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Zhang F, Chai C, Niu R, Diao Y, Zhou Y, Zhang J, Feng L, Yao C, Wu Y, Ma Y, Zan X, Wang W. Genetic characterization of bovine coronavirus strain isolated in Inner Mongolia of China. BMC Vet Res 2024; 20:209. [PMID: 38760785 PMCID: PMC11102244 DOI: 10.1186/s12917-024-04046-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/30/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Bovine coronavirus (BCoV) is implicated in severe diarrhea in calves and contributes to the bovine respiratory disease complex; it shares a close relationship with human coronavirus. Similar to other coronaviruses, remarkable variability was found in the genome and biology of the BCoV. In 2022, samples of feces were collected from a cattle farm. A virus was isolated from 7-day-old newborn calves. In this study, we present the genetic characteristics of a new BCoV isolate. The complete genomic, spike protein, and nucleocapsid protein gene sequences of the BCoV strain, along with those of other coronaviruses, were obtained from the GenBank database. Genetic analysis was conducted using MEGA7.0 and the Neighbor-Joining (NJ) method. The reference strains' related genes were retrieved from GenBank for comparison and analysis using DNAMAN. RESULTS The phylogenetic tree and whole genome consistency analysis showed that it belonged to the GIIb subgroup, which is epidemic in Asia and America, and was quite similar to the Chinese strains in the same cluster. Significantly, the S gene was highly consistent with QH1 (MH810151.1) isolated from yak. This suggests that the strain may have originated from interspecies transmission involving mutations of wild strains. The N gene was conserved and showed high sequence identity with the epidemic strains in China and the USA. CONCLUSIONS Genetic characterization suggests that the isolated strain could be a new mutant from a wild-type lineage, which is in the same cluster as most Chinese epidemic strains but on a new branch.
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Affiliation(s)
- Fan Zhang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010030, China
- Veterinary Research Institute, Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, 010031, China
| | - Chunxia Chai
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010030, China
| | - Rui Niu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010030, China
| | - Yun Diao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010030, China
| | - Yanyan Zhou
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010030, China
| | - Jinlong Zhang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010030, China
| | - Lin Feng
- Helinger County Bureau of Agriculture and Animal Husbandry, Hohhot, 011500, China
| | - Chunming Yao
- Helinger County Bureau of Agriculture and Animal Husbandry, Hohhot, 011500, China
| | - Youzhi Wu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010030, China
| | - Yanhua Ma
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010030, China
| | - Xiaohui Zan
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010030, China
| | - Wei Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010030, China.
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Park GN, Choe S, Song S, Kim KS, Shin J, An BH, Moon SH, Hyun BH, An DJ. Characterization and Spike Gene Analysis of a Candidate Attenuated Live Bovine Coronavirus Vaccine. Animals (Basel) 2024; 14:389. [PMID: 38338032 PMCID: PMC10854572 DOI: 10.3390/ani14030389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
The bovine coronavirus (BCoV) KBR-1 strain, obtained from calf diarrhea samples collected in 2017, belongs to group GIIa. To attenuate this strain, it was subcultured continuously (up to 79 times) in HRT-18 cells, followed by 80-120 passages in MDBK cells. The KBR-1-p120 strain harvested from MDBK cells at passage 120 harbored 13 amino acid mutations in the spike gene. Additionally, the KBR-1-p120 strain showed a high viral titer and cytopathogenic effects in MDBK cells. Seven-day-old calves (negative for BCoV antigen and antibodies) that did not consume colostrum were orally inoculated with the attenuated candidate strain (KBR-1-p120), or with KBR-1 passaged 10 times (KBR-1-p10) in HRT-18 cells. Calves inoculated with KBR-1-p10 had a low diarrhea score, and BCoV RNA was detected at 3-7 days post-inoculation (DPI). The virus was also present in the duodenum, jejunum, and ileum at autopsy; however, calves inoculated with KBR-1-p120 had low levels of BCoV RNA in feces at 4-6 DPI, and no diarrhea. In addition, an extremely small amount of BCoV RNA was present in the jejunum and ileum at autopsy. The small intestines of calves inoculated with KBR-1-p120 were emulsified and used to infect calves two more times, but pathogenicity was not recovered. Therefore, the KBR-1-p120 strain has potential as a live vaccine candidate.
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Affiliation(s)
- Gyu-Nam Park
- Virus Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea; (G.-N.P.); (S.C.); (S.S.); (K.-S.K.); (J.S.); (S.H.M.); (B.-H.H.)
| | - SeEun Choe
- Virus Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea; (G.-N.P.); (S.C.); (S.S.); (K.-S.K.); (J.S.); (S.H.M.); (B.-H.H.)
| | - Sok Song
- Virus Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea; (G.-N.P.); (S.C.); (S.S.); (K.-S.K.); (J.S.); (S.H.M.); (B.-H.H.)
| | - Ki-Sun Kim
- Virus Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea; (G.-N.P.); (S.C.); (S.S.); (K.-S.K.); (J.S.); (S.H.M.); (B.-H.H.)
| | - Jihye Shin
- Virus Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea; (G.-N.P.); (S.C.); (S.S.); (K.-S.K.); (J.S.); (S.H.M.); (B.-H.H.)
| | - Byung-Hyun An
- Department of Virology, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea;
| | - Soo Hyun Moon
- Virus Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea; (G.-N.P.); (S.C.); (S.S.); (K.-S.K.); (J.S.); (S.H.M.); (B.-H.H.)
| | - Bang-Hun Hyun
- Virus Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea; (G.-N.P.); (S.C.); (S.S.); (K.-S.K.); (J.S.); (S.H.M.); (B.-H.H.)
| | - Dong-Jun An
- Virus Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea; (G.-N.P.); (S.C.); (S.S.); (K.-S.K.); (J.S.); (S.H.M.); (B.-H.H.)
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Poonsin P, Wiwatvisawakorn V, Chansaenroj J, Poovorawan Y, Piewbang C, Techangamsuwan S. Canine respiratory coronavirus in Thailand undergoes mutation and evidences a potential putative parent for genetic recombination. Microbiol Spectr 2023; 11:e0226823. [PMID: 37707446 PMCID: PMC10581155 DOI: 10.1128/spectrum.02268-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 07/27/2023] [Indexed: 09/15/2023] Open
Abstract
Canine respiratory coronavirus (CRCoV) is associated with canine infectious respiratory disease complex. Although its detection has been reported worldwide, the genomic characteristics and evolutionary patterns of this virus remain poorly defined. In this study, 21 CRCoV sequences obtained from dogs in Thailand during two episodes (2013-2015, group A; 2021-2022, group B) were characterized and analyzed. The genomic characteristics of Thai CRCoVs changed from 2013 to 2022 and showed a distinct phylogenetic cluster. Phylogenetic analysis of the spike (S) genes divided the analyzed CRCoV strains into five clades. The full-length genome characterization revealed that all Thai CRCoVs possessed a nonsense mutation within the nonstructural gene located between the S and envelope genes, leading to a truncated putative nonstructural protein. Group B Thai CRCoV strains represented the signature nonsynonymous mutations in the S gene that was not identified in group A Thai CRCoVs, suggesting the ongoing evolutionary process of Thai CRCoVs. Although no evidence of recombination of Thai CRCoV strains was found, our analysis identified one Thai CRCoV strain as a potential parent virus for a CRCoV strain found in the United States. Selective pressure analysis of the hypervariable S region indicated that the CRCoV had undergone purifying selection during evolution. Evolutionary analysis suggested that the CRCoV was emerged in 1992 and was first introduced in Thailand in 2004, sharing a common ancestor with Korean CRCoV strains. These findings regarding the genetic characterization and evolutionary analysis of CRCoVs add to the understanding of CRCoVs. IMPORTANCE Knowledge of genomic characterization of the CRCoV is still limited and its evolution remains poorly investigated. We, therefore, investigated the full-length genome of CRCoV in Thailand for the first time and analyzed the evolutionary dynamic of CRCoV. Genomic characterization of Thai CRCoV strains revealed that they possess unique genome structures and have undergone nonsynonymous mutations, which have not been reported in previously described CRCoV strains. Our work suggests that the Thai CRCoVs were not undergone mutation through genetic recombination for their evolution. However, one Thai CRCoV strain PP158_THA_2015 was found to be a potential parent virus for the CRCoV strains found in the United States. This study provides an understanding of the genomic characterization and highlights the signature mutations and ongoing evolutionary process of CRCoV that could be crucial for monitoring in the future.
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Affiliation(s)
- Panida Poonsin
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | | | - Jira Chansaenroj
- Department of Pediatrics, Faculty of Medicine, Center of Excellence in Clinical Virology, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Department of Pediatrics, Faculty of Medicine, Center of Excellence in Clinical Virology, Chulalongkorn University, Bangkok, Thailand
| | - Chutchai Piewbang
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Somporn Techangamsuwan
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
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Shaw B, Gatherer D. Candidate historical events for the emergence of Human Coronavirus OC43: A critical reassessment of the molecular evidence. PLoS One 2023; 18:e0285481. [PMID: 37155606 PMCID: PMC10166493 DOI: 10.1371/journal.pone.0285481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/25/2023] [Indexed: 05/10/2023] Open
Abstract
The "Russian Influenza"-coronavirus theory (RICT) proposes that the pandemic of 1889-1892, conventionally regarded as an influenza pandemic, was caused by the emergence of human coronavirus OC43 (HCoV-OC43) as a zoonosis of bovine coronavirus (BCoV). RICT is based on a Bayesian phylogenetic calculation of the date of the most recent common ancestor (MRCA) of HCoV-OC43 and BCoV. The theory also draws on comparison of both symptoms and some epidemiological parameters of the best studied coronavirus pandemic, i.e. COVID-19, with those reported in 1889-1892. The case is completed with circumstantial evidence involving a panzoonotic among cattle in the decade prior to the "Russian Influenza", with characteristics suggesting it may have been caused by BCoV. In this paper, we review the Bayesian phylogenetic evidence for RICT, replicating previous studies and adding our own, in each case critically reviewing the suitability of the datasets used and the parameters applied. We conclude that the most probable date for the MRCA of HCoV-OC43 and BCoV is 1898-1902. This is a decade too late for compatibility with RICT but happens to coincide with another serious outbreak of respiratory illness, reported in both the USA and the UK, in the winter of 1899-1900.
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Affiliation(s)
- Brandon Shaw
- Division of Biomedical & Life Sciences, Faculty of Health & Medicine, Lancaster University, Lancaster, United Kingdom
| | - Derek Gatherer
- Division of Biomedical & Life Sciences, Faculty of Health & Medicine, Lancaster University, Lancaster, United Kingdom
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Kim EM, Cho HC, Shin SU, Park J, Choi KS. Prevalence and genetic characterization of bovine coronavirus identified from diarrheic pre-weaned native Korean calves from 2019 to 2021. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 100:105263. [PMID: 35276339 DOI: 10.1016/j.meegid.2022.105263] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/13/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Bovine coronavirus (BCoV) is associated with severe diarrhea in calves, winter dysentery in adult cattle, and respiratory diseases in cattle. However, there is currently limited information regarding its molecular characterization in the Republic of Korea (KOR). Therefore, this study investigated the prevalence of BCoV in diarrheic pre-weaned calves (aged ≤60 days) and compared BCoV genome sequences identified globally. A total of 846 fecal samples were collected from calves with diarrhea across 100 beef farms in the KOR. The samples were divided into three groups based on age as follows: 1-10 days (n = 490), 11-30 days (n = 277), and 31-60 days (n = 79). BCoV infection was detected in 50 calves by real-time RT-PCR analysis. The results showed that the prevalence of BCoV was associated with calf age (P = 0.028) and was significantly higher in calves aged 31-60 days (odds ratio: 2.69, 95% confidence interval: 1.24-5.85; P = 0.012) than in those aged 1-10 days. Our findings show that BCoV is an important etiological agent of diarrhea in calves aged 31-60 days. Fifteen full genome sequences (2019-2021 variants) of the spike, hemagglutinin/esterase, and nucleocapsid were obtained from the 50 BCoV-positive samples. Phylogenetic analysis of each gene revealed that BCoVs circulating worldwide might have no boundary between enteric and respiratory tropisms, demonstrating the presence of three BCoVs groups: the classical, Asia/USA, and European. Initially, Korean BCoVs were originated from the USA, but diverged since the 1980s and rapidly evolved independently, unlike in other Asian countries. In this study, Korean BCoVs are more recent BCoVs and present relatively high nucleotide substitution rates in all genes compared with other BCoVs. Our results showed that the 2019-2021 variants undergo continuous genetic evolution and that there are genetic differences among globally distributed BCoVs.
