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1.
J Virol ; 96(3): e0156121, 2022 02 09.
Article in English | MEDLINE | ID: covidwho-1529876

ABSTRACT

Historically part of the coronavirus (CoV) family, torovirus (ToV) was recently classified in the new family Tobaniviridae. While reverse genetics systems have been established for various CoVs, none exist for ToVs. Here, we developed a reverse genetics system using an infectious full-length cDNA clone of bovine ToV (BToV) in a bacterial artificial chromosome (BAC). Recombinant BToV harboring genetic markers had the same phenotype as wild-type (wt) BToV. To generate two types of recombinant virus, the hemagglutinin-esterase (HE) gene was edited, as cell-adapted wtBToV generally loses full-length HE (HEf), resulting in soluble HE (HEs). First, recombinant viruses with HEf and hemagglutinin (HA)-tagged HEf or HEs genes were rescued. These exhibited no significant differences in their effect on virus growth in HRT18 cells, suggesting that HE is not essential for viral replication in these cells. Thereafter, we generated a recombinant virus (rEGFP) wherein HE was replaced by the enhanced green fluorescent protein (EGFP) gene. rEGFP expressed EGFP in infected cells but showed significantly lower levels of viral growth than wtBToV. Moreover, rEGFP readily deleted the EGFP gene after one passage. Interestingly, rEGFP variants with two mutations (C1442F and I3562T) in nonstructural proteins (NSPs) that emerged during passage exhibited improved EGFP expression, EGFP gene retention, and viral replication. An rEGFP into which both mutations were introduced displayed a phenotype similar to that of these variants, suggesting that the mutations contributed to EGFP gene acceptance. The current findings provide new insights into BToV, and reverse genetics will help advance the current understanding of this neglected pathogen. IMPORTANCE ToVs are diarrhea-causing pathogens detected in various species, including humans. Through the development of a BAC-based BToV, we introduced the first reverse genetics system for Tobaniviridae. Utilizing this system, recombinant BToVs with a full-length HE gene were generated. Remarkably, although clinical BToVs generally lose the HE gene after a few passages, some recombinant viruses generated in the current study retained the HE gene for up to 20 passages while accumulating mutations in NSPs, which suggested that these mutations may be involved in HE gene retention. The EGFP gene of recombinant viruses was unstable, but rEGFP into which two NSP mutations were introduced exhibited improved EGFP expression, gene retention, and viral replication. These data suggested the existence of an NSP-based acceptance or retention mechanism for exogenous RNA or HE genes. Recombinant BToVs and reverse genetics are powerful tools for understanding fundamental viral processes, pathogenesis, and BToV vaccine development.


Subject(s)
DNA, Complementary , Genome, Viral , Reverse Genetics , Torovirus/genetics , Animals , Cattle , Cattle Diseases/virology , Cell Line , Cells, Cultured , Chromosomes, Artificial, Bacterial , Cloning, Molecular , Genes, Reporter , Hemagglutinins, Viral/genetics , Hemagglutinins, Viral/metabolism , Mutation , Plasmids/genetics , Torovirus/isolation & purification , Torovirus Infections , Transfection
2.
Arch Virol ; 166(9): 2461-2468, 2021 Sep.
Article in English | MEDLINE | ID: covidwho-1292555

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.


Subject(s)
Cattle Diseases/epidemiology , Coronavirus Infections/veterinary , Coronavirus, Bovine/genetics , Diarrhea/veterinary , RNA, Viral/genetics , Respiratory Tract Infections/veterinary , Spike Glycoprotein, Coronavirus/genetics , Agriculture , Amino Acid Substitution , Animals , Cattle , Cattle Diseases/virology , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Coronavirus, Bovine/classification , Diarrhea/epidemiology , Diarrhea/virology , Epidemiological Monitoring/veterinary , Evolution, Molecular , Feces/virology , Humans , Mutation , Nasal Cavity/virology , Phylogeny , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/virology , Reverse Transcriptase Polymerase Chain Reaction , Sequence Analysis, DNA , Turkey/epidemiology
3.
Viruses ; 13(4)2021 04 15.
Article in English | MEDLINE | ID: covidwho-1184510

ABSTRACT

Coronaviruses (CoV) are widely distributed pathogens of human and animals and can cause mild or severe respiratory and gastrointestinal disease. Antigenic and genetic similarity of some CoVs within the Betacoronavirus genus is evident. Therefore, for the first time in Slovenia, we investigated the genetic diversity of partial 390-nucleotides of RNA-dependent-RNA polymerase gene (RdRp) for 66 human (HCoV) and 24 bovine CoV (BCoV) positive samples, collected between 2010 and 2016 from human patients and cattle with respiratory disease. The characterized CoV strains belong to four different clusters, in three separate human clusters HCoV-HKU1 (n = 34), HCoV-OC43 (n = 31) and HCoV 229E (n = 1) and bovine grouping only as BCoVs (n = 24). BCoVs from cattle and HCoV-OC43 were genetically the most closely related and share 96.4-97.1% nucleotide and 96.9-98.5% amino acid identity.


