1
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Shum MHH, Lee Y, Tam L, Xia H, Chung OLW, Guo Z, Lam TTY. Binding affinity between coronavirus spike protein and human ACE2 receptor. Comput Struct Biotechnol J 2024; 23:759-770. [PMID: 38304547 PMCID: PMC10831124 DOI: 10.1016/j.csbj.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Coronaviruses (CoVs) pose a major risk to global public health due to their ability to infect diverse animal species and potential for emergence in humans. The CoV spike protein mediates viral entry into the cell and plays a crucial role in determining the binding affinity to host cell receptors. With particular emphasis on α- and β-coronaviruses that infect humans and domestic animals, current research on CoV receptor use suggests that the exploitation of the angiotensin-converting enzyme 2 (ACE2) receptor poses a significant threat for viral emergence with pandemic potential. This review summarizes the approaches used to study binding interactions between CoV spike proteins and the human ACE2 (hACE2) receptor. Solid-phase enzyme immunoassays and cell binding assays allow qualitative assessment of binding but lack quantitative evaluation of affinity. Surface plasmon resonance, Bio-layer interferometry, and Microscale Thermophoresis on the other hand, provide accurate affinity measurement through equilibrium dissociation constants (KD). In silico modeling predicts affinity through binding structure modeling, protein-protein docking simulations, and binding energy calculations but reveals inconsistent results due to the lack of a standardized approach. Machine learning and deep learning models utilize simulated and experimental protein-protein interaction data to elucidate the critical residues associated with CoV binding affinity to hACE2. Further optimization and standardization of existing approaches for studying binding affinity could aid pandemic preparedness. Specifically, prioritizing surveillance of CoVs that can bind to human receptors stands to mitigate the risk of zoonotic spillover.
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Affiliation(s)
- Marcus Ho-Hin Shum
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
| | - Yang Lee
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Centre for Immunology and Infection (C2i), Hong Kong Science Park, Hong Kong, China
| | - Leighton Tam
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
| | - Hui Xia
- Department of Chemistry, South University of Science and Technology of China, China
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Oscar Lung-Wa Chung
- Department of Chemistry, South University of Science and Technology of China, China
| | - Zhihong Guo
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
- Centre for Immunology and Infection (C2i), Hong Kong Science Park, Hong Kong, China
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2
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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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3
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Carossino M, Balasuriya UBR, Thieulent CJ, Barrandeguy ME, Vissani MA, Parreño V. Quadruplex Real-Time TaqMan ® RT-qPCR Assay for Differentiation of Equine Group A and B Rotaviruses and Identification of Group A G3 and G14 Genotypes. Viruses 2023; 15:1626. [PMID: 37631969 PMCID: PMC10459720 DOI: 10.3390/v15081626] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/23/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Equine rotavirus A (ERVA) is the leading cause of diarrhea in foals, with G3P[12] and G14P[12] genotypes being the most prevalent. Recently, equine G3-like RVA was recognized as an emerging infection in children, and a group B equine rotavirus (ERVB) was identified as an emergent cause of foal diarrhea in the US. Thus, there is a need to adapt molecular diagnostic tools for improved detection and surveillance to identify emerging strains, understand their molecular epidemiology, and inform future vaccine development. We developed a quadruplex TaqMan® RT-qPCR assay for differentiation of ERVA and ERVB and simultaneous G-typing of ERVA strains, evaluated its analytical and clinical performance, and compared it to (1) a previously established ERVA triplex RT-qPCR assay and (2) standard RT-PCR assay and Sanger sequencing of PCR products. This quadruplex RT-qPCR assay demonstrated high sensitivity (>90%)/specificity (100%) for every target and high overall agreement (>96%). Comparison between the triplex and quadruplex assays revealed only a slightly higher sensitivity for the ERVA NSP3 target using the triplex format (p-value 0.008) while no significant differences were detected for other targets. This quadruplex RT-qPCR assay will significantly enhance rapid surveillance of both ERVA and ERVB circulating and emerging strains with potential for interspecies transmission.
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Affiliation(s)
- Mariano Carossino
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA;
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Udeni B. R. Balasuriya
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA;
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Côme J. Thieulent
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA;
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Maria E. Barrandeguy
- Escuela de Veterinaria, Universidad del Salvador, Buenos Aires B1630, Argentina; (M.E.B.); (M.A.V.)
- Instituto de Virología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires B1686, Argentina;
| | - Maria Aldana Vissani
- Escuela de Veterinaria, Universidad del Salvador, Buenos Aires B1630, Argentina; (M.E.B.); (M.A.V.)
- Instituto de Virología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires B1686, Argentina;
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1425, Argentina
| | - Viviana Parreño
- Instituto de Virología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires B1686, Argentina;
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1425, Argentina
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Pusterla N. Equine Coronaviruses. Vet Clin North Am Equine Pract 2023; 39:55-71. [PMID: 36737293 DOI: 10.1016/j.cveq.2022.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Coronaviruses are a group of related RNA viruses that cause diseases in mammals and birds. In equids, equine coronavirus has been associated with diarrhea in foals and lethargy, fever, anorexia, and occasional gastrointestinal signs in adult horses. Although horses seem to be susceptible to the human severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) based on the high homology to the ACE-2 receptor, they seem to be incidental hosts because of occasional SARS-CoV-2 spillover from humans. However, until more clinical and seroepidemiological data are available, it remains important to monitor equids for possible transmission from humans with clinical or asymptomatic COVID-19.
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Affiliation(s)
- Nicola Pusterla
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, One Shields Avenue, Davis, CA 95616, USA.
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5
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Characterisation of the Upper Respiratory Tract Virome of Feedlot Cattle and Its Association with Bovine Respiratory Disease. Viruses 2023; 15:v15020455. [PMID: 36851669 PMCID: PMC9961997 DOI: 10.3390/v15020455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 02/10/2023] Open
Abstract
Bovine respiratory disease (BRD) is a major health problem within the global cattle industry. This disease has a complex aetiology, with viruses playing an integral role. In this study, metagenomics was used to sequence viral nucleic acids in the nasal swabs of BRD-affected cattle. The viruses detected included those that are well known for their association with BRD in Australia (bovine viral diarrhoea virus 1), as well as viruses known to be present but not fully characterised (bovine coronavirus) and viruses that have not been reported in BRD-affected cattle in Australia (bovine rhinitis, bovine influenza D, and bovine nidovirus). The nasal swabs from a case-control study were subsequently tested for 10 viruses, and the presence of at least one virus was found to be significantly associated with BRD. Some of the more recently detected viruses had inconsistent associations with BRD. Full genome sequences for bovine coronavirus, a virus increasingly associated with BRD, and bovine nidovirus were completed. Both viruses belong to the Coronaviridae family, which are frequently associated with disease in mammals. This study has provided greater insights into the viral pathogens associated with BRD and highlighted the need for further studies to more precisely elucidate the roles viruses play in BRD.
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Abstract
The existence of coronaviruses has been known for many years. These viruses cause significant disease that primarily seems to affect agricultural species. Human coronavirus disease due to the 2002 outbreak of Severe Acute Respiratory Syndrome and the 2012 outbreak of Middle East Respiratory Syndrome made headlines; however, these outbreaks were controlled, and public concern quickly faded. This complacency ended in late 2019 when alarms were raised about a mysterious virus responsible for numerous illnesses and deaths in China. As we now know, this novel disease called Coronavirus Disease 2019 (COVID-19) was caused by Severe acute respiratory syndrome-related-coronavirus-2 (SARS-CoV-2) and rapidly became a worldwide pandemic. Luckily, decades of research into animal coronaviruses hastened our understanding of the genetics, structure, transmission, and pathogenesis of these viruses. Coronaviruses infect a wide range of wild and domestic animals, with significant economic impact in several agricultural species. Their large genome, low dependency on host cellular proteins, and frequent recombination allow coronaviruses to successfully cross species barriers and adapt to different hosts including humans. The study of the animal diseases provides an understanding of the virus biology and pathogenesis and has assisted in the rapid development of the SARS-CoV-2 vaccines. Here, we briefly review the classification, origin, etiology, transmission mechanisms, pathogenesis, clinical signs, diagnosis, treatment, and prevention strategies, including available vaccines, for coronaviruses that affect domestic, farm, laboratory, and wild animal species. We also briefly describe the coronaviruses that affect humans. Expanding our knowledge of this complex group of viruses will better prepare us to design strategies to prevent and/or minimize the impact of future coronavirus outbreaks.
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Key Words
- bcov, bovine coronavirus
- ccov, canine coronavirus
- cov(s), coronavirus(es)
- covid-19, coronavirus disease 2019
- crcov, canine respiratory coronavirus
- e, coronaviral envelope protein
- ecov, equine coronavirus
- fcov, feline coronavirus
- fipv, feline infectious peritonitis virus
- gfcov, guinea fowl coronavirus
- hcov, human coronavirus
- ibv, infectious bronchitis virus
- m, coronaviral membrane protein
- mers, middle east respiratory syndrome-coronavirus
- mhv, mouse hepatitis virus
- pedv, porcine epidemic diarrhea virus
- pdcov, porcine deltacoronavirus
- phcov, pheasant coronavirus
- phev, porcine hemagglutinating encephalomyelitis virus
- prcov, porcine respiratory coronavirus
- rt-pcr, reverse transcriptase polymerase chain reaction
- s, coronaviral spike protein
- sads-cov, swine acute diarrhea syndrome-coronavirus
- sars-cov, severe acute respiratory syndrome-coronavirus
- sars-cov-2, severe acute respiratory syndrome–coronavirus–2
- tcov, turkey coronavirus
- tgev, transmissible gastroenteritis virus
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Affiliation(s)
- Alfonso S Gozalo
- Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland;,
| | - Tannia S Clark
- Office of Laboratory Animal Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - David M Kurtz
- Comparative Medicine Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, North Carolina
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7
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Qi PF, Gao XY, Ji JK, Zhang Y, Yang SH, Cheng KH, Cui N, Zhu ML, Hu T, Dong X, Yan B, Wang CF, Yang HJ, Shi WF, Zhang W. Identification of a recombinant equine coronavirus in donkey, China. Emerg Microbes Infect 2022; 11:1010-1013. [PMID: 35311478 PMCID: PMC8986280 DOI: 10.1080/22221751.2022.2056522] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Equine coronavirus (ECoV) was first identified in the USA and has been previously described in several countries. In order to test the presence of ECoV in China, we collected 51 small intestinal samples from donkey foals with diarrhoea from a donkey farm in Shandong Province, China between August 2020 and April 2021. Two samples tested positive for ECoV and full-length genome sequences were successfully obtained using next-generation sequencing, one of which was further confirmed by Sanger sequencing. The two strains shared 100% sequence identity at the scale of whole genome. Bioinformatics analyses further showed that the two Chinese strains represent a novel genetic variant of ECoV and shared the highest sequence identity of 97.05% with the first identified ECoV strain - NC99. In addition, it may be a recombinant, with the recombination region around the NS2 gene. To our knowledge, this is the first documented report of ECoV in China, highlighting its risk to horse/donkey breeding. In addition, its potential risk to public health also warrants further investigation.
