corresponding to 5.95% (63/1058) of the diarrhea cases in 239 beef and 324 dairy farms. The detection rate of BCoV was significantly higher in dairy than in beef herds: 12.13% (29/239) vs. 4.32% (14/324) respectively. Phylogenetic analysis of the hypervariable S1 region of seven representative samples (from different husbandry systems, farm locations and years of sampling) indicated that BCoV strains circulating in Argentinean beef and dairy herds formed a cluster distinct from other geographical regions. Interestingly, Argentinean strains are distantly related (at both the nucleotide and amino acid levels) with the Mebus historic reference BCoV strain included in the vaccines currently available in Argentina. However, Mebus-induced antibodies were capable of neutralizing the BCoV Arg95, a field strain adapted to grow in vitro, and vice versa, indicating that both strains belong to the same CoV serotype reported in cattle. This work represents the first large survey describing BCoV circulation in Argentinean cattle.
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Affiliation(s)
- M Bok
- Virology Institute, CICVyA, National Institute of Agricultural Technology (INTA), Buenos Aires, Argentina
| | - S Miño
- Virology Institute, CICVyA, National Institute of Agricultural Technology (INTA), Buenos Aires, Argentina; State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agriculture Sciences, Harbin, 150001 Heilongjiang, China
| | - D Rodriguez
- Virology Institute, CICVyA, National Institute of Agricultural Technology (INTA), Buenos Aires, Argentina
| | - A Badaracco
- Virology Institute, CICVyA, National Institute of Agricultural Technology (INTA), Buenos Aires, Argentina
| | - I Nuñes
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo, Brazil
| | - S P Souza
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo, Brazil
| | - G Bilbao
- Laboratory of Animal Health, EEA INTA- Balcarce, Buenos Aires, Argentina
| | | | - R Galarza
- EEA, INTA Rafaela, Santa Fe, Argentina
| | - C Vega
- Virology Institute, CICVyA, National Institute of Agricultural Technology (INTA), Buenos Aires, Argentina
| | - A Odeon
- Laboratory of Animal Health, EEA INTA- Balcarce, Buenos Aires, Argentina
| | - L J Saif
- Food Animal Health Research Program, The Ohio State University, Wooster, OH, USA
| | - V Parreño
- Virology Institute, CICVyA, National Institute of Agricultural Technology (INTA), Buenos Aires, Argentina.
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