Improved detection of bovine coronavirus N gene in faeces of calves infected naturally by a semi-nested PCR assay and an internal control

Bovine Coronavirus in diarrheic pre-weaned calves in Egypt: prevalence, risk factors, and the associated biochemical alterations

Bovine coronavirus (BCoV) is a common viral enteric pathogen responsible for diarrhea in newborn calves. Despite its economic significance, there is limited research on this virus in Egypt. This study aimed to detect the prevalence of BCoV, the associated risk factors, and the biochemical changes during infection. A cross-sectional study included 196 pre-weaned diarrheic calves chosen randomly from 16 farms. Fecal samples were obtained from these diarrheic calves, and a questionnaire was administered to investigate the positivity of BCoV and the potential risk factors. Moreover, blood samples were collected to evaluate the biochemical changes in the infected calves. Logistic regression models were used to assess the strength of the risk factors associated with bovine coronavirus. The prevalence of BCoV among pre-weaned diarrheic calves was 11.22%. The final multivariate analysis revealed that the infection of BCoV was 3.8, 5.96, and 3.2 times higher in males, age ≥ 15 days, and winter season than in female calves, age < 15 days, and other seasons, respectively. The acute phase proteins and the inflammatory biomarkers were changed in infected calves compared to healthy ones. The results indicated that calf age, gender, and exposure to cold temperatures were potential risk factors for BCoV infection. Conversely, no evidence was found to support the hypothesis that BCoV prevalence is linked to locality or ground type. Moreover, the observed biochemical changes in calves with BCoV could assist in the early diagnosis of the infection and provide valuable insights for evaluating prognosis.

Establishment of an indirect ELISA method for detecting bovine coronavirus antibodies based on N protein

Bovine Coronavirus (BCoV) is a significant pathogen responsible for neonatal calf diarrhea, winter dysentery in adult cattle, and bovine respiratory diseases. Infection with the virus can result in hemorrhagic diarrhea, decreased milk production, and potentially fatal outcomes in cattle, leading to considerable economic repercussions for the cattle industry. Efficient management of BCoV relies on swift and precise detection techniques. CHO cells were utilized to express a secreted recombinant nucleocapsid protein (N), whereby rabbit polyclonal antibodies (pAb) were generated through immunization. An indirect enzyme-linked immunosorbent assay (iELISA) based on N protein was established for the detection of BCoV antibodies. Reaction conditions were optimized using a checkerboard approach, with the optimal antigen concentration at 1.25 μg/mL and the optimal antibody dilution at 1:200, the cutoff value distinguishing negative and positive serum samples was 0.986. The sensitivity test indicated that this rabbit pAb had a maximum dilution of 218 within the assay range, did not cross-react with BHV-1, BVDV, BRV, and BRSV positive serum samples, and shown great specificity. The developed iELISA method and commercial kit were used to test 58 bovine serum samples, and the concordance rate was 94.83%. In summary, we have developed a cost-efficient and precise iELISA method based on N protein that serves as a useful diagnostic tool for BCoV in clinical samples and epidemiological research.

Molecular detection of coronavirus in camelids and bovines using real-time quantitative polymerase chain reaction in Wasit Province, Iraq

Background

Coronaviruses (CoVs) are a diverse group of RNA viruses that cause respiratory and gastrointestinal diseases in humans and animals. Over the past two decades, outbreaks of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) and bovine coronavirus (BCoV) have affected animal populations, especially in regions with close animal-human interactions, such as the Arabian Peninsula and Iraq. Given the potential for zoonotic transmission, understanding the prevalence and spread of CoVs among livestock is essential for managing potential risks to animal and human health.

Aim

This study aimed to investigate the prevalence of MERS-CoV in camels and BCoV in bovines within the Wasit Governorate of Iraq to assess the infection rates and potential interspecies transmission risks.

Methods

One hundred and fifty nasal swab samples (75 from camels and 75 from bovines) were collected between November 2022 and April 2023. The samples were analyzed for the presence of MERS-CoV and BCoV using real- time quantitative reverse transcription PCR (qRT-PCR) targeting the nucleocapsid (N) gene for each virus. Standard procedures for RNA extraction were followed, and qRT-PCR assays were conducted using specific primers to ensure high sensitivity and specificity.

Results

MERS-CoV was present in (42%) of the camel samples, whereas BCoV was detected in (34%) of the bovine samples. Statistical analysis indicated a significant difference (p < 0.05) in infection rates between camels and bovines, with a higher prevalence observed in camels. The clinical signs observed in infected camels included fever, nasal discharge, and appetite loss, whereas infected bovines exhibited symptoms such as diarrhea and respiratory distress.

Conclusion

The high prevalence of MERS-CoV and BCoV in camels and bovines in the Wasit region indicates a substantial risk for the continued spread of these viruses within animal populations. These findings underscore the importance of surveillance and biosecurity measures to control the spread of coronavirus among livestock, potentially reducing zoonotic transmission risks. Further research is required to understand the transmission dynamics of CoVs in mixed livestock farming systems.

Specific and sensitive detection of bovine coronavirus using CRISPR-Cas13a combined with RT-RAA technology

Introduction

Bovine coronavirus (BCoV) is an important pathogen of enteric and respiratory disease in cattle, resulting in huge economic losses to the beef and dairy industries worldwide. A specific and sensitive detection assay for BCoV is critical to the early-stage disease prevention and control.

Methods

We established a specific, sensitive, and stable assay for BCoV nucleic acid detection based on CRISPR/Cas13a combined with reverse transcription recombinase-aided amplification (RT-RAA) technology. The specific primers for RT-RAA and CRISPR RNA (crRNA) were designed in the conserved region of the BCoV nucleocapsid (N) gene.

Results

The detection limit of the RT-RAA CRISPR/Cas13a assays for BCoV detection was 1.72 copies/μl, and there were no cross-reactions with the other 10 common bovine enteric and respiratory disease-associated pathogens. The coefficient of variations (CVs) of within and between batches were less than 4.98 and 4.58%, respectively. The RT-RAA-CRISPR/Cas13a assays work well in clinical samples of cattle and yak, the BCoV positive rate of 84 clinical samples detected by RT-RAA-CRISPR/Cas13a assays was 58.3% (49/84), it was notably higher than that of RT-qPCR (2.4%, 2/84; p < 0.001). The 49 positive samples detected by RT-RAA-CRISPR/Cas13a assays were further confirmed as BCoV by Sanger sequencing.

Discussion

A specific, sensitive, and stable assay based on RT-RAA-CRISPR/Cas13a assays for BCoV was developed, providing new technical support for the clinical detection and epidemiological monitoring of BCoV.

Comparative Insights into Acute Gastroenteritis in Cattle Caused by Bovine Rotavirus A and Bovine Coronavirus

Acute gastroenteritis (AGE) in cattle significantly impacts the economy due to relatively high morbidity and mortality and decreased production. Its multifactorial nature drives its global persistence, involving enteric viruses, bacteria, protozoa, and environmental factors. Bovine Rotavirus A (BoRVA) and bovine coronavirus (BCoV) are among the most important enteric RNA viruses causing AGE in cattle. These viruses infect intestinal enterocytes, leading to cell damage and consequently to malabsorption and diarrhea. BoRVA primarily affects calves under 14 days old with gastrointestinal clinical signs, while BCoV affects all ages, causing gastrointestinal and respiratory distress. The economic impact of BoRVA and BCoV, along with their interspecies transmission potential, warrants attention. This concise review discusses the molecular structure, epidemiology, pathogenesis, clinical signs, diagnosis, treatment, and preventive measures of BoRVA and BCoV while providing a comparative analysis. By offering practical guidance on managing such viral infections in cattle, these comparative insights may prove valuable for veterinarians in clinical practice.

Respiratory illness in young and adult cattle caused by bovine viral diarrhea virus subgenotype 2b in singular and mixed bacterial infection in a BVDV-vaccinated dairy herd

Bovine respiratory disease (BRD) is a common global health problem in dairy cattle. The definitive diagnosis of BRD is complex because its etiology involves several predisposing and determining factors. This report describes the etiology of a BRD outbreak in a dairy herd in the mesoregion of Central Eastern Paraná, which simultaneously affected young (calves and heifers) and adult (cows) Holstein-Friesian cattle. Nine biological samples, consisting of five lung samples from two cows and three suckling calves, and four nasal swab samples from heifers, were used for etiological diagnosis. The nucleic acids extracted from lung fragments and nasal swabs were subjected to PCR and RT-PCR assays for partial amplification of the genes of five viruses [bovine viral diarrhea virus (BVDV), bovine alphaherpesvirus 1 (BoAHV1), bovine respiratory syncytial virus (BRSV), bovine parainfluenza virus 3 (BPIV-3), and bovine coronavirus (BCoV)] and four bacteria (Mycoplasma bovis, Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni) involved in the etiology of BRD. All nine biological samples from the animals with BRD tested negative for BoAHV1, BRSV, BPIV-3, BCoV, and H. somni. Therefore, the involvement of these microorganisms in the etiology of BRD outbreak can be ruled out. It was possible to identify the presence of BVDV and M. bovis in singular and mixed infections of the lower respiratory tract in cattle. BVDV was also identified in two nasal swabs: one as a single etiological agent and the other in association with two bacteria (P. multocida and M. haemolytica). The phylogenetic analysis conducted in the nucleotide sequence of the 5'UTR region and Npro gene of the BVDV amplicons demonstrated that the BVDV field strains of this BRD outbreak belong to subgenotype 2b. To the best of our knowledge, this is the first report of BVDV-2b involvement in the etiology of BRD in Brazil. Finally, it is necessary to highlight that the cattle were obtained from an open dairy herd with biannual vaccinations for BVDV-1a and - 2a.