Subject(s)
Cattle Diseases/virology , Coronavirus/classification , Coronavirus/genetics , Animals , Cattle , Cattle Diseases/transmission , Coronavirus 229E, Human/genetics , Coronavirus Infections/transmission , Coronavirus OC43, Human/genetics , Coronavirus, Bovine/genetics , Female , Genetic Variation , Humans , Male , Slovenia
4.
J Dairy Sci ; 104(2): 2151-2163, 2021 Feb.
Article in English | MEDLINE | ID: covidwho-1031655

ABSTRACT

The objective of this prospective cohort study was to investigate the effect of bovine coronavirus (BCoV), bovine rotavirus (BRoV), and Cryptosporidiumparvum on dairy calf health and performance and to determine the prevalence of these pathogens. A total of 198 male dairy calves housed at a grain-fed veal facility were examined from June 11, 2018, to October 9, 2018. Calves were fed milk replacer twice daily and housed individually until weaning at 56 d. Once weaned, calves were moved into groups of 5 until they were moved to a finishing facility at 77 d. At the grain-fed veal facility, calves were scored for fecal consistency for the first 28 d and had fecal samples taken on arrival and at 7 and 14 d. Fecal samples were frozen and submitted to a commercial laboratory, where they were tested for BCoV, C.parvum, and 2 groups of BRoV: group A (BRoV A) and group B (BRoV B). Calves were weighed on arrival and at 14, 49, 56, and 77 d using a digital body scale. Treatments for disease and mortalities that occurred over the 77 d were also recorded. Statistical models, including Cox proportional hazards and repeated measures models, were built to determine the effect of infection with 1 of the pathogens. Over the 3 sampling points, 151 (85.8%), 178 (94.2%), 3 (1.5%), and 97 (57.4%) calves tested positive at least once for BCoV, BRoV A, BRoV B, and C.parvum, respectively. The source of the calves and the level of serum total protein measured on arrival were associated with testing positive for a pathogen. Calves that tested positive for C.parvum had an increased proportion of days with diarrhea and severe diarrhea; calves that tested positive for BCoV and BRoV A had an increased proportion of days with severe diarrhea. In addition, calves that tested positive for C.parvum had a higher hazard of being treated for respiratory disease. With respect to body weight, calves that had diarrhea or severe diarrhea had lower body weight at 49, 56, and 77 d. Specifically, calves that had an increased proportion of days with diarrhea showed a reduction in weight gain of up to 15 kg compared to calves without diarrhea. Calves that tested positive for C.parvum had a lower body weight at 49, 56, and 77 d; calves that tested positive for BCoV had a lower body weight at 56 and 77 d. This study demonstrates that the prevalence of BCoV, BRoV A, and C.parvum infection is high in this population of calves and has significant effects on the occurrence of diarrhea and body weight gain. Future studies should evaluate approaches for minimizing the effect of infection with these pathogens to improve the welfare, health, and productivity of dairy calves.


Subject(s)
Cattle Diseases/physiopathology , Coronavirus Infections/veterinary , Coronavirus, Bovine , Cryptosporidiosis/physiopathology , Cryptosporidium parvum , Rotavirus Infections/veterinary , Animals , Cattle , Cattle Diseases/epidemiology , Cattle Diseases/parasitology , Cattle Diseases/virology , Cohort Studies , Coronavirus Infections/epidemiology , Coronavirus Infections/physiopathology , Cryptosporidiosis/parasitology , Diarrhea/parasitology , Diarrhea/veterinary , Diarrhea/virology , Feces/chemistry , Feces/parasitology , Feces/virology , Male , Prevalence , Prospective Studies , Respiratory Tract Diseases/therapy , Respiratory Tract Diseases/veterinary , Rotavirus , Rotavirus Infections/epidemiology , Rotavirus Infections/physiopathology , Weight Gain
5.
Prev Vet Med ; 181: 104494, 2020 Aug.
Article in English | MEDLINE | ID: covidwho-761798