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Affiliation(s)
- Eun-Mi Kim
- Department of Animal Science and Biotechnology, College of Ecology and Environmental Science, Kyungpook National University, Sangju 37224, Republic of Korea
| | - Hyung-Chul Cho
- Department of Animal Science and Biotechnology, College of Ecology and Environmental Science, Kyungpook National University, Sangju 37224, Republic of Korea
| | - Seung-Uk Shin
- Department of Animal Science and Biotechnology, College of Ecology and Environmental Science, Kyungpook National University, Sangju 37224, Republic of Korea
| | - Jinho Park
- College of Veterinary Medicine, Jeonbuk National University, Iksan 54596, Republic of Korea
| | - Kyoung-Seong Choi
- Department of Animal Science and Biotechnology, College of Ecology and Environmental Science, Kyungpook National University, Sangju 37224, Republic of Korea.
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Zhu Q, Li B, Sun D. Advances in Bovine Coronavirus Epidemiology. Viruses 2022; 14:v14051109. [PMID: 35632850 PMCID: PMC9147158 DOI: 10.3390/v14051109] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/02/2022] [Accepted: 05/19/2022] [Indexed: 11/16/2022] Open
Abstract
Bovine coronavirus (BCoV) is a causative agent of enteric and respiratory disease in cattle. BCoV has also been reported to cause a variety of animal diseases and is closely related to human coronaviruses, which has attracted extensive attention from both cattle farmers and researchers. However, there are few comprehensive epidemiological reviews, and key information regarding the effect of S-gene differences on tissue tendency and potential cross-species transmission remain unclear. In this review, we summarize BCoV epidemiology, including the transmission, infection-associated factors, co-infection, pathogenicity, genetic evolution, and potential cross-species transmission. Furthermore, the potential two-receptor binding motif system for BCoV entry and the association between BCoV and SARS-CoV-2 are also discussed in this review. Our aim is to provide valuable information for the prevention and treatment of BCoV infection throughout the world.
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Affiliation(s)
- Qinghe Zhu
- Heilongjiang Provincial Key Laboratory of the Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China;
| | - Bin Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
- Correspondence: (B.L.); (D.S.); Tel.: +86-045-9681-9121 (D.S.)
| | - Dongbo Sun
- Heilongjiang Provincial Key Laboratory of the Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China;
- Correspondence: (B.L.); (D.S.); Tel.: +86-045-9681-9121 (D.S.)
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Forni D, Cagliani R, Pozzoli U, Mozzi A, Arrigoni F, De Gioia L, Clerici M, Sironi M. Dating the Emergence of Human Endemic Coronaviruses. Viruses 2022; 14:v14051095. [PMID: 35632836 PMCID: PMC9148137 DOI: 10.3390/v14051095] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 01/09/2023] Open
Abstract
Four endemic coronaviruses infect humans and cause mild symptoms. Because previous analyses were based on a limited number of sequences and did not control for effects that affect molecular dating, we re-assessed the timing of endemic coronavirus emergence. After controlling for recombination, selective pressure, and molecular clock model, we obtained similar tMRCA (time to the most recent common ancestor) estimates for the four coronaviruses, ranging from 72 (HCoV-229E) to 54 (HCoV-NL63) years ago. The split times of HCoV-229E and HCoV-OC43 from camel alphacoronavirus and bovine coronavirus were dated ~268 and ~99 years ago. The split times of HCoV-HKU1 and HCoV-NL63 could not be calculated, as their zoonoticic sources are unknown. To compare the timing of coronavirus emergence to that of another respiratory virus, we recorded the occurrence of influenza pandemics since 1500. Although there is no clear relationship between pandemic occurrence and human population size, the frequency of influenza pandemics seems to intensify starting around 1700, which corresponds with the initial phase of exponential increase of human population and to the emergence of HCoV-229E. The frequency of flu pandemics in the 19th century also suggests that the concurrence of HCoV-OC43 emergence and the Russian flu pandemic may be due to chance.
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Affiliation(s)
- Diego Forni
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy; (R.C.); (U.P.); (A.M.); (M.S.)
- Correspondence:
| | - Rachele Cagliani
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy; (R.C.); (U.P.); (A.M.); (M.S.)
| | - Uberto Pozzoli
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy; (R.C.); (U.P.); (A.M.); (M.S.)
| | - Alessandra Mozzi
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy; (R.C.); (U.P.); (A.M.); (M.S.)
| | - Federica Arrigoni
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, 20126 Milan, Italy; (F.A.); (L.D.G.)
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, 20126 Milan, Italy; (F.A.); (L.D.G.)
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, 20122 Milan, Italy;
- Don Carlo Gnocchi Foundation ONLUS, IRCCS, 20148 Milan, Italy
| | - Manuela Sironi
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy; (R.C.); (U.P.); (A.M.); (M.S.)
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Thakor JC, Dinesh M, Manikandan R, Bindu S, Sahoo M, Sahoo D, Dhawan M, Pandey MK, Tiwari R, Emran TB, Dhama K, Chaicumpa W. Swine coronaviruses (SCoVs) and their emerging threats to swine population, inter-species transmission, exploring the susceptibility of pigs for SARS-CoV-2 and zoonotic concerns. Vet Q 2022; 42:125-147. [PMID: 35584308 PMCID: PMC9225692 DOI: 10.1080/01652176.2022.2079756] [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: 12/23/2022] Open
Abstract
Swine coronaviruses (SCoVs) are one of the most devastating pathogens affecting the livelihoods of farmers and swine industry across the world. These include transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), porcine respiratory coronavirus (PRCV), porcine hemagglutinating encephalomyelitis virus (PHEV), swine acute diarrhea syndrome coronavirus (SADS-CoV), and porcine delta coronavirus (PDCoV). Coronaviruses infect a wide variety of animal species and humans because these are having single stranded-RNA that accounts for high mutation rates and thus could break the species barrier. The gastrointestinal, cardiovascular, and nervous systems are the primary organ systems affected by SCoVs. Infection is very common in piglets compared to adult swine causing high mortality in the former. Bat is implicated to be the origin of all CoVs affecting animals and humans. Since pig is the only domestic animal in which CoVs cause a wide range of diseases; new coronaviruses with high zoonotic potential could likely emerge in the future as observed in the past. The recently emerged severe acute respiratory syndrome coronavirus virus-2 (SARS-CoV-2), causing COVID-19 pandemic in humans, has been implicated to have animal origin, also reported from few animal species, though its zoonotic concerns are still under investigation. This review discusses SCoVs and their epidemiology, virology, evolution, pathology, wildlife reservoirs, interspecies transmission, spill-over events and highlighting their emerging threats to swine population. The role of pigs amid ongoing SARS-CoV-2 pandemic will also be discussed. A thorough investigation should be conducted to rule out zoonotic potential of SCoVs and to design appropriate strategies for their prevention and control.
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Affiliation(s)
- Jigarji C Thakor
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh-243122, India
| | - Murali Dinesh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh-243122, India
| | - Rajendran Manikandan
- Immunology Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh-243122, India
| | - Suresh Bindu
- Immunology Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh-243122, India
| | - Monalisa Sahoo
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh-243122, India
| | - Diptimayee Sahoo
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh-243122, India
| | - Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana-141004, India.,The Trafford Group of Colleges, Manchester-WA14 5PQ, United Kingdom
| | - Megha Katare Pandey
- Department of Translational Medicine Center, All India Institute of Medical Sciences, Bhopal-462043, Madhya Pradesh, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, Uttar Pradesh Pandit Deen Dayal Upadhyaya Pashu Chikitsa Vigyan Vishwavidyalaya Evam Go Anusandhan Sansthan (DUVASU), Mathura-281001, India
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong-4381, Bangladesh
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh-243122, India
| | - Wanpen Chaicumpa
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok-10700, Thailand
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Known Cellular and Receptor Interactions of Animal and Human Coronaviruses: A Review. Viruses 2022; 14:v14020351. [PMID: 35215937 PMCID: PMC8878323 DOI: 10.3390/v14020351] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/03/2022] [Accepted: 02/05/2022] [Indexed: 12/12/2022] Open
Abstract
This article aims to review all currently known interactions between animal and human coronaviruses and their cellular receptors. Over the past 20 years, three novel coronaviruses have emerged that have caused severe disease in humans, including SARS-CoV-2 (severe acute respiratory syndrome virus 2); therefore, a deeper understanding of coronavirus host-cell interactions is essential. Receptor-binding is the first stage in coronavirus entry prior to replication and can be altered by minor changes within the spike protein-the coronavirus surface glycoprotein responsible for the recognition of cell-surface receptors. The recognition of receptors by coronaviruses is also a major determinant in infection, tropism, and pathogenesis and acts as a key target for host-immune surveillance and other potential intervention strategies. We aim to highlight the need for a continued in-depth understanding of this subject area following on from the SARS-CoV-2 pandemic, with the possibility for more zoonotic transmission events. We also acknowledge the need for more targeted research towards glycan-coronavirus interactions as zoonotic spillover events from animals to humans, following an alteration in glycan-binding capability, have been well-documented for other viruses such as Influenza A.
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Pratelli A, Lucente MS, Cordisco M, Ciccarelli S, Di Fonte R, Sposato A, Mari V, Capozza P, Pellegrini F, Carelli G, Azzariti A, Buonavoglia C. Natural Bovine Coronavirus Infection in a Calf Persistently Infected with Bovine Viral Diarrhea Virus: Viral Shedding, Immunological Features and S Gene Variations. Animals (Basel) 2021; 11:ani11123350. [PMID: 34944126 PMCID: PMC8697958 DOI: 10.3390/ani11123350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 12/01/2022] Open
Abstract
Simple Summary The evolution of a bovine coronavirus (BCoV) natural infection in a calf persistently infected with bovine viral diarrhea virus (BVDV) was described. The infected calf developed intermittent nasal discharge, diarrhea and hyperthermia. The total number of leukocytes/mL and the absolute differential number of neutrophils and lymphocytes resulted within the normal range, but the monocytes increased at T28 (time 28 post-infection) and the CD8+ subpopulation increased at T7 and between T28 and T35. BCoV shedding in nasal discharges and feces was detected up to three weeks post infection (p.i.) and high antibody titers persisted for up to 8 weeks p.i. Virus shedding increased until T14, contrary to what was observed in a previous study where BCoV was detected with a lower load in the co-infected (BCoV/BVDV) calves than in the calves infected with BCoV only. We can suppose that BVDV may have exacerbated the long viral excretion, as well as favoring the onset of mutations in the genome of BCoV. An extensive study was performed to verify if the selective pressure in the S gene could be a natural mode of variation of BCoV. Abstract The evolution of a bovine coronavirus (BCoV) natural infection in a calf persistently infected with bovine viral diarrhea virus (BVDV) was described. The infected calf developed intermittent nasal discharge, diarrhea and hyperthermia. The total number of leukocytes/mL and the absolute differential number of neutrophils and lymphocytes resulted within the normal range, but monocytes increased at T28 (time 28 post-infection). Flow-cytometry analysis evidenced that the CD8+ subpopulation increased at T7 and between T28 and T35. BCoV shedding in nasal discharges and feces was detected up to three weeks post infection and high antibody titers persisted up to T56. The RNA BCoV load increased until T14, contrary to what was observed in a previous study where the fecal excretion of BCoV was significantly lower in the co-infected (BCoV/BVDV) calves than in the calves infected with BCoV only. We can suppose that BVDV may have modulated the BCoV infection exacerbating the long viral excretion, as well as favoring the onset of mutations in the genome of BCoV detected in fecal samples at T21. An extensive study was performed to verify if the selective pressure in the S gene could be a natural mode of variation of BCoV, providing data for the identification of new epidemic strains, genotypes or recombinant betacoronaviruses.