Microbiological Profile of the Upper and Lower Respiratory Tract of Suckling and Weaned Dairy Calves with Acute Respiratory Disease

Bovine respiratory disease (BRD) is a significant global health issue in cattle farming, leading to substantial economic losses. This study analyzed the microbiological profiles of BRD outbreaks in nine dairy cattle herds in southern Brazil. We examined 36 biological samples, including 24 deep nasopharyngeal swabs (NS) and 12 lung tissue, from 29 suckling and 7 weaned heifer calves with acute BRD. PCR and RT-PCR techniques were used to partially amplify the genes of five viruses and four respiratory bacteria. A total of 8 different microorganisms, 4 viruses (bovine viral diarrhea virus, n = 5; bovine coronavirus, n = 3; bovine alphaherpesvirus 1, n = 3; and bovine parainfluenza virus 3, n = 2), and 4 bacteria (Pasteurella multocida, n = 16; Mycoplasma bovis, n = 8; Histophilus somni, n = 7; and Mannheimia haemolytica, n = 4) were identified in 29 (80.5%) samples. Seven samples (four lung tissue and three NS) were negative for all the microorganisms. Mixed infections were more common (62.1%) than single infections (37.9%). Bacterial nucleic acids were more commonly co-detected in NS than in lung tissue. Nucleic acids from a single pathogen were more frequently detected in lung tissues than in NS. M. bovis was the only bacterium detected in the lower respiratory tract. Understanding the microbiological profiles of the respiratory tracts of dairy calves with clinical signs of BRD is crucial for implementing effective biosecurity measures to prevent BRD in suckling and weaned dairy heifer calves.

Development of the Intestinal Microbiota of Dairy Calves and Changes Associated with Cryptosporidium spp. Infection in Brazil

Cryptosporidium spp. is one of the most important pathogens infecting nursing calves worldwide. This study aimed to investigate the intestinal microbiota of dairy calves during the first month of life and the impact of diarrhea caused by Cryptosporidium on a Brazilian farm. Fecal samples from 30 calves were collected during the first month of life, and fecal scores were recorded. Samples from the second, third, and fourth days of life were analyzed by DNA sequencing of the 16S rRNA gene. In addition, samples of sixteen calves positive for Cryptosporidium spp. were retrospectively chosen according to the development of diarrhea: four and two days before diarrhea, at the onset of diarrhea, after four days of diarrhea, at the end of diarrhea, and after six days of diarrhea resolution. Diarrhea was observed in all calves (100%), starting at day 5 of life, and all calves tested positive for Cryptosporidium in at least one sample. The microbiota richness increased with age but was retarded by diarrhea. Compositional changes associated with Cryptosporidium infection included increases in Fusobacterium, Prevotella, and Peptostreptococcus, as well as decreases in Collinsella and Lachnospiraceae. In conclusion, Cryptosporidium infection has the potential to decrease richness and change the composition of the intestinal microbiota of dairy calves.

Screening of Bovine Coronavirus Multiepitope Vaccine Candidates: An Immunoinformatics Approach

Bovine coronavirus (BCoV) is a causative agent of enteric and respiratory disease in cattle. BCoV has been reported to cause a variety of animal diseases and is closely related to human coronaviruses; moreover, it has attracted extensive attention from both cattle farmers and researchers. With the rise of BCoV, a vaccine that is prophylactic and immunotherapeutic has to be utilized for a preemptive and adroit therapeutic approach. The aim of this study was to develop a novel multiepitope-based BCoV vaccine that can induce an immune response using a silicon reverse vaccinology approach. In this study, an immunoinformatics approach was employed to identify potential vaccine targets against BCoV, and four candidate antigen proteins were selected to predict B-cell and T-cell epitopes. To identify dominant epitopes, we employed a variety of bioinformatics techniques, including antigenicity prediction, immunogenicity assessment, allergenicity analysis, conservative analysis, and toxicity assessment. Finally, six multiepitope vaccines were developed using dominant epitopes, suitable adjuvants, Pan HLADR-binding epitope (PADRE), and linkers. Then based on the antigenicity score, solubility analysis, allergenicity evaluation, physicochemical property assessment, and tertiary structure verification score, construct 6 was selected as the best candidate vaccine; it was named CY. Molecular modeling and structural validation ensured the high-quality 3D structure of construct CY. The immunogenicity and complex stability of the vaccine were evaluated by molecular docking and kinetic simulation. In silicon clones, the BCoV vaccine had high levels of gene expression in the insect expression system. These results may contribute to the development of experimental BCoV vaccines with higher potency and safety.

Advances in Laboratory Diagnosis of Coronavirus Infections in Cattle

Coronaviruses cause infections in humans and diverse species of animals and birds with a global distribution. Bovine coronavirus (BCoV) produces predominantly two forms of disease in cattle: a respiratory form and a gastrointestinal form. All age groups of cattle are affected by the respiratory form of coronavirus, whereas the gastroenteric form causes neonatal diarrhea or calf scours in young cattle and winter dysentery in adult cattle. The tremendous impacts of bovine respiratory disease and the associated losses are well-documented and underscore the importance of this pathogen. Beyond this, studies have demonstrated significant impacts on milk production associated with outbreaks of winter dysentery, with up to a 30% decrease in milk yield. In North America, BCoV was identified for the first time in 1972, and it continues to be a significant economic concern for the cattle industry. A number of conventional and molecular diagnostic assays are available for the detection of BCoV from clinical samples. Conventional assays for BCoV detection include virus isolation, which is challenging from clinical samples, electron microscopy, fluorescent antibody assays, and various immunoassays. Molecular tests are mainly based on nucleic acid detection and predominantly include conventional and real-time polymerase chain reaction (PCR) assays. Isothermal amplification assays and genome sequencing have gained increased interest in recent years for the detection, characterization, and identification of BCoV. It is believed that isothermal amplification assays, such as loop-mediated isothermal amplification and recombinase polymerase amplification, among others, could aid the development of barn-side point-of-care tests for BCoV. The present study reviewed the literature on coronavirus infections in cattle from the last three and a half decades and presents information mainly on the current and advancing diagnostics in addition to epidemiology, clinical presentations, and the impact of the disease on the cattle industry.

A comprehensive molecular analysis of bovine coronavirus strains isolated from Brazil and comparison of a wild-type and cell culture-adapted strain associated with respiratory disease

Bovine coronavirus (BCoV) has dual tropisms that can trigger enteric and respiratory diseases in cattle. Despite its global distribution, BCoV field strains from Brazil remain underexplored in studies investigating the virus's worldwide circulation. Another research gap involves the comparative analysis of S protein sequences in BCoV isolates from passages in cell lines versus direct sequencing from clinical samples. Therefore, one of the objectives of our study was to conduct a comprehensive phylogenetic analysis of BCoV strains identified from Brazil, including a respiratory strain obtained during this study, comparing them with global and ancestral BCoV strains. Additionally, we performed a comparative analysis between wild-type BCoV directly sequenced from the clinical sample (nasal secretion) and the cell culture-adapted strain, utilizing the Sanger method. The field strain and multiple cell passage in cell culture (HRT-18) adapted BCoV strain (BOV19 NS) detected in this study were characterized through molecular and phylogenetic analyses based on partial fragments of 1,448 nt covering the hypervariable region of the S gene. The analyses have demonstrated that different BCoV strains circulating in Brazil, and possibly Brazilian variants, constitute a new genotype (putative G15 genotype). Compared with the ancestral prototype (Mebus strain) of BCoV, 33 nt substitutions were identified of which 15 resulted in non-synonymous mutations (nine transitions and six transversions). Now, compared with the wild-type strain was identified only one nt substitution in nt 2,428 from the seventh passage onwards, which resulted in transversion, neutral-neutral charge, and one substitution of asparagine for tyrosine at aa residue 810 (N810Y).

The Role of Mycoplasma bovirhinis in the Development of Singular and Concomitant Respiratory Infections in Dairy Calves from Southern Brazil

The role of Mycoplasma bovirhinis in the development of pulmonary disease in cattle is controversial and was never evaluated in cattle from Latin America. This study investigated the respiratory infection dynamics associated with M. bovirhinis in suckling calves from 15 dairy cattle herds in Southern Brazil. Nasal swabs were obtained from asymptomatic (n = 102) and calves with clinical manifestations (n = 103) of bovine respiratory disease (BRD) and used in molecular assays to identify the specific genes of viral and bacterial disease pathogens of BRD. Only M. bovirhinis, bovine coronavirus (BCoV), ovine gammaherpesvirus 2 (OvGHV2), Histophilus somni, Pasteurella multocida, and Mannheimia haemolytica were detected. M. bovirhinis was the most frequently diagnosed pathogen in diseased (57.8%; 59/102) and asymptomatic (55.3%; 57/103) calves at all farms. BCoV-related infections were diagnosed in diseased (52%; 53/102) and asymptomatic (51.4%; 53/103) calves and occurred in 93.3% (14/15) of all farms. Similarly, infectious due to OvGHV2 occurred in diseased (37.2%; 38/102) and asymptomatic (27.2%; /28/103) calves and were diagnosed in 80% (12/15) of all farms investigated. Significant statistical differences were not identified when the two groups of calves were compared at most farms, except for infections due to OvGHV2 that affected five calves at one farm. These results demonstrated that the respiratory infection dynamics of M. bovirhinis identified in Southern Brazil are similar to those observed worldwide, suggesting that there is not enough sufficient collected data to consider M. bovirhinis as a pathogen of respiratory infections in cattle. Additionally, the possible roles of BCoV and OvGHV2 in the development of BRD are discussed.