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Affiliation(s)
- Peng-Fei Qi
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, and Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Ji'nan, People's Republic of China
| | - Xing-Yi Gao
- School of Medicine, Shandong University of Traditional Chinese Medicine, Ji'nan, People's Republic of China
| | - Jing-Kai Ji
- School of Life Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, People's Republic of China
| | - Yan Zhang
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji'nan, People's Republic of China
| | - Shao-Hua Yang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, and Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Ji'nan, People's Republic of China
| | - Kai-Hui Cheng
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, and Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Ji'nan, People's Republic of China
| | - Ning Cui
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, and Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Ji'nan, People's Republic of China
| | - Man-Ling Zhu
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, and Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Ji'nan, People's Republic of China
| | - Tao Hu
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, People's Republic of China
| | - Xuan Dong
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China
| | - Bin Yan
- School of Medicine, Shandong University of Traditional Chinese Medicine, Ji'nan, People's Republic of China
| | - Chang-Fa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, People's Republic of China
| | - Hong-Jun Yang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, and Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Ji'nan, People's Republic of China
| | - Wei-Feng Shi
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, People's Republic of China
| | - Wei Zhang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, and Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Ji'nan, People's Republic of China
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8
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Goldstein SA, Brown J, Pedersen BS, Quinlan AR, Elde NC. Extensive Recombination-driven Coronavirus Diversification Expands the Pool of Potential Pandemic Pathogens. Genome Biol Evol 2022; 14:6795266. [PMID: 36477201 PMCID: PMC9730504 DOI: 10.1093/gbe/evac161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2022] [Indexed: 11/06/2022] Open
Abstract
The ongoing SARS-CoV-2 pandemic is the third zoonotic coronavirus identified in the last 20 years. Enzootic and epizootic coronaviruses of diverse lineages also pose a significant threat to livestock, as most recently observed for virulent strains of porcine epidemic diarrhea virus (PEDV) and swine acute diarrhea-associated coronavirus (SADS-CoV). Unique to RNA viruses, coronaviruses encode a proofreading exonuclease (ExoN) that lowers point mutation rates to increase the viability of large RNA virus genomes, which comes with the cost of limiting virus adaptation via point mutation. This limitation can be overcome by high rates of recombination that facilitate rapid increases in genetic diversification. To compare the dynamics of recombination between related sequences, we developed an open-source computational workflow (IDPlot) that bundles nucleotide identity, recombination, and phylogenetic analysis into a single pipeline. We analyzed recombination dynamics among three groups of coronaviruses with noteworthy impacts on human health and agriculture: SARSr-CoV, Betacoronavirus-1, and SADSr-CoV. We found that all three groups undergo recombination with highly diverged viruses from undersampled or unsampled lineages, including in typically highly conserved regions of the genome. In several cases, no parental origin of recombinant regions could be found in genetic databases, demonstrating our shallow characterization of coronavirus diversity and expanding the genetic pool that may contribute to future zoonotic events. Our results also illustrate the limitations of current sampling approaches for anticipating zoonotic threats to human and animal health.
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Affiliation(s)
| | | | - Brent S Pedersen
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Aaron R Quinlan
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA
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Kambayashi Y, Kishi D, Ueno T, Ohta M, Bannai H, Tsujimura K, Kinoshita Y, Nemoto M. Distribution of equine coronavirus RNA in the intestinal and respiratory tracts of experimentally infected horses. Arch Virol 2022; 167:1611-1618. [PMID: 35639190 PMCID: PMC9152306 DOI: 10.1007/s00705-022-05488-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 04/15/2022] [Indexed: 01/12/2023]
Affiliation(s)
- Yoshinori Kambayashi
- Equine Research Institute, Japan Racing Association, 1400-4 Shiba, Shimotsuke, Tochigi, Japan
| | - Daiki Kishi
- Equine Research Institute, Japan Racing Association, 1400-4 Shiba, Shimotsuke, Tochigi, Japan
| | - Takanori Ueno
- Equine Research Institute, Japan Racing Association, 1400-4 Shiba, Shimotsuke, Tochigi, Japan
| | - Minoru Ohta
- Equine Research Institute, Japan Racing Association, 1400-4 Shiba, Shimotsuke, Tochigi, Japan
| | - Hiroshi Bannai
- Equine Research Institute, Japan Racing Association, 1400-4 Shiba, Shimotsuke, Tochigi, Japan
| | - Koji Tsujimura
- Equine Research Institute, Japan Racing Association, 1400-4 Shiba, Shimotsuke, Tochigi, Japan
| | - Yuta Kinoshita
- Equine Research Institute, Japan Racing Association, 1400-4 Shiba, Shimotsuke, Tochigi, Japan
| | - Manabu Nemoto
- Equine Research Institute, Japan Racing Association, 1400-4 Shiba, Shimotsuke, Tochigi, Japan.
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10
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Hierweger MM, Remy-Wohlfender F, Franzen J, Koch MC, Blau D, Schoster A, Nicholson P, Gerber V, Gurtner C, Fouché N, Unger L, Seuberlich T. Outbreak of equine coronavirus disease in adult horses, Switzerland 2021. Transbound Emerg Dis 2022; 69:1691-1694. [PMID: 35243797 DOI: 10.1111/tbed.14501] [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: 12/07/2021] [Revised: 02/14/2022] [Accepted: 02/27/2022] [Indexed: 11/29/2022]
Abstract
Coronaviruses are causing severe respiratory and enteric diseases in humans and animals. Here, we report an outbreak of equine coronavirus disease in adult horses, detected by a voluntary syndromic surveillance scheme for equine diseases in Switzerland. This scheme allowed a rapid concerted action to diagnose and contain the disease.
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Affiliation(s)
- Melanie M Hierweger
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | | | - Jan Franzen
- Institute of Animal Pathology, Vetsuisse-Faculty, University of Bern, Bern, Switzerland
| | - Michel C Koch
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | | | - Angelika Schoster
- Clinic for Equine Internal Medicine, Equine Hospital, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Pamela Nicholson
- Next Generation Sequencing Platform, University of Bern, Bern, Switzerland
| | - Vinzenz Gerber
- Swiss Institute of Equine Medicine, Vetsuisse-Faculty, University of Bern, Bern, Switzerland
| | - Corinne Gurtner
- Institute of Animal Pathology, Vetsuisse-Faculty, University of Bern, Bern, Switzerland
| | - Nathalie Fouché
- Swiss Institute of Equine Medicine, Vetsuisse-Faculty, University of Bern, Bern, Switzerland
| | - Lucia Unger
- Swiss Institute of Equine Medicine, Vetsuisse-Faculty, University of Bern, Bern, Switzerland
| | - Torsten Seuberlich
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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11
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Khandker SS, Godman B, Jawad MI, Meghla BA, Tisha TA, Khondoker MU, Haq MA, Charan J, Talukder AA, Azmuda N, Sharmin S, Jamiruddin MR, Haque M, Adnan N. A Systematic Review on COVID-19 Vaccine Strategies, Their Effectiveness, and Issues. Vaccines (Basel) 2021; 9:1387. [PMID: 34960133 PMCID: PMC8708628 DOI: 10.3390/vaccines9121387] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/18/2021] [Accepted: 11/18/2021] [Indexed: 12/13/2022] Open
Abstract
COVID-19 vaccines are indispensable, with the number of cases and mortality still rising, and currently no medicines are routinely available for reducing morbidity and mortality, apart from dexamethasone, although others are being trialed and launched. To date, only a limited number of vaccines have been given emergency use authorization by the US Food and Drug Administration and the European Medicines Agency. There is a need to systematically review the existing vaccine candidates and investigate their safety, efficacy, immunogenicity, unwanted events, and limitations. The review was undertaken by searching online databases, i.e., Google Scholar, PubMed, and ScienceDirect, with finally 59 studies selected. Our findings showed several types of vaccine candidates with different strategies against SARS-CoV-2, including inactivated, mRNA-based, recombinant, and nanoparticle-based vaccines, are being developed and launched. We have compared these vaccines in terms of their efficacy, side effects, and seroconversion based on data reported in the literature. We found mRNA vaccines appeared to have better efficacy, and inactivated ones had fewer side effects and similar seroconversion in all types of vaccines. Overall, global variant surveillance and systematic tweaking of vaccines, coupled with the evaluation and administering vaccines with the same or different technology in successive doses along with homologous and heterologous prime-booster strategy, have become essential to impede the pandemic. Their effectiveness appreciably outweighs any concerns with any adverse events.
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Affiliation(s)
- Shahad Saif Khandker
- Gonoshasthaya-RNA Molecular Diagnostic & Research Center, Dhanmondi, Dhaka 1205, Bangladesh; (S.S.K.); (M.U.K.); (M.A.H.); (M.R.J.)
| | - Brian Godman
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G1 1XQ, UK;
- Division of Public Health Pharmacy and Management, School of Pharmacy, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman P.O. Box 346, United Arab Emirates
| | - Md. Irfan Jawad
- Department of Microbiology, Jahangirnagar University, Savar 1342, Bangladesh; (M.I.J.); (B.A.M.); (T.A.T.); (A.A.T.); (N.A.)
| | - Bushra Ayat Meghla
- Department of Microbiology, Jahangirnagar University, Savar 1342, Bangladesh; (M.I.J.); (B.A.M.); (T.A.T.); (A.A.T.); (N.A.)
| | - Taslima Akter Tisha
- Department of Microbiology, Jahangirnagar University, Savar 1342, Bangladesh; (M.I.J.); (B.A.M.); (T.A.T.); (A.A.T.); (N.A.)
| | - Mohib Ullah Khondoker
- Gonoshasthaya-RNA Molecular Diagnostic & Research Center, Dhanmondi, Dhaka 1205, Bangladesh; (S.S.K.); (M.U.K.); (M.A.H.); (M.R.J.)
- Department of Community Medicine, Gonoshasthaya Samaj Vittik Medical College, Savar 1344, Bangladesh
| | - Md. Ahsanul Haq
- Gonoshasthaya-RNA Molecular Diagnostic & Research Center, Dhanmondi, Dhaka 1205, Bangladesh; (S.S.K.); (M.U.K.); (M.A.H.); (M.R.J.)
| | - Jaykaran Charan
- Department of Pharmacology, All India Institute of Medical Sciences, Jodhpur 342005, India;
| | - Ali Azam Talukder
- Department of Microbiology, Jahangirnagar University, Savar 1342, Bangladesh; (M.I.J.); (B.A.M.); (T.A.T.); (A.A.T.); (N.A.)
| | - Nafisa Azmuda
- Department of Microbiology, Jahangirnagar University, Savar 1342, Bangladesh; (M.I.J.); (B.A.M.); (T.A.T.); (A.A.T.); (N.A.)
| | - Shahana Sharmin
- Department of Pharmacy, BRAC University, Dhaka 1212, Bangladesh;
| | - Mohd. Raeed Jamiruddin
- Gonoshasthaya-RNA Molecular Diagnostic & Research Center, Dhanmondi, Dhaka 1205, Bangladesh; (S.S.K.); (M.U.K.); (M.A.H.); (M.R.J.)
- Department of Pharmacy, BRAC University, Dhaka 1212, Bangladesh;
| | - Mainul Haque
- The Unit of Pharmacology, Faculty of Medicine and Defence Health, Universiti Pertahanan Nasional Malaysia (National Defence University of Malaysia), Kem Perdana Sugai Besi, Kuala Lumpur 57000, Malaysia
| | - Nihad Adnan
- Gonoshasthaya-RNA Molecular Diagnostic & Research Center, Dhanmondi, Dhaka 1205, Bangladesh; (S.S.K.); (M.U.K.); (M.A.H.); (M.R.J.)
- Department of Microbiology, Jahangirnagar University, Savar 1342, Bangladesh; (M.I.J.); (B.A.M.); (T.A.T.); (A.A.T.); (N.A.)
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12
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Uzal FA, Arroyo LG, Navarro MA, Gomez DE, Asín J, Henderson E. Bacterial and viral enterocolitis in horses: a review. J Vet Diagn Invest 2021; 34:354-375. [PMID: 34763560 DOI: 10.1177/10406387211057469] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Enteritis, colitis, and enterocolitis are considered some of the most common causes of disease and death in horses. Determining the etiology of these conditions is challenging, among other reasons because different causes produce similar clinical signs and lesions, and also because some agents of colitis can be present in the intestine of normal animals. We review here the main bacterial and viral causes of enterocolitis of horses, including Salmonella spp., Clostridium perfringens type A NetF-positive, C. perfringens type C, Clostridioides difficile, Clostridium piliforme, Paeniclostridium sordellii, other clostridia, Rhodococcus equi, Neorickettsia risticii, Lawsonia intracellularis, equine rotavirus, and equine coronavirus. Diarrhea and colic are the hallmark clinical signs of colitis and enterocolitis, and the majority of these conditions are characterized by necrotizing changes in the mucosa of the small intestine, colon, cecum, or in a combination of these organs. The presumptive diagnosis is based on clinical, gross, and microscopic findings, and confirmed by detection of some of the agents and/or their toxins in the intestinal content or feces.
