Bovine respiratory coronavirus

Occurrence and Epidemiology of Bovine Coronavirus in Cattle in Kazakhstan

Bovine coronavirus (BCoV) causes gastrointestinal and respiratory diseases in cattle, but its prevalence in Kazakhstan remains unknown. This nationwide cross-sectional study aimed to assess BCoV prevalence in cattle and to investigate its epidemiological characteristics. Between April and August 2024, serum, nasal and rectal swab samples were collected from 2,237 clinically healthy cattle across 390 farms in 17 oblasts of Kazakhstan. None of the farm owners reported vaccinating against BCoV. Serum samples were tested for BCoV-specific antibodies using a commercially available ELISA, while nested RT-PCR assays were performed on pooled nasal and rectal swabs to detect BCoV RNA. Sequencing and phylogenetic analysis were performed following RT-PCR testing. A univariate GEE model was used to assess the risk factors and a multivariate model was employed to refine the discovered associations. The animal-level seroprevalence of BCoV was 88.2% (95% CI: 84.3%-92.0%), while the herd-level seroprevalence was 89.6% (95% CI: 85.4%-92.9%). The eastern region of Kazakhstan had the lowest seroprevalence compared to other regions. Seropositivity was not associated with age, sex or breed, but correlated with the proportion of cattle in backyards, cattle density and farm size. BCoV shedding was detected in 2.4% (95% CI: 1.4 5% - 3.4%) of sampled animals and in 7.8% (95%CI: 5.3% - 11.0%) of cattle operations across 12 oblasts. Phylogenetic analysis of the complete hemagglutinin/esterase and spike genes revealed that the Kazakhstani BCoV strains belonged to the GIIa group. This first report on BCoV in Kazakhstan confirms its endemic presence, highlighting the need for a national control program.

Detection of avian, murine, bovine, shrew, and bat coronaviruses in wild mammals from Mexico

Coronaviruses infect a wide range of animal and human hosts. Some human coronaviruses, such as SARS-CoV, MERS-CoV, and SARS-CoV-2, originated in animals, with bats often serving as ancestral hosts. This study analyzed samples from wild animals in three Mexican states, using an RT-PCR assay targeting the RdRp gene to detect and genotype coronaviruses, assessing their potential role as reservoirs. Phylogenetic analysis was conducted to determine the genetic relationships of the identified coronaviruses. Gammacoronavirus RNA was identified in fallow deer, llamas, spider monkeys, and mouflons; Betacoronavirus RNA in mouflons and dwarf goats; and Alphacoronavirus RNA in dwarf goats and ponies. The detected viral sequences exhibited high nucleotide identity with known coronaviruses, including Avian coronavirus (Gammacoronavirus), Murine coronavirus (Betacoronavirus), Betacoronavirus 1 (Betacoronavirus), Wénchéng shrew coronavirus (unclassified Alphacoronavirus), and Bat coronavirus HKU10 (Alphacoronavirus). These findings represent the first report of Avian coronavirus, Murine coronavirus, Wénchéng shrew coronavirus, and Bat coronavirus HKU10 in these species, as well as the first detection of Avian coronavirus in llamas, spider monkeys, and mouflons. This study provides valuable insights into the potential role of wildlife as coronavirus reservoirs, highlighting the importance of monitoring these viruses to mitigate future zoonotic transmission risks.

[New drugs for horses and production animals in 2024]

In 2024, there was no release of a novel pharmaceutical agent for horses and food-producing animals or an extension of existing active ingredients to other animal species on the German veterinary medicinal products market. Formic acid is now available for a new form of treatment, the short-term treatment of honeybees, and clenbuterol is available in a new dosage form, as an oral solution for horses. In the field of immunological veterinary medicinal products, three new vaccines were launched on the German veterinary medicinal products market. For the first time, a vaccine against Cryptosporidium parvum in cattle, against Mycoplasma bovis also in cattle and against the H9 subtype of avian influenza in chicken are available. For pigs, a new vaccine with a known pathogen combination with type 2d of porcine circovirus, a new miscibility and needle-free application of products against respiratory pathogens and a new combination with serovar 11 in addition to serovars 2 and 9 of Actinobacillus pleuropneumoniae were approved. Furthermore, a new trivalent combination of three known vaccine antigens and a new miscibility of two products against diarrheal pathogens are available for pigs. A new recombinant combination product against infectious bursitis, infectious laryngotracheitis and Marek's disease has been approved for chicken. New administration methods were introduced to the market for a vaccine against bovine coronavirus (nasal) in cattle and porcine circovirus and Mycoplasma hyopneumoniae (needleless) in pigs.

Bovine coronavirus presence in domestic bovine and antelopes sub-Saharan Africa: evidence from Namibia

BACKGROUND

Bovine coronavirus (BoCV) causes significant economic losses to cattle farming due to mortality in calves, reduced growth performances and milk production in feedlots and dairy cattle. Worldwide distribution of BoCV has been demonstrated, although knowledge of its epidemiology in Africa, especially in the sub-Saharan region, is limited.

RESULTS

In the present study, a total of 208 swab samples of wild ruminants and 435 bovines from different regions of Namibia were obtained and tested by a BoCV-specific qRT-PCR. Twenty-six bovine samples tested positive [26/435 (5.98%; 95CI: 3.94-8.64%)] while, among the wild ruminants, only Greater Kudu (Tragelaphus strepsiceros) were shown to be positive [13/52 (25.00%; 95CI: 14.03-38.95%)] of which 8 showed clinical signs. Analysis of partial nucleoprotein and spike protein gene sequences and comparison with international reference sequences demonstrated the existence of a unique Namibian clade, resulting from a single introduction event around 2010 followed by local evolution. Although the introduction source remains unknown, contact between bovine and wild animals appears likely.

CONCLUSIONS

The present study represents the first report of BoCV circulation in southern Africa, which showed a relatively high frequency and the ability of persisting and evolving locally in the absence of further foreign introductions. The implications for disease spread among domestic bovines and the potential impact on wildlife should encourage broader investigations on BoCV involving other African countries. Moreover, the Greater Kudu's susceptibility to BoCV infection was also proven, further highlighting the host plasticity of this virus.

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.

Discovery of a novel Betacoronavirus 1, cpCoV, in goats in China: The new risk of cross-species transmission

Betacoronavirus is a causative agent of respiratory and enteric diseases in humans and animals. Several ruminants are recognized to be intermediate hosts in the transmission of emerging coronaviruses from reservoir hosts to humans. Here, we first report a novel Betacoronavirus isolated from goats suffering from diarrhea in China, putatively named caprine coronavirus (cpCoV). Full-genome characterization and nuclear acid comparisons demonstrated that this virus is an evolutionarily distinct Betacoronavirus belonging to the subgenus Embecovirus and is a Betacoronavirus 1 species. Notably, on phylogenetic trees based on complete genomes and RdRp, S, and N genes, the cpCoVs were grouped into a clade distinct from other Betacoronavirus strains and were closely related to the HKU23- and HKU23-associated coronaviruses. CpCoV possessed a unique genome organization with a truncated NS4a protein and an elongated NS4b protein that showed no significant matches in the GenBank database. The homology of the S and NS4a-4b genes between cpCoV and Embecovirus was less than 95%. Analysis revealed possible recombination events occurred during the evolution of cpCoV and HKU23, and there are striking similarities between the two viruses in evolutionary terms. In addition, cpCoV showed a narrow cell tropism, replicating in human- and bovine-origin cells in vitro, and caused diarrhea and enteric pathologic changes in goats and calves in vivo. We have provided epidemiological, virological, evolutionary, and experimental evidence that cpCoV is a novel etiological agent for enteric disease in goats. Evidently, a spilling-over event might have occurred between ruminants, including goats, camels, cattle, and wild animals. This study highlights the importance of identifying coronavirus diversity and inter-species transmission in ruminants worldwide, broadens our understanding of the ecology of coronaviruses, and aids in the prevention of animal-to-human transmission and outbreaks.