ABSTRACT

A national control program against bovine respiratory syncytial virus (BRSV) and bovine coronavirus (BCV) was launched in Norway in 2016. A key strategy in the program is to test for presence of antibodies and protect test-negative herds from infection. Because these viruses are endemic, the rate of re-introduction can be high, and a disease-free status will become more uncertain as time from testing elapses. The aim of this study was to estimate the probability of freedom (PostPFree) from BRSV and BCV antibodies over time by use of bulk tank milk (BTM) antibody-testing, geographic information and animal movement data, and to validate the herd-level estimates against subsequent BTM testing. BTM samples were collected from 1148 study herds in West Norway in 2013 and 2016, and these were analyzed for BRSV and BCV antibodies. PostPFree was calculated for herds that were negative in 2013/2014, and updated periodically with new probabilities every three months. Input variables were test sensitivity, the probability of introduction through animal purchase and local transmission. Probability of introduction through animal purchase was calculated by using real animal movement data and herd prevalence in the region of the source herd. The PostPFree from the final three months in 2015 was compared to BTM test results from March 2016 using a Wilcoxon Rank Sum Test. The probability of freedom was generally high for test-negative herds immediately after testing, reflecting the high sensitivity of the tests. It did however, decrease with time since testing, and was greatly affected by purchase of livestock. When comparing the median PostPFree for the final three months to the test results in 2016, it was significantly lower (p < 0.01) for test positive herds. Furthermore, there was a large difference in the proportion of test positive herds between the first and fourth quartile of PostPFree. The results show that PostPFree provides a better estimate of herd-level BTM status for both BRSV and BCV than what can be achieved by relying solely on the previous test-result.


Subject(s)
Cattle Diseases/prevention & control , Coronavirus Infections/veterinary , Coronavirus, Bovine , Respiratory Syncytial Virus Infections/veterinary , Respiratory Syncytial Virus, Bovine , Animals , Antibodies, Viral/immunology , Cattle/virology , Cattle Diseases/epidemiology , Cattle Diseases/virology , Coronavirus Infections/epidemiology , Coronavirus Infections/prevention & control , Female , Infection Control/methods , Milk/immunology , Norway/epidemiology , Probability , Respiratory Syncytial Virus Infections/epidemiology , Respiratory Syncytial Virus Infections/prevention & control
6.
J Clin Microbiol ; 58(8)2020 Jul 23.
Article in English | MEDLINE | ID: covidwho-1006147

ABSTRACT

Discovery of bats with severe acute respiratory syndrome (SARS)-related coronaviruses (CoVs) raised the specter of potential future outbreaks of zoonotic SARS-CoV-like disease in humans, which largely went unheeded. Nevertheless, the novel SARS-CoV-2 of bat ancestral origin emerged to infect humans in Wuhan, China, in late 2019 and then became a global pandemic. Less than 5 months after its emergence, millions of people worldwide have been infected asymptomatically or symptomatically and at least 360,000 have died. Coronavirus disease 2019 (COVID-19) in severely affected patients includes atypical pneumonia characterized by a dry cough, persistent fever, and progressive dyspnea and hypoxia, sometimes accompanied by diarrhea and often followed by multiple organ failure, especially of the respiratory and cardiovascular systems. In this minireview, we focus on two endemic respiratory CoV infections of livestock: bovine coronavirus (BCoV) and porcine respiratory coronavirus (PRCV). Both animal respiratory CoVs share some common features with SARS-CoV and SARS-CoV-2. BCoV has a broad host range including wild ruminants and a zoonotic potential. BCoV also has a dual tropism for the respiratory and gastrointestinal tracts. These aspects, their interspecies transmission, and certain factors that impact disease severity in cattle parallel related facets of SARS-CoV or SARS-CoV-2 in humans. PRCV has a tissue tropism for the upper and lower respiratory tracts and a cellular tropism for type 1 and 2 pneumocytes in lung but is generally a mild infection unless complicated by other exacerbating factors, such as bacterial or viral coinfections and immunosuppression (corticosteroids).


Subject(s)
Betacoronavirus/growth & development , Cattle Diseases/physiopathology , Coronavirus Infections/veterinary , Coronavirus, Bovine/growth & development , Pneumonia, Viral/physiopathology , Respiratory Tract Infections/veterinary , Swine Diseases/physiopathology , Animals , Betacoronavirus/pathogenicity , COVID-19 , Cattle , Cattle Diseases/pathology , Cattle Diseases/virology , Coronavirus Infections/pathology , Coronavirus Infections/physiopathology , Coronavirus, Bovine/pathogenicity , Host Specificity , Humans , Pandemics , Pneumonia, Viral/pathology , Porcine Respiratory Coronavirus/growth & development , Porcine Respiratory Coronavirus/pathogenicity , Respiratory Tract Infections/pathology , Respiratory Tract Infections/physiopathology , SARS-CoV-2 , Swine , Swine Diseases/pathology , Swine Diseases/virology , Viral Tropism
7.
J Dairy Sci ; 104(2): 2151-2163, 2021 Feb.
Article in English | MEDLINE | ID: covidwho-973226