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Affiliation(s)
- Francisco A Uzal
- California Animal Health and Food Safety Laboratory, University of California-Davis, San Bernardino Laboratory, USA
| | - Luis G Arroyo
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Mauricio A Navarro
- California Animal Health and Food Safety Laboratory, University of California-Davis, San Bernardino Laboratory, USA.,Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Diego E Gomez
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Javier Asín
- California Animal Health and Food Safety Laboratory, University of California-Davis, San Bernardino Laboratory, USA
| | - Eileen Henderson
- California Animal Health and Food Safety Laboratory, University of California-Davis, San Bernardino Laboratory, USA
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13
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A Novel Potentially Recombinant Rodent Coronavirus with a Polybasic Cleavage Site in the Spike Protein. J Virol 2021; 95:e0117321. [PMID: 34431700 PMCID: PMC8549509 DOI: 10.1128/jvi.01173-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has reignited global interest in animal coronaviruses and their potential for human transmission. While bats are thought to be the wildlife reservoir of SARS-CoV and SARS-CoV-2, the widespread human coronavirus OC43 is thought to have originated in rodents. Here, we sampled 297 rodents and shrews, representing eight species, from three municipalities of southern China. We report coronavirus prevalences of 23.3% and 0.7% in Guangzhou and Guilin, respectively, with samples from urban areas having significantly higher coronavirus prevalences than those from rural areas. We obtained three coronavirus genome sequences from Rattus norvegicus, including a Betacoronavirus (rat coronavirus [RCoV] GCCDC3), an Alphacoronavirus (RCoV-GCCDC5), and a novel Betacoronavirus (RCoV-GCCDC4). Recombination analysis suggests that there was a potential recombination event involving RCoV-GCCDC4, murine hepatitis virus (MHV), and Longquan Rl rat coronavirus (LRLV). Furthermore, we uncovered a polybasic cleavage site, RARR, in the spike (S) protein of RCoV-GCCDC4, which is dominant in RCoV. These findings provide further information on the potential for interspecies transmission of coronaviruses and demonstrate the value of a One Health approach to virus discovery. IMPORTANCE Surveillance of viruses among rodents in rural and urban areas of South China identified three rodent coronaviruses, RCoV-GCCDC3, RCoV-GCCDC4, and RCoV-GCCDC5, one of which was identified as a novel potentially recombinant coronavirus with a polybasic cleavage site in the spike (S) protein. Through reverse transcription-PCR (RT-PCR) screening of coronaviruses, we found that coronavirus prevalence in urban areas is much higher than that in rural areas. Subsequently, we obtained three coronavirus genome sequences by deep sequencing. After different method-based analyses, we found that RCoV-GCCDC4 was a novel potentially recombinant coronavirus with a polybasic cleavage site in the S protein, dominant in RCoV. This newly identified coronavirus RCoV-GCCDC4 with its potentially recombinant genome and polybasic cleavage site provides a new insight into the evolution of coronaviruses. Furthermore, our results provide further information on the potential for interspecies transmission of coronaviruses and demonstrate the necessity of a One Health approach for zoonotic disease surveillance.
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14
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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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15
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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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16
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Goldstein SA, Brown J, Pedersen BS, Quinlan AR, Elde NC. Extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.03.429646. [PMID: 33564759 PMCID: PMC7872347 DOI: 10.1101/2021.02.03.429646] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The ongoing SARS-CoV-2 pandemic is the third zoonotic coronavirus identified in the last twenty years. Enzootic and epizootic coronaviruses of diverse lineages also pose a significant threat to livestock, as most recently observed for virulent strains of porcine epidemic diarrhea virus (PEDV) and swine acute diarrhea-associated coronavirus (SADS-CoV). Unique to RNA viruses, coronaviruses encode a proofreading exonuclease (ExoN) that lowers point mutation rates to increase the viability of large RNA virus genomes, which comes with the cost of limiting virus adaptation via point mutation. This limitation can be overcome by high rates of recombination that facilitate rapid increases in genetic diversification. To compare dynamics of recombination between related sequences, we developed an open-source computational workflow (IDPlot) to measure nucleotide identity, locate recombination breakpoints, and infer phylogenetic relationships. We analyzed recombination dynamics among three groups of coronaviruses with noteworthy impacts on human health and agriculture: SARSr-CoV, Betacoronavirus-1, and SADSr-CoV. We found that all three groups undergo recombination with highly diverged viruses from sparsely sampled or undescribed lineages, which can disrupt the inference of phylogenetic relationships. In most cases, no parental origin of recombinant regions could be found in genetic databases, suggesting that much coronavirus diversity remains unknown. These patterns of recombination expand the genetic pool that may contribute to future zoonotic events. Our results also illustrate the limitations of current sampling approaches for anticipating zoonotic threats to human and animal health.
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Affiliation(s)
- Stephen A. Goldstein
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.,Corresponding authors. (S.A.G), (N.C.E)
| | - Joe Brown
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Brent S. Pedersen
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Aaron R. Quinlan
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Nels C. Elde
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.,Corresponding authors. (S.A.G), (N.C.E)
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17
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Outbreak of equine coronavirus infection among riding horses in Tokyo, Japan. Comp Immunol Microbiol Infect Dis 2021; 77:101668. [PMID: 34004508 DOI: 10.1016/j.cimid.2021.101668] [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: 01/19/2021] [Revised: 04/28/2021] [Accepted: 05/06/2021] [Indexed: 11/20/2022]
Abstract
In 2020, an outbreak of equine coronavirus (ECoV) infection occurred among 41 horses at a riding stable in Tokyo, Japan. This stable had 16 Thoroughbreds and 25 horses of other breeds, including Andalusians, ponies and miniature horses. Fifteen horses (37 %) showed mild clinical signs such as fever, lethargy, anorexia and diarrhoea, and they recovered within 3 days of onset. A virus neutralization test showed that all 41 horses were infected with ECoV, signifying that 26 horses (63 %) were subclinical. The results suggest that subclinical horses played an important role as spreaders. A genome sequence analysis revealed that the lengths from genes p4.7 to p12.7 or NS2 in ECoV differed from those of ECoVs detected previously, suggesting that this outbreak was caused by a virus different from those that caused previous outbreaks among draughthorses in Japan. Among 30 horses that tested positive by real-time RT-PCR, ECoV shedding periods of non-Thoroughbreds were significantly longer than those of Thoroughbreds. The difference in shedding periods may indicate that some breeds excrete ECoV longer than other breeds and can contribute to the spread of ECoV.
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18
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Seroprevalence and Risk Factors for Exposure to Equine Coronavirus in Apparently Healthy Horses in Israel. Animals (Basel) 2021; 11:ani11030894. [PMID: 33800990 PMCID: PMC8004030 DOI: 10.3390/ani11030894] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/11/2021] [Accepted: 03/18/2021] [Indexed: 01/14/2023] Open
Abstract
Simple Summary Equine coronavirus (ECoV) is a β-coronavirus that, together with other coronaviruses, are pathogenic to both human and animals, as seen in the recent COVID-19 pandemic. ECoV is considered as a diarrheic pathogen in foals and is included in the list of viral causes of enteritis. During the last decade, outbreaks of ECoV were reported in adult horses in the USA, EU and Japan. In Israel, other coronaviruses were reported in cattle, camels and in humans; however, coronaviruses have not been reported in horses. In this study, we aimed to determine the exposure of healthy horses to ECoV and determine the selected risk factors for infection. For this purpose, serum samples were collected from 333 healthy horses, 41 (12.3%) of which had anti-ECoV antibodies. Seropositive horses were found in more than half (58.6%) of the farms and horses located in central Israel were more likely to be positive. ECoV should be included in the differential diagnosis list of pathogens in cases of adult horses with acute onset of anorexia, lethargy, fever and gastrointestinal signs in Israel. Abstract Equine coronavirus (ECoV) infection is the cause of an emerging enteric disease of adult horses. Outbreaks have been reported in the USA, EU and Japan, as well as sporadic cases in the UK and Saudi Arabia. Infection of ECoV in horses in Israel has never been reported, and the risk of exposure is unknown. Importation and exportation of horses from and into Israel may have increased the exposure of horses in Israel to ECoV. While the disease is mostly self-limiting, with or without supportive treatment, severe complications may occur in some animals, and healthy carriers may pose a risk of infection to other horses. This study was set to evaluate the risk of exposure to ECoV of horses in Israel by using a previously validated, S1-based enzyme-linked immunosorbent assay (ELISA). A total of 41 out of 333 horses (12.3%) were seropositive. Exposure to ECoV was detected in 17 of 29 farms (58.6%) and the seroprevalence varied between 0 and 37.5% amongst farms. The only factor found to be significantly associated with ECoV exposure in the multivariable model was the geographical area (p < 0.001). ECoV should be included in the differential diagnosis list of pathogens in cases of adult horses with anorexia, lethargy, fever and gastrointestinal signs in Israel.
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19
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Colina SE, Serena MS, Echeverría MG, Metz GE. Clinical and molecular aspects of veterinary coronaviruses. Virus Res 2021; 297:198382. [PMID: 33705799 PMCID: PMC7938195 DOI: 10.1016/j.virusres.2021.198382] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/20/2020] [Accepted: 03/04/2021] [Indexed: 12/12/2022]
Abstract
Coronaviruses are a large group of RNA viruses that infect a wide range of animal species. The replication strategy of coronaviruses involves recombination and mutation events that lead to the possibility of cross-species transmission. The high plasticity of the viral receptor due to a continuous modification of the host species habitat may be the cause of cross-species transmission that can turn into a threat to other species including the human population. The successive emergence of highly pathogenic coronaviruses such as the Severe Acute Respiratory Syndrome (SARS) in 2003, the Middle East Respiratory Syndrome Coronavirus in 2012, and the recent SARS-CoV-2 has incentivized a number of studies on the molecular basis of the coronavirus and its pathogenesis. The high degree of interrelatedness between humans and wild and domestic animals and the modification of animal habitats by human urbanization, has favored new viral spreads. Hence, knowledge on the main clinical signs of coronavirus infection in the different hosts and the distinctive molecular characteristics of each coronavirus is essential to prevent the emergence of new coronavirus diseases. The coronavirus infections routinely studied in veterinary medicine must be properly recognized and diagnosed not only to prevent animal disease but also to promote public health.
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Affiliation(s)
- Santiago Emanuel Colina
- Virology, Faculty of Veterinary Sciences, National University of La Plata, La Plata, Argentina; CONICET (National Scientific and Technical Research Council), CCT La Plata, Argentina
| | - María Soledad Serena
- Virology, Faculty of Veterinary Sciences, National University of La Plata, La Plata, Argentina; CONICET (National Scientific and Technical Research Council), CCT La Plata, Argentina
| | - María Gabriela Echeverría
- Virology, Faculty of Veterinary Sciences, National University of La Plata, La Plata, Argentina; CONICET (National Scientific and Technical Research Council), CCT La Plata, Argentina
| | - Germán Ernesto Metz
- Virology, Faculty of Veterinary Sciences, National University of La Plata, La Plata, Argentina; CONICET (National Scientific and Technical Research Council), CCT La Plata, Argentina.
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20
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Gioti K, Kottaridi C, Voyiatzaki C, Chaniotis D, Rampias T, Beloukas A. Animal Coronaviruses Induced Apoptosis. Life (Basel) 2021; 11:life11030185. [PMID: 33652685 PMCID: PMC7996831 DOI: 10.3390/life11030185] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/21/2021] [Accepted: 02/22/2021] [Indexed: 02/06/2023] Open
Abstract
Apoptosis is a form of programmed death that has also been observed in cells infected by several viruses. It is considered one of the most critical innate immune mechanisms that limits pathogen proliferation and propagation before the initiation of the adaptive immune response. Recent studies investigating the cellular responses to SARS-CoV and SARS-CoV-2 infection have revealed that coronaviruses can alter cellular homeostasis and promote cell death, providing evidence that the modulation of apoptotic pathways is important for viral replication and propagation. Despite the genetic diversity among different coronavirus clades and the infection of different cell types and several hosts, research studies in animal coronaviruses indicate that apoptosis in host cells is induced by common molecular mechanisms and apoptotic pathways. We summarize and critically review current knowledge on the molecular aspects of cell-death regulation during animal coronaviruses infection and the viral–host interactions to this process. Future research is expected to lead to a better understanding of the regulation of cell death during coronavirus infection. Moreover, investigating the role of viral proteins in this process will help us to identify novel antiviral targets related to apoptotic signaling pathways.