Neglected bacterial infections associated to bovine respiratory disease in lactating cows from high-yielding dairy cattle herds

Bovine respiratory disease (BRD) is a multifactorial and predominantly multietiological disease that affects dairy cattle herds worldwide, being more frequent in young animals. The occurrence of BRD was investigated in lactating cows from two high-yielding dairy herds in southern Brazil. To determine the etiology of the clinical cases of acute respiratory disease, nasal swab samples were collected from cows with clinical signs of BRD and evaluated using PCR and RT-PCR for nucleic acid detection of the main BRD etiological agents, including Mycoplasma bovis, Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, bovine respiratory syncytial virus, bovine coronavirus, bovine viral diarrhea virus, bovine alphaherpesvirus 1, and bovine parainfluenza virus 3. Only three microorganisms (M. bovis, H. somni, and P. multocida) were identified in both single and mixed infections. We concluded that 40.0% of the cows were infected with M. bovis and 75.0% with H. somni in herd A. Considering both single and mixed infections, the analyses performed in herd B showed that 87.5%, 25.0%, and 50.0% of the cows were infected with M. bovis, H. somni, and P. multocida, respectively. M. bovis and H. somni are considered fastidious bacteria and laboratory diagnosis is neglected. Subsequently, most clinical cases of mycoplasmosis and histophilosis in cattle remain undiagnosed. This study demonstrates the importance of M. bovis and H. somni infections in adult cows with BRD. These results highlight the importance of including these bacteria in the group of etiological agents responsible for the occurrence of BRD in cattle, especially in adult cows with unfavorable immunological conditions, such as recent calving and peak lactation.

Histophilus somni disease conditions with simultaneous infections by ovine gammaherpesvirus 2 in cattle herds from Southern Brazil

This report investigated the cause of cattle mortality in two farms in Southern Brazil. The tissues of one animal from each farm (animals #1 and #2) respectively were used in pathological and molecular investigations to determine the possible cause of death. The principal pathological findings observed in animal #1 were pulmonary, myocardial, and encephalitic hemorrhages with vasculitis, and lymphoplasmacytic interstitial pneumonia with proliferative vascular lesions (PVL). The main pathological findings observed in animal #2 were purulent bronchopneumonia, hemorrhagic myocarditis, and lymphoplasmacytic interstitial pneumonia with PVL. An immunohistochemical assay detected intralesional antigens of a malignant catarrhal fever virus (MCFV) from multiple tissues of animal #2 while PCR confirmed that the MCFV amplified was ovine gammaherpesvirus 2 (OvGHV2), genus Macavirus, subfamily Gammaherpesvirinae; OvGHV2 was also amplified from multiple tissues of animal #1. Furthermore, PCR assays amplified Histophilus somni DNA from multiple fragments of both animals. However, the nucleic acids of Mannheimia haemolytica, Pasteurella multocida, Mycoplasma bovis, bovine respiratory syncytial virus, bovine alphaherpesvirus virus 1 and 5, bovine coronavirus, and bovine parainfluenza virus 3 were not amplified from any of the tissues analyzed, suggesting that these pathogens did not participate in the development of the lesions herein described. These findings demonstrated that both animals were concomitantly infected by H. somni and OvGHV2 and developed the septicemic and encephalitic manifestations of H. somni. Furthermore, the interstitial pneumonia observed in cow #2 was more likely associated with infection by OvGHV2.

Association of ovine gammaherpesvirus 2 with an outbreak of acute respiratory disease in dairy cattle

This study investigated the cause of an outbreak of an acute respiratory disease syndrome followed by episodes of diarrhea in a dairy cattle herd from Southern Brazil. Deep nasal swabs (DNS) from asymptomatic calves, calves with pulmonary discomfort, and diarrheic calves after episodes of respiratory distress were used in molecular assays designed to detect the principal pathogens associated with bovine respiratory disease (BRD). Fecal samples were used for the molecular detection of bovine enteric disease agents. Pulmonary tissues from three calves and a cow that died were evaluated by molecular assays to identify 11 agents associated with the development of BRD. The intestinal and pulmonary fragments of one calf and the cow revealed atrophic enteritis and interstitial pneumonia by histopathology, respectively. Immunohistochemistry (IHC) identified intralesional antigens of a malignant catarrhal fever virus, genus Macavirus, within epithelial cells of the lungs and intestines. Molecular assays amplified ovine gammaherpesvirus 2 (OvGHV2) from most of the DNS, and the pulmonary and intestinal fragments from the animals that died, confirming that the Macavirus identified by IHC was OvGHV2. Concomitant pulmonary infections of OvGHV2 with bovine gammaherpesvirus 6 and bovine coronavirus were identified. Additionally, bovine viral diarrhea virus 1b and Aichivirus B were detected in the fecal samples. These findings demonstrated that OvGHV2, a Macavirus, was the disease agent most frequently (81.2%; 13/16) associated with singular pulmonary infections during this outbreak of BRD, suggesting that this virus may be another potential agent of respiratory disease of cattle.

[Genetic diversity of Siberian bovine coronavirus isolates (Coronaviridae: Coronavirinae: Betacoronavirus-1: Bovine-Like coronaviruses)]

INTRODUCTION

Bovine coronaviruses (BCoVs) are causative agents of diarrhea, respiratory diseases in calves and winter cow dysentery. The study of genetic diversity of these viruses is topical issue. The purpose of the research is studying the genetic diversity of BCoV isolates circulating among dairy cattle in Siberia.

MATERIALS AND METHODS

Specimens used in this study were collected from animals that died or was forcedly slaughtered before the start of the study. The target for amplification were nucleotide sequences of S and N gene regions.

RESULTS

Based on the results of RT-PCR testing, virus genome was present in 16.3% of samples from calves with diarrheal syndrome and in 9.9% with respiratory syndrome. The nucleotide sequences of S gene region were determined for 18 isolates, and N gene sequences - for 12 isolates. Based on S gene, isolates were divided into two clades each containing two subclades. First subclade of first clade (European line) included 11 isolates. Second one included classic strains Quebec and Mebus, strains from Europe, USA and Korea, but none of sequences from this study belonged to this subclade. 6 isolates belonged to first subclade of second clade (American-Asian line). Second subclade (mixed line) included one isolate. N gene sequences formed two clades, one of them included two subclades. First subclade included 3 isolates (American-Asian line), and second subclade (mixed) included one isolate. Second clade (mixed) included 8 sequences. No differences in phylogenetic grouping between intestinal and respiratory isolates, as well as according to their geographic origin were identified.

CONCLUSION

The studied population of BCoV isolates is heterogeneous. Nucleotide sequence analysis is a useful tool for studying molecular epidemiology of BCoV. It can be beneficial for choice of vaccines to be used in a particular geographic region.

Possible Association of Bovine Gammaherpesvirus 6 with Pulmonary Disease in a Cow

Bovine gammaherpesvirus 6 (BoGHV6), previously known as bovine lymphotropic virus, is a member of the Macavirus genus, subfamily Gammaherpesvirinae. Other members of the genus Macavirus include viruses that produce malignant catarrhal fever (MCF) in mammalian hosts, collectively referred to as the MCF virus (MCFV) complex, and the porcine lymphotropic herpesvirus (PLHV). However, the current role of BoGHV6 in the development of diseases and/or disease syndromes remains uncertain and controversial. This paper investigated the participation of BoGHV6 in the development of pulmonary disease in a cow with interstitial pneumonia by histopathology and molecular testing. Tissue antigens of common viral agents of respiratory diseases and Mycoplasma bovis were not identified by immunohistochemistry. Additionally, molecular assays designed to amplify common bacterial and viral pathogens of pulmonary disease did not amplify the nucleic acids of these agents. However, a pan-PCR assay amplified the DNA of the herpesvirus polymerase gene, while the specific BoGHV6 nested-PCR assay amplified the partial fragment of the BoGHV6 polymerase gene derived from the pulmonary tissue with interstitial pneumonia. Phylogenetic analysis revealed that the BoGHV6 strain herein identified had 99.8% nucleotide (nt) sequence identity with reference strains of BoGHV6, but only 72.2-73.5% and 67.9-68.6% nt identity with reference strains of MCFV and PLHV, respectively. Consequently, these results suggest that BoGHV6 was associated with the pulmonary disease observed in this cow.