Betacoronavirus internal protein: role in immune evasion and viral pathogenesis

Betacoronaviruses express a small internal (I) protein that is encoded by the same subgenomic RNA (sgRNA) as the nucleocapsid (N) protein. Translation of the +1 reading frame of the N sgRNA through leaky ribosomal scanning leads to expression of the I protein. The I protein is an accessory protein reported to evade host innate immune responses during coronavirus infection. Previous studies have shown that the I proteins of severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2, and Middle East respiratory syndrome coronavirus suppress type I interferon production by distinct mechanisms. In this review, we summarize the current knowledge on the I proteins of betacoronaviruses from different subgenera, with emphasis on its function and role in pathogenesis.

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.

Isolation and molecular characterization of an enteric isolate of the genotype-Ia bovine coronavirus with notable mutations in the receptor binding domain of the spike glycoprotein

BCoV new isolate was plaque purified, isolated, and propagated in vitro using MDBK and HRT-18. The full-length genome sequencing of this new BCoV isolate (31 Kbs) was drafted and deported in the GenBank. The genome organization is (5'-UTR-Gene-1-32kDa-HE-S-4.9 kDa-4.8 kDa-12.7 kDa-E-M-N-UTR-3'). Phylogenetic analysis based on the sequences of (the full-length genome, S, HE, and N) showed that the BCoV-13 clustered with other North American BCoV genotype I members. The sequence analysis shows several synonymous mutations among various domains of the S glycoprotein, especially the receptor binding domain. We found nine notable nucleotide deletions immediately downstream of the RNA binding domain of the nucleocapsid gene. Further gene function studies are encouraged to study the function of these mutations on the BCoV molecular pathogenesis and immune regulation. This research enhances our understanding of BCoV genomics and contributes to improved diagnostic and control measures for BCoV infections in cattle.

A Passion for Small Things and Staying Primed: My Career in Virology and Immunology

A love of science and animals, perseverance, and happenstance propelled my career in veterinary virology and immunology. I have focused on deadly enteric and respiratory viral infections in neonatal livestock and humans with an aim to understand their prevalence, pathogenesis, interspecies transmission, and immunity and develop vaccines. Research on animal coronaviruses (CoVs), including their broad interspecies transmission, provided a foundation to understand emerging zoonotic fatal human respiratory CoVs [severe acute respiratory syndrome, Middle East respiratory syndrome, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)] and reverse zoonosis of SARS-CoV-2 to animals. A highlight of my early research was the discovery of the gut-mammary gland-sIgA axis, documenting a common mucosal immune system. The latter remains pivotal to designing maternal vaccines for passive immunity in neonates. Our discovery and innovative cell propagation of fastidious human and animal rotaviruses and caliciviruses and their infectivity in germ-free animals has provided cell-adapted and animal disease models for ongoing virologic and immunologic investigations and vaccines. Nevertheless, besides the research discoveries, my lasting legacy remains the outstanding mentees who have enriched my science and my life.

Herd-level occurrence and risk factors associated with respiratory and enteric pathogens from dairy calves in Ontario: A cross-sectional study

This cross-sectional herd-level study aimed to determine the occurrence of and risk factors for pathogens associated with neonatal calf diarrhea (NCD) and bovine respiratory disease (BRD) on Ontario dairy farms. From April to August 2022, a convenience sample of 100 dairy farms was visited once. A questionnaire covering farm biosecurity, calving and colostrum management, preweaning nutrition, and housing was administered on-farm. At each farm visit, approximately 5 calves between 2 and 35 d old were randomly selected for fecal sampling. Furthermore, approximately 5 calves between 21 to 122 d old were randomly selected for nasopharyngeal sampling. In total, 363 fecal samples (from 83 dairy farms) and 390 nasopharyngeal swab samples (from 80 dairy farms) were collected. Fecal samples were analyzed individually using a multiplex PCR to identify bacterial and parasitic enteric pathogens. Nasopharyngeal swabs were analyzed as one pooled sample per farm using bacterial culture and real-time PCR. The most common enteric pathogens detected at herd-level were Cryptosporidium parvum (67.4%) and Escherichia coli K99+ (13.2%). The most common respiratory pathogens detected at herd-level were Pasteurella multocida (62.5%), bovine coronavirus (42.5%), and Mycoplasma bovis (21.2%). Multivariable logistic models were built to explore associations between the most common pathogens and herd-level predictors selected from the questionnaire. Herd positivity for C. parvum was positively associated with having more than 61 preweaning calves per year and feeding mainly whole milk to calves. The presence of M. bovis was positively associated with herds that combined manual and automatic milk-feeding systems, and the presence of bovine coronavirus was positively associated with having more than 98 preweaning calves during the year. Univariable Poisson regression models were built to explore the association between the most common pathogens and preweaning calf mortality. Herds that were positive for C. parvum, M. bovis, or bovine coronavirus had a greater risk of preweaning calf mortality. These results provide insights for future research on pathogens associated with NCD and BRD and offer guidance for veterinarians and dairy farmers in implementing disease control measures in dairy calf herds.

Investigating bovine coronavirus in Indian calves: Incidence, molecular evidence, and pathological role in bovine respiratory disease complex (BRDC)

Background

Bovine coronavirus (BCoV) and bacterial pathogens contribute to bovine respiratory disease complex (BRDC) in young calves. However, the role of BCoV in BRDC occurrence and site-specific respiratory pathology in India remains poorly explored.

Aims

This study aimed to assess BCoV prevalence in BRDC cases.

Methods

We investigated 406 weaner calves (166 cattle, 240 buffaloes) up to ≤1 year, with respiratory distress and pulmonary lesions.

Results

BRDC cases exhibited 0.98% BCoV occurrence, confirmed by partial N gene amplification (172 bp) via RT-PCR and immunohistochemistry (IHC). Grossly, 4 BCoV positive cases showed variable degrees of consolidation of cranioventral lobes and non-collapsed caudodorsal lobes, associated with congestion and emphysema. Microscopically, the inflated sites of the lung tissue sections showed hallmark changes of interstitial pneumonia characterized by moderate infiltration with lymphocytes and increased numbers of fibroblasts in the interalveolar septa and the stroma of bronchioles and bronchi. In concomitant Pasteurella multocida infected cases, cranioventral lobes exhibited suppurative bronchopneumonia with neutrophilic exudate. The above lesions were well colocalized with BCoV antigen in the epithelial cells and in the debris of the lumen of the alveoli and the bronchi/bronchioles. The sequence comparison of the 172 bp amplicon with the published BCoV N gene showed close relatedness.

Conclusion

The present study implicated BCoV as a component of BRDC in India that should be considered in the diagnosis of BRDC outbreaks.

The ex vivo infection model of the peripheral bovine mononuclear cells (PBMCs) and the bovine spleen cells with the bovine coronavirus (BCoV) induced a differential expression of the host cytokine genes profiles and modulates the virus replication

The adaptive immune response during BCoV infection of peripheral blood mononuclear cells (PBMCs), the bovine spleen cells, and their isolated T lymphocytes was not studied well. Our study confirmed successful BCoV infection in PBMCs and spleen T cells. The BCoV replication was evidenced by measuring genome copy numbers using real-time PCR and expression levels of BCoV spike and nucleocapsid proteins via western blot and immunofluorescence assays. In infected PBMCs, CD4 T-cell levels were 1.45-fold higher, and CD8 T-cell levels were 1.6-fold lower compared to sham-infected cells. Conversely, infected splenocytes showed a 0.88-fold decrease in CD4 T-cells and a 1.88-fold increase in CD8 T-cells. The cytokine gene expression analysis revealed that BCoV infection activated type I interferon and upregulated IL-6 expression in PBMCs and splenocytes. These findings demonstrate that BCoV successfully infects immune cells from PBMCs and spleen, inducing differential host cytokine gene expression that favors virus replication.