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Affiliation(s)
- Katerina Gioti
- Department of Biomedical Sciences, University of West Attica, 12243 Athens, Greece; (K.G.); (C.K.); (C.V.); (D.C.)
| | - Christine Kottaridi
- Department of Biomedical Sciences, University of West Attica, 12243 Athens, Greece; (K.G.); (C.K.); (C.V.); (D.C.)
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Chrysa Voyiatzaki
- Department of Biomedical Sciences, University of West Attica, 12243 Athens, Greece; (K.G.); (C.K.); (C.V.); (D.C.)
| | - Dimitrios Chaniotis
- Department of Biomedical Sciences, University of West Attica, 12243 Athens, Greece; (K.G.); (C.K.); (C.V.); (D.C.)
| | - Theodoros Rampias
- Biomedical Research Foundation of the Academy of Athens, Basic Research Center, 11527 Athens, Greece
- Correspondence: (T.R.); (A.B.)
| | - Apostolos Beloukas
- Department of Biomedical Sciences, University of West Attica, 12243 Athens, Greece; (K.G.); (C.K.); (C.V.); (D.C.)
- Institute of Infection & Global Health, University of Liverpool, Liverpool L69 7BE, UK
- Correspondence: (T.R.); (A.B.)
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21
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Identification of Host Cellular Protein Substrates of SARS-COV-2 Main Protease. Int J Mol Sci 2020; 21:ijms21249523. [PMID: 33333742 PMCID: PMC7765187 DOI: 10.3390/ijms21249523] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 12/20/2022] Open
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease-19 (COVID-19) being associated with severe pneumonia. Like with other viruses, the interaction of SARS-CoV-2 with host cell proteins is necessary for successful replication, and cleavage of cellular targets by the viral protease also may contribute to the pathogenesis, but knowledge about the human proteins that are processed by the main protease (3CLpro) of SARS-CoV-2 is still limited. We tested the prediction potentials of two different in silico methods for the identification of SARS-CoV-2 3CLpro cleavage sites in human proteins. Short stretches of homologous host-pathogen protein sequences (SSHHPS) that are present in SARS-CoV-2 polyprotein and human proteins were identified using BLAST analysis, and the NetCorona 1.0 webserver was used to successfully predict cleavage sites, although this method was primarily developed for SARS-CoV. Human C-terminal-binding protein 1 (CTBP1) was found to be cleaved in vitro by SARS-CoV-2 3CLpro, the existence of the cleavage site was proved experimentally by using a His6-MBP-mEYFP recombinant substrate containing the predicted target sequence. Our results highlight both potentials and limitations of the tested algorithms. The identification of candidate host substrates of 3CLpro may help better develop an understanding of the molecular mechanisms behind the replication and pathogenesis of SARS-CoV-2.
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22
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Haake C, Cook S, Pusterla N, Murphy B. Coronavirus Infections in Companion Animals: Virology, Epidemiology, Clinical and Pathologic Features. Viruses 2020; 12:E1023. [PMID: 32933150 PMCID: PMC7551689 DOI: 10.3390/v12091023] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/11/2020] [Accepted: 09/11/2020] [Indexed: 12/17/2022] Open
Abstract
Coronaviruses are enveloped RNA viruses capable of causing respiratory, enteric, or systemic diseases in a variety of mammalian hosts that vary in clinical severity from subclinical to fatal. The host range and tissue tropism are largely determined by the coronaviral spike protein, which initiates cellular infection by promoting fusion of the viral and host cell membranes. Companion animal coronaviruses responsible for causing enteric infection include feline enteric coronavirus, ferret enteric coronavirus, canine enteric coronavirus, equine coronavirus, and alpaca enteric coronavirus, while canine respiratory coronavirus and alpaca respiratory coronavirus result in respiratory infection. Ferret systemic coronavirus and feline infectious peritonitis virus, a mutated feline enteric coronavirus, can lead to lethal immuno-inflammatory systemic disease. Recent human viral pandemics, including severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and most recently, COVID-19, all thought to originate from bat coronaviruses, demonstrate the zoonotic potential of coronaviruses and their potential to have devastating impacts. A better understanding of the coronaviruses of companion animals, their capacity for cross-species transmission, and the sharing of genetic information may facilitate improved prevention and control strategies for future emerging zoonotic coronaviruses. This article reviews the clinical, epidemiologic, virologic, and pathologic characteristics of nine important coronaviruses of companion animals.
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Affiliation(s)
- Christine Haake
- School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Sarah Cook
- Graduate Group Integrative Pathobiology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA;
| | - Nicola Pusterla
- Department of Medicine & Epidemiology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA;
| | - Brian Murphy
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA;
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23
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Pusterla N. Science-in-brief: Equine coronavirus - a decade long journey to investigate an emerging enteric virus of adult horses. Equine Vet J 2020; 52:651-653. [PMID: 32589298 DOI: 10.1111/evj.13288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 05/15/2020] [Indexed: 01/24/2023]
Affiliation(s)
- Nicola Pusterla
- Department of Veterinary Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA
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24
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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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25
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Development and Validation of a S1 Protein-Based ELISA for the Specific Detection of Antibodies against Equine Coronavirus. Viruses 2019; 11:v11121109. [PMID: 31801275 PMCID: PMC6950238 DOI: 10.3390/v11121109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/26/2019] [Accepted: 11/29/2019] [Indexed: 02/06/2023] Open
Abstract
Equine coronavirus (ECoV) is considered to be involved in enteric diseases in foals. Recently, several outbreaks of ECoV infection have also been reported in adult horses from the USA, France and Japan. Epidemiological studies of ECoV infection are still limited, and the seroprevalence of ECoV infection in Europe is unknown. In this study, an indirect enzyme-linked immunosorbent assay (ELISA) method utilizing ECoV spike S1 protein was developed in two formats, and further validated by analyzing 27 paired serum samples (acute and convalescent sera) from horses involved in an ECoV outbreak and 1084 sera of horses with unknown ECoV exposure. Both formats showed high diagnostic accuracy compared to virus neutralization (VN) assay. Receiver-operating characteristic (ROC) analyses were performed to determine the best cut-off values for both ELISA formats, assuming a test specificity of 99%. Employing the developed ELISA method, we detected seroconversion in 70.4% of horses from an ECoV outbreak. Among the 1084 horse sera, seropositivity varied from 25.9% (young horses) to 82.8% (adult horses) in Dutch horse populations. Further, sera of Icelandic horses were included in this study and a significant number of sera (62%) were found to be positive. Overall, the results demonstrated that the ECoV S1-based ELISA has reliable diagnostic performance compared to the VN assay and is a useful assay to support seroconversion in horses involved with ECoV outbreaks and to estimate ECoV seroprevalence in populations of horses.
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26
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Nemoto M, Schofield W, Cullinane A. The First Detection of Equine Coronavirus in Adult Horses and Foals in Ireland. Viruses 2019; 11:E946. [PMID: 31615132 PMCID: PMC6832964 DOI: 10.3390/v11100946] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 10/10/2019] [Accepted: 10/12/2019] [Indexed: 11/16/2022] Open
Abstract
The objective of this study was to investigate the presence of equine coronavirus (ECoV) in clinical samples submitted to a diagnostic laboratory in Ireland. A total of 424 clinical samples were examined from equids with enteric disease in 24 Irish counties between 2011 and 2015. A real-time reverse transcription polymerase chain reaction was used to detect ECoV RNA. Nucleocapsid, spike and the region from the p4.7 to p12.7 genes of positive samples were sequenced, and sequence and phylogenetic analyses were conducted. Five samples (1.2%) collected in 2011 and 2013 tested positive for ECoV. Positive samples were collected from adult horses, Thoroughbred foals and a donkey foal. Sequence and/or phylogenetic analysis showed that nucleocapsid, spike and p12.7 genes were highly conserved and were closely related to ECoVs identified in other countries. In contrast, the region from p4.7 and the non-coding region following the p4.7 gene had deletions or insertions. The differences in the p4.7 region between the Irish ECoVs and other ECoVs indicated that the Irish viruses were distinguishable from those circulating in other countries. This is the first report of ECoV detected in both foals and adult horses in Ireland.
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Affiliation(s)
- Manabu Nemoto
- Virology Unit, The Irish Equine Centre, Johnstown, Naas, Co. Kildare W91 RH93, Ireland.
- Equine Research Institute, Japan Racing Association, Shimotsuke, Tochigi 329-0412, Japan.
| | - Warren Schofield
- Troytown Grey Abbey Equine Hospital, Green Road, Co. Kildare R51 YV04, Ireland.
| | - Ann Cullinane
- Virology Unit, The Irish Equine Centre, Johnstown, Naas, Co. Kildare W91 RH93, Ireland.
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27
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Abstract
RNA viruses carry out selective packaging of their genomes in a variety of ways, many involving a genomic packaging signal. The first coronavirus packaging signal was discovered nearly thirty years ago, but how it functions remains incompletely understood. This review addresses the current state of knowledge of coronavirus genome packaging, which has mainly been studied in two prototype species, mouse hepatitis virus and transmissible gastroenteritis virus. Despite the progress that has been made in the mapping and characterization of some packaging signals, there is conflicting evidence as to whether the viral nucleocapsid protein or the membrane protein plays the primary role in packaging signal recognition. The different models for the mechanism of genomic RNA packaging that have been prompted by these competing views are described. Also discussed is the recent exciting discovery that selective coronavirus genome packaging is critical for in vivo evasion of the host innate immune response. Selective incorporation of the coronavirus genome into virions is mediated by a cis-acting RNA packaging signal. Packaging signals vary across different coronavirus genera and lineages. Different lines of evidence attribute packaging signal recognition to either the nucleocapsid or the membrane protein. Selective coronavirus genome packaging plays a role in evasion of host innate immunity.
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Affiliation(s)
- Paul S Masters
- Wadsworth Center, New York State Department of Health, Albany, NY, 12201, United States.
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28
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Carossino M, Barrandeguy ME, Erol E, Li Y, Balasuriya UBR. Development and evaluation of a one-step multiplex real-time TaqMan ® RT-qPCR assay for the detection and genotyping of equine G3 and G14 rotaviruses in fecal samples. Virol J 2019; 16:49. [PMID: 31023319 PMCID: PMC6482509 DOI: 10.1186/s12985-019-1149-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 03/20/2019] [Indexed: 11/23/2022] Open
Abstract
Background Equine rotavirus A (ERVA) is the leading cause of diarrhea in neonatal foals and has a negative impact on equine breeding enterprises worldwide. Among ERVA strains infecting foals, the genotypes G3P[12] and G14P[12] are the most prevalent, while infections by strains with other genomic arrangements are infrequent. The identification of circulating strains of ERVA is critical for diagnostic and surveillance purposes, as well as to understand their molecular epidemiology. Current genotyping methods available for ERVA and rotaviruses affecting other animal species rely on Sanger sequencing and are significantly time-consuming, costly and labor intensive. Here, we developed the first one-step multiplex TaqMan® real-time reverse transcription polymerase chain reaction (RT-qPCR) assay targeting the NSP3 and VP7 genes of ERVA G3 and G14 genotypes for the rapid detection and G-typing directly from fecal specimens. Methods A one-step multiplex TaqMan® RT-qPCR assay targeting the NSP3 and VP7 genes of ERVA G3 and G14 genotypes was designed. The analytical sensitivity was assessed using serial dilutions of in vitro transcribed RNA containing the target sequences while the analytical specificity was determined using RNA and DNA derived from a panel of group A rotaviruses along with other equine viruses and bacteria. The clinical performance of this multiplex assay was evaluated using a panel of 177 fecal samples and compared to a VP7-specific standard RT-PCR assay and Sanger sequencing. Limits of detection (LOD), sensitivity, specificity, and agreement were determined. Results The multiplex G3 and G14 VP7 assays demonstrated high specificity and efficiency, with perfect linearity. A 100-fold difference in their analytical sensitivity was observed when compared to the singleplex assays; however, this difference did not have an impact on the clinical performance. Clinical performance of the multiplex RT-qPCR assay demonstrated that this assay had a high sensitivity/specificity for every target (100% for NSP3, > 90% for G3 VP7 and > 99% for G14 VP7, respectively) and high overall agreement (> 98%) compared to conventional RT-PCR and sequencing. Conclusions This new multiplex RT-qPCR assay constitutes a useful, very reliable tool that could significantly aid in the rapid detection and G-typing of ERVA strains circulating in the field.