Development of a multienzyme isothermal rapid amplification and lateral flow dipstick combination assay for bovine coronavirus detection

Bovine coronavirus (BCoV) is a major cause of infectious disease in cattle, causing huge economic losses to the beef and dairy industries worldwide. BCoV can infect humans and multiple other species of animals. A rapid, reliable, and simple test is needed to detect BCoV infection in suspected farms. In this study, we developed a novel multienzyme isothermal rapid amplification (MIRA) and lateral flow dipstick (LFD) combination assay, targeting a highly conserved region of the viral nucleocapsid (N) gene for BCoV detection. The MIRA-LFD assay was highly specific and sensitive, comparable to a published reverse transcription quantitative PCR (RT-qPCR) assay for BCoV detection. Compared with the published RT-qPCR assay, the κ value of the MIRA-LFD assay in the detection of 192 cattle clinical samples was 0.982. The MIRA-LFD assay did not require sophisticated instruments and the results could be observed with eyes. Our results showed that the MIRA-LFD assay was a useful diagnostic tool for rapid on-site detection of BCoV.

Efficacy of prepartum vaccination against neonatal calf diarrhea in Nelore dams as a prevention measure

Background

Neonatal calf diarrhea (NCD) is the leading cause of calf morbidity and mortality in beef cattle. Cow’s vaccination in last stage of pregnancy is one of the most important measures to mitigate the risk of NCD outbreaks. The aim of this study was to evaluate the efficacy of prepartum single dose vaccination against NCD, especially Bovine Rotavirus type A (BoRVA) and Bovine Coronavirus (BCoV), in Nelore dams and offspring. A total of 117 pregnant cows (n = 81) and heifers (n = 36) were distributed in two groups, vaccinated (VAC: cows = 40; heifers = 19) and non-vaccinated (NVAC: cows = 41; heifers = 17). Vaccination occurred between 60 to 50 days before the expected calving date with a single dose of a water-in-oil (W/O) vaccine, and NVAC group received a dose of saline solution 0.9%. Blood samples were collected before vaccination and 30 days after to evaluate the antibody (Ab) response. Specific IgG1 Abs against BoRVA and BCoV were measured by using an Enzyme Linked Immuno Sorbent Assay (ELISA). Calves’ births were monitored, and the transference of passive immunity was evaluated. Diarrhea was monitored in the first 30 days of age, and fecal samples were collected for identification of the etiological agent.

Results

Higher titers of IgG1 Ab against BoRVA and BCoV was observed in the VAC group than NVAC group in the cow (P < 0.0001) and total dams categories (P < 0.0001). The titer of specific IgG1 Abs in the calves’ serum reflected the dams response, observing higher IgG1 Ab titers for BoRVA (P < 0.0016) and BCoV (P < 0.0095) in the offspring born to VAC cows and higher IgG1 Ab titers for BoRVA(P < 0.0171) and BCoV (P < 0.0200) in the offspring born to VAC total dams. The general incidence of diarrhea observed was 18.6% (11/59) and 29.3% (17/58) in the calves born to the VAC and NVAC group, respectively.

Conclusions

Prepartum vaccination with a single dose of the vaccine tested increased the titers of IgG1 Ab against BCoV and BoRVA, and it could be used as a preventive strategy to decrease the NCD occurrence in Nelore calves.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-022-03391-5.

Bovine Coronavirus Co-infection and Molecular Characterization in Dairy Calves With or Without Clinical Respiratory Disease

Bovine respiratory disease (BRD) is considered a major cause of morbidity and mortality in young calves and is caused by a range of infectious agents, including viruses and bacteria. This study aimed to determine the frequency of viral and bacterial pathogens detected in calves with BRD from high-production dairy cattle herds and to perform the molecular characterization of N and S1 genes in identified bovine coronavirus (BCoV) strains. Nasal swabs were collected from 166 heifer calves, namely, 85 symptomatic and 81 asymptomatic calves aged between 5 and 90 days, from 10 dairy cattle herds. Nasal swabs were evaluated using molecular techniques for the identification of viruses (BCoV, bovine alphaherpesvirus 1, bovine viral diarrhea virus, bovine parainfluenza virus 3, and bovine respiratory syncytial virus) and bacteria (Pasteurella multocida, Mannheimia haemolytica, Histophilus somni, and Mycoplasma bovis). In addition, five and two BCoV-positive samples were submitted to N and S1 gene amplification and nucleotide sequencing, respectively. The frequency of diagnosis of BCoV was higher (56%, 93/166) than the frequency of P. multocida (39.8%, 66/166) and M. haemolytica (33.1%, 55/166). The three microorganisms were identified in the calves of symptomatic and asymptomatic heifer calve groups. All other pathogens included in the analyses were negative. In the phylogenetic analysis of the S1 gene, the Brazilian strains formed a new branch, suggesting a new genotype, called # 15; from the N gene, the strains identified here belonged to cluster II. This study describes high rates of BCoV, P. multocida, and M. haemolytica in heifer calves from high-production dairy cattle herds with BRD. Additionally, the molecular characterization provides evidence that the circulating BCoV strains are ancestrally different from the prototype vaccine strains and even different BCoV strains previously described in Brazil.

Advances in Bovine Coronavirus Epidemiology

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.

Ovine gammaherpesvirus 2 infections in cattle without typical manifestations of sheep-associated malignant catarrhal fever and concomitantly infected with bovine coronavirus

Sheep-associated malignant catarrhal fever (SA-MCF) is a severe, frequently fatal, lymphoproliferative disease that affects a wide variety of ruminants and is caused by ovine gammaherpesvirus 2 (OvHV-2), a member of the MCF virus (MCFV) complex. The typical clinical manifestations of SA-MCF are well known and easily recognized by veterinarians, resulting in clinical diagnosis of MCF when characteristic clinical signs are present. This article describes the findings observed in cattle infected with OvHV-2 but without typical clinical manifestations of SA-MCF. Three calves with episodes of diarrhea before death and a yearling that died suddenly were investigated. Gross alterations were not suggestive of SA-MCF. Histopathology revealed a combination of proliferating vascular lesions (PVLs) and necrotizing vasculitis in three animals (two calves and the yearling); with PVLs being identified only at the carotid rete mirabile of two calves infected with OvHV-2. Additional significant histopathologic lesions included atrophic enteritis, portal lymphocytic hepatitis, interstitial pneumonia, suppurative bacterial bronchopneumonia, and pulmonary hemorrhage. An immunohistochemical assay designed to identify only antigens of MCFV revealed, positive, intralesional, intracytoplasmic immunoreactivity within epithelial cells of multiple tissues of all animals with PVLs. PCR assays amplified OvHV-2 DNA from multiple tissues of the animals that contained MCFV proteins, confirming the MCFV identified as OvHV-2. Additionally, bovine coronavirus (BCoV) nucleic acids were amplified from tissues of all animals, including the animal not infected by OvHV-2. Collectively, these findings confirmed the participation of OvHV-2 in the development of the disease patterns observed in these animals that were concomitantly infected by BCoV and provide additional confirmation that cattle can be subclinically infected with OvHV-2. Consequently, the real occurrence of OvHV-2-related disease may be more elevated than reported, since asymptomatic or subclinically infected animals are not likely to be investigated for OvHV-2. Furthermore, PVLs should be included as possible histologic indicators of OvHV-2-related diseases in ruminants.

Ovine gammaherpesvirus-2 infection associated with chronic interstitial pneumonia in a sheep

Sheep Associated-Malignant Catarrhal Fever (SA-MCF) is severe, frequently lethal, lymphoproliferative disease predominantly of ruminants, that is caused by ovine gammaherpesvirus-2 (OvHV-2), a member of the MCF virus (MCFV) complex. However, SA-MCF in sheep is a rare entity with few demonstrations of natural diseases worldwide. This report documents the clinical, radiographical, pathological, immunohistochemical, and molecular findings of SA-MCF in a sheep. A 4-year-old, female, mixed-breed sheep with progressive emaciation for at least one month was humanely euthanized due to poor prognosis. Clinically, the animal had tachypnea, ruminal hypomotility, productive coughing with bilateral muffling sounds during pulmonary auscultation. Radiographical evaluation revealed alveolar opacity of the cranioventral pulmonary region. Grossly, there were distinct rib impressions on the pleural surface of the lungs, suggestive of interstitial pneumonia. Histopathologic evaluation of the lungs revealed several disease patterns including 1) chronic interstitial pneumonia with vasculitis and proliferating vascular lesions, and thrombosis; 2) pulmonary abscesses associated with embolic dissemination of Corynebacterium pseudotuberculosis from superficial lymph node due to caseous lymphadenitis, CLA; 3) granulomatous pneumonia associated with pulmonary nematodes; and 4) chronic pleuritis, probably due to caseous lymphadenitis. Additional significant histologic findings included widespread lymphocytic vasculitis and proliferating vascular lesions in multiple tissues, atrophic enteritis, segmental degeneration of myocardial fibers with lymphocytic pericarditis, lymphocytic interstitial nephritis, and non-suppurative encephalitis. An immunohistochemistry (IHC) assay, based on the monoclonal antibody 15A (MAb-15A), that is specific to all MCFV known to cause MCF, revealed positive, intracytoplasmic, intralesional immunoreactivity, predominantly within bronchial and bronchiolar epithelial cells of the lungs and cryptal epithelial cells of the small intestine, followed by the renal tubular epithelium, cardiomyocytes, and with patchy immunolabelling within neurons of the cerebral cortex. Molecular testing done to detect a wide range of bacterial and viral agents of ruminant diseases, only amplified OvHV-2 DNA from fresh tissue fragments of the lungs, kidney, liver, spleen, and cerebrum. Direct sequencing confirmed that the PCR amplicon derived from the pulmonary fragments had 99.2-99.7% nucleotide sequence identity with OvHV-2 reference strains and strains of OvHV-2 from Brazil. The clinical, radiographical, gross, histopathologic, IHC, and molecular findings in the lungs are consistent with chronic interstitial pneumonia associated with infection by OvHV-2. Furthermore, the non-detection of other viral agents associated with pulmonary diseases in ruminants suggest that OvHV-2 was directly associated with the development of chronic pneumonia in this sheep. Additionally, the dental alterations, CLA, and the pulmonary nematode may have contributed towards the reduced immunological statue of the animal and facilitated the occurrence of SA-MCF. These findings may indicate that OvHV-2 may be a major participant in the pathogenesis of pulmonary disease of sheep under special conditions. Moreover, the proliferating vascular lesions identified in multiple tissues are additional evidence of chronic manifestations of OvHV-2 infections as described in chronic SA-MCF of cattle, while the widespread vasculitis is consistent with SA-MCF. Additionally, the IHC findings using the MAb-15A confirmed that this diagnostic approach is efficient to identify intralesional antigens of OvHV-2.