The first report on detecting SARS-CoV-2 inside bacteria of the human gut microbiome: A case series on asymptomatic family members and a child with COVID-19

Many studies report the importance of using feces as source sample for detecting SARS-CoV-2 in patients with COVID-19 symptoms but who are negative to oropharyngeal/ nasopharyngeal tests. Here, we report the case of an asymptomatic child whose family members had negative results with the rapid antigen nasopharyngeal swab tests. The 21-month-old child presented with fever, diarrhea, bilateral conjunctivitis, and conspicuous lacrimation. In this study, analysis for the presence of SARS-CoV-2 in fecal samples by using Luminex technology allowed accurate detection of the presence of the viral RNA in the feces of the child and of all her relatives, which thus resulted to be positive but asymptomatic. It is the first time that SARS-CoV-2- is observed inside the bacteria of the human gut microbiome and outside a matrix resembling extracellular bacterial lysates, in agreement with a bacteriophage mechanism with the images obtained by transmission electron microscopy (TEM), post-embedding immunogold, and by fluorescence microscope. In addition to the typical observations of respiratory symptoms, accurate evaluation of clinical gastrointestinal and neurological symptoms, combined with efficient highly sensitive molecular testing on feces, represent an efficient approach for detecting SARS-CoV-2, and for providing the correct therapy in challenging COVID-19 cases, like the one here reported.

Machine learning tools used for mapping some immunogenic epitopes within the major structural proteins of the bovine coronavirus (BCoV) and for the in silico design of the multiepitope-based vaccines

Introduction

BCoV is one of the significant causes of enteritis in young calves; it may also be responsible for many respiratory outbreaks in young calves. BCoV participates in the development of bovine respiratory disease complex in association with other bacterial pathogens. Our study aimed (1) to map the immunogenic epitopes (B and T cells) within the major BCoV structural proteins. These epitopes are believed to induce a robust immune response through the interaction with major histocompatibility complex (MHC class II) molecules (2) to design some novel BCoV multiepitope-based vaccines.

Materials and Methods

The goal is achieved through several integrated in silico prediction computational tools to map these epitopes within the major BCoV structural proteins. The final vaccine was constructed in conjugation with the Choleratoxin B toxin as an adjuvant. The tertiary structure of each vaccine construct was modeled through the AlphaFold2 tools. The constructed vaccine was linked to some immunostimulants such as Toll-like receptors (TLR2 and TLR4). We also predicted the affinity binding of these vaccines with this targeted protein using molecular docking. The stability and purity of each vaccine construct were assessed using the Ramachandran plot and the Z-score values. We created the in silico cloning vaccine constructs using various expression vectors through vector builder and Snap gene.

Results and discussion

The average range of major BCoV structural proteins was detected within the range of 0.4 to 0.5, which confirmed their antigen and allergic properties. The binding energy values were detected between -7.9 and -9.4 eV and also confirmed their best interaction between our vaccine construct and Toll-like receptors. Our in silico cloning method expedited the creation of vaccine constructs and established a strong basis for upcoming clinical trials and experimental validations.

Conclusion

Our designed multiepitope vaccine candidates per each BCoV structural protein showed high antigenicity, immunogenicity, non-allergic, non-toxic, and high-water solubility. Further studies are highly encouraged to validate the efficacy of these novel BCoV vaccines in the natural host.

Bovine Coronavirus Prevalence and Risk Factors in Calves on Dairy Farms in Europe

This study evaluated prevalence and risk factors in health, management, and biosecurity of bovine coronavirus (BCoV) in neonatal and weaned dairy calves on 125 dairy farms in Europe. Nasal and fecal swabs from neonatal calves, weaned calves, and fresh cows were analyzed for BCoV using RT-PCR, and blood and bulk milk samples were collected for BCoV antibody levels using ELISA. Multiple logistic regression models with random effects of herds were used to evaluate the herd health status, husbandry, management, and biosecurity associated with BCoV shedding (nasal and/or fecal PCR positive samples) in neonatal and weaned calves. BCoV was detected in 80% of herds and in 24% of neonatal calves, 23% of weaned calves, and 5% of fresh cows. The biosecurity scored on 109 dairies with Biocheck.Ugent was, on average, 60% (external score 71%, internal score 47%), and there was no clear association between various biosecurity measures on BCoV shedding in calves. Dry cow vaccination against BCoV reduced shedding in neonatal calves, whereas it was linked to increased shedding in weaned calves in these farms. Several husbandry factors, including nutrition (transition milk feeding and milk feeding levels) and management (group housing and weaning age), were associated with BCoV shedding in calves.

Retrospective study of the relative frequency of cattle respiratory disease pathogens in clinical laboratory samples submitted by UK veterinary practices

BACKGROUND

The objective of this study was to explore the relative frequency and seasonality of bovine respiratory pathogens in the UK, based on clinical case submission for laboratory PCR testing.

METHODS

This study used retrospective data generated by a central Scotland laboratory using 407 clinical (pooled) samples collected by 95 veterinary practices located throughout the UK between November 2020 and September 2022. Statistical analyses were performed using descriptive spatial analysis (choropleth maps), chi-squared analysis, Poisson and logistic regression modelling.

RESULTS

The majority (77.6%) of the samples had more than one species of bacteria identified, and 17.7% had multiple viruses identified. In comparison with the colder months of autumn and winter (September to February), the warmer months (March to August) were significantly associated with lower odds of respiratory disease caused by certain pathogens. Poisson models showed small but significant univariable associations between total viruses (coefficient = ‒0.01, standard error [SE] = 0.004, 95% confidence interval [CI] = ‒0.02 to ‒0.003) and total pathogens (coefficient = ‒0.005, SE = 0.002, 95% CI = ‒0.008 to 0.002) and increasing weekly age.

LIMITATIONS

This is an inherently biased population because it only comprises clinical samples submitted to a single UK laboratory, and the data were analysed retrospectively.

CONCLUSIONS

A large majority of clinical bovine respiratory disease (BRD) samples were multipathogenic, and pathogens such as bovine coronavirus (which has generally not been considered a significant contributing pathogen in the BRD complex in the UK) were prevalent.

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.

Novel CRISPR/Cas13-based assay for detection of bovine coronavirus associated with severe diarrhea in calves

Bovine coronavirus (BCoV) is one of the important causes of diarrhoea in cattle. The virus is responsible for the high fatality rate associated with acute diarrhoea in calves. Rapid and accurate tests need to be conducted to detect the virus and minimise economic losses associated with the disease. Nucleic acid-based detection assays including PCR is an accurate test for detecting pathogens. However, these tests need skilled personnel, time and expensive devices. In this study, we developed a novel assay for the detection of BCoV in clinical cases. This novel assay combined reverse transcription-recombinase polymerase amplification with CRISPR/Cas13 and conducted a rapid visualisation of cleavage activity using a Lateral Flow Device. A conserved sequence of the BCV M gene was used as a target gene and the assays were tested in terms of specificity, sensitivity and time consumption. The result showed the specificity of the assay as 100% with no false positives being detected. Ten copies of the input RNA were enough to detect the virus and perform the assay. It took up to forty minutes for reading the results. Conducted together, the assay should be used as a rapid test to clinically diagnose infectious pathogens including bovine coronavirus. However, the assay needed the RNA to be extracted from the clinical sample in order to detect the virus. Therefore, more studies are needed to optimise the assay to be able to detect the virus in the clinical sample without extracting the RNA.