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Affiliation(s)
- Mariano Carossino
- Louisiana Animal Disease Diagnostic Laboratory and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA.,Escuela de Veterinaria, Universidad del Salvador, Champagnat 1599, Ruta Panamericana km54.5 (B1630AHU), Pilar, Buenos Aires, Argentina
| | - Maria E Barrandeguy
- Escuela de Veterinaria, Universidad del Salvador, Champagnat 1599, Ruta Panamericana km54.5 (B1630AHU), Pilar, Buenos Aires, Argentina.,Instituto de Virología, CICVyA, INTA. Las Cabañas y Los Reseros s/n, (1712) Castelar, Buenos Aires, Argentina
| | - Erdal Erol
- Department of Veterinary Science, University of Kentucky Veterinary Diagnostic Laboratory, University of Kentucky, Lexington, KY, USA
| | - Yanqiu Li
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, USA
| | - Udeni B R Balasuriya
- Louisiana Animal Disease Diagnostic Laboratory and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA.
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29
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Lau SKP, Fan RYY, Luk HKH, Zhu L, Fung J, Li KSM, Wong EYM, Ahmed SS, Chan JFW, Kok RKH, Chan KH, Wernery U, Yuen KY, Woo PCY. Replication of MERS and SARS coronaviruses in bat cells offers insights to their ancestral origins. Emerg Microbes Infect 2018; 7:209. [PMID: 30531999 PMCID: PMC6286955 DOI: 10.1038/s41426-018-0208-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 11/08/2018] [Accepted: 11/11/2018] [Indexed: 01/10/2023]
Abstract
Previous findings of Middle East Respiratory Syndrome coronavirus (MERS-CoV)-related viruses in bats, and the ability of Tylonycteris-BatCoV HKU4 spike protein to utilize MERS-CoV receptor, human dipeptidyl peptidase 4 hDPP4, suggest a bat ancestral origin of MERS-CoV. We developed 12 primary bat cell lines from seven bat species, including Tylonycteris pachypus, Pipistrellus abramus and Rhinolophus sinicus (hosts of Tylonycteris-BatCoV HKU4, Pipistrellus-BatCoV HKU5, and SARS-related-CoV respectively), and tested their susceptibilities to MERS-CoVs, SARS-CoV, and human coronavirus 229E (HCoV-229E). Five cell lines, including P. abramus and R. sinicus but not T. pachypus cells, were susceptible to human MERS-CoV EMC/2012. However, three tested camel MERS-CoV strains showed different infectivities, with only two strains capable of infecting three and one cell lines respectively. SARS-CoV can only replicate in R. sinicus cells, while HCoV-229E cannot replicate in any bat cells. Bat dipeptidyl peptidase 4 (DPP4) sequences were closely related to those of human and non-human primates but distinct from dromedary DPP4 sequence. Critical residues for binding to MERS-CoV spike protein were mostly conserved in bat DPP4. DPP4 was expressed in the five bat cells susceptible to MERS-CoV, with significantly higher mRNA expression levels than those in non-susceptible cells (P = 0.0174), supporting that DPP4 expression is critical for MERS-CoV infection in bats. However, overexpression of T. pachypus DPP4 failed to confer MERS-CoV susceptibility in T. pachypus cells, suggesting other cellular factors in determining viral replication. The broad cellular tropism of MERS-CoV should prompt further exploration of host diversity of related viruses to identify its ancestral origin.
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Affiliation(s)
- Susanna K P Lau
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China. .,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China. .,Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China. .,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
| | - Rachel Y Y Fan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Hayes K H Luk
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Longchao Zhu
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Joshua Fung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kenneth S M Li
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Emily Y M Wong
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Syed Shakeel Ahmed
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jasper F W Chan
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Raven K H Kok
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kwok-Hung Chan
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Ulrich Wernery
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China. .,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China. .,Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China. .,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
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30
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Schaefer E, Harms C, Viner M, Barnum S, Pusterla N. Investigation of an experimental infection model of equine coronavirus in adult horses. J Vet Intern Med 2018; 32:2099-2104. [PMID: 30353949 PMCID: PMC6271284 DOI: 10.1111/jvim.15318] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 06/02/2018] [Accepted: 08/09/2018] [Indexed: 11/29/2022] Open
Abstract
Background Equine coronavirus (ECoV) is a recently reported enteric disease of adult horses. Natural infection by ECoV has been reported in adult horses worldwide, whereas experimental infection has only been reported in juvenile horses. An experimental infection model is needed to study the clinical presentation, laboratory abnormalities, and pathophysiological changes associated with ECoV. Objectives To investigate the clinical, hematologic, molecular, and serological features of adult horses experimentally infected with ECoV. Animals Eight adult horses. Methods Four horses were intragastrically infected with fecal material containing 109 genome equivalents of ECoV. Four additional horses were exposed daily to the feces from the experimentally‐infected horses. Monitoring included physical examinations, as well as daily nasal swab, whole blood, and fecal collection for molecular detection of ECoV. Blood was collected every other day for hematologic analysis and weekly for serologic analysis. Results All 8 horses shed ECoV in feces. Six of the 8 horses (75%) exhibited mild, clinical disease with soft, formed manure; 1 horse exhibited transient pyrexia. All horses maintained total white cell counts within normal limits, but 3 horses developed transient lymphopenia. No statistically significant differences (P = .20) were observed in quantity of fecal shedding of ECoV between the 2 groups. Conclusions and Clinical Importance Experimental infection of adult horses with ECoV was associated with mild and self‐limiting clinical signs, transient lymphopenia, and fecal shedding of ECoV, which mimics natural infection. No differences between experimentally‐infected horses and horses exposed to ECoV‐containing feces were identified. Results of our study support a fecal‐oral route of transmission.
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Affiliation(s)
- Emily Schaefer
- William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California, Davis, Davis, California
| | - Corey Harms
- William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California, Davis, Davis, California
| | - Molly Viner
- William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California, Davis, Davis, California
| | - Samantha Barnum
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, Davis, California
| | - Nicola Pusterla
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, Davis, California
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31
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Pusterla N, Vin R, Leutenegger CM, Mittel LD, Divers TJ. Enteric coronavirus infection in adult horses. Vet J 2018; 231:13-18. [PMID: 29429482 PMCID: PMC7110460 DOI: 10.1016/j.tvjl.2017.11.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 11/07/2017] [Accepted: 11/15/2017] [Indexed: 01/10/2023]
Abstract
A new enteric virus of adult horses, equine coronavirus (ECoV), has recently been recognized. It is associated with fever, lethargy, anorexia, and less frequently, colic and diarrhea. This enteric virus is transmitted via the feco-oral route and horses become infected by ingesting fecally contaminated feed and water. Various outbreaks have been reported since 2010 from Japan, Europe and the USA. While the clinical signs are fairly non-specific, lymphopenia and neutropenia are often seen. Specific diagnosis is made by the detection of ECoV in feces by either quantitative real-time PCR, electron microscopy or antigen-capture ELISA. Supportive treatment is usually required, as most infections are self-limiting. However, rare complications, such as endotoxemia, septicemia and hyperammonemia-associated encephalopathy, have been reported, and have been related to the loss of barrier function at the intestinal mucosa. This review article will focus on the latest information pertaining to the virus, epidemiology, clinical signs, diagnosis, pathology, treatment and prevention of ECoV infection in adult horses.
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Affiliation(s)
- N Pusterla
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA.
| | - R Vin
- Myhre Equine Clinic, Rochester, NH 03867, USA
| | | | - L D Mittel
- College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - T J Divers
- College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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32
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NEMOTO M, KANNO T, BANNAI H, TSUJIMURA K, YAMANAKA T, KOKADO H. Antibody response to equine coronavirus in horses inoculated with a bovine coronavirus vaccine. J Vet Med Sci 2017; 79:1889-1891. [PMID: 28993568 PMCID: PMC5709570 DOI: 10.1292/jvms.17-0414] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/24/2017] [Indexed: 11/22/2022] Open
Abstract
A vaccine for equine coronavirus (ECoV) is so far unavailable. Bovine coronavirus (BCoV) is antigenically related to ECoV; it is therefore possible that BCoV vaccine will induce antibodies against ECoV in horses. This study investigated antibody response to ECoV in horses inoculated with BCoV vaccine. Virus neutralization tests showed that antibody titers against ECoV increased in all six horses tested at 14 days post inoculation, although the antibody titers were lower against ECoV than against BCoV. This study showed that BCoV vaccine provides horses with antibodies against ECoV to some extent. It is unclear whether antibodies provided by BCoV vaccine are effective against ECoV, and therefore ECoV challenge studies are needed to evaluate efficacy of the vaccine in the future.
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Affiliation(s)
- Manabu NEMOTO
- Equine Research Institute, Japan Racing Association, 1400-4 Shiba, Shimotsuke, Tochigi 329-0412, Japan
| | - Toru KANNO
- Hokkaido Research Station, National Institute of Animal Health, 4 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-0045, Japan
| | - Hiroshi BANNAI
- Equine Research Institute, Japan Racing Association, 1400-4 Shiba, Shimotsuke, Tochigi 329-0412, Japan
| | - Koji TSUJIMURA
- Equine Research Institute, Japan Racing Association, 1400-4 Shiba, Shimotsuke, Tochigi 329-0412, Japan
| | - Takashi YAMANAKA
- Equine Research Institute, Japan Racing Association, 1400-4 Shiba, Shimotsuke, Tochigi 329-0412, Japan
| | - Hiroshi KOKADO
- Equine Research Institute, Japan Racing Association, 1400-4 Shiba, Shimotsuke, Tochigi 329-0412, Japan
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33
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Novel Alphacoronaviruses and Paramyxoviruses Cocirculate with Type 1 and Severe Acute Respiratory System (SARS)-Related Betacoronaviruses in Synanthropic Bats of Luxembourg. Appl Environ Microbiol 2017; 83:AEM.01326-17. [PMID: 28710271 DOI: 10.1128/aem.01326-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 07/05/2017] [Indexed: 01/21/2023] Open
Abstract
Several infectious disease outbreaks with high mortality in humans have been attributed to viruses that are thought to have evolved from bat viruses. In this study from Luxembourg, the genetic diversity and epidemiology of paramyxoviruses and coronaviruses shed by the bat species Rhinolophus ferrumequinum and Myotis emarginatus were evaluated. Feces collection (n = 624) was performed longitudinally in a mixed-species colony in 2015 and 2016. In addition, feces (n = 254) were collected cross-sectionally from six Myotis emarginatus colonies in 2016. By use of degenerate primers in a nested format, overall prevalences of 1.1% (10/878) and 4.9% (43/878) were determined for paramyxoviruses and coronaviruses. Sequences of the partial RNA-dependent RNA polymerase and spike glycoprotein genes of coronaviruses, as well as sequences of the partial L gene of paramyxoviruses, were obtained. Novel paramyxovirus and Alphacoronavirus strains were identified in different Myotis emarginatus colonies, and severe acute respiratory syndrome (SARS)-related Betacoronavirus strains were shed by Rhinolophus ferrumequinum Logistic regression revealed that the level of Alphacoronavirus shedding was highest in July (odds ratio, 2.8; P < 0.01), probably due to periparturient stress. Phylogenetic analyses point to close virus-host coevolution, and the high genetic similarity of the study strains suggests that the Myotis emarginatus colonies in Luxembourg are socially connected. Most interestingly, we show that bats also host Betacoronavirus1 strains. The high similarity of the spike gene sequences of these viruses with mammalian Betacoronavirus 1 strains may be of concern. Both the SARS-related and Betacoronavirus 1 strains detected in bats in Luxembourg may cross the species barrier after a host adaptation process.IMPORTANCE Bats are a natural reservoir of a number of zoonotic pathogens. Several severe outbreaks in humans (e.g., a Nipah virus outbreak in Malaysia in 1998, and the almost global spread of severe acute respiratory syndrome in 2003) have been caused by bat-borne viruses that were transmitted to humans mostly after virus adaptation (e.g., in intermediate animal hosts). Despite the indigenousness of bat species that host viruses with suspected zoonotic potential and despite the zoonotic transmission of European bat 1 lyssavirus in Luxembourg, knowledge about the diversity and epidemiology of bat viruses remains limited in this country. Moreover, in contrast to other European countries, bat viruses are currently not included in the national surveillance activities of this land-locked country. We suggest that this gap in disease surveillance should be addressed, since we show here that synanthropic bats host viruses that may be able to cross the species barrier.