ABSTRACT

The objective of this prospective cohort study was to investigate the effect of bovine coronavirus (BCoV), bovine rotavirus (BRoV), and Cryptosporidiumparvum on dairy calf health and performance and to determine the prevalence of these pathogens. A total of 198 male dairy calves housed at a grain-fed veal facility were examined from June 11, 2018, to October 9, 2018. Calves were fed milk replacer twice daily and housed individually until weaning at 56 d. Once weaned, calves were moved into groups of 5 until they were moved to a finishing facility at 77 d. At the grain-fed veal facility, calves were scored for fecal consistency for the first 28 d and had fecal samples taken on arrival and at 7 and 14 d. Fecal samples were frozen and submitted to a commercial laboratory, where they were tested for BCoV, C.parvum, and 2 groups of BRoV: group A (BRoV A) and group B (BRoV B). Calves were weighed on arrival and at 14, 49, 56, and 77 d using a digital body scale. Treatments for disease and mortalities that occurred over the 77 d were also recorded. Statistical models, including Cox proportional hazards and repeated measures models, were built to determine the effect of infection with 1 of the pathogens. Over the 3 sampling points, 151 (85.8%), 178 (94.2%), 3 (1.5%), and 97 (57.4%) calves tested positive at least once for BCoV, BRoV A, BRoV B, and C.parvum, respectively. The source of the calves and the level of serum total protein measured on arrival were associated with testing positive for a pathogen. Calves that tested positive for C.parvum had an increased proportion of days with diarrhea and severe diarrhea; calves that tested positive for BCoV and BRoV A had an increased proportion of days with severe diarrhea. In addition, calves that tested positive for C.parvum had a higher hazard of being treated for respiratory disease. With respect to body weight, calves that had diarrhea or severe diarrhea had lower body weight at 49, 56, and 77 d. Specifically, calves that had an increased proportion of days with diarrhea showed a reduction in weight gain of up to 15 kg compared to calves without diarrhea. Calves that tested positive for C.parvum had a lower body weight at 49, 56, and 77 d; calves that tested positive for BCoV had a lower body weight at 56 and 77 d. This study demonstrates that the prevalence of BCoV, BRoV A, and C.parvum infection is high in this population of calves and has significant effects on the occurrence of diarrhea and body weight gain. Future studies should evaluate approaches for minimizing the effect of infection with these pathogens to improve the welfare, health, and productivity of dairy calves.


Subject(s)
Cattle Diseases/physiopathology , Coronavirus Infections/veterinary , Coronavirus, Bovine , Cryptosporidiosis/physiopathology , Cryptosporidium parvum , Rotavirus Infections/veterinary , Animals , Cattle , Cattle Diseases/epidemiology , Cattle Diseases/parasitology , Cattle Diseases/virology , Cohort Studies , Coronavirus Infections/epidemiology , Coronavirus Infections/physiopathology , Cryptosporidiosis/parasitology , Diarrhea/parasitology , Diarrhea/veterinary , Diarrhea/virology , Feces/chemistry , Feces/parasitology , Feces/virology , Male , Prevalence , Prospective Studies , Respiratory Tract Diseases/therapy , Respiratory Tract Diseases/veterinary , Rotavirus , Rotavirus Infections/epidemiology , Rotavirus Infections/physiopathology , Weight Gain
8.
Transbound Emerg Dis ; 68(4): 1779-1785, 2021 Jul.
Article in English | MEDLINE | ID: covidwho-944802

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic with millions of infected humans and hundreds of thousands of fatalities. As the novel disease - referred to as COVID-19 - unfolded, occasional anthropozoonotic infections of animals by owners or caretakers were reported in dogs, felid species and farmed mink. Further species were shown to be susceptible under experimental conditions. The extent of natural infections of animals, however, is still largely unknown. Serological methods will be useful tools for tracing SARS-CoV-2 infections in animals once test systems are evaluated for use in different species. Here, we developed an indirect multi-species ELISA based on the receptor-binding domain (RBD) of SARS-CoV-2. The newly established ELISA was evaluated using 59 sera of infected or vaccinated animals, including ferrets, raccoon dogs, hamsters, rabbits, chickens, cattle and a cat, and a total of 220 antibody-negative sera of the same animal species. Overall, a diagnostic specificity of 100.0% and sensitivity of 98.31% were achieved, and the functionality with every species included in this study could be demonstrated. Hence, a versatile and reliable ELISA protocol was established that enables high-throughput antibody detection in a broad range of animal species, which may be used for outbreak investigations, to assess the seroprevalence in susceptible species or to screen for reservoir or intermediate hosts.


Subject(s)
COVID-19 , Cat Diseases , Cattle Diseases , Rodent Diseases , Animals , Antibodies, Viral , COVID-19/veterinary , Cat Diseases/virology , Cats , Cattle , Cattle Diseases/virology , Chickens , Enzyme-Linked Immunosorbent Assay/veterinary , Ferrets , Humans , Mice , Rabbits , Rodent Diseases/virology , SARS-CoV-2 , Seroepidemiologic Studies
9.
Viruses ; 12(11)2020 11 10.
Article in English | MEDLINE | ID: covidwho-918257

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.