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Affiliation(s)
- Annamaria Pratelli
- Department of Veterinary Medicine, University Aldo Moro of Bari, Strada per Casamassima km 3, 70010 Valenzano (Ba), Italy; (M.S.L.); (M.C.); (S.C.); (A.S.); (V.M.); (P.C.); (F.P.); (G.C.); (C.B.)
- Correspondence: ; Tel.: +39-080-4679835
| | - Maria Stella Lucente
- Department of Veterinary Medicine, University Aldo Moro of Bari, Strada per Casamassima km 3, 70010 Valenzano (Ba), Italy; (M.S.L.); (M.C.); (S.C.); (A.S.); (V.M.); (P.C.); (F.P.); (G.C.); (C.B.)
| | - Marco Cordisco
- Department of Veterinary Medicine, University Aldo Moro of Bari, Strada per Casamassima km 3, 70010 Valenzano (Ba), Italy; (M.S.L.); (M.C.); (S.C.); (A.S.); (V.M.); (P.C.); (F.P.); (G.C.); (C.B.)
| | - Stefano Ciccarelli
- Department of Veterinary Medicine, University Aldo Moro of Bari, Strada per Casamassima km 3, 70010 Valenzano (Ba), Italy; (M.S.L.); (M.C.); (S.C.); (A.S.); (V.M.); (P.C.); (F.P.); (G.C.); (C.B.)
| | - Roberta Di Fonte
- Laboratory of Experimental Pharmacology at IRCCS Istituto Tumori Giovanni Paolo II, Viale Orazio Flacco 65, 70124 Bari, Italy; (R.D.F.); (A.A.)
| | - Alessio Sposato
- Department of Veterinary Medicine, University Aldo Moro of Bari, Strada per Casamassima km 3, 70010 Valenzano (Ba), Italy; (M.S.L.); (M.C.); (S.C.); (A.S.); (V.M.); (P.C.); (F.P.); (G.C.); (C.B.)
| | - Viviana Mari
- Department of Veterinary Medicine, University Aldo Moro of Bari, Strada per Casamassima km 3, 70010 Valenzano (Ba), Italy; (M.S.L.); (M.C.); (S.C.); (A.S.); (V.M.); (P.C.); (F.P.); (G.C.); (C.B.)
| | - Paolo Capozza
- Department of Veterinary Medicine, University Aldo Moro of Bari, Strada per Casamassima km 3, 70010 Valenzano (Ba), Italy; (M.S.L.); (M.C.); (S.C.); (A.S.); (V.M.); (P.C.); (F.P.); (G.C.); (C.B.)
| | - Francesco Pellegrini
- Department of Veterinary Medicine, University Aldo Moro of Bari, Strada per Casamassima km 3, 70010 Valenzano (Ba), Italy; (M.S.L.); (M.C.); (S.C.); (A.S.); (V.M.); (P.C.); (F.P.); (G.C.); (C.B.)
| | - Grazia Carelli
- Department of Veterinary Medicine, University Aldo Moro of Bari, Strada per Casamassima km 3, 70010 Valenzano (Ba), Italy; (M.S.L.); (M.C.); (S.C.); (A.S.); (V.M.); (P.C.); (F.P.); (G.C.); (C.B.)
| | - Amalia Azzariti
- Laboratory of Experimental Pharmacology at IRCCS Istituto Tumori Giovanni Paolo II, Viale Orazio Flacco 65, 70124 Bari, Italy; (R.D.F.); (A.A.)
| | - Canio Buonavoglia
- Department of Veterinary Medicine, University Aldo Moro of Bari, Strada per Casamassima km 3, 70010 Valenzano (Ba), Italy; (M.S.L.); (M.C.); (S.C.); (A.S.); (V.M.); (P.C.); (F.P.); (G.C.); (C.B.)
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Zhu Q, Su M, Li Z, Wang X, Qi S, Zhao F, Li L, Guo D, Feng L, Li B, Sun D. Epidemiological survey and genetic diversity of bovine coronavirus in Northeast China. Virus Res 2021; 308:198632. [PMID: 34793872 DOI: 10.1016/j.virusres.2021.198632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/31/2021] [Accepted: 11/01/2021] [Indexed: 10/19/2022]
Abstract
In 2020, to trace the prevalence and evolution of bovine coronavirus (BCoV) in China, a total of 1383 samples (1016 fecal samples and 367 nasal swab samples) were collected from 1016 cattle exhibiting diarrhea symptoms on dairy farms and beef cattle farms in Heilongjiang Province, Northeast China. All samples were subjected to reverse transcription-polymerase chain reaction (RT-PCR) detection of the BCoV N gene, followed by an analysis of its epidemiology and genetic evolution. The results indicated that of the 1016 diarrhea-affected cattle, 15.45% (157/1016) were positive for BCoV, in which positive rates of the fecal and nasal swab samples were 12.20% (124/1016) and 21.53% (79/367), respectively. Of the 367 cattle whose nasal swab samples were collected, the BCoV positive rate of the corresponding fecal samples was 15.26% (56/367). BCoV infection was significantly associated with age, farming pattern, cattle type, farm latitude, sample type, and clinical symptom (p < 0.05). Of the 203 BCoV-positive samples, 20 spike (S) genes were successfully sequenced. The 20 identified BCoV strains shared nucleotide homologies of 97.7-100.0%, and their N-terminal domain of S1 subunit (S1-NTD: residues 15-298) differed genetically from the reference strains of South Korea and Europe. The 20 identified BCoV strains were clustered in the Asia-North America group (GII group) in the global strain-based phylogenetic tree and formed three clades in the Chinese strain-based phylogenetic tree. The HLJ/HH-10/2020 strain was clustered into the Europe group (GI group) in the S1-NTD-based phylogenetic tree, exhibiting N146/I, D148/G, and L154/F mutations that affect the S protein structure. Of the identified BCoV strains, one potential recombination event occurred between the HLJ/HH-20/2020 and HLJ/HH-10/2020 strains, which led to the generation of the recombinant BCV-AKS-01 strain. A selective pressure analysis on the S protein revealed one positively selected site (Asn509) among the 20 identified BCoV strains located inside the putative receptor binding domain (residues 326-540). These data provide a greater understanding of the epidemiology and evolution of BCoV in China.
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Affiliation(s)
- Qinghe Zhu
- Laboratory for the Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China; Branch of Animal Husbandry and Veterinary of Heilongjiang Academy of Agricultural Sciences, Qiqihar 161000, China
| | - Mingjun Su
- Laboratory for the Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China
| | - Zijian Li
- Laboratory for the Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China
| | - Xiaoran Wang
- Laboratory for the Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China
| | - Shanshan Qi
- Laboratory for the Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China
| | - Feiyu Zhao
- Laboratory for the Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China
| | - Lu Li
- Laboratory for the Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China
| | - Donghua Guo
- Laboratory for the Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China
| | - Li Feng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Bin Li
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Dongbo Sun
- Laboratory for the Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China.
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Forni D, Cagliani R, Arrigoni F, Benvenuti M, Mozzi A, Pozzoli U, Clerici M, De Gioia L, Sironi M. Adaptation of the endemic coronaviruses HCoV-OC43 and HCoV-229E to the human host. Virus Evol 2021; 7:veab061. [PMID: 34527284 PMCID: PMC8344746 DOI: 10.1093/ve/veab061] [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: 04/08/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 12/29/2022] Open
Abstract
Four coronaviruses (HCoV-OC43, HCoV-HKU1, HCoV-NL63, and HCoV-229E) are endemic in human populations. All these viruses are seasonal and generate short-term immunity. Like the highly pathogenic coronaviruses, the endemic coronaviruses have zoonotic origins. Thus, understanding the evolutionary dynamics of these human viruses might provide insight into the future trajectories of SARS-CoV-2 evolution. Because the zoonotic sources of HCoV-OC43 and HCoV-229E are known, we applied a population genetics-phylogenetic approach to investigate which selective events accompanied the divergence of these viruses from the animal ones. Results indicated that positive selection drove the evolution of some accessory proteins, as well as of the membrane proteins. However, the spike proteins of both viruses and the hemagglutinin-esterase (HE) of HCoV-OC43 represented the major selection targets. Specifically, for both viruses, most positively selected sites map to the receptor-binding domains (RBDs) and are polymorphic. Molecular dating for the HCoV-229E spike protein indicated that RBD Classes I, II, III, and IV emerged 3-9 years apart. However, since the appearance of Class V (with much higher binding affinity), around 25 years ago, limited genetic diversity accumulated in the RBD. These different time intervals are not fully consistent with the hypothesis that HCoV-229E spike evolution was driven by antigenic drift. An alternative, not mutually exclusive possibility is that strains with higher affinity for the cellular receptor have out-competed strains with lower affinity. The evolution of the HCoV-OC43 spike protein was also suggested to undergo antigenic drift. However, we also found abundant signals of positive selection in HE. Whereas such signals might result from antigenic drift, as well, previous data showing co-evolution of the spike protein with HE suggest that optimization for human cell infection also drove the evolution of this virus. These data provide insight into the possible trajectories of SARS-CoV-2 evolution, especially in case the virus should become endemic.
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Affiliation(s)
- Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, via don Luigi Monza, 23843 Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, via don Luigi Monza, 23843 Bosisio Parini, Italy
| | - Federica Arrigoni
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza, Milan 20126, Italy
| | - Martino Benvenuti
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza, Milan 20126, Italy
| | - Alessandra Mozzi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, via don Luigi Monza, 23843 Bosisio Parini, Italy
| | - Uberto Pozzoli
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, via don Luigi Monza, 23843 Bosisio Parini, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, via Francesco Sforza, Milan 20122, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza, Milan 20126, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, via don Luigi Monza, 23843 Bosisio Parini, Italy
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Kiser JN, Neibergs HL. Identifying Loci Associated With Bovine Corona Virus Infection and Bovine Respiratory Disease in Dairy and Feedlot Cattle. Front Vet Sci 2021; 8:679074. [PMID: 34409086 PMCID: PMC8364960 DOI: 10.3389/fvets.2021.679074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 07/01/2021] [Indexed: 01/04/2023] Open
Abstract
Bovine coronavirus (BCoV) is associated with respiratory and enteric infections in both dairy and beef cattle worldwide. It is also one of a complex of pathogens associated with bovine respiratory disease (BRD), which affects millions of cattle annually. The objectives of this study were to identify loci and heritability estimates associated with BCoV infection and BRD in dairy calves and feedlot cattle. Dairy calves from California (n = 1,938) and New Mexico (n = 647) and feedlot cattle from Colorado (n = 915) and Washington (n = 934) were tested for the presence of BCoV when classified as BRD cases or controls following the McGuirk scoring system. Two comparisons associated with BCoV were investigated: (1) cattle positive for BCoV (BCoV+) were compared to cattle negative for BCoV (BCoV-) and (2) cattle positive for BCoV and affected with BRD (BCoV+BRD+) were compared to cattle negative for BCoV and BRD (BCoV-BRD-). The Illumina BovineHD BeadChip was used for genotyping, and genome-wide association analyses (GWAA) were performed using EMMAX (efficient mixed-model association eXpedited). The GWAA for BCoV+ identified 51 loci (p < 1 × 10-5; 24 feedlot, 16 dairy, 11 combined) associated with infection with BCoV. Three loci were associated with BCoV+ across populations. Heritability estimates for BCoV+ were 0.01 for dairy, 0.11 for feedlot cattle, and 0.03 for the combined population. For BCoV+BRD+, 80 loci (p < 1 × 10-5; 26 feedlot, 25 dairy, 29 combined) were associated including 14 loci across populations. Heritability estimates for BCoV+BRD+ were 0.003 for dairy, 0.44 for feedlot cattle, and 0.07 for the combined population. Several positional candidate genes associated with BCoV and BRD in this study have been associated with other coronaviruses and respiratory infections in humans and mice. These results suggest that selection may reduce susceptibility to BCoV infection and BRD in cattle.