Severe outbreak of bovine neonatal diarrhea in a dairy calf rearing unit with multifactorial etiology

This study describes the etiological diversity observed in a severe neonatal diarrhea outbreak with morbidity and mortality rates of 80 and 20%, respectively, with detection of mixed infections with viral, bacterial, and protozoan disease agents in a dairy calf rearing unit. Diarrheic fecal samples were collected from eight 5 to 18 days of age calves and were submitted to the investigation of the presence of rotavirus A (RVA), bovine coronavirus (BCoV), bovine kobuvirus (BKV), bovine viral diarrhea virus 1 and 2 (BVDV-1 and BVDV-2), enteropathogenic Escherichia coli (ETEC), Salmonella sp., and Cryptosporidium spp. Fragments of the small intestine of one calf with diarrhea that spontaneously died were submitted for histopathological analyses. The most frequent infectious agent detected in diarrheic fecal samples was BKV (8/8-100%), followed by RVA (5/8-62.5%), BVDV (5/8-62.5%), Cryptosporidium parvum (5/8-62.5%), ETEC (4/8-50%), and Cryptosporidium ryanae (1/8-12.5%). These etiological agents were found in mixed infections with two or more pathogens per diarrheic fecal sample. The association of viral and protozoan pathogens was the most frequently identified (37.5%) in these samples, followed by viral and bacterial (25%); viral, bacterial, and protozoan (25%); and only viral agents (12.5%). BCoV and Salmonella sp. were not identified in the diarrheic fecal samples analyzed. Additionally, histopathology of the small intestine diagnosed chronic lymphocytic enteritis. In conclusion, in calf rearing units, the adoption and strict monitoring of health management practices are critical to the success of this calf creation system.

Clinical and molecular aspects of veterinary coronaviruses

Coronaviruses are a large group of RNA viruses that infect a wide range of animal species. The replication strategy of coronaviruses involves recombination and mutation events that lead to the possibility of cross-species transmission. The high plasticity of the viral receptor due to a continuous modification of the host species habitat may be the cause of cross-species transmission that can turn into a threat to other species including the human population. The successive emergence of highly pathogenic coronaviruses such as the Severe Acute Respiratory Syndrome (SARS) in 2003, the Middle East Respiratory Syndrome Coronavirus in 2012, and the recent SARS-CoV-2 has incentivized a number of studies on the molecular basis of the coronavirus and its pathogenesis. The high degree of interrelatedness between humans and wild and domestic animals and the modification of animal habitats by human urbanization, has favored new viral spreads. Hence, knowledge on the main clinical signs of coronavirus infection in the different hosts and the distinctive molecular characteristics of each coronavirus is essential to prevent the emergence of new coronavirus diseases. The coronavirus infections routinely studied in veterinary medicine must be properly recognized and diagnosed not only to prevent animal disease but also to promote public health.

Fatal Interstitial Pneumonia Associated with Bovine Coronavirus in Cows from Southern Italy

An outbreak of winter dysentery, complicated by severe respiratory syndrome, occurred in January 2020 in a high production dairy cow herd located in a hilly area of the Calabria region. Of the 52 animals belonging to the farm, 5 (9.6%) died with severe respiratory distress, death occurring 3–4 days after the appearance of the respiratory signs (caught and gasping breath). Microbiological analysis revealed absence of pathogenic bacteria whilst Real-time PCR identified the presence of RNA from Bovine Coronavirus (BCoV) in several organs: lungs, small intestine (jejunum), mediastinal lymph nodes, liver and placenta. BCoV was therefore hypothesized to play a role in the lethal pulmonary infection. Like the other CoVs, BCoV is able to cause different syndromes. Its role in calf diarrhea and in mild respiratory disease is well known: we report instead the involvement of this virus in a severe and fatal respiratory disorder, with symptoms and disease evolution resembling those of Severe Acute Respiratory Syndromes (SARS).

Integrative Network Analysis of Predicted miRNA-Targets Regulating Expression of Immune Response Genes in Bovine Coronavirus Infection

Bovine coronavirus (BCoV) infection that causes disease outbreaks among farm animals, resulting in significant economic losses particularly in the cattle industry, has the potential to become zoonotic. miRNAs, which are short non-coding segments of RNA that inhibits the expression of their target genes, have been identified as potential biomarkers and drug targets, though this potential in BCoV remains largely unknown. We hypothesize that certain miRNAs could simultaneously target multiple genes, are significantly conserved across many species, thereby demonstrating the potential to serve as diagnostic or therapeutic tools for bovine coronavirus infection. To this end, we utilized different existing and publicly available computational tools to conduct system analysis predicting important miRNAs that could affect BCoV pathogenesis. Eleven genes including CEBPD, IRF1, TLR9, SRC, and RHOA, significantly indicated in immune-related pathways, were identified to be associated with BCoV, and implicated in other coronaviruses. Of the 70 miRNAs predicted to target the identified genes, four concomitant miRNAs (bta-miR-11975, bta-miR-11976, bta-miR-22-3p, and bta-miR-2325c) were found. Examining the gene interaction network suggests IL-6, IRF1, and TP53 as key drivers. Phylogenetic analysis revealed that miR-22 was completely conserved across all 14 species it was searched against, suggesting a shared and important functional role. Functional annotation and associated pathways of target genes, such as positive regulation of cytokine production, IL-6 signaling pathway, and regulation of leukocyte differentiation, indicate the miRNAs are major participants in multiple aspects of both innate and adaptive immune response. Examination of variants evinced a potentially deleterious SNP in bta-miR-22-3p and an advantageous SNP in bta-miR-2325c. Conclusively, this study provides new insight into miRNAs regulating genes responding to BCoV infection, with bta-miR-22-3p particularly indicated as a potential drug target or diagnostic marker for bovine coronavirus.

Microbial diversity involved in the etiology of a bovine respiratory disease outbreak in a dairy calf rearing unit

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BALF is a good biological sample for the molecular diagnosis of BRD in dairy calves.

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Mixed infections of viruses and bacteria were frequent in dairy calves with respiratory disease.

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BVDV 1d in BALF samples of dairy heifer calves in a BRD outbreak was characterized.

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The calf rearing unit without prophylactic measures for respiratory infections represent a risk factor for BRD.

The etiological agents involved in a bovine respiratory disease (BRD) outbreak were investigated in a dairy heifer calf rearing unit from southern Brazil. A battery of PCR assays was performed to detect the most common viruses and bacteria associated with BRD, such as bovine viral diarrhea virus (BVDV), bovine respiratory syncytial virus (BRSV), bovine alphaherpesvirus 1 (BoHV-1), bovine coronavirus (BCoV), bovine parainfluenza virus 3 (BPIV-3), Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasma bovis. Bronchoalveolar lavage fluid (BALF) samples were taken from 21 heifer calves (symptomatic n = 15; asymptomatic n = 6) that, during the occurrence of the BDR outbreak, were aged between 6 and 90 days. At least one microorganism was detected in 85.7 % (18/21) of the BALF samples. Mixed infections were more frequent (72.2 %) than single infections (27.7 %). The interactions between viruses and bacteria were the most common in coinfections (55.5 %). The frequencies of BRD agents were 38.1 % for BRSV, 28.6 % for BVDV, 33.3 % for BCoV, 42.85 % for P. multocida, 33.3 % for M. bovis, and 19 % for H. somni. BoHV-1, BPIV-3, and M. haemolytica were not identified in any of the 21 BALF samples. Considering that BALF and not nasal swabs were analyzed, these results demonstrate the etiological multiplicity that may be involved in BRD outbreaks in dairy calves.

Molecular characterization of Brazilian wild-type strains of bovine respiratory syncytial virus reveals genetic diversity and a putative new subgroup of the virus

Background

Bovine orthopneumovirus, formerly known as bovine respiratory syncytial virus (BRSV), is frequently associated with bovine respiratory disease (BRD).

Aim

To perform the molecular characterization of the G and F proteins of Brazilian wild-type BRSV strains derived from bovine respiratory infections in both beef and dairy cattle.

Materials and Methods

Ten BRSV strains derived from a dairy heifer rearing unit (n = 3) in 2011 and steers of three other feedlots (n = 7) in 2014 and 2015 were analyzed. For the BRSV G and F partial gene amplifications, RT-nested-PCR assays were performed with sequencing in both directions with forward and reverse primers used.