Brain invasion of bovine coronavirus: molecular analysis of bovine coronavirus infection in calves with severe pneumonia and neurological signs

IMPORTANCE

Although the role of bovine coronavirus (BCoV) in calf diarrhea and respiratory disorders is well documented, its contribution to neurological diseases is unclear.

OBJECTIVE

This study conducted virological investigations of calves showing diarrhea and respiratory and neurological signs.

METHODS

An outbreak of diarrhea, respiratory, and neurological disorders occurred among the 12 calves in July 2022 in Istanbul, Türkiye. Two of these calves exhibited neurological signs and died a few days after the appearance of symptoms. One of these calves was necropsied and analyzed using molecular and histopathological tests.

RESULTS

BCoV RNA was detected in the brain, lung, spleen, liver, and intestine of the calf that had neurological signs by real-time reverse transcription polymerase chain reaction. Immunostaining was also observed in the intestine and brain. A 622 bp S1 gene product was noted on gel electrophoresis only in the brain. Phylogenetic analysis indicated that the BCoV detected in this study had a high proximity to the BCoV strain GIb with 99.19% nucleotide sequence homology to the strains detected in Poland, Israel, Türkiye, and France. No distinct genetic lineages were observed when the brain isolate was compared with the respiratory and enteric strains reported to GenBank. In addition, the highest identity (98,72%) was obtained with the HECV 4408 and L07748 strains of human coronaviruses.

CONCLUSIONS AND RELEVANCE

The strain detected in a calf brain belongs to the GIb-European lineage and shares high sequence homology with BCoV strains detected in Europe and Israel. In addition, the similarity between the human coronaviruses (4408 and L07748) raises questions about the zoonotic potential of the strains detected in this study.

Humoral Immune Response in Immunized Sheep with Bovine Coronavirus Glycoproteins Delivered via an Adenoviral Vector

Bovine coronavirus (BCoV) is distributed globally and mainly causes different clinical manifestations: enteric diarrhea in calves, winter dysentery in adults, and respiratory symptoms in cattle of all ages. Low mortality and high morbidity are the hallmarks of BCoV infection, usually associated with substantial economic losses for the livestock industry. Vaccination, combined with the implementation of biosecurity measures, is the key strategy for the prevention of infections. This pilot study evaluates the immunogenicity of a recombinant vaccine containing two BCoV antigens (S and M) in sheep, compared to vaccines containing only the M or S protein. Three groups of sheep were inoculated intramuscularly at day 0 and day 21 with recombinant adenoviruses expressing BCoV S protein (AdV-BCoV-S), BCoV M protein (AdV-BCoV-M), or both proteins (AdV-BCoV-S + M). Serum antibodies were evaluated using immunofluorescence (IF) and serum neutralization (SN) tests. Moderate seroconversion was observed by day 21, but serum antibodies detected via SN increased from 1:27.5 (day 21) to 1:90 (day 28) in sheep inoculated with the recombinant AdV expressing both the S- and M-BCoV proteins. Based on the SN results, a repeated-measures ANOVA test indicated a more significant difference in immune response between the three groups (F = 20.47; p < 0.001). The experimental investigation produced satisfactory results, highlighting that the S + M recombinant vaccine was immunogenic, stimulating a valid immune response. Despite some inherent limitations, including a small sample size and the absence of challenge tests, the study demonstrated the efficacy of the immune response induced via the recombinant vaccine containing both S and M proteins compared to that induced via the individual proteins S or M.

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.

Isolation and Characterization of Contemporary Bovine Coronavirus Strains

Bovine coronavirus (BCoV) poses a threat to cattle health worldwide, contributing to both respiratory and enteric diseases. However, few contemporary strains have been isolated. In this study, 71 samples (10 nasal and 61 fecal) were collected from one farm in Ohio in 2021 and three farms in Georgia in 2023. They were screened by BCoV-specific real-time reverse transcription-PCR, and 15 BCoV-positive samples were identified. Among them, five BCoV strains from fecal samples were isolated using human rectal tumor-18 (HRT-18) cells. The genomic sequences of five strains were obtained. The phylogenetic analysis illustrated that these new strains clustered with US BCoVs that have been detected since the 1990s. Sequence analyses of the spike proteins of four pairs of BCoVs, with each pair originally collected from the respiratory and enteric sites of one animal, revealed the potential amino acid residue patterns, such as D1180 for all four enteric BCoVs and G1180 for three of four respiratory BCoVs. This project provides new BCoV isolates and sequences and underscores the genetic diversity of BcoVs, the unknown mechanisms of disease types, and the necessity of sustained surveillance and research for BCoVs.

Evaluation of bovine coronavirus in Korean native calves challenged through different inoculation routes

Bovine coronavirus (BCoV) is a pneumoenteric virus that can infect the digestive and respiratory tracts of cattle, resulting in economic losses. Despite its significance, information regarding BCoV pathogenesis is limited. Hence, we investigated clinical signs, patterns of viral shedding, changes in antibody abundance, and cytokine/chemokine production in calves inoculated with BCoV via intranasal and oral. Six clinically healthy Korean native calves (< 30 days old), initially negative for BCoV, were divided into intranasal and oral groups and monitored for 15 days post-infection (dpi). BCoV-infected calves exhibited clinical signs such as nasal discharge and diarrhea, starting at 3 dpi and recovering by 12 dpi, with nasal discharge being the most common symptoms. Viral RNA was detected in nasal and fecal samples from all infected calves. Nasal shedding occurred before fecal shedding regardless of the inoculation route; however, fecal shedding persisted longer. Although the number of partitions was very few, viral RNA was identified in the blood of two calves in the oral group at 7 dpi and 9 dpi using digital RT-PCR analysis. The effectiveness of maternal antibodies in preventing viral replication and shedding appeared limited. Our results showed interleukin (IL)-8 as the most common and highly induced chemokine. During BCoV infection, the levels of IL-8, monocyte chemoattractant protein-1, and macrophage inflammatory protein-1β were significantly affected, suggesting that these emerge as potential and reliable biomarkers for predicting BCoV infection. This study underscores the importance of BCoV as a major pathogen causing diarrhea and respiratory disease.

Comparison of postweaning bovine respiratory disease treatment rates between non-vaccinated control beef calves and calves variably primed and boosted using commercially available bovine coronavirus vaccines

Objective

Bovine respiratory disease (BRD) and overall postweaning treatment rates were compared among 3 groups of calves either differentially primed and boosted with commercially available bovine coronavirus (BCoV) vaccine or not vaccinated against BCoV.

Animals

Commercial heifer and steer beef calves born in April and May 2022.

Procedure

In June 2022, calves were randomly enrolled into 3 treatment groups. Those in 2 groups [V1 (n = 160) and V2 (n = 160)] were administered a mucosal priming dose of 1 of 2 commercial BCoV vaccines; those in the 3rd group [CTL (n = 151)] were unvaccinated against BCoV. The V1 and V2 groups were boosted by intramuscular injection pre-weaning with the same vaccine used for priming. Weaning occurred 3 wk after the last preweaning processing day. Ranch staff used a BRD case definition provided by their herd veterinarian to identify, treat, and record treatments for 45 d post-weaning.

Results

Postweaning BRD treatment rates for V1, V2, and CTL were 7%, 9%, and 14%, respectively. The CTL calves had 2.2× greater odds of receiving treatment for BRD than V1 calves. There were no differences in odds of treatment between CTL and V2 calves or V1 and V2 calves.