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Affiliation(s)
- Jennifer N Kiser
- Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | - Holly L Neibergs
- Department of Animal Sciences, Washington State University, Pullman, WA, United States
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Antigenic sites in SARS-CoV-2 spike RBD show molecular similarity with pathogenic antigenic determinants and harbors peptides for vaccine development. Immunobiology 2021; 226:152091. [PMID: 34303920 PMCID: PMC8297981 DOI: 10.1016/j.imbio.2021.152091] [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: 06/13/2020] [Revised: 03/13/2021] [Accepted: 03/30/2021] [Indexed: 01/22/2023]
Abstract
The spike protein of coronavirus is key target for drug development and other pharmacological interventions. In current study, we performed an integrative approach to predict antigenic sites in SARS-CoV-2 spike receptor binding domain and found nine potential antigenic sites. The predicted antigenic sites were then assessed for possible molecular similarity with other known antigens in different organisms. Out of nine sites, seven sites showed molecular similarity with 54 antigenic determinants found in twelve pathogenic bacterial species (Mycobacterium tuberculosis, Mycobacterium leprae, Bacillus anthracis, Borrelia burgdorferi, Clostridium perfringens, Clostridium tetani, Helicobacter Pylori, Listeria monocytogenes, Staphylococcus aureus, Streptococcus pyogenes, Vibrio cholera and Yersinia pestis), two malarial parasites (Plasmodium falciparum and Plasmodium knowlesi) and influenza virus A. Most of the bacterial antigens that displayed molecular similarity with antigenic sites in SARS-CoV-2 RBD (receptor binding domain) were toxins and virulent factors. Antigens from Mycobacterium that showed similarity were mainly involved in modulating host cell immune response and ensuring persistence and survival of pathogen in host cells. Presence of a large number of antigenic determinants, similar to those in highly pathogenic microorganisms, not merely accounts for complex etiology of the disease but also provides an explanation for observed pathophysiological complications, such as deregulated immune response, unleashed or dysregulated cytokine secretion (cytokine storm), multiple organ failure etc., that are more evident in aged and immune-compromised patients. Over-representation of antigenic determinants from Plasmodium and Mycobacterium in all antigenic sites suggests that anti-malarial and anti-TB drugs can prove to be clinical beneficial for COVID-19 treatment. Besides this, anti-leprosy, anti-lyme, anti-plague, anti-anthrax drugs/vaccine etc. are also expected to be beneficial in COVID-19 treatment. Moreover, individuals previously immunized/vaccinated or had previous history of malaria, tuberculosis or other disease caused by fifteen microorganisms are expected to display a considerable degree of resistance against SARS-CoV-2 infection. Out of the seven antigenic sites predicted in SARS-CoV-2, a part of two antigenic sites were also predicted as potent T-cell epitopes (KVGGNYNYL444-452 and SVLYNSASF366-374) against MHC class I and three (KRISNCVADYSVLYN356-370, DLCFTNVYADSFVI389-402, and YRVVVLSFELLHA508-520) against MHC class II. All epitopes possessed significantly lower predicted IC50 value which is a prerequisite for a preferred vaccine candidate for COVID-19.
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Bovine coronavirus infections in Turkey: molecular analysis of the full-length spike gene sequences of viruses from digestive and respiratory infections. Arch Virol 2021; 166:2461-2468. [PMID: 34212242 PMCID: PMC8247624 DOI: 10.1007/s00705-021-05147-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 05/03/2021] [Indexed: 11/25/2022]
Abstract
Bovine coronavirus (BCoV) can be spread by animal activity. Although cattle farming is widespread in Turkey, there are few studies of BCoV. The aim of this study was to evaluate the current situation regarding BCoV in Turkey. This is the first study reporting the full-length nucleotide sequences of BCoV spike (S) genes in Turkey. Samples were collected from 119 cattle with clinical signs of respiratory (n = 78) or digestive tract (n = 41) infection on different farms located across widely separated provinces in Turkey. The samples were screened for BCoV using RT-nested PCR targeting the N gene, which identified BCoV in 35 samples (9 faeces and 26 nasal discharge). RT-PCR analysis of the S gene produced partial/full-length S gene sequences from 11 samples (8 faeces and 3 nasal discharge samples). A phylogenetic tree of the S gene sequences was made to analyze the genetic relationships among BCoVs from Turkey and other countries. The results showed that the local strains present in faeces and nasal discharge samples had many different amino acid changes. Some of these changes were shown in previous studies to be critical for tropism. This study provides new data on BCoV in Turkey that will be valuable in designing effective vaccine approaches and control strategies.
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Jelinek HF, Mousa M, Alefishat E, Osman W, Spence I, Bu D, Feng SF, Byrd J, Magni PA, Sahibzada S, Tay GK, Alsafar HS. Evolution, Ecology, and Zoonotic Transmission of Betacoronaviruses: A Review. Front Vet Sci 2021; 8:644414. [PMID: 34095271 PMCID: PMC8173069 DOI: 10.3389/fvets.2021.644414] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/25/2021] [Indexed: 12/18/2022] Open
Abstract
Coronavirus infections have been a part of the animal kingdom for millennia. The difference emerging in the twenty-first century is that a greater number of novel coronaviruses are being discovered primarily due to more advanced technology and that a greater number can be transmitted to humans, either directly or via an intermediate host. This has a range of effects from annual infections that are mild to full-blown pandemics. This review compares the zoonotic potential and relationship between MERS, SARS-CoV, and SARS-CoV-2. The role of bats as possible host species and possible intermediate hosts including pangolins, civets, mink, birds, and other mammals are discussed with reference to mutations of the viral genome affecting zoonosis. Ecological, social, cultural, and environmental factors that may play a role in zoonotic transmission are considered with reference to SARS-CoV, MERS, and SARS-CoV-2 and possible future zoonotic events.
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Affiliation(s)
- Herbert F. Jelinek
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Center of Heath Engineering Innovation, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Mira Mousa
- Nuffield Department of Women's and Reproduction Health, Oxford University, Oxford, United Kingdom
| | - Eman Alefishat
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Pharmacology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biopharmaceutics and Clinical Pharmacy, School of Pharmacy, The University of Jordan, Amman, Jordan
| | - Wael Osman
- Department of Chemistry, College of Arts and Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Ian Spence
- Discipline of Pharmacology, University of Sydney, Sydney, NSW, Australia
| | - Dengpan Bu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Samuel F. Feng
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Mathematics, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Jason Byrd
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, United States
| | - Paola A. Magni
- Discipline of Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, WA, Australia
- Murdoch University Singapore, King's Centre, Singapore, Singapore
| | - Shafi Sahibzada
- Antimicrobial Resistance and Infectious Diseases Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Guan K. Tay
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Division of Psychiatry, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, WA, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Habiba S. Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Genetics and Molecular Biology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
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Abstract
Within only one year after the first detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), nearly 100 million infections were reported in the human population globally, with more than two million fatal cases. While SARS-CoV-2 most likely originated from a natural wildlife reservoir, neither the immediate viral precursor nor the reservoir or intermediate hosts have been identified conclusively. Due to its zoonotic origin, SARS-CoV-2 may also be relevant to animals. Thus, to evaluate the host range of the virus and to assess the risk to act as potential animal reservoir, a large number of different animal species were experimentally infected with SARS-CoV-2 or monitored in the field in the last months. In this review, we provide an update on studies describing permissive and resistant animal species. Using a scoring system based on viral genome detection subsequent to SARS-CoV-2 inoculation, seroconversion, the development of clinical signs and transmission to conspecifics or humans, the susceptibility of diverse animal species was classified on a semi-quantitative scale. While major livestock species such as pigs, cattle and poultry are mostly resistant, companion animals appear moderately susceptible, while several model animal species used in research, including several Cricetidae species and non-human primates, are highly susceptible to SARS-CoV-2 infection. By natural infections, it became obvious that American minks (Neovison vison) in fur farms, e.g., in the Netherlands and Denmark are highly susceptible resulting in local epidemics in these animals.
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Rao V, Kannan S, Arakeri G, Subhash A, Batra HV, Kumar J, Gulia A. Interspecies transmission of coronaviruses and immunization: An Indian perspective. INDIAN JOURNAL OF MEDICAL SCIENCES 2020. [PMCID: PMC8219005 DOI: 10.25259/ijms_191_2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The milder form of infection and higher rates of recovery witnessed among COVID-19 patients in India is indicative of the potential intervention of other “unconventional” biological mechanisms. The recently established similarity between beta-coronavirus strains in animals and humans led us to hypothesize that previous contact with infected dogs or cattle could shield humans from the circulating SARS-CoV-2 virus. We further believe that our hypothesis, if confirmed by further studies, could be used as a potential vaccine strategy.
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Affiliation(s)
- Vishal Rao
- Department of Head and Neck Surgical Oncology, HCG Cancer Hospital, Bengaluru, Karnataka, India,
| | - Swetha Kannan
- Department of Immunology, School of Biological Sciences, University of Edinburgh, Scotland, United Kingdom,
| | - Gururaj Arakeri
- Department of Oral and Maxillofacial Surgery, Navodaya Dental College, Raichur, Karnataka, India,
| | - Anand Subhash
- Department of Head and Neck Surgical Oncology, HCG Cancer Hospital, Bengaluru, Karnataka, India,
| | - H. V. Batra
- Shankarnaraya Lifesciences, Bengaluru, Karnataka, India,
| | - Jitendra Kumar
- Bangalore Bio-Innovation Center, Bengaluru, Karnataka, India,
| | - Ashish Gulia
- Bone and Soft Tissue, Tata Memorial Hospital, Mumbai, Maharashtra, India,
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19
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Yuan Y, He J, Gong L, Li W, Jiang L, Liu J, Chen Q, Yu J, Hou S, Shi Y, Lu S, Zhang Z, Ge Y, Sa N, He L, Wu J, Sun Y, Liu Z. Molecular epidemiology of SARS-CoV-2 clusters caused by asymptomatic cases in Anhui Province, China. BMC Infect Dis 2020; 20:930. [PMID: 33287717 PMCID: PMC7719853 DOI: 10.1186/s12879-020-05612-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/11/2020] [Indexed: 01/25/2023] Open
Abstract
Background COVID-19 is a newly emerging disease caused by a novel coronavirus (SARS-CoV-2), which spread globally in early 2020. Asymptomatic carriers of the virus contribute to the propagation of this disease, and the existence of asymptomatic infection has caused widespread fear and concern in the control of this pandemic. Methods In this study, we investigated the origin and transmission route of SARS-CoV-2 in Anhui’s two clusters, analyzed the role and infectiousness of asymptomatic patients in disease transmission, and characterized the complete spike gene sequences in the Anhui strains. Results We conducted an epidemiological investigation of two clusters caused by asymptomatic infections sequenced the spike gene of viruses isolated from 12 patients. All cases of the two clusters we investigated had clear contact histories, both from Wuhan, Hubei province. The viruses isolated from two outbreaks in Anhui were found to show a genetically close link to the virus from Wuhan. In addition, new single nucleotide variations were discovered in the spike gene. Conclusions Both clusters may have resulted from close contact and droplet-spreading and asymptomatic infections were identified as the initial cause. We also analyzed the infectiousness of asymptomatic cases and the challenges to the current epidemic to provided information for the development of control strategies.
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Affiliation(s)
- Yuan Yuan
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China.,Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China
| | - Jun He
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China.,Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China
| | - Lei Gong
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China
| | - Weiwei Li
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China.,Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China
| | - Liangliang Jiang
- Maanshan Center for Disease Control and Prevention, 849, Jiangdong Avenue, Maanshan, China
| | - Jiang Liu
- Huainan Center for Disease Control and Prevention, Linchang Avenue, Huainan, China
| | - Qingqing Chen
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China.,Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China
| | - Junling Yu
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China.,Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China
| | - Sai Hou
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China
| | - Yonglin Shi
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China.,Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China
| | - Siqi Lu
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China
| | - Zhuhui Zhang
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China.,Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China
| | - Yinglu Ge
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China.,Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China
| | - Nan Sa
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China.,Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China
| | - Lan He
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China
| | - Jiabing Wu
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China
| | - Yong Sun
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China. .,Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China.
| | - Zhirong Liu
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China.