Results

The G gene-based analysis revealed that two strains were highly similar to the BRSV sequences representative of subgroup III, including the Bayovac vaccine strain. However, the remaining seven Brazilian BRSV strains were diverse when compared with strains representative of the BRSV I to VIII subgroups. The central hydrophobic region of the Brazilian BRSV G gene showed the replacement of conserved cysteines and other residues of importance to antibody reactivity. The deduced F gene amino acid sequences from the Brazilian BRSV strains showed changes that were absent in the representative sequences of the known subgroups. Viral isolation on the nasopharyngeal swab suspensions failed to isolate BRSV.

Conclusion

Results suggest that these strains represent a putative new subgroup of BRSV with mutations observed in the immunodominant region of the G protein. However, further studies on these Brazilian BRSV strains should be performed to establish their pathogenic potential.

Prevalence and risk factors for agents causing diarrhea (Coronavirus, Rotavirus, Cryptosporidium spp., Eimeria spp., and nematodes helminthes) according to age in dairy calves from Brazil

The present study attempted to verify the prevalence of and risk factors for diarrhea-causing agents in dairy calves from Brazil. Additionally, ages with a higher risk of occurrence for each agent were verified by means of the receiver operating characteristic (ROC) curve. The collections were performed on 39 farms, belonging to 29 municipalities located in eight states of Brazil. It was possible to conclude that the prevalence of Coronavirus, Rotavirus, Cryptosporidium spp., Eimeria spp., and nematodes was 7.20% (95% CI 4.54-9.78), 6.37% (95% CI 3.85-8.89), 51.52% (95% CI 45.26-55.57), 3.46% (95% CI 2.24-4.67), and 3.46% (95% CI 2.24-4.67), respectively. Ages with higher probabilities of occurrence of these diseases in calves were < 10, > 8, > 6, > 37, and > 36 days, respectively. Diarrhea occurred more significantly (P < 0.0001) in animals less than 21 days old and mainly on those receiving milk through automatic feeders (P < 0.001). Cryptosporidium spp. were a risk factor for the occurrence of Rotavirus, and vice versa (P = 0.0039) and presented a positive correlation with Coronavirus (P = 0.0089). Calves that drink water from rivers, streams, and ponds had a higher chance of being infected by Eimeria spp. (P < 0.0001), as well as developing infection by nematodes (P < 0.0001). The results found in this study highlight the importance of studying the agents of diarrhea together, once they act as coinfection where the losses triggered for the owners will involve some of these agents simultaneously.

Dairy calf rearing unit and infectious diseases: diarrhea outbreak by bovine coronavirus as a model for the dispersion of pathogenic microorganisms

Dairy calf rearing unit is a management system that is only recently being implemented by some milk producer’s cooperatives in southern Brazil. However, aspects related to the health profile of the heifer calves that arrive in the rearing unit as well as about biosecurity practices and microbiological challenges have not yet been evaluated in this rearing system in a tropical country. Diarrhea is the main and most frequent consequence of enteric infections in newborn calves. This study, through some etiological and epidemiological characteristics of an outbreak of neonatal diarrhea, has the aim to alert to the possibility of pathogenic microorganism spread in a dairy heifer calf rearing unit. The diarrhea outbreak presented some non-regular characteristics observed in bovine coronavirus (BCoV) enteric infections in dairy calves. The spread of infection was extremely rapid (1 week); the attack rate (> 50%) was much higher than that observed in calves subjected to conventional rearing; and the age range (5 to 90 days) of the affected heifer calves was much broader than that often observed in the BCoV diarrhea worldwide. These unusual epidemiological characteristics observed in this BCoV diarrhea outbreak raise awareness of the health threat present in calf rearing units as well as of the easy and rapid viral spread in a population of young animals from different dairy herds and, therefore, with very distinct immunological status.

Phylogenetic analysis of VP1 and RdRP genes of Brazilian aichivirus B strains involved in a diarrhea outbreak in dairy calves

Aichivirus B has been reported worldwide in calves and adult cattle with and without diarrhea. The aim of this study was to describe the molecular characteristics of the RdRP and VP1 genes of aichivirus B strains identified as the most frequent etiologic agent in a neonatal diarrhea outbreak in a high-production Brazilian dairy cattle herd. Preliminary laboratory analysis ruled out important enteropathogens (Cryptosporidium spp; Eimeria spp., E. coli F5, and bovine coronavirus). Fecal samples from diarrheic (n = 24) and asymptomatic (n = 5) calves up to 30 days old were collected for virological analysis. RT-PCR assays were performed for the detection of aichivirus B RdRP and VP1 genes and for rotavirus A VP7 and VP4 genes in fecal samples. Asymptomatic calves (control group) were negative for both viruses. Aichivirus B and rotavirus A G10P[11] genotypes were found in 54.2% (13/24) and 25% (6/24) of the diarrheic fecal samples, respectively. Aichivirus B was only identified (83.3%, 10/12) in calves up to two weeks old. Phylogenetic analysis based on the RdRP gene grouped the Brazilian strains in a new branch within the aichivirus B group. Comparative analysis of the nucleotide sequence of the VP1 gene of Brazilian and Chinese aichivirus B strains allowed the strains identified in this study to be classified in the putative lineage 1. This is the first description of a high rate of aichivirus B detection in a diarrhea outbreak in dairy calves, and the first phylogenetic study of the VP1 gene of aichivirus B wild-type strains performed in South America.

Detection of Bovine Coronavirus by Conventional Reverse Transcription Polymerase Chain Reaction

Bovine coronavirus (BCoV) is an economically significant cause of enteric and respiratory diseases in cattle throughout the world. BCoV is a known cause of neonatal calf diarrhea, winter dysentery in adult cattle, and respiratory disorders in cattle of all ages. In this chapter, we describe a simple and efficient protocol for total nucleic acids extraction to be used in conventional RT-PCR assay. This is a technique used routinely in our virology laboratory to detect BCoV from stool and nasopharyngeal samples of cattle.

Molecular detection of bovine coronavirus in a diarrhea outbreak in pasture-feeding Nellore steers in southern Brazil

Worldwide diarrhea outbreaks in cattle herds are more frequently detected in calves being that diarrhea outbreaks in adult cattle are not common. Winter dysentery (WD) is a bovine coronavirus (BCoV) enteric infection that is more reported in Northern hemisphere. Seasonal outbreaks of WD in adult cattle occur mainly in dairy cows. WD has not been described in beef cattle herds of tropical countries. This study describes the molecular detection of BCoV in a diarrhea outbreak in beef cattle steers (Nellore) raised on pasture in Parana, southern Brazil. During the outbreak, the farm had about 600 fattening steers. Watery and bloody diarrhea unresponsive to systemic broad-spectrum antibiotic therapy reveals a morbidity rate of approximately 15 %. The BCoV N gene was identified in 42.9 % (6/14) of the diarrheic fecal samples evaluated by semi-nested polymerase chain reaction (SN-PCR) technique. Other enteric microorganisms occasionally identified in adult cattle and evaluated in this study such as bovine groups A, B, and C rotavirus, bovine viral diarrhea virus, bovine torovirus, aichivirus B, and Eimeria sp. were not identified in the fecal samples. To the best knowledge of the authors, this is the first description of the BCoV diagnosis in fecal samples collected in a diarrhea outbreak in adult beef cattle grazing in the grass in a tropical country.

Prevalence of endemic enteropathogens of calves in New Zealand dairy farms

AIM

To conduct a country-wide prevalence study of bovine group A rotavirus, coronavirus, Cryptosporidium parvum, Salmonella spp. and enterotoxigenic K99(+) Escherichia coli (K99) in calves on New Zealand dairy farms.

METHODS

Faecal samples (n=1,283) were collected during the 2011 calving season from calves that were 1-5 and 9-21 days-old on 97 dairy farms, and were analysed for the presence of bovine group A rotavirus, coronavirus, Cryptosporidium and Salmonella spp., and K99. Farm-level prevalences were calculated and relationships between demographic variables and the presence of enteropathogens were examined using logistic regression models.

RESULTS

Of the 97 farms, 93 (96%) had at least one sample infected with enteropathogens. The standardised farm prevalences of bovine group A rotavirus, bovine coronavirus and C. parvum were 46, 14 and 18%, respectively, in calves that were 1-5 days-old, and 57, 31 and 52%, respectively, in calves that were 9-21 days-old. The farm-level prevalence of K99 was 11% in calves that were 1-5 days-old. Salmonella spp. were found in three and four samples, from calves that were 1-5 and 9-21 days-old, respectively. No associations between explanatory variables and the presence of the enteropathogens were identified at the farm level. At the calf level, the odds of C. parvum shedding and of co-infection with any combination of pathogens were greater in calves that were 9-21 than 1-5 days-old.

CONCLUSIONS AND CLINICAL RELEVANCE

This study provides epidemiological estimates of the prevalence of calves' enteropathogens in New Zealand, which could be used for infection risk assessment or estimation of the environmental loads of pathogens shed in cattle faeces.

