Detection and molecular characterisation of bovine corona and toroviruses from Croatian cattle

Classification, replication, and transcription of Nidovirales

Nidovirales is one order of RNA virus, with the largest single-stranded positive sense RNA genome enwrapped with membrane envelope. It comprises four families (Arterividae, Mesoniviridae, Roniviridae, and Coronaviridae) and has been circulating in humans and animals for almost one century, posing great threat to livestock and poultry，as well as to public health. Nidovirales shares similar life cycle: attachment to cell surface, entry, primary translation of replicases, viral RNA replication in cytoplasm, translation of viral proteins, virion assembly, budding, and release. The viral RNA synthesis is the critical step during infection, including genomic RNA (gRNA) replication and subgenomic mRNAs (sg mRNAs) transcription. gRNA replication requires the synthesis of a negative sense full-length RNA intermediate, while the sg mRNAs transcription involves the synthesis of a nested set of negative sense subgenomic intermediates by a discontinuous strategy. This RNA synthesis process is mediated by the viral replication/transcription complex (RTC), which consists of several enzymatic replicases derived from the polyprotein 1a and polyprotein 1ab and several cellular proteins. These replicases and host factors represent the optimal potential therapeutic targets. Hereby, we summarize the Nidovirales classification, associated diseases, "replication organelle," replication and transcription mechanisms, as well as related regulatory factors.

Literature Review: Coinfection in Young Ruminant Livestock-Cryptosporidium spp. and Its Companions

The protozoan Cryptosporidium parvum is one of the major causative pathogens of diarrhoea in young ruminants; therefore, it causes economic losses and impairs animal welfare. Besides C. parvum, there are many other non-infectious and infectious factors, such as rotavirus, Escherichia coli, and Giardia duodenalis, which may lead to diarrhoeic disease in young livestock. Often, more than one infectious agent is detected in affected animals. Little is known about the interactions bet-ween simultaneously occurring pathogens and their potential effects on the course of disease. In this review, a brief overview about pathogens associated with diarrhoea in young ruminants is presented. Furthermore, information about coinfections involving Cryptosporidium is provided.

Reverse Genetics with a Full-length Infectious cDNA Clone of Bovine Torovirus

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

Epidemiological survey and genetic diversity of bovine coronavirus in Northeast China

In 2020, to trace the prevalence and evolution of bovine coronavirus (BCoV) in China, a total of 1383 samples (1016 fecal samples and 367 nasal swab samples) were collected from 1016 cattle exhibiting diarrhea symptoms on dairy farms and beef cattle farms in Heilongjiang Province, Northeast China. All samples were subjected to reverse transcription-polymerase chain reaction (RT-PCR) detection of the BCoV N gene, followed by an analysis of its epidemiology and genetic evolution. The results indicated that of the 1016 diarrhea-affected cattle, 15.45% (157/1016) were positive for BCoV, in which positive rates of the fecal and nasal swab samples were 12.20% (124/1016) and 21.53% (79/367), respectively. Of the 367 cattle whose nasal swab samples were collected, the BCoV positive rate of the corresponding fecal samples was 15.26% (56/367). BCoV infection was significantly associated with age, farming pattern, cattle type, farm latitude, sample type, and clinical symptom (p < 0.05). Of the 203 BCoV-positive samples, 20 spike (S) genes were successfully sequenced. The 20 identified BCoV strains shared nucleotide homologies of 97.7-100.0%, and their N-terminal domain of S1 subunit (S1-NTD: residues 15-298) differed genetically from the reference strains of South Korea and Europe. The 20 identified BCoV strains were clustered in the Asia-North America group (GII group) in the global strain-based phylogenetic tree and formed three clades in the Chinese strain-based phylogenetic tree. The HLJ/HH-10/2020 strain was clustered into the Europe group (GI group) in the S1-NTD-based phylogenetic tree, exhibiting N¹⁴⁶/I, D¹⁴⁸/G, and L¹⁵⁴/F mutations that affect the S protein structure. Of the identified BCoV strains, one potential recombination event occurred between the HLJ/HH-20/2020 and HLJ/HH-10/2020 strains, which led to the generation of the recombinant BCV-AKS-01 strain. A selective pressure analysis on the S protein revealed one positively selected site (Asn⁵⁰⁹) among the 20 identified BCoV strains located inside the putative receptor binding domain (residues 326-540). These data provide a greater understanding of the epidemiology and evolution of BCoV in China.