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20
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Bovine Coronavirus: Variability, Evolution, and Dispersal Patterns of a No Longer Neglected Betacoronavirus. Viruses 2020; 12:v12111285. [PMID: 33182765 PMCID: PMC7697035 DOI: 10.3390/v12111285] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 12/13/2022] Open
Abstract
Bovine coronavirus (BoCV) is an important pathogen of cattle, causing severe enteric disease and playing a role in the bovine respiratory disease complex. Similar to other coronaviruses, a remarkable variability characterizes both its genome and biology. Despite their potential relevance, different aspects of the evolution of BoCV remain elusive. The present study reconstructs the history and evolution of BoCV using a phylodynamic approach based on complete genome and spike protein sequences. The results demonstrate high mutation and recombination rates affecting different parts of the viral genome. In the spike gene, this variability undergoes significant selective pressures—particularly episodic pressure—located mainly on the protein surface, suggesting an immune-induced selective pressure. The occurrence of compensatory mutations was also identified. On the contrary, no strong evidence in favor of host and/or tissue tropism affecting viral evolution has been proven. The well-known plasticity is thus ascribable to the innate broad viral tropism rather than mid- or long-term adaptation. The evaluation of the geographic spreading pattern clearly evidenced two clusters: a European cluster and an American–Asian cluster. While a relatively dense and quick migration network was identified in the former, the latter was dominated by the primary role of the United States (US) as a viral exportation source. Since the viral spreading pattern strongly mirrored the cattle trade, the need for more intense monitoring and preventive measures cannot be underestimated as well as the need to enforce the vaccination of young animals before international trade, to reduce not only the clinical impact but also the transferal and mixing of BoCV strains.
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21
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Tizaoui K, Zidi I, Lee KH, Ghayda RA, Hong SH, Li H, Smith L, Koyanagi A, Jacob L, Kronbichler A, Shin JI. Update of the current knowledge on genetics, evolution, immunopathogenesis, and transmission for coronavirus disease 19 (COVID-19). Int J Biol Sci 2020; 16:2906-2923. [PMID: 33061805 PMCID: PMC7545713 DOI: 10.7150/ijbs.48812] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/23/2020] [Indexed: 01/08/2023] Open
Abstract
In December 2019, an acute respiratory disease caused by novel species of coronavirus (SARS-CoV-2), emerged in China and has spread throughout the world. On 11th March 2020, the World Health Organization (WHO) officially declared coronavirus disease 19 (COVID-19) a pandemic, severe coronavirus-mediated human disease. Based on genomic and phylogenetic studies, SARS-CoV-2 might originate from bat coronaviruses and infects humans directly or through intermediate zoonotic hosts. However, the exact origin or the host intermediate remains unknown. Genetically, SARS-CoV-2 is similar to several existing coronaviruses, particularly SARS-CoV, but differs by silent and non-silent mutations. The virus uses different transmission routes and targets cells and tissues with angiotensin-converting enzyme 2 (ACE2) protein, which makes it contagious. COVID-19 shares both the main clinical features and excessive/dysregulated cell responses with the two previous Middle East respiratory syndrome coronavirus (MERS) and severe acute respiratory syndrome coronavirus (SARS) epidemics. In this review, we provide an update of the current knowledge on the COVID-19 pandemic. Gaining a deeper understanding of SARS-CoV-2 structure, transmission routes, and molecular responses, will assist in the prevention and control of COVID-19 outbreaks in the future.
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Affiliation(s)
- Kalthoum Tizaoui
- Laboratory Microorganismes and Active Biomolecules, Sciences Faculty of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Ines Zidi
- Laboratory Microorganismes and Active Biomolecules, Sciences Faculty of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Keum Hwa Lee
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ramy Abou Ghayda
- Division of Urology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston MA, USA
| | - Sung Hwi Hong
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston MA, USA
- Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Han Li
- University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Lee Smith
- The Cambridge Centre for Sport and Exercise Science, Anglia Ruskin University, Cambridge, CB1 1PT, UK
| | - Ai Koyanagi
- Research and Development Unit, Parc Sanitari Sant Joan de Déu, CIBERSAM, 08830 Barcelona, Spain
- ICREA, Pg. Lluis Companys 23, 08010 Barcelona, Spain
| | - Louis Jacob
- Research and Development Unit, Parc Sanitari Sant Joan de Déu, CIBERSAM, 08830 Barcelona, Spain
- Faculty of Medicine, University of Versailles Saint-Quentin-en-Yvelines, 78000 Versailles, France
| | - Andreas Kronbichler
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck 6020, Austria
| | - Jae Il Shin
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea
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22
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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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23
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Morenikeji OB, Strutton E, Wallace M, Bernard K, Yip E, Thomas BN. Dissecting Transcription Factor-Target Interaction in Bovine Coronavirus Infection. Microorganisms 2020; 8:E1323. [PMID: 32872640 PMCID: PMC7564962 DOI: 10.3390/microorganisms8091323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/27/2020] [Accepted: 08/27/2020] [Indexed: 02/06/2023] Open
Abstract
Coronaviruses are RNA viruses that cause significant disease within many species, including cattle. Bovine coronavirus (BCoV) infects cattle and wild ruminants, both as a respiratory and enteric pathogen, and possesses a significant economic threat to the cattle industry. Transcription factors are proteins that activate or inhibit transcription through DNA binding and have become new targets for disease therapies. This study utilized in silico tools to identify potential transcription factors that can serve as biomarkers for regulation of BCoV pathogenesis in cattle, both for testing and treatment. A total of 11 genes were identified as significantly expressed during BCoV infection through literature searches and functional analyses. Eleven transcription factors were predicted to target those genes (AREB6, YY1, LMO2, C-Rel, NKX2-5, E47, RORAlpha1, HLF, E4BP4, ARNT, CREB). Function, network, and phylogenetic analyses established the significance of many transcription factors within the immune response. This study establishes new information on the transcription factors and genes related to host-pathogen interactome in BCoV infection, particularly transcription factors YY1, AREB6, LMO2, and NKX2, which appear to have strong potential as diagnostic markers, and YY1 as a potential target for drug therapies.
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Affiliation(s)
- Olanrewaju B. Morenikeji
- Department of Biology, Hamilton College, Clinton, NY 13323, USA; (O.B.M.); (E.S.); (M.W.); (K.B.); (E.Y.)
| | - Ellis Strutton
- Department of Biology, Hamilton College, Clinton, NY 13323, USA; (O.B.M.); (E.S.); (M.W.); (K.B.); (E.Y.)
| | - Madeleine Wallace
- Department of Biology, Hamilton College, Clinton, NY 13323, USA; (O.B.M.); (E.S.); (M.W.); (K.B.); (E.Y.)
| | - Kahleel Bernard
- Department of Biology, Hamilton College, Clinton, NY 13323, USA; (O.B.M.); (E.S.); (M.W.); (K.B.); (E.Y.)
| | - Elaine Yip
- Department of Biology, Hamilton College, Clinton, NY 13323, USA; (O.B.M.); (E.S.); (M.W.); (K.B.); (E.Y.)
| | - Bolaji N. Thomas
- Department of Biomedical Sciences, College of Health Sciences and Technology, Rochester Institute of Technology, Rochester, NY 14623, USA
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24
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Global Transmission, Spatial Segregation, and Recombination Determine the Long-Term Evolution and Epidemiology of Bovine Coronaviruses. Viruses 2020; 12:v12050534. [PMID: 32414076 PMCID: PMC7290379 DOI: 10.3390/v12050534] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 01/15/2023] Open
Abstract
Bovine coronavirus (BCoV) is widespread in cattle and wild ruminant populations throughout the world. The virus causes neonatal calf diarrhea and winter dysentery in adult cattle, as well as upper and lower respiratory tract infection in young cattle. We isolated and deep sequenced whole genomes of BCoV from calves with respiratory distress in the south–west of France and conducted a comparative genome analysis using globally collected BCoV sequences to provide insights into the genomic characteristics, evolutionary origins, and global diversity of BCoV. Molecular clock analyses allowed us to estimate that the BCoV ancestor emerged in the 1940s, and that two geographically distinct lineages diverged from the 1960s–1970s. A recombination event in the spike gene (breakpoint at nt 1100) may be at the origin of the genetic divergence sixty years ago. Little evidence of genetic mixing between the spatially segregated lineages was found, suggesting that BCoV genetic diversity is a result of a global transmission pathway that occurred during the last century. However, we found variation in evolution rates between the European and non-European lineages indicating differences in virus ecology.
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25
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Anand K, Karade S, Sen S, Gupta R. SARS-CoV-2: Camazotz's Curse. Med J Armed Forces India 2020; 76:136-141. [PMID: 32341622 PMCID: PMC7183968 DOI: 10.1016/j.mjafi.2020.04.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 04/22/2020] [Indexed: 02/08/2023] Open
Abstract
The world is currently face to face with a pandemic which is spreading rapidly across the globe caused by SARS-CoV-2, a strain of Coronaviruses (CoVs) belonging to subgenus Sarbecovirus of genus Betacoronavirus. World Health Organisation (WHO) on 11 Feb 20 named this disease caused by SARS-CoV-2 as Covid-19. This pandemic is spreading rapidly and more than 20,00,000 cases have occurred globally. The human Coronaviruses discovered in 1960s were considered potentially harmless endemic viruses with seasonal distribution before late 2002. The CoVs are found in a large number of domestic and wild animals and birds. The first pandemic caused by Coronavirus caused by SARS-CoV was recognized in the late 2002 in Guangdong Province and resulted in widespread morbidity and mortality. This was followed by MERS-CoV which began in 2012 in the Arabian peninsula with multiple outbreaks related to it in various parts of the globe. Various studies have suggested how these viruses made their entry from their natural reservoir bats via intermediate host like civets and camels in case of SARS-CoV and MERS-CoV respectively. The intermediate host of the SARS-CoV-2 still needs to be established. The SARS-CoV-2 has 96.2% similarity to the bat Severe Acute Respiratory Syndrome related-Coronavirus (SARSr-CoV RaTG13). SARS-CoV-2 has been found to be more distant in relation to SARS-CoV (79%) and MERS-CoV (50%). At the whole genome sequence level pangolin CoV and SARSr-CoV RaTG13 show 91.02% and 96.2% similarity with SARS-CoV-2 but the S1 subunit of spike protein of pangolin CoV is more closely related to SARS-CoV-2 than SARSr-CoV RaTG13. The genetic analysis of the currently circulating strains of the pandemic have shown 99.98-100% similarity in their genomes implying a recent shift to humans. The animal source of SARS-CoV-2 needs to be identified to implement control measures in the present pandemic. Also, how the virus moves interspecies will help predict and prevent future pandemics.
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Affiliation(s)
- K.B. Anand
- Associate Professor, Department of Microbiology, Armed Forces Medical College, Pune 411040, India
| | - S. Karade
- Assistant Professor, Department of Microbiology, Armed Forces Medical College, Pune 411040, India
| | - S. Sen
- Professor & Head, Department of Microbiology, Armed Forces Medical College, Pune 411040, India
| | - R.M. Gupta
- Professor (Microbiology) & Dean and Deputy Commandant, Armed Forces Medical College, Pune 411040, India
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26
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Suzuki T, Otake Y, Uchimoto S, Hasebe A, Goto Y. Genomic Characterization and Phylogenetic Classification of Bovine Coronaviruses Through Whole Genome Sequence Analysis. Viruses 2020; 12:v12020183. [PMID: 32041103 PMCID: PMC7077292 DOI: 10.3390/v12020183] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 01/31/2020] [Accepted: 02/04/2020] [Indexed: 01/18/2023] Open
Abstract
Bovine coronavirus (BCoV) is zoonotically transmissible among species, since BCoV-like viruses have been detected in wild ruminants and humans. BCoV causing enteric and respiratory disease is widespread in cattle farms worldwide; however, limited information is available regarding the molecular characterization of BCoV because of its large genome size, despite its significant economic impact. This study aimed to better understand the genomic characterization and evolutionary dynamics of BCoV via comparative sequence and phylogenetic analyses through whole genome sequence analysis using 67 BCoV isolates collected throughout Japan from 2006 to 2017. On comparing the genomic sequences of the 67 BCoVs, genetic variations were detected in 5 of 10 open reading frames (ORFs) in the BCoV genome. Phylogenetic analysis using whole genomes from the 67 Japanese BCoV isolates in addition to those from 16 reference BCoV strains, revealed the existence of two major genotypes (classical and US wild ruminant genotypes). All Japanese BCoV isolates originated from the US wild ruminant genotype, and they tended to form the same clusters based on the year and farm of collection, not the disease type. Phylogenetic trees on hemagglutinin-esterase protein (HE), spike glycoprotein (S), nucleocapsid protein (N) genes and ORF1 revealed clusters similar to that on whole genome, suggesting that the evolution of BCoVs may be closely associated with variations in these genes. Furthermore, phylogenetic analysis of BCoV S genes including those of European and Asian BCoVs and human enteric coronavirus along with the Japanese BCoVs revealed that BCoVs differentiated into two major types (European and American types). Moreover, the European and American types were divided into eleven and three genotypes, respectively. Our analysis also demonstrated that BCoVs with different genotypes periodically emerged and predominantly circulated within the country. These findings provide useful information to elucidate the detailed molecular characterization of BCoVs, which have spread worldwide. Further genomic analyses of BCoV are essential to deepen the understanding of the evolution of this virus.