Longitudinal study of Salmonella spp., diarrheagenic Escherichia coli, Rotavirus, and Coronavirus isolated from healthy and diarrheic calves in a Brazilian dairy herd

This prospective longitudinal study investigated the epidemiology of enteric disease associated with infections in calves aging up to 70 days. A total of 850 fecal samples were collected from 67 calves. Seventeen isolates of Salmonella spp. were recovered from feces of 11 calves (16.4%), and statistical analysis revealed no association between the presence of Salmonella spp. and clinical signs of diarrhea or age. Virulence factors of Escherichia coli were identified in 103 strains: eae (7), K99/STa (7), Stx1 (7), Stx1/eae (36), Stx1/Stx2/eae (2), Stx2 (43), and Stx2/eae (1). There was statistical association between diarrheic animals carrying E. coli Stx1/eae (+) in their feces at 2 and 4 weeks of age (P = 0.003) and E. coli Stx2 (+) at 5 weeks of age (P = 0.03). Rotavirus was detected in 49 (5.76%) fecal samples collected from 33 calves (49.2%). The presence of rotavirus was correlated with diarrheic feces (P < 0.0001) rather than feces with normal consistency. There was a significant relationship between age group and diarrhea (P = 0.001). Bovine coronavirus (BCoV) was detected in 93 fecal samples collected from 46 calves (68.6%). There was an association (P < 0.0001) between diarrheic animals positive for BCoV and age groups. The results demonstrate the importance of the pathogens studied in the etiology of diarrhea in calves.

Phylogenetic analysis of a G6P[5] bovine rotavirus strain isolated in a neonatal diarrhea outbreak in a beef cattle herd vaccinated with G6P[1] and G10P[11] genotypes

The aim of this study was to perform the molecular characterization of the eleven genes of a G6P[5] bovine group A rotavirus (RVA) strain detected in a diarrhea outbreak from a vaccinated beef cattle herd. The outbreak affected 80 % of calves between 15–30 days old. RVA was identified by RT-PCR in 12 (70.6 %) out of 17 diarrheic fecal samples evaluated. The rotavirus wild-type strain had the genotype constellation G6(IV)-P[5](IX)-I2c-R2-C2-M2-A3-N2-T6-E2e-H3a. This study confirms the importance of homotypic immunity against the bovine RVA P[5] genotype in neonatal diarrhea in cattle herds that are regularly vaccinated against rotaviruses.

Severe diarrhea outbreak in beef calves (Bos indicus) caused by G6P[11], an emergent genotype of bovine rotavirus group A

The episodes of diarrhea caused by neonatal bovine rotavirus group A (BoRVA) constitute one of the major health problems in the calf rearing worldwide. The main G (VP7) and P (VP4) genotypes of BoRVA strains involved in the etiology of diarrhea in calves are G6P[1], G10P[11], G6P[5], and G8P[1]. However, less frequently, other G and P genotypes have been described in BoRVA strains identified in diarrheic fecal samples of calves. This study describes the identification and molecular characterization of an emerging genotype (G6P[11]) in BoRVA strains involved in the etiology of a diarrhea outbreak in beef calves in a cattle herd of high production in extensive management system. The diarrhea outbreak, which showed high morbidity (60%) and lethality (7%) rates, occurred in calves (n= 384) Nelore (Bos indicus) up to 30-day-old from the State of Mato Grosso do Sul, Brazil. BoRVA was identified in 80% (16/20) of the fecal samples analyzed by polyacrylamide gel electrophoresis (PAGE) technique. In all PAGE-positive fecal samples were amplified products with 1,062-bp and 876-bp in the RT-PCR assays for VP7 (G type) and VP4 (VP8*) (P type) of BoRVA, respectively. The nucleotide sequence analysis of VP7 and VP4 genes of four wild-type BoRVA strains showed G6-III P[11]-III genotype/lineage. The G6P[11] genotype has been described in RVA strains of human and animal hosts, however, in calves this genotype was only identified in some cross-sectional studies and not as a single cause of diarrhea outbreaks in calves with high morbidity and lethality rates as described in this study. The monitoring of the G and P genotypes of BoRVA strains involved in diarrhea outbreaks in calves is important for both animal and public health by allowing the identification of the most frequent genotypes, the characterization of novel genotypes and to identify reassortments with genotypes described in animal and human hosts. The results of this study show the importance of the monitoring of the genotypes of BoRVA strains involved in episodes of bovine neonatal diarrhea as for characterization of frequency of occurrence and pathogenic potential of uncommon genotypes as for monitoring of the emergency of different BoRVA genotypes not included in commercial vaccines.

Kobuvirus (Aichivirus B) infection in Brazilian cattle herds

There are few studies involving the detection of Aichivirus B in cattle herds worldwide, and this virus has never been diagnosed in South America. This study evaluated 222 diarrhoeic faecal samples from four Brazilian geographical regions (South, Southeast, Midwest, and North), collected between February 2010 to May 2012. To evaluate the frequency of occurrence in different types of livestock, samples from beef (n = 105) and dairy (n = 117) cattle herds were evaluated. To determine the category of animals more susceptible to infection, the sampling included samples from calves (n = 182) and adults animals (n = 40). The 216 bp fragment of the Aichivirus RdRp gene was amplified by a RT-PCR assay in 18.2 % (40/222) of the samples evaluated in both beef and dairy cattle animals. The highest (P < 0.05) detection rate (20.9 %; 38/182) of the Aichivirus B was found in calves. The nucleotide sequencing analysis showed that the Brazilian Aichivirus B strains clustered in a distinct branch in the phylogenetic tree of the European and Asiatic strains. This is the first description of Aichivirus B infection in Brazilian cattle herds.

Histophilus somni-induced infections in cattle from southern Brazil

The sudden death of three calves, one diarrheic calf, and one aborted fetus from four farms in southern Brazil was investigated. Two Histophilus somni-associated syndromes were identified: systemic histophilosis (n = 4) and abortion (n = 1). The principal pathological findings included vasculitis, meningoencephalitis with thrombosis, necrotizing myocarditis, renal infarctions, hepatic abscesses, and bronchopneumonia. PCR assays were used to amplify specific amplicons of the ovine herpesvirus 2, bovine herpesvirus 1 and -5, Listeria monocytogenes, H. somni, and pestivirus; bovine group A rotavirus (BoRV-A) and bovine coronavirus (BCoV) were investigated in calves with diarrhea. H. somni DNA was amplified in tissues from all calves and the brain of the aborted fetus with pathological alterations consistent with histophilosis. All other PCR assays were negative; BoRV-A and BCoV were not identified. These findings confirm the participation of H. somni in the pathological alterations observed in this study and represent the first description of histophilosis in cattle from Brazil.

A new approach for diagnosis of bovine coronavirus using a reverse transcription recombinase polymerase amplification assay

Bovine coronavirus (BCoV) is an economically significant cause of calf scours and winter dysentery of adult cattle, and may induce respiratory tract infections in cattle of all ages. Early diagnosis of BCoV helps to diminish its burden on the dairy and beef industry. Real-time RT-PCR assay for the detection of BCoV has been described, but it is relatively expensive, requires well-equipped laboratories and is not suitable for on-site screening. A novel assay, using reverse transcription recombinase polymerase amplification (RT-RPA), for the detection of BCoV is developed. The BCoV RT-RPA was rapid (10-20 min) and has an analytical sensitivity of 19 molecules. No cross-reactivity with other viruses causing bovine gastrointestinal and/or respiratory infections was observed. The assay performance on clinical samples was validated by testing 16 fecal and 14 nasal swab specimens and compared to real-time RT-PCR. Both assays provided comparable results. The RT-RPA assay was significantly more rapid than the real-time RT-PCR assay. The BCoV RT-RPA constitutes a suitable accurate, sensitive and rapid alternative to the common measures used for BCoV diagnosis. In addition, the use of a portable fluorescence reading device extends its application potential to use in the field and point-of-care diagnosis.

Comparison of three diagnostic techniques for detection of rotavirus and coronavirus in calf faeces in Australia

Objective  Compare real‐time reverse transcription polymerase chain reaction (qRT‐PCR), a commercially available enzyme‐linked immunosorbent assay (ELISA) and lateral flow immunochromatography assay (LAT) for the detection of rotavirus and coronavirus in faecal samples collected from diarrhoeic calves.

Design  Prospective survey.

Method  Samples were tested at two separate facilities using a commercial ELISA and an in‐house qRT‐PCR. Simple logistic regression was performed to examine the relationship between the two tests. A subset of samples was screened using qRT‐PCR, ELISA and a commercial LAT dipstick (132 faecal samples were tested for coronavirus and 122 samples for rotavirus).

Results  Of the 586 samples tested, 131 (22.39%) and 468 (79.86%) were positive for coronavirus and group A rotavirus, respectively, using qRT‐PCR. The number of samples positive on ELISA for coronavirus and rotavirus was 73 (12.46%) and 225 (38.40%), respectively. Using LAT, 30 (22.73%) and 43 (35.35%) samples were positive for coronavirus and rotavirus, respectively. Simple linear regression revealed a statistically significant (P < 0.05) but weak (r²=−0.07 and −0.40) correlation between the rotavirus/coronavirus qRT‐PCR and ELISA, respectively. There was also poor agreement between the LAT and qRT‐PCR assays.

Conclusion  The sensitivity and specificity of the commercial ELISA and LAT assays evaluated in this study were low compared with qRT‐PCR. The low positive and negative predictive values of the assays suggests that they were of limited diagnostic benefit in the population sampled.