Subject(s)
Coronavirus Infections/transmission , Coronavirus Infections/veterinary , Coronavirus, Bovine/genetics , Coronavirus, Bovine/pathogenicity , Evolution, Molecular , Genetic Variation , Animals , Cattle , Cattle Diseases/transmission , Cattle Diseases/virology , Coronavirus Infections/epidemiology , Genome, Viral , Livestock , Mutation , Phylogeny , Phylogeography , Recombination, Genetic , Sequence Analysis, DNA , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics , Transportation , United States/epidemiology
10.
Prev Vet Med ; 185: 105196, 2020 Dec.
Article in English | MEDLINE | ID: covidwho-894168

ABSTRACT

A total of 237 faecal specimens from diarrheic calves younger than two months were collected and submitted for diagnosis of enteropathogens over a two-year period (2017-2018) to a veterinary laboratory. Samples originated from 193 dairy and beef farms in 29 provinces distributed throughout Spain, and were tested for the occurrence of three target enteric pathogens by reverse transcription real-time PCR (RT-qPCR): bovine rotavirus A (RVA), Cryptosporidium parvum and bovine coronavirus (BCoV). RT-PCR and nucleotide sequencing analysis were used to determine the G (VP7 gene) and P (VP4 gene) genotypes of 26 specimens positive for RVA. A total of 188 specimens (79.3 %) were positive for at least one of the three target enteric pathogens, and 101 samples (42.6 %) harbored mixed infections. The individual prevalence was 57.8 %, 50.6 % and 23.6 % for C. parvum, RVA and BCoV, respectively. Molecular analysis of selected RVA strains revealed the presence of the G6, G10, G3, P[5] and P[11] genotypes, with the combinations G6P[5] and G6P[11] being the most prevalent. Alignments of nucleotide sequences of the VP7 and VP4 markers showed a high frequency of single nucleotide polymorphisms (SNPs), with up to 294 SNPs found in 869bp of sequence at the G6 genotype (0.338 SNPs/nt), which reveals the extensive genetic diversity of RVA strains. Phylogenetic analysis of the VP7 gene of the G6 strains revealed four distinct lineages, with most strains clustering in the G6-IV lineage. The discrepancies between the RVA genotypes circulating in the sampled cattle farms and the genotypes contained in commercial vaccines currently available in Spain are discussed. We believe that this is the first study on the molecular characterization of rotavirus infecting cattle in Spain.


Subject(s)
Cattle Diseases/virology , Diarrhea/veterinary , Rotavirus Infections/veterinary , Rotavirus/genetics , Animals , Cattle , Cattle Diseases/epidemiology , Coinfection , Coronavirus/isolation & purification , Coronavirus Infections/epidemiology , Coronavirus Infections/veterinary , Coronavirus Infections/virology , Cryptosporidiosis/complications , Cryptosporidiosis/epidemiology , Cryptosporidium parvum/isolation & purification , Diarrhea/epidemiology , Diarrhea/virology , Feces/virology , Genetic Variation , Genotype , Rotavirus Infections/epidemiology , Rotavirus Infections/virology , Spain/epidemiology
11.
BMC Vet Res ; 16(1): 405, 2020 Oct 27.
Article in English | MEDLINE | ID: covidwho-895005

ABSTRACT

BACKGROUND: Apart from the huge worldwide economic losses often occasioned by bovine coronavirus (BCoV) to the livestock industry, particularly with respect to cattle rearing, continuous surveillance of the virus in cattle and small ruminants is essential in monitoring variations in the virus that could enhance host switching. In this study, we collected rectal swabs from a total of 1,498 cattle, sheep and goats. BCoV detection was based on reverse transcriptase polymerase chain reaction. Sanger sequencing of the partial RNA-dependent RNA polymerase (RdRp) region for postive samples were done and nucleotide sequences were compared with homologous sequences from the GenBank. RESULTS: The study reports a BCoV prevalence of 0.3%, consisting of 4 positive cases; 3 goats and 1 cattle. Less than 10% of all the animals sampled showed clinical signs such as diarrhea and respiratory distress except for high temperature which occurred in > 1000 of the animals. However, none of the 4 BCoV positive animals manifested any clinical signs of the infection at the time of sample collection. Bayesian majority-rule cladogram comparing partial and full length BCoV RdRp genes obtained in the study to data from the GenBank revealed that the sequences obtained from this study formed one large monophyletic group with those from different species and countries. The goat sequences were similar to each other and clustered within the same clade. No major variations were thus observed between our isolates and those from elsewhere. CONCLUSIONS: Given that Ghana predominantly practices the extensive and semi-intensive systems of animal rearing, our study highlights the potential for spillover of BCoV to small ruminants in settings with mixed husbandry and limited separation between species.