Conclusion

In a herd with previously diagnosed BCoV BRD cases, prime-boost vaccination of calves is associated with a difference in odds of BRD treatment post-weaning compared to not vaccinating calves against BCoV.

Clinical relevance

Prime-boost vaccination with commercial BCoV vaccine may be an important management tool for herds with known BCoV BRD outbreaks.

The Potential Roles of Host Cell miRNAs in Fine-Tuning Bovine Coronavirus (BCoV) Molecular Pathogenesis, Tissue Tropism, and Immune Regulation

Bovine coronavirus (BCoV) infection causes significant economic loss to the dairy and beef industries worldwide. BCoV exhibits dual tropism, infecting the respiratory and enteric tracts of cattle. The enteric BCoV isolates could also induce respiratory manifestations under certain circumstances. However, the mechanism of this dual tropism of BCoV infection has not yet been studied well. MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression and play a dual role in virus infection, mediating virus or modulating host immune regulatory genes through complex virus-host cell interactions. However, their role in BCoV infection remains unclear. This study aims to identify bovine miRNAs crucial for regulating virus-host interaction, influencing tissue tropism, and explore their potential as biomarkers and therapeutic agents against BCoV. We downloaded 18 full-length BCoV genomes (10 enteric and eight respiratory) from GenBank. We applied several bioinformatic tools to study the host miRNAs targeting various regions in the viral genome. We used the criteria of differential targeting between the enteric/respiratory isolates to identify some critical miRNAs as biological markers for BCoV infection. Using various online bioinformatic tools, we also searched for host miRNA target genes involved in BCoV infection, immune evasion, and regulation. Our results show that four bovine miRNAs (miR-2375, miR-193a-3p, miR-12059, and miR-494) potentially target the BCoV spike protein at multiple sites. These miRNAs also regulate the host immune suppressor pathways, which negatively impacts BCoV replication. Furthermore, we found that bta-(miR-2338, miR-6535, miR-2392, and miR-12054) also target the BCoV genome at certain regions but are involved in regulating host immune signal transduction pathways, i.e., type I interferon (IFN) and retinoic acid-inducible gene I (RIG-I) pathways. Moreover, both miR-2338 and miR-2392 also target host transcriptional factors RORA, YY1, and HLF, which are potential diagnostic markers for BCoV infection. Therefore, miR-2338, miR-6535, miR-2392, and miR-12054 have the potential to fine-tune BCoV tropism and immune evasion and enhance viral pathogenesis. Our results indicate that host miRNAs play essential roles in the BCoV tissue tropism, pathogenesis, and immune regulation. Four bovine miRNAs (miR-2375, bta-miR-193a-3p, bta-miR-12059, and bta-miR-494) target BCoV-S glycoprotein and are potentially involved in several immune suppression pathways during the viral infection. These miRNA candidates could serve as good genetic markers for BCoV infection. However, further studies are urgently needed to validate these identified miRNAs and their target genes in the context of BCoV infection and dual tropism and as genetic markers.

Molecular and Serological Detection of Bovine Coronaviruses in Marmots (Marmota marmota) in the Alpine Region

In this study, virological surveillance focused on coronaviruses in marmots in the Alpine region in 2022, captured as part of a population control reduction program in the Livigno area. Seventy-six faecal samples were randomly collected from marmots at the time of capture and release and tested for genome detection of pan-coronavirus, pan-pestivirus, canine distemper virus, and influenza A and D virus. Nine faecal samples were positive in the Pan-CoV RT-PCR, while all were negative for the other viruses. Pan-coronavirus positives were further identified using Illumina's complete genome sequencing, which showed the highest homology with Bovine Coronavirus previously detected in roe deer in the Alps. Blood samples (n.35) were collected randomly from animals at release and tested for bovine coronavirus (BCoV) antibodies using competitive ELISA and VNT. Serological analyses revealed that 8/35 sera were positive for BCoV antibodies in both serological tests. This study provides molecular and serological evidence of the presence of BCoV in an alpine marmot population due to a likely spillover event. Marmots share areas and pastures with roe deer and other wild ruminants, and environmental transmission is a concrete possibility.

Who Is the Intermediate Host of RNA Viruses? A Study Focusing on SARS-CoV-2 and Poliovirus

The COVID-19 pandemic has sparked a surge in research on microbiology and virology, shedding light on overlooked aspects such as the infection of bacteria by RNA virions in the animal microbiome. Studies reveal a decrease in beneficial gut bacteria during COVID-19, indicating a significant interaction between SARS-CoV-2 and the human microbiome. However, determining the origins of the virus remains complex, with observed phenomena such as species jumps adding layers to the narrative. Prokaryotic cells play a crucial role in the disease's pathogenesis and transmission. Analyzing previous studies highlights intricate interactions from clinical manifestations to the use of the nitrogen isotope test. Drawing parallels with the history of the Poliovirus underscores the need to prioritize investigations into prokaryotic cells hosting RNA viruses.

Comparison of virus-neutralizing and virus-specific ELISA antibody responses among bovine neonates differentially primed and boosted against bovine coronavirus

Objective

This study addressed the current gap in knowledge of neonatal prime-boost immune responses for the control of bovine coronavirus (BCoV) respiratory disease in weaning-age beef cattle.

Animals

Study 1 and Study 2 had 33 and 22 commercial cross neonatal beef calves, respectively.

Procedures

Study 1 compared BCoV-neutralizing antibody concentrations of control calves with 3 groups of calves differentially vaccinated with mucosal and/or systemic BCoV modified live virus (MLV) vaccines. Study 2 compared specific and neutralizing antibody concentrations among mucosally BCoV primed groups of calves that were differentially systemically boosted.

Results

In Study 1, calves that were mucosally primed and systemically boosted had higher BCoV-neutralizing antibody concentrations than the control group at weaning. In Study 2, boosting mucosally primed calves by injecting inactivated or MLV vaccine resulted in anamnestic BCoV-specific antibody responses at weaning.

Conclusion

Neonatal mucosal priming and systemic boosting resulted in anamnestic BCoV antibody responses at weaning.

Clinical relevance

Prime-boost vaccination should be considered for control of BCoV respiratory disease.

A multiplex real-time fluorescence-based quantitative PCR assay for calf diarrhea viruses

Introduction

Calf diarrhea is a significant condition that has a strong effect on the cattle industry, resulting in huge economic losses annually. Bovine torovirus (BToV), bovine enterovirus (BEV), bovine norovirus (BNoV), bovine coronavirus (BCoV), bovine rotavirus (BRV), and bovine viral diarrhea virus (BVDV) are key pathogens that have been implicated in calf diarrhea. Among these viruses, there remains limited research on BToV, BEV, and BNoV, with no available vaccines or drugs for their prevention and control. Although commercial vaccines exist for BCoV, BRV, and BVDV, the prevalence of these diseases remains high.

Methods

To address this issue, we developed a multiplex real-time fluorescence quantitative PCR method for detecting BToV, BEV, BNoV, BCoV, BRV, and BVDV. This method can be used to effectively monitor the prevalence of these six viruses and serve as a reference for future prevention and control strategies. In this study, we specifically designed primers and probes for the BNoV Rdrp, BEV 5'UTR, BToV M, BCoV N, BRV NSP5, and BVDV 5'UTR genes.

Results

This method was determined to be efficient, stable, and sensitive. The lowest detectable levels of plasmids for BNoV, BEV, BToV, BRV, BCoV, and BVDV were 1.91 copies/μL, 96.0 copies/μL, 12.8 copies/μL, 16.4 copies/μL, 18.2 copies/μL, and 65.3 copies/μL, respectively. Moreover, the coefficients of variation for all six detection methods were < 3%; they also exhibited a strong linear relationship (R2 ≥ 0.98), and an amplification efficiency of 90%-110%. A total of 295 fecal and anal swabs were collected from calves with diarrhea in Guangdong, China. The positive rates for BToV, BEV, BNoV, BCoV, BR, and BVDV were determined to be 0.34% (1/295), 6.10% (18/295), 0.68% (2/295), 1.36% (4/295), 10.85% (32/295), and 2.03% (6/295), respectively. Notably, BEV and BRV exhibited the highest prevalence.