Identification of a novel single-stranded, circular DNA virus from bovine stool

We report the identification of a novel single-stranded, circular DNA virus isolated from bovine stool. The virus, named bovine stool-associated circular DNA virus (BoSCV), has a genome comprising 2600 bases of circular ssDNA, with two putative ORFs encoding replicase and capsid proteins, arranged inversely. The stem–loop structure was located between the 3′ ends of the two putative ORFs, as in chimpanzee stool-associated circular virus (ChimpSCV) and unlike other circular DNA viruses, including members of the families Circoviridae, Nanoviridae and Geminiviridae. BoSCV was also genetically similar to ChimpSCV, with approximately 30 % identity in the replicase and capsid proteins. A phylogenetic analysis based on the replicase protein showed that BoSCV and ChimpSCV are in the same clade. A field survey using BoSCV-specific PCRs targeting ORF1 detected BoSCV and BoSCV-like sequences in bovine and porcine stool samples. BoSCV appears to belong to a new genus of circular DNA viruses.

Rapid detection of Betacoronavirus 1 from clinical fecal specimens by a novel reverse transcription loop-mediated isothermal amplification assay

Betacoronavirus 1 (BCoV-1) is an important pathogen causing diarrhea in calves. In the current study, a novel reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for rapid detection of BCoV-1 was successfully developed. The primers were designed to target the highly conserved fragment of BCoV-1 nucleocapsid gene. The assay displayed high specificity detecting only BCoV-1 with no cross reaction with other viruses. When 418 clinical samples from 6 different geographical areas of Xinjiang province were tested by the RT-LAMP method, the results indicated that this test is a simple, rapid, accurate, and sensitive method for the detection of BCoV-1.

Bovine coronavirus (BCV) infections in transported commingled beef cattle and sole-source ranch calves

This study investigated bovine coronavirus (BCV) in both beef calves direct from the ranch and commingled, mixed-source calves obtained from an auction market. The level of BCV-neutralizing antibodies found in the calves varied among ranches in 2 different studies in a retained-ownership program (ROP), from the ranch to the feedlot. Calves with low levels of BCV-neutralizing antibodies (16 or less) were more likely to be treated for bovine respiratory disease (BRD) than those with higher titers. In 3 studies of commingled, mixed-source calves, BCV was recovered from calves at entry to the feedlot and the infections were cleared by day 8. The BCV was identified in lung samples [bronchoalveolar lavage (BAL) collection] as well as in nasal swabs. Calves with low levels of BCV-neutralizing antibodies at entry were most likely to be shedding BCV. Bovine coronavirus was isolated from both healthy and sick calves, but not from sick calves after 4 d arrival at the feedlot. Bovine coronavirus (BCV) should be considered along with other bovine respiratory viruses in the diagnosis of etiologies in bovine respiratory disease, especially for animals that become sick shortly after arrival. If approved vaccines are developed, it would be best to carry out vaccination programs before calves are weaned, giving them sufficient time to gain active immunity before commingling with other cattle.

Development of a SYBR Green I based real-time RT-PCR assay for detection and quantification of bovine coronavirus

A novel two-step, SYBR Green I based real-time RT-PCR assay was developed for detection and quantification of BCoV using ABI PRISM 7500 sequence detection system. The assay was carried out using two sets of primers designed to amplify highly conserved sequences of the nucleocapsid gene of BCoV and the internal control, bovine glyceraldehyde-3-phosphate dehydrogenase, RNA. Specific identification of both targets was elucidated by melt curve analysis, in which the BCoV amplified product generated a melt peak at 78.35 ± 0.26 °C and the internal control RNA at 82.54 ± 0.32 °C. The assay was highly specific since all negative controls and other viruses of clinical and structural relevance failed to develop any positive results. The detection limit of the reaction was 10(3) plasmid copies and 1.17 × 10(-3) TCID(50) of the tissue culture propagated virus. Standard deviation and coefficient of variation was low for both intra-assay and inter-assay variability. The assay performance on field samples was evaluated on 103 (68 fecal and 35 nasal) swab specimens and compared with the conventional RT-PCR assay. The results of both assays matched for the diagnosis of 65 fecal and 33 nasal samples. However, three fecal and two nasal samples tested negative in gel-based assay were positive for the real-time RT-PCR. The robustness and a high-throughput performance of the developed assay make it a powerful tool in diagnostic applications and in BCoV research.

Multiplex semi-nested RT-PCR with exogenous internal control for simultaneous detection of bovine coronavirus and group A rotavirus

Neonatal calf diarrhea is a multi-etiology syndrome of cattle and direct detection of the two major agents of the syndrome, group A rotavirus and Bovine coronavirus (BCoV) is hampered by their fastidious growth in cell culture. This study aimed at developing a multiplex semi-nested RT-PCR for simultaneous detection of BCoV (N gene) and group A rotavirus (VP1 gene) with the addition of an internal control (mRNA ND5). The assay was tested in 75 bovine feces samples tested previously for rotavirus using PAGE and for BCoV using nested RT-PCR targeted to RdRp gene. Agreement with reference tests was optimal for BCoV (kappa = 0.833) and substantial for rotavirus detection (kappa = 0.648). the internal control, ND5 mRNA, was detected successfully in all reactions. Results demonstrated that this multiplex semi-nested RT-PCR was effective in the detection of BCoV and rotavirus, with high sensitivity and specificity for simultaneous detection of both viruses at a lower cost, providing an important tool for studies on the etiology of diarrhea in cattle.

Lung Pathology and Infectious Agents in Fatal Feedlot Pneumonias and Relationship with Mortality, Disease Onset, and Treatments

This study charted 237 fatal cases of bovine respiratory disease (BRD) observed from May 2002 to May 2003 in a single Oklahoma feed yard. Postmortem lung samples were used for agent identification and histopathology. Late in the study, 94 skin samples (ear notches) were tested for Bovine viral diarrhea virus (BVDV) by immunohistochemistry (IHC). Bovine respiratory disease morbidity was 14.7%, and the mortality rate of all causes was 1.3%, with more than half (53.8%) attributed to BRD (0.7% total of all causes). The agents isolated were the following: Mannheimia haemolytica (25.0%), Pasteurella multocida (24.5%), Histophilus somni (10.0%), Arcanobacterium pyogenes (35.0%), Salmonella spp. (0.5%), and Mycoplasma spp. (71.4%). Viruses recovered by cell culture were BVDV-1a noncytopathic (NCP; 2.7%), BVDV-1a cytopathic (CP) vaccine strain (1.8%), BVDV-1b NCP (2.7%), BVDV-2a NCP (3.2%), BVDV-2b CP (0.5%), and Bovine herpesvirus 1 (2.3%). Gel-based polymerase chain reaction (PCR) assays were 4.6% positive for Bovine respiratory syncytial virus and 10.8% positive for Bovine coronavirus. Bovine viral diarrhea virus IHC testing was positive in 5.3% of the animals. The mean values were determined for the treatment data: fatal disease onset (32.65 days), treatment interval (29.15 days), number of antibiotic treatments (2.65), number of different antibiotics (1.89), and day of death (61.81 days). Lesions included the following: 1) duration: acute (21%), subacute (15%), chronic (40.2%), healing (2.8%), normal (18.1%), and autolyzed (2.8%); 2) type of pneumonia: lobar bronchopneumonia (LBP; 27.1 %), LBP with pleuritis (49.1 %), interstitial pneumonia (5.1 %), bronchointerstitial pneumonia (1.4%), septic (0.9%), embolic foci (0.5%), other (2.8%), normal (10.3%), and autolyzed (2.8%); and 3) bronchiolar lesions: bronchiolitis obliterans (39.7%), bronchiolar necrosis (26.6%), bronchiolitis obliterans/bronchiolar necrosis (1.4%), other bronchiolar lesions (6.5%), and bronchiolar lesion negative (25.7%). Statistically significant relationships were present among the agents, lesions, and the animal treatment, disease onset, and mortality data. Clinical illnesses observed in this study were lengthier than those reported 16–20 years ago, based on fatal disease onset, treatment interval, and day of death.

Frequency of BCoV detection by a semi-nested PCR assay in faeces of calves from Brazilian cattle herds

Bovine coronavirus (BCoV) is one of the main causes of neonatal calf diarrhoea. Several diagnostic assays have been employed to detect the presence of the virus in stool samples from calves. Despite this, the frequency of BCoV infection among Brazilian and even South American cattle herds has yet to be well characterised. This study describes the occurrence of BCoV infection among calves from dairy and beef herds in four Brazilian states. A total of 282 stool samples from 1 to 60-day-old calves were evaluated for the presence of BCoV by a semi-nested (SN) PCR assay. The animals were from herds (n = 23) located in three geographical regions in Brazil (south, southeast, and center-west). The specific BCoV amplicon was detected in 15.6% (44/282) of the faecal specimens examined, of which 95.4% (42/44) were from diarrhoeic and 4.6% (2/44) from asymptomatic calves. The specificity of the SN-PCR amplicons was evaluated by restriction fragment length polymorphism (RFLP) analysis. The results show that the BCoV is widespread, mainly among calves from 16 to 30-days-old (p = 0.0023), and verify the association between BCoV infection and clinical signs of diarrhoea (p = 0.005). These findings emphasise the importance of this virus in enteric infections of Brazilian cattle herds.