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Hemida MG, Chu DKW, Perera RAPM, Ko RLW, So RTY, Ng BCY, Chan SMS, Chu S, Alnaeem AA, Alhammadi MA, Webby RJ, Poon LLM, Balasuriya UBR, Peiris M. Coronavirus infections in horses in Saudi Arabia and Oman. Transbound Emerg Dis 2017; 64:2093-2103. [PMID: 28296228 PMCID: PMC7169745 DOI: 10.1111/tbed.12630] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Indexed: 12/01/2022]
Abstract
Equine coronaviruses (ECoV) are the only coronavirus known to infect horses. So far, data on ECoV infection in horses remain limited to the USA, France and Japan and its geographic distribution is not well understood. We carried out RT‐PCR on 306 nasal and 315 rectal swabs and tested 243 sera for antibodies to detect coronavirus infections in apparently healthy horses in Saudi Arabia and Oman. We document evidence of infection with ECoV and HKU23 coronavirus by RT‐PCR. There was no conclusive evidence of Middle East respiratory syndrome coronavirus infection in horses. Serological data suggest that lineage A betacoronavirus infections are commonly infecting horses in Saudi Arabia and Oman but antibody cross‐reactivities between these viruses do not permit us to use serological data alone to identify which coronaviruses are causing these infections.
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Affiliation(s)
- M G Hemida
- Department of Microbiology and Parasitology, College of Veterinary Medicine, King Faisal University, Al-Hasa, Saudi Arabia.,Department of Virology Faculty of Veterinary Medicine, Kaferelsheik University, Kaferelsheik, Egypt
| | - D K W Chu
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - R A P M Perera
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - R L W Ko
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - R T Y So
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - B C Y Ng
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - S M S Chan
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - S Chu
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - A A Alnaeem
- Department of Clinical Studies, College of Veterinary Medicine, King Faisal University, Al-Hasa, Saudi Arabia
| | - M A Alhammadi
- Department of Microbiology and Parasitology, College of Veterinary Medicine, King Faisal University, Al-Hasa, Saudi Arabia
| | - R J Webby
- Division of Virology, Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - L L M Poon
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - U B R Balasuriya
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA.,Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - M Peiris
- School of Public Health, The University of Hong Kong, Hong Kong, China
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Lineage A Betacoronavirus NS2 Proteins and the Homologous Torovirus Berne pp1a Carboxy-Terminal Domain Are Phosphodiesterases That Antagonize Activation of RNase L. J Virol 2017; 91:JVI.02201-16. [PMID: 28003490 DOI: 10.1128/jvi.02201-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 12/13/2016] [Indexed: 01/22/2023] Open
Abstract
Viruses in the family Coronaviridae, within the order Nidovirales, are etiologic agents of a range of human and animal diseases, including both mild and severe respiratory diseases in humans. These viruses encode conserved replicase and structural proteins as well as more diverse accessory proteins, encoded in the 3' ends of their genomes, that often act as host cell antagonists. We previously showed that 2',5'-phosphodiesterases (2',5'-PDEs) encoded by the prototypical Betacoronavirus, mouse hepatitis virus (MHV), and by Middle East respiratory syndrome-associated coronavirus antagonize the oligoadenylate-RNase L (OAS-RNase L) pathway. Here we report that additional coronavirus superfamily members, including lineage A betacoronaviruses and toroviruses infecting both humans and animals, encode 2',5'-PDEs capable of antagonizing RNase L. We used a chimeric MHV system (MHVMut) in which exogenous PDEs were expressed from an MHV backbone lacking the gene for a functional NS2 protein, the endogenous RNase L antagonist. With this system, we found that 2',5'-PDEs encoded by the human coronavirus HCoV-OC43 (OC43; an agent of the common cold), human enteric coronavirus (HECoV), equine coronavirus (ECoV), and equine torovirus Berne (BEV) are enzymatically active, rescue replication of MHVMut in bone marrow-derived macrophages, and inhibit RNase L-mediated rRNA degradation in these cells. Additionally, PDEs encoded by OC43 and BEV rescue MHVMut replication and restore pathogenesis in wild-type (WT) B6 mice. This finding expands the range of viruses known to encode antagonists of the potent OAS-RNase L antiviral pathway, highlighting its importance in a range of species as well as the selective pressures exerted on viruses to antagonize it.IMPORTANCE Viruses in the family Coronaviridae include important human and animal pathogens, including the recently emerged viruses severe acute respiratory syndrome-associated coronavirus (SARS-CoV) and Middle East respiratory syndrome-associated coronavirus (MERS-CoV). We showed previously that two viruses within the genus Betacoronavirus, mouse hepatitis virus (MHV) and MERS-CoV, encode 2',5'-phosphodiesterases (2',5'-PDEs) that antagonize the OAS-RNase L pathway, and we report here that these proteins are furthermore conserved among additional coronavirus superfamily members, including lineage A betacoronaviruses and toroviruses, suggesting that they may play critical roles in pathogenesis. As there are no licensed vaccines or effective antivirals against human coronaviruses and few against those infecting animals, identifying viral proteins contributing to virulence can inform therapeutic development. Thus, this work demonstrates that a potent antagonist of host antiviral defenses is encoded by multiple and diverse viruses within the family Coronaviridae, presenting a possible broad-spectrum therapeutic target.
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Kooijman LJ, James K, Mapes SM, Theelen MJP, Pusterla N. Seroprevalence and risk factors for infection with equine coronavirus in healthy horses in the USA. Vet J 2017; 220:91-94. [PMID: 28190504 PMCID: PMC7110631 DOI: 10.1016/j.tvjl.2017.01.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 11/30/2022]
Abstract
Equine coronavirus has only recently been associated with emerging infections in adult horses. Seroprevalence data is needed to better understand the epidemiology of equine coronavirus in adult horses. The seroprevalence to equine coronavirus was 9.6% in 5247 healthy, adult horses from 18 states in the USA. Seropositivity was significantly associated with horses from the Mid-West, draft horses and ranch/farm and breeding use.
Equine coronavirus (ECoV) is considered an enteric pathogen of foals and has only recently been associated with infections in adult horses. Seroprevalence data is needed to better understand the epidemiology of ECoV in adult horses, evaluate diagnostic modalities and develop preventive measures. The objective of this study was to investigate the seroprevalence and selective risk factors for ECoV in 5247 healthy adult horses in the USA, using a recently established and validated IgG enzyme-linked immunosorbent assay. Prevalence factors analysed in this study included geographic region, age, breed, sex and use. A total of 504/5247 horses (9.6%) horses tested seropositive. Geographic region (Mid-West; P = 0.008), breed (Draft horses; P = 0.003) and specific uses of horses (ranch/farm, P = 0.034; breeding use, P = 0.016) were all statistically significant risk factors for seropositivity.
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Affiliation(s)
- L J Kooijman
- Department of Equine Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 114, Utrecht 3584CM, The Netherlands
| | - K James
- Department of Veterinary Medicine and Epidemiology, School of Veterinary Medicine, University of California, One Shields Avenue, Davis, California 95616, USA
| | - S M Mapes
- Department of Veterinary Medicine and Epidemiology, School of Veterinary Medicine, University of California, One Shields Avenue, Davis, California 95616, USA
| | - M J P Theelen
- Department of Equine Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 114, Utrecht 3584CM, The Netherlands
| | - N Pusterla
- Department of Veterinary Medicine and Epidemiology, School of Veterinary Medicine, University of California, One Shields Avenue, Davis, California 95616, USA.
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Diseases of the Alimentary Tract. Vet Med (Auckl) 2017. [PMCID: PMC7167529 DOI: 10.1016/b978-0-7020-5246-0.00007-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Fang P, Fang L, Liu X, Hong Y, Wang Y, Dong N, Ma P, Bi J, Wang D, Xiao S. Identification and subcellular localization of porcine deltacoronavirus accessory protein NS6. Virology 2016; 499:170-177. [PMID: 27661736 PMCID: PMC7111631 DOI: 10.1016/j.virol.2016.09.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/14/2016] [Accepted: 09/15/2016] [Indexed: 12/27/2022]
Abstract
Porcine deltacoronavirus (PDCoV) is an emerging swine enteric coronavirus. Accessory proteins are genus-specific for coronavirus, and two putative accessory proteins, NS6 and NS7, are predicted to be encoded by PDCoV; however, this remains to be confirmed experimentally. Here, we identified the leader-body junction sites of NS6 subgenomic RNA (sgRNA) and found that the actual transcription regulatory sequence (TRS) utilized by NS6 is non-canonical and is located upstream of the predicted TRS. Using the purified NS6 from an Escherichia coli expression system, we obtained two anti-NS6 monoclonal antibodies that could detect the predicted NS6 in cells infected with PDCoV or transfected with NS6-expressing plasmids. Further studies revealed that NS6 is always localized in the cytoplasm of PDCoV-infected cells, mainly co-localizing with the endoplasmic reticulum (ER) and ER-Golgi intermediate compartments, as well as partially with the Golgi apparatus. Together, our results identify the NS6 sgRNA and demonstrate its expression in PDCoV-infected cells.
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Affiliation(s)
- Puxian Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Liurong Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Xiaorong Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Yingying Hong
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Yongle Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Nan Dong
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Panpan Ma
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Jing Bi
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Department of Immunology and Aetology, College of Basic Medicine, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Dang Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China.
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Kooijman LJ, Mapes SM, Pusterla N. Development of an equine coronavirus-specific enzyme-linked immunosorbent assay to determine serologic responses in naturally infected horses. J Vet Diagn Invest 2016; 28:414-8. [PMID: 27216723 DOI: 10.1177/1040638716649643] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Equine coronavirus (EqCoV) infection has been documented in most reports through quantitative qPCR analysis of feces and viral genome sequencing. Although qPCR is used to detect antigen during the acute disease phase, there is no equine-specific antibody test available to study EqCoV seroprevalence in various horse populations. We developed an enzyme-linked immunosorbent assay (ELISA) targeting antibodies to the spike (S) protein of EqCoV and validated its use, using acute and convalescent sera from 83 adult horses involved in 6 outbreaks. The EqCoV S protein-based ELISA was able to reliably detect antibodies to EqCoV in naturally infected horses. The greatest seroconversion rate was observed in horses with clinical signs compatible with EqCoV infection and EqCoV qPCR detection in feces. The EqCoV S protein-based ELISA could be used effectively for seroepidemiologic studies in order to better characterize the overall infection rate of EqCoV in various horse populations.