Discussion

Additionally, this study identified the occurrence of BToV and BNoV in Guangdong for the first time. In summary, this study successfully established an effective method for detecting several important bovine viruses; ultimately, this holds strong implications for the future development of the cattle industry.

MALDI-TOF MS analysis for detection of bovine coronavirus with tryptic peptides from viral proteins

Bovine coronavirus (BCoV）, a significant cattle pathogen causing enteric and respiratory diseases, is primarily detected using reverse transcription-polymerase chain reaction. Our objective was to develop a novel detection method for BCoV by matrix-assisted laser desorption/ionization‒time-of-flight mass spectrometry (MALDI-TOF MS）. Peptide mass fingerprint analysis revealed that nucleocapsid (N）, membrane (M）, and hemagglutinin-esterase (HE) were three main BCoV proteins. Their tryptic peptides were used as target molecules for BCoV detection. When the tryptic digest of 107.0 viral copies was analyzed by MALDI-TOF MS, five peptides with relatively strong peaks were detected. The detection limit was between 105.0 and 106.0 copies per test for BCoV alone. To detect BCoV in the swab eluate, ultrafiltration purification achieved a detection limit between 106.0 and 107.0 copies per test, sufficient to detect BCoV-infected calves. Our findings offer valuable insights for BCoV detection by MALDI-TOF MS.

A Rapid and Novel Multiplex PCR Assay for Simultaneous Detection of Multiple Viruses Associated with Bovine Gastroenteritis

Bovine viral diarrheal virus (BVDV) and bovine coronavirus (BCoV) are prevalent viral infections in buffalo calves that result in significant economic losses globally. However, Bovine picobirnavirus (BPBV) Group I and II has been an emerging causes of gastrointestinal infection as has been detected with mixed of BVDV as well as BCV. To combat economic losses and viral infection, a rapid and innovative multiplex-PCR assay (M-PCR) was developed to simultaneously identify BVDV, BCV, and BPBV. The assay employed three primer pairs, each specific to a particular virus. Notably, the primers for BCV and BVDV, targeting the transmembrane (M) Mebus gene and 5'UTR genes, respectively, were self-designed. To validate the assay, 300 samples of buffalo calf feces were subjected to the standardized multiplex PCR. The results demonstrated that 54 (18%) samples tested positive for multiple viruses, with 16.67% samples infected by BVDV, 0.9% by BCoV, and 0.13% by BPBV, as detected by the M-PCR assay. In summary, this developed assay is characterized by high specificity, sensitivity, throughput, and speed, enabling the simultaneous detection of the three viruses in a single reaction tube. Consequently, it holds potential for epidemiological investigations. It is worth noting that, to the best of our knowledge, this is the first reported multiplex assay for the worldwide detection of BVDV, BCoV, and BPBV. This novel assay promises to aid in the detection of mixed infections in the gastrointestinal tract.

Development of real-time RT-PCR systems for detection and quantitation of bovine enteric viral pathogens

The enteric viruses in animals are responsible for severe and devastating losses to the livestock owners with a profound negative impact on animal, health, welfare, and productivity. These viruses are usually transmitted via the feco-oral route and primarily infect the digestive tract of the humans, bovines and different mammals as well as birds. Some of the important enteric viruses in ruminants are: Rotavirus A (RVA), Peste des petits virus (PPRV), Norovirus (NV), Bovine corona virus (BoCV) and Bluetongue virus (BTV). In the present study, sensitive, specific and reliable TaqMan probe-based RT-qPCRs were developed and standardized for the rapid detection and quantification of enteric viruses from fecal samples. The assays result in efficient amplification of the RVA, BTV and BoCV RNA with a limit of detection (LoD) of 5, 5 and 4 copies, respectively, which is 1000 times more sensitive than the traditional gel-based RT-PCR. The reproducibility of each assay was satisfactory, thus allowing for a sensitive and accurate measurement of the viral RNA load in clinical samples. In conclusion, real time PCR developed for these viruses are highly specific and sensitive technique for the detection of diarrheic viral pathogens of cattle and buffalo.

Impacts of Surface Characteristics and Dew Point on the Blue-Light (BL405) Inactivation of Viruses

The increased prevalence of multidrug-resistant organisms (MDROs), healthcare associated infections (HAIs), and the recent COVID-19 pandemic has caused the photoinactivation industry to explore alternative wavelengths. Blue light (BL405) has gained significant interest as it is much less harmful to the skin and eyes than traditional germicidal wavelengths; therefore, in theory, it can be used continuously with human exposure. At present, the viricidal effects of BL405 are largely unknown as the literature predominately addresses bacterial disinfection performed with this wavelength. This work provides novel findings to the industry, reporting on the virucidal effects of BL405 on surfaces. This research utilizes three surfaces: ceramic, PTFE, and stainless steel. The efficacy of BL405 inactivation varied by surface type, which was due to surface characteristics, such as the contact angle, porosity, zeta potential, and reflectivity. Additionally, the effect of the dew point on BL405 inactivation efficacy was determined. This research is the first to study the effects of the dew point on the virucidal effectiveness of BL405 surface inactivation. The effects of the dew point were significant for all surfaces and the control experiments. The high-dew-point conditions (18 °C) yielded higher levels of BL405 inactivation and viral degradation for the experiments and controls, respectively.

SARS-CoV-2 prevalence in domestic and wildlife animals: A genomic and docking based structural comprehensive review

The SARS-CoV-2 virus has been identified as the infectious agent that led to the COVID-19 pandemic, which the world has seen very recently. Researchers have linked the SARS-CoV-2 outbreak to bats for the zoonotic spread of the virus to humans. Coronaviruses have a crown-like shape and positive-sense RNA nucleic acid. It attaches its spike glycoprotein to the host angiotensin-converting enzyme 2 (ACE2) receptor. Coronavirus genome comprises 14 ORFs and 27 proteins, spike glycoprotein being one of the most critical proteins for viral pathogenesis. Many mammals and reptiles, including bats, pangolins, ferrets, snakes, and turtles, serve as the principal reservoirs for this virus. But many experimental investigations have shown that certain domestic animals, including pigs, chickens, dogs, cats, and others, may also be able to harbor this virus, whether they exhibit any symptoms. These animals act as reservoirs for SARS-CoV, facilitating its zoonotic cross-species transmission to other species, including humans. In this review, we performed a phylogenetic analysis with multiple sequence alignment and pairwise evolutionary distance analysis, which revealed the similarity of ACE2 receptors in humans, chimpanzees, domestic rabbits, house mice, and golden hamsters. Pairwise RMSD analysis of the spike protein from some commonly reported SARS-CoV revealed that bat and pangolin coronavirus shared the highest structural similarity with human coronavirus. In a further experiment, molecular docking confirmed a higher affinity of pig, bat, and pangolin coronavirus spike proteins' affinity to the human ACE2 receptor. Such comprehensive structural and genomic analysis can help us to forecast the next likely animal source of these coronaviruses that may infect humans. To combat these zoonotic illnesses, we need a one health strategy that considers the well-being of people and animals and the local ecosystem.

Complete Genome Sequence of a Bovine Coronavirus Isolated from a Goat in Pennsylvania, USA

We report a complete genome sequence of bovine coronavirus (BCoV) isolated from a goat in the state of Pennsylvania in 2022. BCoV often causes calf scours and winter dysentery in cattle.