Subject(s)
Cattle Diseases/virology , Coronavirus Infections/veterinary , Coronavirus, Bovine/isolation & purification , Goat Diseases/virology , Sheep Diseases/virology , Animals , Base Sequence , Bayes Theorem , Cattle , Cattle Diseases/epidemiology , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Coronavirus, Bovine/genetics , Diarrhea/veterinary , Ghana/epidemiology , Goat Diseases/epidemiology , Goats , Phylogeny , Prevalence , RNA-Dependent RNA Polymerase/genetics , Respiratory Distress Syndrome/veterinary , Reverse Transcriptase Polymerase Chain Reaction/veterinary , Sheep , Sheep Diseases/epidemiology
12.
Transbound Emerg Dis ; 68(4): 1824-1834, 2021 Jul.
Article in English | MEDLINE | ID: covidwho-842343

ABSTRACT

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causing coronavirus disease-2019 (COVID-19) likely has evolutionary origins in other animals than humans based on genetically related viruses existing in rhinolophid bats and pangolins. Similar to other animal coronaviruses, SARS-CoV-2 contains a functional furin cleavage site in its spike protein, which may broaden the SARS-CoV-2 host range and affect pathogenesis. Whether ongoing zoonotic infections are possible in addition to efficient human-to-human transmission remains unclear. In contrast, human-to-animal transmission can occur based on evidence provided from natural and experimental settings. Carnivores, including domestic cats, ferrets and minks, appear to be particularly susceptible to SARS-CoV-2 in contrast to poultry and other animals reared as livestock such as cattle and swine. Epidemiologic evidence supported by genomic sequencing corroborated mink-to-human transmission events in farm settings. Airborne transmission of SARS-CoV-2 between experimentally infected cats additionally substantiates the possibility of cat-to-human transmission. To evaluate the COVID-19 risk represented by domestic and farmed carnivores, experimental assessments should include surveillance and health assessment of domestic and farmed carnivores, characterization of the immune interplay between SARS-CoV-2 and carnivore coronaviruses, determination of the SARS-CoV-2 host range beyond carnivores and identification of human risk groups such as veterinarians and farm workers. Strategies to mitigate the risk of zoonotic SARS-CoV-2 infections may have to be developed in a One Health framework and non-pharmaceutical interventions may have to consider free-roaming animals and the animal farming industry.


Subject(s)
COVID-19 , Cattle Diseases , Swine Diseases , Animals , COVID-19/veterinary , Cattle , Cattle Diseases/virology , Ferrets , Humans , Macaca mulatta , Phylogeny , Rabbits , SARS-CoV-2 , Seroepidemiologic Studies , Swine , Swine Diseases/virology
13.
Transbound Emerg Dis ; 68(4): 2209-2218, 2021 Jul.
Article in English | MEDLINE | ID: covidwho-838157

ABSTRACT

Bovine respiratory disease (BRD) has a complex pathogenesis and aetiology, being the costliest disease affecting the cattle industry in North America. In this study, we applied Nanopore-based viral metagenomic sequencing to explore the nasal virome of cattle upon arrival at feedlot and related the findings to the development of BRD. Deep nasal swabs (DNS) from 310 cattle for which BRD outcomes were known (155 cattle developed BRD within 40 days and 155 remained healthy) were included. The most prevalent virus in on-arrival samples was bovine coronavirus (BCV) (45.2%, 140/310), followed by bovine rhinitis virus B (BRBV) (21.9%, 68/310), enterovirus E (EVE) (19.6%, 60/310), bovine parainfluenza virus 3 (BPIV3) (10.3%, 32/310), ungulate tetraparvovirus 1 (UTPV1) (9.7%, 30/310) and influenza D virus (7.1%, 22/310). No relationship was found between BRD development and the number of viruses detected, the presence of any specific individual virus or combination of viruses. Bovine kobuvirus (BKV) was detected in 2.6% of animals (8/310), being the first report of this virus in Canada. Results of this study demonstrate the diversity of viruses in bovine DNS collected upon arrival at feedlot and highlights the need for further research into prediction of BRD development in the context of mixed infections.