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Affiliation(s)
- Tohru Suzuki
- Division of Viral Disease and Epidemiology, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 3050856, Japan
- Correspondence: ; Tel.: +81-29-838-7914
| | - Yoshihiro Otake
- Central Tochigi Prefectural Livestock Health and Hygiene Center, Utsunomiya, Tochigi 3210905, Japan;
| | - Satoko Uchimoto
- Shiga Prefectural Livestock Health and Hygiene Center, Omihachiman, Shiga 5230813, Japan;
| | - Ayako Hasebe
- Central Gifu Prefectural Livestock Health and Hygiene Center, Gifu 5011112, Japan;
| | - Yusuke Goto
- Central Iwate Prefectural Livestock Health and Hygiene Center, Takizawa, Iwate 0200605, Japan;
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27
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Castells M, Giannitti F, Caffarena RD, Casaux ML, Schild C, Castells D, Riet-Correa F, Victoria M, Parreño V, Colina R. Bovine coronavirus in Uruguay: genetic diversity, risk factors and transboundary introductions from neighboring countries. Arch Virol 2019; 164:2715-2724. [PMID: 31456086 PMCID: PMC7087214 DOI: 10.1007/s00705-019-04384-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 07/30/2019] [Indexed: 11/15/2022]
Abstract
Bovine coronavirus (BCoV) is a recognized cause of severe neonatal calf diarrhea, with a negative impact on animal welfare, leading to economic losses to the livestock industry. Cattle production is one of the most important economic sectors in Uruguay. The aim of this study was to determine the frequency of BCoV infections and their genetic diversity in Uruguayan calves and to describe the evolutionary history of the virus in South America. The overall detection rate of BCoV in Uruguay was 7.8% (64/824): 7.7% (60/782) in dairy cattle and 9.5% (4/42) in beef cattle. The detection rate of BCoV in samples from deceased and live calves was 10.0% (6/60) and 7.6% (58/763), respectively. Interestingly, there was a lower frequency of BCoV detection in calves born to vaccinated dams (3.3%, 8/240) than in calves born to unvaccinated dams (12.2%, 32/263) (OR: 4.02, 95%CI: 1.81–8.90; p = 0.00026). The frequency of BCoV detection was higher in colder months (11.8%, 44/373) than in warmer months (1.5%, 3/206) (OR: 9.05, 95%CI: 2.77–29.53, p = 0.000013). Uruguayan strains grouped together in two different lineages: one with Argentinean strains and the other with Brazilian strains. Both BCoV lineages were estimated to have entered Uruguay in 2013: one of them from Brazil (95%HPD interval: 2011–2014) and the other from Argentina (95%HPD interval: 2010–2014). The lineages differed by four amino acid changes, and both were divergent from the Mebus reference strain. Surveillance should be maintained to detect possible emerging strains that can clearly diverge at the antigenic level from vaccine strains.
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Affiliation(s)
- Matías Castells
- Laboratorio de Virología Molecular, CENUR Litoral Norte, Centro Universitario de Salto, Universidad de la República, Rivera 1350, 50000, Salto, Uruguay.,Instituto Nacional de Investigación Agropecuaria (INIA), Plataforma de Investigación en Salud Animal, Ruta 50 km 11, La Estanzuela, 70000, Colonia, Uruguay
| | - Federico Giannitti
- Instituto Nacional de Investigación Agropecuaria (INIA), Plataforma de Investigación en Salud Animal, Ruta 50 km 11, La Estanzuela, 70000, Colonia, Uruguay
| | - Rubén Darío Caffarena
- Instituto Nacional de Investigación Agropecuaria (INIA), Plataforma de Investigación en Salud Animal, Ruta 50 km 11, La Estanzuela, 70000, Colonia, Uruguay.,Facultad de Veterinaria, Universidad de la República, Alberto Lasplaces 1620, Montevideo, Uruguay
| | - María Laura Casaux
- Instituto Nacional de Investigación Agropecuaria (INIA), Plataforma de Investigación en Salud Animal, Ruta 50 km 11, La Estanzuela, 70000, Colonia, Uruguay
| | - Carlos Schild
- Instituto Nacional de Investigación Agropecuaria (INIA), Plataforma de Investigación en Salud Animal, Ruta 50 km 11, La Estanzuela, 70000, Colonia, Uruguay
| | - Daniel Castells
- Centro de Investigación y Experimentación Dr. Alejandro Gallinal, Secretariado Uruguayo de la Lana, Ruta 7 km 140, Cerro Colorado, Florida, Uruguay
| | - Franklin Riet-Correa
- Instituto Nacional de Investigación Agropecuaria (INIA), Plataforma de Investigación en Salud Animal, Ruta 50 km 11, La Estanzuela, 70000, Colonia, Uruguay
| | - Matías Victoria
- Laboratorio de Virología Molecular, CENUR Litoral Norte, Centro Universitario de Salto, Universidad de la República, Rivera 1350, 50000, Salto, Uruguay
| | - Viviana Parreño
- Sección de Virus Gastroentéricos, Instituto de Virología, CICV y A, INTA Castelar, Buenos Aires, Argentina
| | - Rodney Colina
- Laboratorio de Virología Molecular, CENUR Litoral Norte, Centro Universitario de Salto, Universidad de la República, Rivera 1350, 50000, Salto, Uruguay.
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28
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Keha A, Xue L, Yan S, Yue H, Tang C. Prevalence of a novel bovine coronavirus strain with a recombinant hemagglutinin/esterase gene in dairy calves in China. Transbound Emerg Dis 2019; 66:1971-1981. [PMID: 31077561 PMCID: PMC7168545 DOI: 10.1111/tbed.13228] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 03/07/2019] [Accepted: 05/04/2019] [Indexed: 11/29/2022]
Abstract
Bovine coronavirus (BCoV) is the causative agent of diarrhoea in newborn calves, winter dysentery in adult cattle and respiratory tract illnesses in cattle across the world. In this study, a total of 190 faecal samples from dairy calves with diarrhoea were collected from 14 farms in six Chinese provinces, and BCoV was detected in 18.95% (36/190) of the samples by reverse transcriptase polymerase chain reaction. Full-length spike, hemagglutinin/esterase (HE), nucleocapsid and transmembrane genes were simultaneously cloned from 13 clinical samples (eight farms in four provinces), and most of the BCoV strains showed a unique evolutionary pattern based on the phylogenetic analysis of these genes. Interesting, 10 of the 13 strains were identified as HE recombinant strains, and these strains had experienced the same recombination event and carried the same recombination sites located between the esterase and lectin domain. They also shared an identical aa variant (F181V) in the R2-loop. Moreover, 9/10 strains displayed another identical aa variant (P, S158A) in the adjacent R1-loop of the HE gene, which differs from the other available BCoV HE sequences in the GenBank database. Our results showed that BCoV is widely circulating in dairy cattle in China, contributing to the diagnosis and control of dairy calves diarrhoea. Furthermore, a BCoV strain that carries a recombinant HE gene has spread in dairy calves in China. To the best of our knowledge, this is the first description of an HE recombination event occurring in BCoV; this is also the first description of the molecular prevalence of BCoV in China. Our findings will enhance current understanding about the genetic evolution of BCoV.
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Affiliation(s)
- Abi Keha
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, China
| | - Luo Xue
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, China
| | - Shen Yan
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, China
| | - Hua Yue
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu, China
| | - Cheng Tang
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu, China
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Szczepanski A, Owczarek K, Bzowska M, Gula K, Drebot I, Ochman M, Maksym B, Rajfur Z, Mitchell JA, Pyrc K. Canine Respiratory Coronavirus, Bovine Coronavirus, and Human Coronavirus OC43: Receptors and Attachment Factors. Viruses 2019; 11:v11040328. [PMID: 30959796 PMCID: PMC6521053 DOI: 10.3390/v11040328] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 03/31/2019] [Accepted: 04/02/2019] [Indexed: 01/19/2023] Open
Abstract
Despite high similarity of canine respiratory coronavirus (CRCoV), bovine coronavirus, (BCoV) and human coronavirus OC43 (HCoV-OC43), these viruses differ in species specificity. For years it was believed that they share receptor specificity, utilizing sialic acids for cell surface attachment, internalization, and entry. Interestingly, careful literature analysis shows that viruses indeed bind to the cell surface via sialic acids, but there is no solid data that these moieties mediate virus entry. In our study, using a number of techniques, we showed that all three viruses are indeed able to bind to sialic acids to a different extent, but these molecules render the cells permissive only for the clinical strain of HCoV-OC43, while for others they serve only as attachment receptors. CRCoV and BCoV appear to employ human leukocyte antigen class I (HLA-1) as the entry receptor. Furthermore, we identified heparan sulfate as an alternative attachment factor, but this may be related to the cell culture adaptation, as in ex vivo conditions, it does not seem to play a significant role. Summarizing, we delineated early events during CRCoV, BCoV, and HCoV-OC43 entry and systematically studied the attachment and entry receptor utilized by these viruses.
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Affiliation(s)
- Artur Szczepanski
- Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland.
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland.
| | - Katarzyna Owczarek
- Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland.
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland.
| | - Monika Bzowska
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland.
| | - Katarzyna Gula
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland.
| | - Inga Drebot
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland.
| | - Marek Ochman
- Department of Cardiac, Vascular and Endovascular Surgery and Transplantology, Medical University of Silesia in Katowice, Silesian Centre for Heart Diseases, Marii Curie Sklodowskiej 9, 41-800 Zabrze, Poland.
| | - Beata Maksym
- Department of Pharmacology, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia in Katowice, ul. Jordana 19, 41-808 Zabrze, Poland.
| | - Zenon Rajfur
- Institute of Physics, Faculty of Physics, Astronomy and Applied Computer Sciences, Jagiellonian University, Lojasiewicza 11, 30-348 Krakow, Poland.
| | - Judy A Mitchell
- Department of Pathology and Pathogen Biology, The Royal Veterinary College, Hatfield, Hertfordshire AL9 7TA, UK.
| | - Krzysztof Pyrc
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland.
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He Q, Guo Z, Zhang B, Yue H, Tang C. First detection of bovine coronavirus in Yak (Bos grunniens) and a bovine coronavirus genome with a recombinant HE gene. J Gen Virol 2019; 100:793-803. [PMID: 30932810 PMCID: PMC7079584 DOI: 10.1099/jgv.0.001254] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The yak (Bosgrunniens) is a unique domestic bovine species that plays an indispensable role for herdsmen in the Qinghai–Tibet Plateau. Here, 336 diarrhoeic samples were collected from yaks on 29 farms in the Qinghai–Tibet Plateau from 2015 to 2017. Approximately 69.05 % (232/336) of the diarrhoeic samples were assessed as bovine coronavirus (BCoV)-positive by RT-PCR assay, and most of the detected strains showed a unique evolution based on 40 spike (S), nucleocapsid (N) and haemagglutinin-esterase (HE) gene fragments. Notably, the 12 complete S genes detected shared 1 identical amino acid mutation (E121V) in the S1 subunit compared with the other 150 complete S genes in the GenBank database. Furthermore, a BCoV strain (designated YAK/HY24/CH/2017) was isolated from one diarrhoeic sample (virus titre : 108.17TCID50 ml−1), and a phylogenetic analysis based on complete genome sequences revealed that strain YAK/HY24/CH/2017 has the closest genetic relationship with the BCoV prototype strain Mebus. Interestingly, 2 significant characteristics were observed in the genome of strain YAK/HY24/CH/2017 : (1) the strain had 26 unique amino acid variations in the S gene compared with the other 150 BCoV S genes in the GenBank database and (2) a recombination event was identified between the esterase and lectin domains of the HE gene. In conclusion, this study revealed the high prevalence of BCoV in yaks in the Qinghai–Tibet Plateau. To the best of our knowledge, this is the first description of the molecular prevalence of BCoV in yaks and of a BCoV genome with an HE gene recombination.