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Affiliation(s)
- Lotte J Kooijman
- Department of Veterinary Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA
| | - Samantha M Mapes
- Department of Veterinary Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA
| | - Nicola Pusterla
- Department of Veterinary Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA
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Woo PCY, Lau SKP, Fan RYY, Lau CCY, Wong EYM, Joseph S, Tsang AKL, Wernery R, Yip CCY, Tsang CC, Wernery U, Yuen KY. Isolation and Characterization of Dromedary Camel Coronavirus UAE-HKU23 from Dromedaries of the Middle East: Minimal Serological Cross-Reactivity between MERS Coronavirus and Dromedary Camel Coronavirus UAE-HKU23. Int J Mol Sci 2016; 17:ijms17050691. [PMID: 27164099 PMCID: PMC4881517 DOI: 10.3390/ijms17050691] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 04/21/2016] [Accepted: 04/25/2016] [Indexed: 01/20/2023] Open
Abstract
Recently, we reported the discovery of a dromedary camel coronavirus UAE-HKU23 (DcCoV UAE-HKU23) from dromedaries in the Middle East. In this study, DcCoV UAE-HKU23 was successfully isolated in two of the 14 dromedary fecal samples using HRT-18G cells, with cytopathic effects observed five days after inoculation. Northern blot analysis revealed at least seven distinct RNA species, corresponding to predicted subgenomic mRNAs and confirming the core sequence of transcription regulatory sequence motifs as 5′-UCUAAAC-3′ as we predicted previously. Antibodies against DcCoV UAE-HKU23 were detected in 58 (98.3%) and 59 (100%) of the 59 dromedary sera by immunofluorescence and neutralization antibody tests, respectively. There was significant correlation between the antibody titers determined by immunofluorescence and neutralization assays (Pearson coefficient = 0.525, p < 0.0001). Immunization of mice using recombinant N proteins of DcCoV UAE-HKU23 and Middle East respiratory syndrome coronavirus (MERS-CoV), respectively, and heat-inactivated DcCoV UAE-HKU23 showed minimal cross-antigenicity between DcCoV UAE-HKU23 and MERS-CoV by Western blot and neutralization antibody assays. Codon usage and genetic distance analysis of RdRp, S and N genes showed that the 14 strains of DcCoV UAE-HKU23 formed a distinct cluster, separated from those of other closely related members of Betacoronavirus 1, including alpaca CoV, confirming that DcCoV UAE-HKU23 is a novel member of Betacoronavirus 1.
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Affiliation(s)
- Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong.
- Department of Microbiology, the University of Hong Kong, Pokfulam, Hong Kong.
- Research Centre of Infection and Immunology, the University of Hong Kong, Pokfulam, Hong Kong.
- Carol Yu Centre for Infection, the University of Hong Kong, Pokfulam, Hong Kong.
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310006, China.
| | - Susanna K P Lau
- State Key Laboratory of Emerging Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong.
- Department of Microbiology, the University of Hong Kong, Pokfulam, Hong Kong.
- Research Centre of Infection and Immunology, the University of Hong Kong, Pokfulam, Hong Kong.
- Carol Yu Centre for Infection, the University of Hong Kong, Pokfulam, Hong Kong.
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310006, China.
| | - Rachel Y Y Fan
- Department of Microbiology, the University of Hong Kong, Pokfulam, Hong Kong.
| | - Candy C Y Lau
- Department of Microbiology, the University of Hong Kong, Pokfulam, Hong Kong.
| | - Emily Y M Wong
- Department of Microbiology, the University of Hong Kong, Pokfulam, Hong Kong.
| | | | - Alan K L Tsang
- Department of Microbiology, the University of Hong Kong, Pokfulam, Hong Kong.
| | | | - Cyril C Y Yip
- Department of Microbiology, the University of Hong Kong, Pokfulam, Hong Kong.
| | - Chi-Ching Tsang
- Department of Microbiology, the University of Hong Kong, Pokfulam, Hong Kong.
| | | | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong.
- Department of Microbiology, the University of Hong Kong, Pokfulam, Hong Kong.
- Research Centre of Infection and Immunology, the University of Hong Kong, Pokfulam, Hong Kong.
- Carol Yu Centre for Infection, the University of Hong Kong, Pokfulam, Hong Kong.
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310006, China.
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Irigoyen N, Firth AE, Jones JD, Chung BYW, Siddell SG, Brierley I. High-Resolution Analysis of Coronavirus Gene Expression by RNA Sequencing and Ribosome Profiling. PLoS Pathog 2016; 12:e1005473. [PMID: 26919232 PMCID: PMC4769073 DOI: 10.1371/journal.ppat.1005473] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/04/2016] [Indexed: 02/07/2023] Open
Abstract
Members of the family Coronaviridae have the largest genomes of all RNA viruses, typically in the region of 30 kilobases. Several coronaviruses, such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and Middle East respiratory syndrome-related coronavirus (MERS-CoV), are of medical importance, with high mortality rates and, in the case of SARS-CoV, significant pandemic potential. Other coronaviruses, such as Porcine epidemic diarrhea virus and Avian coronavirus, are important livestock pathogens. Ribosome profiling is a technique which exploits the capacity of the translating ribosome to protect around 30 nucleotides of mRNA from ribonuclease digestion. Ribosome-protected mRNA fragments are purified, subjected to deep sequencing and mapped back to the transcriptome to give a global "snap-shot" of translation. Parallel RNA sequencing allows normalization by transcript abundance. Here we apply ribosome profiling to cells infected with Murine coronavirus, mouse hepatitis virus, strain A59 (MHV-A59), a model coronavirus in the same genus as SARS-CoV and MERS-CoV. The data obtained allowed us to study the kinetics of virus transcription and translation with exquisite precision. We studied the timecourse of positive and negative-sense genomic and subgenomic viral RNA production and the relative translation efficiencies of the different virus ORFs. Virus mRNAs were not found to be translated more efficiently than host mRNAs; rather, virus translation dominates host translation at later time points due to high levels of virus transcripts. Triplet phasing of the profiling data allowed precise determination of translated reading frames and revealed several translated short open reading frames upstream of, or embedded within, known virus protein-coding regions. Ribosome pause sites were identified in the virus replicase polyprotein pp1a ORF and investigated experimentally. Contrary to expectations, ribosomes were not found to pause at the ribosomal frameshift site. To our knowledge this is the first application of ribosome profiling to an RNA virus.
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Affiliation(s)
- Nerea Irigoyen
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Joshua D Jones
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Betty Y-W Chung
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Stuart G Siddell
- Department of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Ian Brierley
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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Pusterla N, Vin R, Leutenegger C, Mittel LD, Divers TJ. Equine coronavirus: An emerging enteric virus of adult horses. EQUINE VET EDUC 2015; 28:216-223. [PMID: 32313392 PMCID: PMC7163714 DOI: 10.1111/eve.12453] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Equine coronavirus (ECoV) is an emerging virus associated clinically and epidemiologically with fever, depression, anorexia and less frequently colic and diarrhoea in adult horses. Sporadic cases and outbreaks have been reported with increased frequency since 2010 from Japan, the USA and more recently from Europe. A faeco‐oral transmission route is suspected and clinical or asymptomatic infected horses appear to be responsible for direct and indirect transmission of ECoV. A presumptive clinical diagnosis of ECoV infection may be suggested by clinical presentation, haematological abnormalities such as leucopenia due to lymphopenia and/or neutropenia. Confirmation of ECoV infection is provided by specific ECoV nucleic acid detection in faeces by quantitative PCR (qPCR) or demonstration of coronavirus antigen by immunohistochemistry or electron microscopy in intestinal biopsy material obtained ante or post mortem. The disease is generally self‐limiting and horses typically recover with symptomatic supportive care. Complications associated with disruption of the gastrointestinal barrier have been reported in some infected horses and include endotoxaemia, septicaemia and hyperammonaemia‐associated encephalopathy. Although specific immunoprophylactic measures have been shown to be effective in disease prevention for closely‐related coronaviruses such as bovine coronavirus (BCoV), such strategies have yet not been investigated for horses and disease prevention is limited to basic biosecurity protocols. This article reviews current knowledge concerning the aetiology, epidemiology, clinical signs, diagnosis, pathology, treatment and prevention of ECoV infection in adult horses.
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Affiliation(s)
- N Pusterla
- Department of Medicine and Epidemiology School of Veterinary Medicine University of California Davis USA
| | - R Vin
- IDEXX Laboratories, Inc. West Sacramento California USA
| | - C Leutenegger
- IDEXX Laboratories, Inc. West Sacramento California USA
| | - L D Mittel
- The Animal Health Diagnostic Center Cornell University Ithaca New York USA
| | - T J Divers
- College of Veterinary Medicine Cornell University Ithaca New York USA
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Nemoto M, Oue Y, Higuchi T, Kinoshita Y, Bannai H, Tsujimura K, Yamanaka T, Kondo T. Low prevalence of equine coronavirus in foals in the largest thoroughbred horse breeding region of Japan, 2012-2014. Acta Vet Scand 2015; 57:53. [PMID: 26395082 PMCID: PMC4579792 DOI: 10.1186/s13028-015-0149-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 08/30/2015] [Indexed: 12/04/2022] Open
Abstract
Background Equine coronavirus (ECoV) is considered to be a diarrheic pathogen in foals. In central Kentucky in the United States, it has been shown that approximately 30 % of thoroughbred foals are infected with ECoV and thus it is considered widely prevalent. In contrast, the epidemiology of ECoV and its relationship to diarrhea in foals are poorly understood in Japan. We investigated ECoV in rectal swabs collected from thoroughbred foals in Japan. Results We collected 337 rectal swabs from 307 diarrheic foals in the Hidaka district of Hokkaido, the largest thoroughbred horse breeding region in Japan, between 2012 and 2014. In addition, 120 rectal swabs were collected from 120 healthy foals in 2012. These samples were tested by reverse transcription loop-mediated isothermal amplification and a real-time reverse transcription-polymerase chain reaction. All samples collected from diarrheic foals were negative, and only three samples (2.5 %) collected from healthy foals were positive for ECoV. Compared with central Kentucky, ECoV is not prevalent among thoroughbred foals in the Hidaka district of Hokkaido. Conclusion ECoV is not prevalent and was not related to diarrhea in thoroughbred foals in the Hidaka district of Hokkaido between 2012 and 2014.
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Nemoto M, Oue Y, Murakami S, Kanno T, Bannai H, Tsujimura K, Yamanaka T, Kondo T. Complete genome analysis of equine coronavirus isolated in Japan. Arch Virol 2015; 160:2903-6. [PMID: 26271151 PMCID: PMC7086706 DOI: 10.1007/s00705-015-2565-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 08/04/2015] [Indexed: 11/27/2022]
Abstract
Equine coronavirus has been responsible for several outbreaks of disease in the United States and Japan. Only one complete genome sequence (NC99 isolated in the US) had been reported for this pathogenic RNA virus. Here, we report the complete genome sequences of three equine coronaviruses isolated in 2009 and 2012 in Japan. The genome sequences of Tokachi09, Obihiro12-1 and Obihiro12-2 were 30,782, 30,916 and 30,916 nucleotides in length, respectively, excluding the 3'-poly (A) tails. All three isolates were genetically similar to NC99 (98.2-98.7%), but deletions and insertions were observed in the genes nsp3 of ORF1a, NS2 and p4.7.
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Affiliation(s)
- Manabu Nemoto
- Epizootic Research Center, Equine Research Institute, Japan Racing Association, 1400-4 Shiba, Shimotsuke, Tochigi, 329-0412, Japan.
| | - Yasuhiro Oue
- Hokkaido Kushiro Livestock Hygiene Service Center, 127-1 Otanoshike, Kushiro, Hokkaido, 084-0917, Japan
| | - Satoshi Murakami
- Thermo Fisher Scientific, Life technologies Japan Ltd., Sumitomo Fudosan Mita Twin Bldg., 4-2-8 Shibaura, Minato-ku, Tokyo, 108-0023, Japan
| | - Toru Kanno
- Dairy Hygiene Research Division, Hokkaido Research Station, National Institute of Animal Health, 4 Hitsujigaoka, Toyohira, Sapporo, Hokkaido, 062-0045, Japan
| | - Hiroshi Bannai
- Epizootic Research Center, Equine Research Institute, Japan Racing Association, 1400-4 Shiba, Shimotsuke, Tochigi, 329-0412, Japan
| | - Koji Tsujimura
- Epizootic Research Center, Equine Research Institute, Japan Racing Association, 1400-4 Shiba, Shimotsuke, Tochigi, 329-0412, Japan
| | - Takashi Yamanaka
- Epizootic Research Center, Equine Research Institute, Japan Racing Association, 1400-4 Shiba, Shimotsuke, Tochigi, 329-0412, Japan
| | - Takashi Kondo
- Epizootic Research Center, Equine Research Institute, Japan Racing Association, 1400-4 Shiba, Shimotsuke, Tochigi, 329-0412, Japan
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Kin N, Miszczak F, Lin W, Ar Gouilh M, Vabret A. Genomic Analysis of 15 Human Coronaviruses OC43 (HCoV-OC43s) Circulating in France from 2001 to 2013 Reveals a High Intra-Specific Diversity with New Recombinant Genotypes. Viruses 2015; 7:2358-77. [PMID: 26008694 PMCID: PMC4452910 DOI: 10.3390/v7052358] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 04/23/2015] [Accepted: 05/04/2015] [Indexed: 01/19/2023] Open
Abstract
Human coronavirus OC43 (HCoV-OC43) is one of five currently circulating human coronaviruses responsible for respiratory infections. Like all coronaviruses, it is characterized by its genome’s high plasticity. The objectives of the current study were to detect genetically distinct genotypes and eventually recombinant genotypes in samples collected in Lower Normandy between 2001 and 2013. To this end, we sequenced complete nsp12, S, and N genes of 15 molecular isolates of HCoV-OC43 from clinical samples and compared them to available data from the USA, Belgium, and Hong-Kong. A new cluster E was invariably detected from nsp12, S, and N data while the analysis of nsp12 and N genes revealed the existence of new F and G clusters respectively. The association of these different clusters of genes in our specimens led to the description of thirteen genetically distinct genotypes, among which eight recombinant viruses were discovered. Identification of these recombinant viruses, together with temporal analysis and tMRCA estimation, provides important information for understanding the dynamics of the evolution of these epidemic coronaviruses.