Subject(s)
Cattle Diseases , Coronavirus, Bovine , Respiratory Tract Diseases/veterinary , Animals , Canada/epidemiology , Cattle , Cattle Diseases/epidemiology , Cattle Diseases/virology , Respiratory Tract Diseases/virology , Virome , Viruses
14.
Arch Virol ; 165(12): 3011-3015, 2020 Dec.
Article in English | MEDLINE | ID: covidwho-833995

ABSTRACT

The hemagglutinin-esterase (HE) protein of betacoronavirus lineage A is a secondary receptor in the infection process and is involved in the emergence of new betacoronavirus genotypes with altered host specificity and tissue tropism. We previously reported a novel recombinant bovine coronavirus (BCoV) strain that was circulating in dairy cattle in China, but this virus was not successfully isolated, and the genetic characteristics of BCoV are still largely unknown. In this study, 20 diarrheic faecal samples were collected from a farm in Liaoning province that had an outbreak of calf diarrhea (≤ 3 months of age) in November 2018, and all of the samples tested positive for BCoV by RT-PCR. In addition, a BCoV strain with a recombinant HE (designated as SWUN/A1/2018) and another BCoV strain with a recombinant HE containing an insertion (designated as SWUN/A10/2018) were successfully isolated in cell culture (TCID50: 104.25/mL and 104.73/mL, respectively). Unexpectedly, we identified the emergence of a novel BCoV variant characterized by a 12-nt bovine gene insertion in the receptor-binding domain in a natural recombinant HE gene, suggesting a novel evolutionary pattern in BCoV.


Subject(s)
Cattle Diseases/epidemiology , Coronavirus Infections/veterinary , Coronavirus, Bovine/genetics , Diarrhea/veterinary , Hemagglutinins, Viral/genetics , RNA, Viral/genetics , Viral Fusion Proteins/genetics , Animals , Cattle , Cattle Diseases/pathology , Cattle Diseases/virology , China/epidemiology , Coronavirus Infections/epidemiology , Coronavirus Infections/pathology , Coronavirus Infections/virology , Coronavirus, Bovine/classification , Coronavirus, Bovine/isolation & purification , Diarrhea/epidemiology , Diarrhea/pathology , Diarrhea/virology , Evolution, Molecular , Feces/virology , Gene Expression , Genotype , Models, Molecular , Mutagenesis, Insertional , Phylogeny , Protein Structure, Secondary , Reverse Transcriptase Polymerase Chain Reaction , Sequence Analysis, DNA
15.
Emerg Infect Dis ; 26(1): 168-171, 2020 01.
Article in English | MEDLINE | ID: covidwho-829054

ABSTRACT

Influenza D virus (IDV) can potentially cause respiratory diseases in livestock. We isolated a new IDV strain from diseased cattle in Japan; this strain is phylogenetically and antigenically distinguished from the previously described IDVs.


Subject(s)
Cattle Diseases/epidemiology , Orthomyxoviridae Infections/veterinary , Thogotovirus/genetics , Animals , Cattle/virology , Cattle Diseases/virology , Japan/epidemiology , Orthomyxoviridae Infections/epidemiology , Orthomyxoviridae Infections/virology , Phyllachorales , Real-Time Polymerase Chain Reaction/veterinary
16.
Arch Virol ; 165(7): 1577-1583, 2020 Jul.
Article in English | MEDLINE | ID: covidwho-827686

ABSTRACT

Bovine torovirus (BToV) is a diarrhea-causing pathogen. In this study, 92 diarrheic fecal samples from five farms in four provinces in China were collected and tested for BToV using a RT-PCR assay, and 21.73% samples were found to be BToV positive. Moreover, two complete BToV genome sequences (MN073058 and MN073059) were obtained from the clinical samples, which were 28,297 and 28,301 nucleotides in length, respectively. Sequence analysis showed that the two isolates shared 10 identical amino acid mutations in the S protein compared to the complete S sequences of BToV available in the GenBank database. In addition, seven consecutive amino acid mutations were found from aa 1,486 to 1,492 in the S protein of isolate MN073058. Moreover, the two isolates shared one identical amino acid mutation in the receptor binding sites of the HE protein. To the best of our knowledge, this is the first report on the epidemic and genomic characterization of BToV in China, which is helpful for further understanding the genetic evolution of BToV.


Subject(s)
Cattle Diseases/virology , Diarrhea/veterinary , Torovirus Infections/veterinary , Torovirus/isolation & purification , Animals , Cattle , Diarrhea/virology , Feces/virology , Genome, Viral , Genomics , Phylogeny , Torovirus/classification , Torovirus/genetics , Torovirus Infections/virology , Viral Proteins/genetics
17.
Vet Clin North Am Food Anim Pract ; 36(2): 321-332, 2020 Jul.
Article in English | MEDLINE | ID: covidwho-825203

ABSTRACT

Advances in viral detection in bovine respiratory disease (BRD) have resulted from advances in viral sequencing of respiratory tract samples. New viruses detected include influenza D virus, bovine coronavirus, bovine rhinitis A, bovine rhinitis B virus, and others. Serosurveys demonstrate widespread presence of some of these viruses in North American cattle. These viruses sometimes cause disease after animal challenge, and some have been found in BRD cases more frequently than in healthy cattle. Continued work is needed to develop reagents for identification of new viruses, to confirm their pathogenicity, and to determine whether vaccines have a place in their control.