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Affiliation(s)
- Qifu He
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, PR China
| | - Zijing Guo
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, PR China
| | - Bin Zhang
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, PR China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation, Chengdu, PR China
| | - Hua Yue
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, PR China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation, Chengdu, PR China
- *Correspondence: Hua Yue,
| | - Cheng Tang
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, PR China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation, Chengdu, PR China
- Cheng Tang,
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Shin J, Tark D, Le VP, Choe S, Cha RM, Park GN, Cho IS, Nga BTT, Lan NT, An DJ. Genetic characterization of bovine coronavirus in Vietnam. Virus Genes 2019; 55:415-420. [PMID: 30771080 PMCID: PMC7088966 DOI: 10.1007/s11262-019-01647-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/04/2019] [Indexed: 11/29/2022]
Abstract
A maximum clade credibility tree constructed using the full-length spike (S) and hemagglutinin-esterase genes revealed that Vietnamese Bovine coronavirus (BCoV) strains belong to a single cluster (C1); therefore, they might share a common origin with Cuban and Chinese BCoV strains. The omega values of cluster 1 (C1) and cluster 2 (C2) were 0.15734 and 0.11613, respectively, and naive empirical bayes analysis identified two amino acid positions (179 and 501) in the S protein in C1 and three amino acid positions (113, 501, and 525) in that of C2 that underwent positive selection (p > 99%). The evolutionary rate of C1 was estimated to be 7.6206 × 10-4 substitutions/site/year, and the most recent common ancestor (tMRCA) of Vietnamese BCoVs was estimated to date back to 1962 (95% HPD 1950-1973). The effective population sizes of C1 and C2 underwent a rapid reduction after 2000 and 2004, respectively.
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Affiliation(s)
- Jihye Shin
- Viral Disease Division, Animal and Plant Quarantine Agency (QIA), Gimcheon, Gyeongbuk, 39660, Republic of Korea
| | - Dongseob Tark
- Korea Zoonosis Research Institute, Chonbuk National University, Iksan, Jeonbuk, 54531, Republic of Korea
| | - Van Phan Le
- Faculty of Veterinary Medicine, Vietnam National University of Agriculture (VNUA), Hanoi, Vietnam
| | - SeEun Choe
- Viral Disease Division, Animal and Plant Quarantine Agency (QIA), Gimcheon, Gyeongbuk, 39660, Republic of Korea
| | - Ra Mi Cha
- Viral Disease Division, Animal and Plant Quarantine Agency (QIA), Gimcheon, Gyeongbuk, 39660, Republic of Korea
| | - Gyu-Nam Park
- Viral Disease Division, Animal and Plant Quarantine Agency (QIA), Gimcheon, Gyeongbuk, 39660, Republic of Korea
| | - In-Soo Cho
- Viral Disease Division, Animal and Plant Quarantine Agency (QIA), Gimcheon, Gyeongbuk, 39660, Republic of Korea
| | - Bui Thi To Nga
- Faculty of Veterinary Medicine, Vietnam National University of Agriculture (VNUA), Hanoi, Vietnam
| | - Nguyen Thi Lan
- Faculty of Veterinary Medicine, Vietnam National University of Agriculture (VNUA), Hanoi, Vietnam
| | - Dong-Jun An
- Viral Disease Division, Animal and Plant Quarantine Agency (QIA), Gimcheon, Gyeongbuk, 39660, Republic of Korea.
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32
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Brandão PE. Could human coronavirus OC43 have co-evolved with early humans? Genet Mol Biol 2018; 41:692-698. [PMID: 30004106 PMCID: PMC6136381 DOI: 10.1590/1678-4685-gmb-2017-0192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 01/05/2018] [Indexed: 12/24/2022] Open
Abstract
This paper reports on an investigation of the role of codon usage evolution on the suggested bovine-to-human spillover of Bovine coronavirus (BCoV), an enteric/respiratory virus of cattle, resulting in the emergence of the exclusively respiratory Human coronavirus OC43 (HCoV-OC43). Analyses based on full genomes of BCoV and HCoV-OC43 and on both human and bovine mRNAs sequences of cholecystokinin (CCK) and surfactant protein 1 A (SFTP1-A), representing the enteric and respiratory tract codon usage, respectively, have shown natural selection leading to optimization or deoptimization of viral codon usage to the human enteric and respiratory tracts depending on the virus genes under consideration. A higher correlation was found for the nucleotide distance at the 3rd nucleotide position of codons and codon usage optimization to the human respiratory tract when BCoV and HCoV-OC43 were compared. An MCC tree based on relative synonymous codon usage (RSCU) data integrating data from both viruses and hosts into a same analysis indicated three putative host/virus contact dates ranging from 1.54E8 to 2.44E5 years ago, suggesting that an ancestor coronavirus might have followed human evolution.
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Affiliation(s)
- Paulo Eduardo Brandão
- Departmento de Medicina Veterinaria Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, SP, Brazil
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33
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de Mira Fernandes A, Brandão PE, dos Santos Lima M, de Souza Nunes Martins M, da Silva TG, da Silva Cardoso Pinto V, de Paula LT, Vicente MES, Okuda LH, Pituco EM. Genetic diversity of BCoV in Brazilian cattle herds. Vet Med Sci 2018; 4:183-189. [PMID: 29687958 PMCID: PMC6090412 DOI: 10.1002/vms3.102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Bovine coronavirus (BCoV) is one of the main aetiological agents of gastroenteritis in calves, causing significant economic damage to livestock. This study aims to characterise BCoV genetically on the basis of the N gene. A total of 114 faecal samples from beef and dairy calves with or without clinical symptoms of diarrhoea from five Brazilian states (São Paulo, Minas Gerais, Santa Catarina, Mato Grosso and Bahia) were evaluated between 2008 and 2015 by technique of Semi-nested RT-PCR for gene N and genealogical analysis. Of the 114 samples analysed, 14.91% (17/114) were positive. BCoV was detected in 22.72% (10/44) of the animals with diarrhoea and in 10% (7/70) of asymptomatic animals. BCoV was identified in calves from rural properties located in all of the regions sampled. Genealogical analysis showed that the Brazilian sequences of BCoV for the gene which codes for the N protein can be broken down into two distinct clusters, and the samples from this study were closely linked to Asian strains. These results contribute to the molecular characterization of BCoV in Brazil and are the first report of the circulation of BCoV in the states of Santa Catarina and Bahia.
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Affiliation(s)
- Adeline de Mira Fernandes
- Laboratory of Bovine VirusesCenter of Research and Development of Animal HealthBiological Institute of São PauloSão PauloBrazil
| | - Paulo E. Brandão
- Department of Preventative Veterinary Medicine and Animal HealthFaculty of Veterinary and Zootechnical MedicineUniversity of São PauloSão PauloBrazil
| | - Michele dos Santos Lima
- Laboratory of Bovine VirusesCenter of Research and Development of Animal HealthBiological Institute of São PauloSão PauloBrazil
| | - Maira de Souza Nunes Martins
- Laboratory of Bovine VirusesCenter of Research and Development of Animal HealthBiological Institute of São PauloSão PauloBrazil
| | - Thais G. da Silva
- Laboratory of Bovine VirusesCenter of Research and Development of Animal HealthBiological Institute of São PauloSão PauloBrazil
| | - Vivian da Silva Cardoso Pinto
- Laboratory of Bovine VirusesCenter of Research and Development of Animal HealthBiological Institute of São PauloSão PauloBrazil
| | - Larissa T. de Paula
- Laboratory of Bovine VirusesCenter of Research and Development of Animal HealthBiological Institute of São PauloSão PauloBrazil
| | - Marta Elisabete S. Vicente
- Laboratory of Bovine VirusesCenter of Research and Development of Animal HealthBiological Institute of São PauloSão PauloBrazil
| | - Liria H. Okuda
- Laboratory of Bovine VirusesCenter of Research and Development of Animal HealthBiological Institute of São PauloSão PauloBrazil
| | - Edviges M. Pituco
- Laboratory of Bovine VirusesCenter of Research and Development of Animal HealthBiological Institute of São PauloSão PauloBrazil
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34
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Kim JH, Jang JH, Yoon SW, Noh JY, Ahn MJ, Kim Y, Jeong DG, Kim HK. Detection of bovine coronavirus in nasal swab of non-captive wild water deer, Korea. Transbound Emerg Dis 2018; 65:627-631. [PMID: 29508550 PMCID: PMC7169857 DOI: 10.1111/tbed.12847] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Indexed: 11/29/2022]
Abstract
Bovine coronavirus (BCoV) is a causative agent of respiratory and enteric diseases in cattle and calves. BCoV infection was also evident in captive wild ruminants. Recently, water deer are recognized as the most common wildlife to approach farmhouses and livestock barns in Korea. Therefore, we investigated 77 nasal swab samples from non‐captive wild water deer (Hydropotes inermis) between November 2016 and September 2017 and identified three samples positive for coronavirus, indicating potential for respiratory shedding. The full genomic sequences of the water deer coronavirus were closely related to BCoV (>98%). Therefore, effective biosecurity system in bovine farms would be necessary to prevent contact between farm ruminants and free‐ranging wild water deer.
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Affiliation(s)
- J H Kim
- Infectious Diseases Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - J-H Jang
- Chungnam Wild Animal Rescue Center, Yesan, Korea
| | - S-W Yoon
- Infectious Diseases Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea.,Bio-Analytical Science Division, University of Science and Technology (UST), Daejeon, Korea
| | - J Y Noh
- Infectious Diseases Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea.,College of Veterinary Medicine, Chungbuk National University, Cheongju, Korea
| | - M-J Ahn
- Infectious Diseases Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea.,Bio-Analytical Science Division, University of Science and Technology (UST), Daejeon, Korea
| | - Y Kim
- Infectious Diseases Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea.,College of Veterinary Medicine, Chungbuk National University, Cheongju, Korea
| | - D G Jeong
- Infectious Diseases Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea.,Bio-Analytical Science Division, University of Science and Technology (UST), Daejeon, Korea
| | - H K Kim
- Infectious Diseases Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
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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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Luna L, Brandão PE, Maturrano L, Rosadio R, Silva FDF, Soares RM, Gregori F. Betacoronavirus 1 in alpacas ( Vicugna pacos) in the High Peruvian Andes. Small Rumin Res 2015; 133:7-9. [PMID: 32288207 PMCID: PMC7127686 DOI: 10.1016/j.smallrumres.2015.10.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/08/2015] [Accepted: 10/13/2015] [Indexed: 12/31/2022]
Abstract
The detection of a BCoV-like coronavirus in fecal samples from Peruvian alpacas crias suggests possible role of this virus on enteric disorders etiology in the High Andes, an environment in which coronaviruses have not previously been reported.
Genetic sequences highly related to Bovine coronavirus (BCoV) were detected in fecal samples from Peruvian 1–3 week old alpaca crias located on six farms in Puno department, some of which shared pastures with cattle. A total of 60 samples were screened for coronavirus using a nested PCR amplification of a fragment of the RNA-dependent RNA polymerase (RdRp) gene. Sequences from 11 positive samples were highly similar to the Kakegawa, Quebec and Mebus BCoV strains (99.5–100.0%) and 99.2% identical to an alpaca Coronavirus (CoV) previously detected in the USA. The detection of genetic sequences related to BCoV from Peruvian alpaca crias suggests possible role of this virus on enteric disorders etiology in the High Andes.