Development of an IgY-Based Treatment to Control Bovine Coronavirus Diarrhea in Dairy Calves

Bovine Coronavirus (BCoV) is a major pathogen associated with neonatal calf diarrhea. Standard practice dictates that to prevent BCoV diarrhea, dams should be immunized in the last stage of pregnancy to increase BCoV-specific antibody (Ab) titers in serum and colostrum. For the prevention to be effective, calves need to suck maternal colostrum within the first six to twelve hours of life before gut closure to ensure a good level of passive immunity. The high rate of maternal Ab transfer failure resulting from this process posed the need to develop alternative local passive immunity strategies to strengthen the prevention and treatment of BCoV diarrhea. Immunoglobulin Y technology represents a promising tool to address this gap. In this study, 200 laying hens were immunized with BCoV to obtain spray-dried egg powder enriched in specific IgY Abs to BCoV on a large production scale. To ensure batch-to-batch product consistency, a potency assay was statistically validated. With a sample size of 241, the BCoV-specific IgY ELISA showed a sensitivity and specificity of 97.7% and 98.2%, respectively. ELISA IgY Abs to BCoV correlated with virus-neutralizing Ab titers (Pearson correlation, R2 = 0.92, p < 0.001). Most importantly, a pilot efficacy study in newborn calves showed a significant delay and shorter duration of BCoV-associated diarrhea and shedding in IgY-treated colostrum-deprived calves. Calves were treated with milk supplemented with egg powder (final IgY Ab titer to BCoV ELISA = 512; VN = 32) for 14 days as a passive treatment before a challenge with BCoV and were compared to calves fed milk with no supplementation. This is the first study with proof of efficacy of a product based on egg powder manufactured at a scale that successfully prevents BCoV-associated neonatal calf diarrhea.

Prevalence of bovine coronavirus in cattle in China: A systematic review and meta-analysis

Bovine coronavirus (BCoV) is one of the important pathogens that cause calf diarrhea (CD), winter dysentery (WD), and the bovine respiratory disease complex (BRDC), and spreads worldwide. An infection of BCoV in cattle can lead to death of young animals, stunted growth, reduced milk production, and milk quality, thus bringing serious economic losses to the bovine industry. Therefore, it is necessary to prevent and control the spread of BCoV. Here, a systematic review and meta-analysis was conducted to assess the prevalence of BCoV in cattle in China before 2022. A total of 57 articles regarding the prevalence of BCoV in cattle in China were collected from five databases (PubMed, ScienceDirect, CNKI, VIP, and Wan Fang). Based on the inclusion criteria, a total of 15,838 samples were included, and 6,136 were positive cases. The overall prevalence of BCoV was 30.8%, with the highest prevalence rate (60.5%) identified in South China and the lowest prevalence (15.6%) identified in Central China. We also analyzed other subgroup information, included sampling years, sample sources, detection methods, breeding methods, age, type of cattle, presence of diarrhea, and geographic and climatic factors. The results indicated that BCoV was widely prevalent in China. Among all subgroups, the sample sources, detection methods, breeding methods, and presence or absence of diarrheal might be potential risk factors responsible for BCoV prevalence. It is recommended to strengthen the detection of BCoV in cattle, in order to effectively control the spread of BCoV.

Assessment of GO-Based Protein Interaction Affinities in the Large-Scale Human-Coronavirus Family Interactome

SARS-CoV-2 is a novel coronavirus that replicates itself via interacting with the host proteins. As a result, identifying virus and host protein-protein interactions could help researchers better understand the virus disease transmission behavior and identify possible COVID-19 drugs. The International Committee on Virus Taxonomy has determined that nCoV is genetically 89% compared to the SARS-CoV epidemic in 2003. This paper focuses on assessing the host-pathogen protein interaction affinity of the coronavirus family, having 44 different variants. In light of these considerations, a GO-semantic scoring function is provided based on Gene Ontology (GO) graphs for determining the binding affinity of any two proteins at the organism level. Based on the availability of the GO annotation of the proteins, 11 viral variants, viz., SARS-CoV-2, SARS, MERS, Bat coronavirus HKU3, Bat coronavirus Rp3/2004, Bat coronavirus HKU5, Murine coronavirus, Bovine coronavirus, Rat coronavirus, Bat coronavirus HKU4, Bat coronavirus 133/2005, are considered from 44 viral variants. The fuzzy scoring function of the entire host-pathogen network has been processed with ~180 million potential interactions generated from 19,281 host proteins and around 242 viral proteins. ~4.5 million potential level one host-pathogen interactions are computed based on the estimated interaction affinity threshold. The resulting host-pathogen interactome is also validated with state-of-the-art experimental networks. The study has also been extended further toward the drug-repurposing study by analyzing the FDA-listed COVID drugs.

[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.

Coronaviruses: Troubling Crown of the Animal Kingdom

The existence of coronaviruses has been known for many years. These viruses cause significant disease that primarily seems to affect agricultural species. Human coronavirus disease due to the 2002 outbreak of Severe Acute Respiratory Syndrome and the 2012 outbreak of Middle East Respiratory Syndrome made headlines; however, these outbreaks were controlled, and public concern quickly faded. This complacency ended in late 2019 when alarms were raised about a mysterious virus responsible for numerous illnesses and deaths in China. As we now know, this novel disease called Coronavirus Disease 2019 (COVID-19) was caused by Severe acute respiratory syndrome-related-coronavirus-2 (SARS-CoV-2) and rapidly became a worldwide pandemic. Luckily, decades of research into animal coronaviruses hastened our understanding of the genetics, structure, transmission, and pathogenesis of these viruses. Coronaviruses infect a wide range of wild and domestic animals, with significant economic impact in several agricultural species. Their large genome, low dependency on host cellular proteins, and frequent recombination allow coronaviruses to successfully cross species barriers and adapt to different hosts including humans. The study of the animal diseases provides an understanding of the virus biology and pathogenesis and has assisted in the rapid development of the SARS-CoV-2 vaccines. Here, we briefly review the classification, origin, etiology, transmission mechanisms, pathogenesis, clinical signs, diagnosis, treatment, and prevention strategies, including available vaccines, for coronaviruses that affect domestic, farm, laboratory, and wild animal species. We also briefly describe the coronaviruses that affect humans. Expanding our knowledge of this complex group of viruses will better prepare us to design strategies to prevent and/or minimize the impact of future coronavirus outbreaks.

Evaluating the transmission feasibility of SARS-CoV-2 Omicron (B.1.1.529) variant to 143 mammalian hosts: insights from S protein RBD and host ACE2 interaction studies

In comparison to previously known severe respiratory syndrome coronavirus 2 (SARS-CoV-2) variants, the newly emerged Omicron (B.1.1.529) variant shows higher infectivity in humans. Exceptionally high infectivity of this variant raises concern of its possible transmission via other intermediate hosts. The SARS-CoV-2 infectivity is established via the association of spike (S) protein receptor binding domain (RBD) with host angiotensin I converting enzyme 2 (hACE2) receptor. In the course of this study, we investigated the interaction between Omicron S protein RBD with the ACE2 receptor of 143 mammalian hosts including human by protein-protein interaction analysis. The goal of this study was to forecast the likelihood that the virus may infect other mammalian species that coexist with or are close to humans in the household, rural, agricultural, or zoological environments. The Omicron RBD was found to interact with higher binding affinity with the ACE2 receptor of 122 mammalian hosts via different amino acid residues from the human ACE2 (hACE2). The rat (Rattus rattus) ACE2 was found to show the strongest interaction with Omicron RBD with a binding affinity of -1393.6 kcal/mol. These distinct strong binding affinity of RBD of Omicron with host ACE2 indicates a greater potential of new host transmissibility and infection via intermediate hosts. Though expected but the phylogenetic position of the mammalian species may not dictate the Omicron RBD binding to the host ACE2 receptor suggesting an involvement of multiple factors in guiding host divergence of the variant.