Subject(s)
Cattle Diseases/virology , Coronavirus, Bovine/genetics , Diarrhea Viruses, Bovine Viral/genetics , Genetic Testing/veterinary , Herpesvirus 1, Bovine/genetics , Respiratory Tract Diseases/veterinary , Animals , Cattle , Coronavirus, Bovine/isolation & purification , Diarrhea Viruses, Bovine Viral/isolation & purification , Genomics/methods , Herpesvirus 1, Bovine/isolation & purification , Respiratory Tract Diseases/virology
18.
Vet Microbiol ; 241: 108544, 2020 Feb.
Article in English | MEDLINE | ID: covidwho-823170

ABSTRACT

Cattle, goats and sheep are dominant livestock species in sub-Saharan Africa, with sometimes limited information on the prevalence of major infectious diseases. Restrictions due to notifiable epizootics complicate the exchange of samples in surveillance studies and suggest that laboratory capacities should be established domestically. Bovine Coronavirus (BCoV) causes mainly enteric disease in cattle. Spillover to small ruminants is possible. Here we established BCoV serology based on a recombinant immunofluorescence assay for cattle, goats and sheep, and studied the seroprevalence of BCoV in these species in four different locations in the Greater Accra, Volta, Upper East, and Northern provinces of Ghana. The whole sampling and testing was organized and conducted by a veterinary school in Kumasi, Ashanti Region of Ghana. Among sampled sheep (n = 102), goats (n = 66), and cattle (n = 1495), the seroprevalence rates were 25.8 %, 43.1 % and 55.8 %. For cattle, seroprevalence was significantly higher on larger farms (82.2 % vs 17.8 %, comparing farms with >50 or <50 animals; p = 0.027). Highest prevalence was seen in the Northern province with dry climate, but no significant trend following the north-south gradient of sampling sites was detected. Our study identifies a considerable seroprevalence for BCoV in Ghana and provides further support for the spillover of BCoV to small ruminants in settings with mixed husbandry and limited separation between species.


Subject(s)
Cattle Diseases/epidemiology , Coronavirus Infections/veterinary , Coronavirus, Bovine/immunology , Goat Diseases/epidemiology , Sheep Diseases/epidemiology , Age Distribution , Animals , Cattle , Cattle Diseases/immunology , Cattle Diseases/transmission , Cattle Diseases/virology , Cluster Analysis , Coronavirus Infections/epidemiology , Coronavirus Infections/immunology , Coronavirus Infections/transmission , Cross-Sectional Studies , Female , Ghana/epidemiology , Goat Diseases/immunology , Goat Diseases/transmission , Goat Diseases/virology , Goats , Lactation , Male , Multivariate Analysis , Risk Factors , Seroepidemiologic Studies , Sex Distribution , Sheep , Sheep Diseases/immunology , Sheep Diseases/transmission , Sheep Diseases/virology
19.
Viruses ; 12(2)2020 02 06.
Article in English | MEDLINE | ID: covidwho-789512

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.


Subject(s)
Cattle Diseases/virology , Coronavirus Infections/veterinary , Coronavirus, Bovine/classification , Coronavirus, Bovine/genetics , Animals , Cattle , Cattle Diseases/epidemiology , Cell Line, Tumor , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Coronavirus, Bovine/isolation & purification , Evolution, Molecular , Genetic Variation , Genome, Viral/genetics , Genotype , Humans , Japan/epidemiology , Phylogeny , RNA, Viral/genetics , Sequence Analysis, DNA , Spike Glycoprotein, Coronavirus/genetics
20.
Med Lav ; 111(4): 321-325, 2020 Aug 31.
Article in English | MEDLINE | ID: covidwho-738017

ABSTRACT

Although Bernardino Ramazzini is usually regarded only as the father of occupational medicine, his approach to fight the devastating rinderpest epidemic in 1711 is worth mentioning in the light of the public health emergency represented by Coronavirus Disease-2019 (COVID-19). This commentary (i) focuses on Ramazzini's xiii oration describing that event, (ii) analyses the approach suggested to fight the cattle epidemic and economic threats, (iii) highlights some similar aspects between the 1711 rinderpest epidemic and the current COVID-19 pandemic (team expertise, contagion transmissibility, drug treatment, preventive measures, decision timeliness).


Subject(s)
Cattle Diseases/history , Coronavirus Infections/epidemiology , Pneumonia, Viral/epidemiology , Rinderpest/history , Animals , Betacoronavirus , COVID-19 , Cattle , Cattle Diseases/virology , History, 18th Century , Humans , Pandemics , Public Health , SARS-CoV-2
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