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Affiliation(s)
- L Luna
- Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, Av. Professor Dr. Orlando Marques de Paiva, 87, Cidade Universitária, CEP 05508-270 São Paulo, Brazil
| | - P E Brandão
- Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, Av. Professor Dr. Orlando Marques de Paiva, 87, Cidade Universitária, CEP 05508-270 São Paulo, Brazil
| | - L Maturrano
- Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Avenida Circunvalación 2800, San Borja, Lima, Peru
| | - R Rosadio
- Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Avenida Circunvalación 2800, San Borja, Lima, Peru
| | - F D F Silva
- Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, Av. Professor Dr. Orlando Marques de Paiva, 87, Cidade Universitária, CEP 05508-270 São Paulo, Brazil
| | - R M Soares
- Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, Av. Professor Dr. Orlando Marques de Paiva, 87, Cidade Universitária, CEP 05508-270 São Paulo, Brazil
| | - F Gregori
- Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, Av. Professor Dr. Orlando Marques de Paiva, 87, Cidade Universitária, CEP 05508-270 São Paulo, Brazil
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37
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Bok M, Miño S, Rodriguez D, Badaracco A, Nuñes I, Souza SP, Bilbao G, Louge Uriarte E, Galarza R, Vega C, Odeon A, Saif LJ, Parreño V. Molecular and antigenic characterization of bovine Coronavirus circulating in Argentinean cattle during 1994-2010. Vet Microbiol 2015; 181:221-9. [PMID: 26520931 PMCID: PMC7185509 DOI: 10.1016/j.vetmic.2015.10.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 08/28/2015] [Accepted: 10/13/2015] [Indexed: 12/11/2022]
Abstract
Detection rate of BCoV was statistically higher in dairy than in beef calves. Argentinean strains are distant from the Mebus strain included in local vaccines. In vitro cross-protection between Arg95 field strain and Mebus reference strain.
Bovine coronavirus (BCoV) is an important viral pathogen associated with neonatal calf diarrhea. Our aim was to investigate the incidence of BCoV in diarrhea outbreaks in beef and dairy herds from Argentina during 1994–2010. A total of 5.365 fecal samples from diarrheic calves were screened for BCoV diagnosis by ELISA. The virus was detected in 1.71% (92/5365) of the samples corresponding to 5.95% (63/1058) of the diarrhea cases in 239 beef and 324 dairy farms. The detection rate of BCoV was significantly higher in dairy than in beef herds: 12.13% (29/239) vs. 4.32% (14/324) respectively. Phylogenetic analysis of the hypervariable S1 region of seven representative samples (from different husbandry systems, farm locations and years of sampling) indicated that BCoV strains circulating in Argentinean beef and dairy herds formed a cluster distinct from other geographical regions. Interestingly, Argentinean strains are distantly related (at both the nucleotide and amino acid levels) with the Mebus historic reference BCoV strain included in the vaccines currently available in Argentina. However, Mebus-induced antibodies were capable of neutralizing the BCoV Arg95, a field strain adapted to grow in vitro, and vice versa, indicating that both strains belong to the same CoV serotype reported in cattle. This work represents the first large survey describing BCoV circulation in Argentinean cattle.
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Affiliation(s)
- M Bok
- Virology Institute, CICVyA, National Institute of Agricultural Technology (INTA), Buenos Aires, Argentina
| | - S Miño
- Virology Institute, CICVyA, National Institute of Agricultural Technology (INTA), Buenos Aires, Argentina; State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agriculture Sciences, Harbin, 150001 Heilongjiang, China
| | - D Rodriguez
- Virology Institute, CICVyA, National Institute of Agricultural Technology (INTA), Buenos Aires, Argentina
| | - A Badaracco
- Virology Institute, CICVyA, National Institute of Agricultural Technology (INTA), Buenos Aires, Argentina
| | - I Nuñes
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo, Brazil
| | - S P Souza
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo, Brazil
| | - G Bilbao
- Laboratory of Animal Health, EEA INTA- Balcarce, Buenos Aires, Argentina
| | | | - R Galarza
- EEA, INTA Rafaela, Santa Fe, Argentina
| | - C Vega
- Virology Institute, CICVyA, National Institute of Agricultural Technology (INTA), Buenos Aires, Argentina
| | - A Odeon
- Laboratory of Animal Health, EEA INTA- Balcarce, Buenos Aires, Argentina
| | - L J Saif
- Food Animal Health Research Program, The Ohio State University, Wooster, OH, USA
| | - V Parreño
- Virology Institute, CICVyA, National Institute of Agricultural Technology (INTA), Buenos Aires, Argentina.
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Metegnier G, Becking T, Chebbi MA, Giraud I, Moumen B, Schaack S, Cordaux R, Gilbert C. Comparative paleovirological analysis of crustaceans identifies multiple widespread viral groups. Mob DNA 2015; 6:16. [PMID: 26388953 PMCID: PMC4573495 DOI: 10.1186/s13100-015-0047-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 09/10/2015] [Indexed: 01/08/2023] Open
Abstract
Background The discovery of many fragments of viral genomes integrated in the genome of their eukaryotic host (endogenous viral elements; EVEs) has recently opened new avenues to further our understanding of viral evolution and of host-virus interactions. Here, we report the results of a comprehensive screen for EVEs in crustaceans. Following up on the recent discovery of EVEs in the terrestrial isopod, Armadillidium vulgare, we scanned the genomes of six crustacean species: a terrestrial isopod (Armadillidium nasatum), two water fleas (Daphnia pulex and D. pulicaria), two copepods (the salmon louse, Lepeophtheirus salmonis and Eurytemora affinis), and a freshwater amphipod (Hyalella azteca). Results In total, we found 210 EVEs representing 14 different lineages belonging to five different viral groups that are present in two to five species: Bunyaviridae (−ssRNA), Circoviridae (ssDNA), Mononegavirales (−ssRNA), Parvoviridae (ssDNA) and Totiviridae (dsRNA). The identification of shared orthologous insertions between A. nasatum and A. vulgare indicates that EVEs have been maintained over several millions of years, although we did not find any evidence supporting exaptation. Overall, the different degrees of EVE degradation (from none to >10 nonsense mutations) suggest that endogenization has been recurrent during the evolution of the various crustacean taxa. Our study is the first to report EVEs in D. pulicaria, E. affinis and H. azteca, many of which are likely to result from recent endogenization of currently circulating viruses. Conclusions In conclusion, we have unearthed a large diversity of EVEs from crustacean genomes, and shown that four of the five viral groups we uncovered (Bunyaviridae, Circoviridae, Mononegavirales, Parvoviridae) were and may still be present in three to four highly divergent crustacean taxa. In addition, the discovery of recent EVEs offers an interesting opportunity to characterize new exogenous viruses currently circulating in economically or ecologically important copepod species. Electronic supplementary material The online version of this article (doi:10.1186/s13100-015-0047-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gabriel Metegnier
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, building B8-B35, 6 rue Michel Brunet, TSA 51106 F-86073 Poitiers, Cedex 9 France
| | - Thomas Becking
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, building B8-B35, 6 rue Michel Brunet, TSA 51106 F-86073 Poitiers, Cedex 9 France
| | - Mohamed Amine Chebbi
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, building B8-B35, 6 rue Michel Brunet, TSA 51106 F-86073 Poitiers, Cedex 9 France
| | - Isabelle Giraud
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, building B8-B35, 6 rue Michel Brunet, TSA 51106 F-86073 Poitiers, Cedex 9 France
| | - Bouziane Moumen
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, building B8-B35, 6 rue Michel Brunet, TSA 51106 F-86073 Poitiers, Cedex 9 France
| | - Sarah Schaack
- Department of Biology, Reed College, Portland, OR USA
| | - Richard Cordaux
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, building B8-B35, 6 rue Michel Brunet, TSA 51106 F-86073 Poitiers, Cedex 9 France
| | - Clément Gilbert
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, building B8-B35, 6 rue Michel Brunet, TSA 51106 F-86073 Poitiers, Cedex 9 France
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39
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Genetic drift of human coronavirus OC43 spike gene during adaptive evolution. Sci Rep 2015; 5:11451. [PMID: 26099036 PMCID: PMC4476415 DOI: 10.1038/srep11451] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 05/26/2015] [Indexed: 11/08/2022] Open
Abstract
Coronaviruses (CoVs) continuously threaten human health. However, to date, the evolutionary mechanisms that govern CoV strain persistence in human populations have not been fully understood. In this study, we characterized the evolution of the major antigen-spike (S) gene in the most prevalent human coronavirus (HCoV) OC43 using phylogenetic and phylodynamic analysis. Among the five known HCoV-OC43 genotypes (A to E), higher substitution rates and dN/dS values as well as more positive selection sites were detected in the S gene of genotype D, corresponding to the most dominant HCoV epidemic in recent years. Further analysis showed that the majority of substitutions were located in the S1 subunit. Among them, seven positive selection sites were chronologically traced in the temporal evolution routes of genotype D, and six were located around the critical sugar binding region in the N-terminal domain (NTD) of S protein, an important sugar binding domain of CoV. These findings suggest that the genetic drift of the S gene may play an important role in genotype persistence in human populations, providing insights into the mechanisms of HCoV-OC43 adaptive evolution.
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40
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Prevalence and genetic diversity analysis of human coronavirus OC43 among adult patients with acute respiratory infections in Beijing, 2012. PLoS One 2014; 9:e100781. [PMID: 24987849 PMCID: PMC4079595 DOI: 10.1371/journal.pone.0100781] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 05/27/2014] [Indexed: 02/08/2023] Open
Abstract
To determine the prevalence, epidemiology and genetic diversity of human coronavirus OC43 (HCoV-OC43) among adult patients with acute respiratory infections (ARI) in Beijing,five hundred and fifty-nine nasopharyngeal swab samples were collected from adult patients with ARI in Beijing. The prevalence of HCoV-OC43 infection among these patients was assessed using two different OneStep reverse transcription polymerase chain reaction (RT-PCR) assays. The epidemiological profiles of the patients with HCoV-OC43 infection were described. Partial S and N genes of HCoV-OC43 circulating strains were sequenced followed by phylogenetic analysis and amino acid alignment. Our results showed that the prevalence of HCoV-OC43 infection was 12.52% (95% CI: 9.78–15.26%), and the epidemic peak occurred in autumn. Fifty partial S and 40 partial N fragments were obtained from these patients. Phylogenetic analysis based on neighbour-joining method showed that at least three distinct clusters (A, B, C/D) of HCoV-OC43 strains were circulating among adult patients with ARI in Beijing. In addition, some novel unique clusters (UNT) of HCoV-OC43 were found in the S- and N-based phylogenetic trees. Furthermore, consensus amino acids substitutes for each cluster were also found after alignment of partial S or N sequence coding region in this study. In conclusion, we herein describe the prevalence of HCoV-OC43 among adult patients and provide substantial evidence for the genetic diversity of HCoV-OC43 circulating in Beijing.
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41
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Potential applications for antiviral therapy and prophylaxis in bovine medicine. Anim Health Res Rev 2014; 15:102-17. [PMID: 24810855 DOI: 10.1017/s1466252314000048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Viral disease is one of the major causes of financial loss and animal suffering in today's cattle industry. Increases in global commerce and average herd size, urbanization, vertical integration within the industry and alterations in global climate patterns have allowed the spread of pathogenic viruses, or the introduction of new viral species, into regions previously free of such pathogens, creating the potential for widespread morbidity and mortality in naïve cattle populations. Despite this, no antiviral products are currently commercially licensed for use in bovine medicine, although significant progress has been made in the development of antivirals for use against bovine viral diarrhea virus (BVDV), foot and mouth disease virus (FMDV) and bovine herpesvirus (BHV). BVDV is extensively studied as a model virus for human antiviral studies. Consequently, many compounds with efficacy have been identified and a few have been successfully used to prevent infection in vivo although commercial development is still lacking. FMDV is also the subject of extensive antiviral testing due to the importance of outbreak containment for maintenance of export markets. Thirdly, BHV presents an attractive target for antiviral development due to its worldwide presence. Antiviral studies for other bovine viral pathogens are largely limited to preliminary studies. This review summarizes the current state of knowledge of antiviral compounds against several key bovine pathogens and the potential for commercial antiviral applications in the prevention and control of several selected bovine diseases.
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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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