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.

Recent Emergence of Bovine Coronavirus Variants with Mutations in the Hemagglutinin-Esterase Receptor Binding Domain in U.S. Cattle

Bovine coronavirus (BCoV) has spilled over to many species, including humans, where the host range variant coronavirus OC43 is endemic. The balance of the opposing activities of the surface spike (S) and hemagglutinin-esterase (HE) glycoproteins controls BCoV avidity, which is critical for interspecies transmission and host adaptation. Here, 78 genomes were sequenced directly from clinical samples collected between 2013 and 2022 from cattle in 12 states, primarily in the Midwestern U.S. Relatively little genetic diversity was observed, with genomes having >98% nucleotide identity. Eleven isolates collected between 2020 and 2022 from four states (Nebraska, Colorado, California, and Wisconsin) contained a 12 nucleotide insertion in the receptor-binding domain (RBD) of the HE gene similar to one recently reported in China, and a single genome from Nebraska collected in 2020 contained a novel 12 nucleotide deletion in the HE gene RBD. Isogenic HE proteins containing either the insertion or deletion in the HE RBD maintained esterase activity and could bind bovine submaxillary mucin, a substrate enriched in the receptor 9-O-acetylated-sialic acid, despite modeling that predicted structural changes in the HE R3 loop critical for receptor binding. The emergence of BCoV with structural variants in the RBD raises the possibility of further interspecies transmission.

Routine Decontamination of Surfaces Relevant to Working Dogs: Neutralization of Superficial Coronavirus Contamination

Given the increased deployment of working dogs to settings with pathogenic biological agents, a safe, effective, and logistically feasible surface decontamination protocol is essential to protect both the animals and their human handlers. Our group previously found that superficial contamination on surfaces relevant to the working dog community, including leashes and toys, could be significantly reduced using a standardized wiping protocol with various cleansing products. To expand upon this work, we analyzed the ability of this protocol to decontaminate surface-deposited bovine coronavirus, which was used as a BSL2 surrogate for SARS-CoV-2. Unsurprisingly, the physical characteristics of a given surface, including porosity and texture, had a significant effect on the ability to recover viable virus remaining on the surface post treatment. After correcting for these differences, however, wiping with 70% isopropyl alcohol (IPA) and 0.5% chlorhexidine performed best, reducing viral titers by >3 log on plastic bumper toys and nylon collars, and by >2 log on rubber toys and tennis balls. Leather leashes and Velcro proved more difficult to decontaminate, but both still showed significant loss of viral contamination following wiping with IPA or chlorhexidine. This work (i) validates the utility of a simple protocol for the neutralization of viruses on several surfaces, (ii) identifies materials that are more difficult to decontaminate, which should, thus, be considered for removal from field use, and (iii) highlights the need for further development of protocols testing porous or textured surfaces.

Gastrointestinal symptoms and fecal shedding of SARS-CoV-2 RNA suggest prolonged gastrointestinal infection

Background

COVID-19 manifests with respiratory, systemic, and gastrointestinal (GI) symptoms.^1, SARS-CoV-2 RNA is detected in respiratory and fecal samples, and recent reports demonstrate viral replication in both the lung and intestinal tissue.2, 3, 4 Although much is known about early fecal RNA shedding, little is known about long-term shedding, especially in those with mild COVID-19. Furthermore, most reports of fecal RNA shedding do not correlate these findings with GI symptoms.⁵.

Methods

We analyzed the dynamics of fecal RNA shedding up to 10 months after COVID-19 diagnosis in 113 individuals with mild to moderate disease. We also correlated shedding with disease symptoms.

Findings

Fecal SARS-CoV-2 RNA is detected in 49.2% [95% confidence interval, 38.2%-60.3%] of participants within the first week after diagnosis. Whereas there was no ongoing oropharyngeal SARS-CoV-2 RNA shedding in subjects at 4 months, 12.7% [8.5%-18.4%] of participants continued to shed SARS-CoV-2 RNA in the feces at 4 months after diagnosis and 3.8% [2.0%-7.3%] shed at 7 months. Finally, we found that GI symptoms (abdominal pain, nausea, vomiting) are associated with fecal shedding of SARS-CoV-2 RNA.

Conclusions

The extended presence of viral RNA in feces, but not in respiratory samples, along with the association of fecal viral RNA shedding with GI symptoms suggest that SARS-CoV-2 infects the GI tract and that this infection can be prolonged in a subset of individuals with COVID-19.

Funding

This research was supported by a Stanford ChemH-IMA grant; fellowships from the AACR and NSF; and NIH R01-AI148623, R01-AI143757, and UL1TR003142.

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.

Infectivity and Morphology of Bovine Coronavirus Inactivated In Vitro by Cationic Photosensitizers

Bovine coronaviruses (BCoVs), which cause gastrointestinal and respiratory diseases in cattle, and are genetically related to the human coronavirus HCoV-OC43, which is responsible for up to 10% of common colds, attract increased attention. We applied the method of photodynamic inactivation with cationic photosensitizers (PSs) to reduce the titers of BCoV and studied the morphological structure of viral particles under various modes of photodynamic exposure. The samples of virus containing liquid with an initial virus titer of 5 Log₁₀ TCID50/mL were incubated with methylene blue (MB) or octakis(cholinyl)zinc phthalocyanine (Zn-PcChol₈₊) at concentrations of 1–5 μM for 10 min in the dark at room temperature. After incubation, samples were irradiated with LED (emission with maximum at 663 nm for MB or at 686 nm for Zn-PcChol₈₊) with light doses of 1.5 or 4 J/cm². Next, the irradiation titrated virus containing liquid was studied using negative staining transmission electron microscopy. MB and Zn-PcChol₈₊ at concentrations of 1–5 μM, in combination with red light from LED sources in the low doses of 1.5–4.0 J/cm², led to a decrease in BCoV titers by at least four orders of magnitude from the initial titer 5 Log₁₀ TCID50/mL. Morphological changes in photodamaged BCoVs with increasing PS concentrations were loss of spikes, change in shape, decreased size of virus particles, destruction of the envelope, and complete disintegration of viruses. BCoV has been found to be sensitive to MB, which is the well-known approved drug, even in the absence of light.

Bovine Coronavirus Infects the Respiratory Tract of Cattle Challenged Intranasally

Bovine Coronavirus (BCoV) is a member of a family of viruses associated with both enteric and respiratory diseases in a wide range of hosts. BCoV has been well-established as a causative agent of diarrhea in cattle, however, its role as a respiratory pathogen is controversial. In this study, fifteen calves were challenged intranasally with virulent BCoV in order to observe the clinical manifestation of the BCoV infection for up to 8 days after initial challenge, looking specifically for indication of symptoms, pathology, and presence of viral infection in the respiratory tract, as compared to six unchallenged control calves. Throughout the study, clinical signs of disease were recorded and nasal swabs were collected daily. Additionally, bronchoalveolar lavage (BAL) was performed at 4 days Post-challenge, and blood and tissue samples were collected from calves at 4, 6, or 8 days Post-challenge to be tested for the presence of BCoV and disease pathology. The data collected support that this BCoV challenge resulted in respiratory infections as evidenced by the isolation of BCoV in BAL fluids and positive qPCR, immunohistochemistry (IHC), and histopathologic lesions in the upper and lower respiratory tissues. This study can thus be added to a growing body of data supporting that BCoV is a respiratory pathogen and contributor to respiratory disease in cattle.