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Affiliation(s)
- Nathalie Kin
- Normandie Université, 14032 Caen, France; E-Mails: (F.M.); (M.A.G.); (A.V.)
- Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France; E-Mails: (W.L.); (E.C.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +33-0-2-31-27-25-54
| | - Fabien Miszczak
- Normandie Université, 14032 Caen, France; E-Mails: (F.M.); (M.A.G.); (A.V.)
- Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France; E-Mails: (W.L.); (E.C.)
- Department of Virology, University Hospital of Caen, F-14033 Caen, France
| | - Wei Lin
- Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France; E-Mails: (W.L.); (E.C.)
| | - Meriadeg Ar Gouilh
- Normandie Université, 14032 Caen, France; E-Mails: (F.M.); (M.A.G.); (A.V.)
- Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France; E-Mails: (W.L.); (E.C.)
- Institut Pasteur, Environment and Infectious Risks Research and Expertise Unit, F-75015 Paris, France
| | - Astrid Vabret
- Normandie Université, 14032 Caen, France; E-Mails: (F.M.); (M.A.G.); (A.V.)
- Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France; E-Mails: (W.L.); (E.C.)
- Department of Virology, University Hospital of Caen, F-14033 Caen, France
| | - Epicorem Consortium
- Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France; E-Mails: (W.L.); (E.C.)
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Giannitti F, Diab S, Mete A, Stanton JB, Fielding L, Crossley B, Sverlow K, Fish S, Mapes S, Scott L, Pusterla N. Necrotizing Enteritis and Hyperammonemic Encephalopathy Associated With Equine Coronavirus Infection in Equids. Vet Pathol 2015; 52:1148-56. [PMID: 25648965 DOI: 10.1177/0300985814568683] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Equine coronavirus (ECoV) is a Betacoronavirus recently associated clinically and epidemiologically with emerging outbreaks of pyrogenic, enteric, and/or neurologic disease in horses in the United States, Japan, and Europe. We describe the pathologic, immunohistochemical, ultrastructural, and molecular findings in 2 horses and 1 donkey that succumbed to natural infection with ECoV. One horse and the donkey (case Nos. 1, 3) had severe diffuse necrotizing enteritis with marked villous attenuation, epithelial cell necrosis at the tips of the villi, neutrophilic and fibrinous extravasation into the small intestinal lumen (pseudomembrane formation), as well as crypt necrosis, microthrombosis, and hemorrhage. The other horse (case No. 2) had hyperammonemic encephalopathy with Alzheimer type II astrocytosis throughout the cerebral cortex. ECoV was detected by quantitative polymerase chain reaction in small intestinal tissue, contents, and/or feces, and coronavirus antigen was detected by immunohistochemistry in the small intestine in all cases. Coronavirus-like particles characterized by spherical, moderately electron lucent, enveloped virions with distinct peplomer-like structures projecting from the surface were detected by negatively stained transmission electron microscopy in small intestine in case No. 1, and transmission electron microscopy of fixed small intestinal tissue from the same case revealed similar 85- to 100-nm intracytoplasmic particles located in vacuoles and free in the cytoplasm of unidentified (presumably epithelial) cells. Sequence comparison showed 97.9% to 99.0% sequence identity with the ECoV-NC99 and Tokachi09 strains. All together, these results indicate that ECoV is associated with necrotizing enteritis and hyperammonemic encephalopathy in equids.
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Affiliation(s)
- F Giannitti
- California Animal Health and Food Safety Laboratory, School of Veterinary Medicine, University of California, Davis, CA, USA Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, USA
| | - S Diab
- California Animal Health and Food Safety Laboratory, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - A Mete
- California Animal Health and Food Safety Laboratory, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - J B Stanton
- Department of Veterinary Microbiology and Pathology and Washington Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - L Fielding
- Loomis Basin Equine Medical Center, Loomis, CA, USA
| | - B Crossley
- California Animal Health and Food Safety Laboratory, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - K Sverlow
- California Animal Health and Food Safety Laboratory, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - S Fish
- California Animal Health and Food Safety Laboratory, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - S Mapes
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - L Scott
- Idaho Equine Hospital, Nampa, ID, USA
| | - N Pusterla
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA
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Discovery of a novel coronavirus, China Rattus coronavirus HKU24, from Norway rats supports the murine origin of Betacoronavirus 1 and has implications for the ancestor of Betacoronavirus lineage A. J Virol 2014; 89:3076-92. [PMID: 25552712 DOI: 10.1128/jvi.02420-14] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
UNLABELLED We discovered a novel Betacoronavirus lineage A coronavirus, China Rattus coronavirus (ChRCoV) HKU24, from Norway rats in China. ChRCoV HKU24 occupied a deep branch at the root of members of Betacoronavirus 1, being distinct from murine coronavirus and human coronavirus HKU1. Its unique putative cleavage sites between nonstructural proteins 1 and 2 and in the spike (S) protein and low sequence identities to other lineage A betacoronaviruses (βCoVs) in conserved replicase domains support ChRCoV HKU24 as a separate species. ChRCoV HKU24 possessed genome features that resemble those of both Betacoronavirus 1 and murine coronavirus, being closer to Betacoronavirus 1 in most predicted proteins but closer to murine coronavirus by G+C content, the presence of a single nonstructural protein (NS4), and an absent transcription regulatory sequence for the envelope (E) protein. Its N-terminal domain (NTD) demonstrated higher sequence identity to the bovine coronavirus (BCoV) NTD than to the mouse hepatitis virus (MHV) NTD, with 3 of 4 critical sugar-binding residues in BCoV and 2 of 14 contact residues at the MHV NTD/murine CEACAM1a interface being conserved. Molecular clock analysis dated the time of the most recent common ancestor of ChRCoV HKU24, Betacoronavirus 1, and rabbit coronavirus HKU14 to about the year 1400. Cross-reactivities between other lineage A and B βCoVs and ChRCoV HKU24 nucleocapsid but not spike polypeptide were demonstrated. Using the spike polypeptide-based Western blot assay, we showed that only Norway rats and two oriental house rats from Guangzhou, China, were infected by ChRCoV HKU24. Other rats, including Norway rats from Hong Kong, possessed antibodies only against N protein and not against the spike polypeptide, suggesting infection by βCoVs different from ChRCoV HKU24. ChRCoV HKU24 may represent the murine origin of Betacoronavirus 1, and rodents are likely an important reservoir for ancestors of lineage A βCoVs. IMPORTANCE While bats and birds are hosts for ancestors of most coronaviruses (CoVs), lineage A βCoVs have never been found in these animals and the origin of Betacoronavirus lineage A remains obscure. We discovered a novel lineage A βCoV, China Rattus coronavirus HKU24 (ChRCoV HKU24), from Norway rats in China with a high seroprevalence. The unique genome features and phylogenetic analysis supported the suggestion that ChRCoV HKU24 represents a novel CoV species, occupying a deep branch at the root of members of Betacoronavirus 1 and being distinct from murine coronavirus. Nevertheless, ChRCoV HKU24 possessed genome characteristics that resemble those of both Betacoronavirus 1 and murine coronavirus. Our data suggest that ChRCoV HKU24 represents the murine origin of Betacoronavirus 1, with interspecies transmission from rodents to other mammals having occurred centuries ago, before the emergence of human coronavirus (HCoV) OC43 in the late 1800s. Rodents are likely an important reservoir for ancestors of lineage A βCoVs.
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48
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Oue Y, Morita Y, Kondo T, Nemoto M. Epidemic of equine coronavirus at Obihiro Racecourse, Hokkaido, Japan in 2012. J Vet Med Sci 2014; 75:1261-5. [PMID: 23648375 DOI: 10.1292/jvms.13-0056] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Equine coronavirus (ECoV) outbreaks have occurred three times at Obihiro Racecourse in Hokkaido, Japan. The third ECoV outbreak occurred between late February and early April 2012. The main clinical signs of affected horses were anorexia, pyrexia and leucopenia; gastrointestinal disease was observed in about 10% of affected horses. Two ECoV strains were isolated from diarrheal samples. All paired sera (9/9) collected from febrile horses showed seroconversion by neutralization test. Sequence and phylogenetic analysis of the ECoV isolated showed that putative amino acid sequences in S and N genes were highly conserved among ECoV strains. In contrast, sequences of the region coding 4.7 kDa non-structural protein (p 4.7) differed among the strains. Because of the diversity of the p4.7 region, this region should be useful for epidemiological investigation of ECoV.
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Affiliation(s)
- Yasuhiro Oue
- Hokkaido Tokachi Livestock Hygiene Service Center, 59-6 Kisen, Kawanishicho, Obihiro, Hokkaido 089-1182, Japan
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49
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Miszczak F, Tesson V, Kin N, Dina J, Balasuriya UBR, Pronost S, Vabret A. First detection of equine coronavirus (ECoV) in Europe. Vet Microbiol 2014; 171:206-9. [PMID: 24768449 PMCID: PMC7117151 DOI: 10.1016/j.vetmic.2014.03.031] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 03/17/2014] [Accepted: 03/21/2014] [Indexed: 01/24/2023]
Abstract
Equine coronavirus (ECoV) is involved mainly in enteric infections. Following the recent description of ECoV in 2000, this study reports for the first time the presence of ECoV in France and, on a wider scale, in Europe. ECoV was molecularly detected from diarrheic and respiratory specimens. Sequencing and phylogenetic analyses demonstrated that European strains are most closely related to the reference North American strain (ECoV-NC99) than the Asian strain (ECoV-Tokachi09).
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Affiliation(s)
- Fabien Miszczak
- Normandie Univ, France; UNICAEN, EA4655, U2RM, F-14032 Caen, France; Department of Virology, University Hospital, F-14033 Caen, France; Frank Duncombe Laboratory-LABEO, F-14053 Caen, France.
| | - Vincent Tesson
- Normandie Univ, France; UNICAEN, EA4655, U2RM, F-14032 Caen, France; Department of Virology, University Hospital, F-14033 Caen, France
| | - Nathalie Kin
- Normandie Univ, France; UNICAEN, EA4655, U2RM, F-14032 Caen, France; Department of Virology, University Hospital, F-14033 Caen, France
| | - Julia Dina
- Normandie Univ, France; UNICAEN, EA4655, U2RM, F-14032 Caen, France; Department of Virology, University Hospital, F-14033 Caen, France
| | - Udeni B R Balasuriya
- Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY, USA
| | - Stéphane Pronost
- Normandie Univ, France; UNICAEN, EA4655, U2RM, F-14032 Caen, France; Frank Duncombe Laboratory-LABEO, F-14053 Caen, France
| | - Astrid Vabret
- Normandie Univ, France; UNICAEN, EA4655, U2RM, F-14032 Caen, France; Department of Virology, University Hospital, F-14033 Caen, France
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50
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Dhama K, Pawaiya R, Chakrabort S, Tiwari R, Saminathan M, Verma A. Coronavirus Infection in Equines: A Review. ACTA ACUST UNITED AC 2014. [DOI: 10.3923/ajava.2014.164.176] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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