Identifying Loci Associated With Bovine Corona Virus Infection and Bovine Respiratory Disease in Dairy and Feedlot Cattle

Bovine coronavirus (BCoV) is associated with respiratory and enteric infections in both dairy and beef cattle worldwide. It is also one of a complex of pathogens associated with bovine respiratory disease (BRD), which affects millions of cattle annually. The objectives of this study were to identify loci and heritability estimates associated with BCoV infection and BRD in dairy calves and feedlot cattle. Dairy calves from California (n = 1,938) and New Mexico (n = 647) and feedlot cattle from Colorado (n = 915) and Washington (n = 934) were tested for the presence of BCoV when classified as BRD cases or controls following the McGuirk scoring system. Two comparisons associated with BCoV were investigated: (1) cattle positive for BCoV (BCoV⁺) were compared to cattle negative for BCoV (BCoV^-) and (2) cattle positive for BCoV and affected with BRD (BCoV⁺BRD⁺) were compared to cattle negative for BCoV and BRD (BCoV^-BRD^-). The Illumina BovineHD BeadChip was used for genotyping, and genome-wide association analyses (GWAA) were performed using EMMAX (efficient mixed-model association eXpedited). The GWAA for BCoV⁺ identified 51 loci (p < 1 × 10^-5; 24 feedlot, 16 dairy, 11 combined) associated with infection with BCoV. Three loci were associated with BCoV⁺ across populations. Heritability estimates for BCoV⁺ were 0.01 for dairy, 0.11 for feedlot cattle, and 0.03 for the combined population. For BCoV⁺BRD⁺, 80 loci (p < 1 × 10^-5; 26 feedlot, 25 dairy, 29 combined) were associated including 14 loci across populations. Heritability estimates for BCoV⁺BRD⁺ were 0.003 for dairy, 0.44 for feedlot cattle, and 0.07 for the combined population. Several positional candidate genes associated with BCoV and BRD in this study have been associated with other coronaviruses and respiratory infections in humans and mice. These results suggest that selection may reduce susceptibility to BCoV infection and BRD in cattle.

Development and use of a reverse transcription insulated isothermal PCR assay for detection and characterization of bovine torovirus in yaks

Bovine torovirus (BToV) is an important diarrhea-causing pathogen affecting bovines. To facilitate BToV detection, a reverse transcription insulated isothermal PCR (RT-iiPCR) assay was developed that targets the BToV M gene with high specificity and reproducibility. The assay has a limit of detection of 23 copies/μL. Out of 69 diarrheic fecal samples from yaks collected on six farms in Tibet and Sichuan provinces in China, 11.59% (8/69) tested positive for BToV using this assay. The full-length spike (S) and hemagglutinin-esterase (HE) genes of three positive samples were subsequently sequenced. Notably, an identical recombination event was identified in the S1 subunit of the S protein of three isolates. All of the HE genes were found to belong to genotype III and shared the same unique aa variation (P44S) in the esterase domain. This study is the first confirmation of BToV in yaks and the first report of an S gene recombination event in BToV. Our findings will enhance the current understanding of the molecular characteristics and genetic evolution of BToV.

Characterization of Localization and Export Signals of Bovine Torovirus Nucleocapsid Protein Responsible for Extensive Nuclear and Nucleolar Accumulation and Their Importance for Virus Growth

Torovirus (ToV) has recently been classified into the new family Tobaniviridae, although historically, it belonged to the Coronavirus (CoV) family. The nucleocapsid (N) proteins of CoVs are predominantly localized in the cytoplasm, where the viruses replicate, but in some cases the proteins are partially located in the nucleolus. Many studies have investigated the subcellular localization and nucleocytoplasmic trafficking signals of the CoV N proteins, but little is known about ToV N proteins. Here, we studied the subcellular localization of the bovine ToV (BToV) N protein (BToN) and characterized its nucleocytoplasmic trafficking signals. Unlike other CoVs, BToN in infected cells was transported mainly to the nucleolus during early infection but was distributed predominantly in the nucleoplasm rather than in the nucleolus during late infection. Interestingly, a small quantity of BToN was detected in the cytoplasm during infection. Examination of a comprehensive set of substitution or deletion mutants of BToN fused with enhanced green fluorescent protein (EGFP) revealed that clusters of arginine (R) residues comprise nuclear/nucleolar localization signals (NLS/NoLS), and the C-terminal region served as a chromosomal maintenance 1 (CRM1)-independent nuclear export signal (NES). Moreover, recombinant viruses with mutations in the NLS/NoLS, but retaining nuclear accumulation, were successfully rescued and showed slightly reduced growth ability, while the virus that lost the NLS/NoLS-mediated nuclear accumulation of BToN was not rescued. These results indicate that BToN uniquely accumulates mainly in nuclear compartments during infection, regulated by an R-rich NLS/NoLS and a CRM1-independent NES, and that the BToN accumulation in the nuclear compartment driven by NLS/NoLS is important for virus growth.IMPORTANCE ToVs are diarrhea-causing pathogens detected in many species, including humans. BToV has spread worldwide, leading to economic loss, and there is currently no treatment or vaccine available. Positive-stranded RNA viruses, including ToVs, replicate in the cytoplasm, and their structural proteins generally accumulate in the cytoplasm. Interestingly, BToN accumulated predominantly in the nucleus/nucleolus during all infectious processes, with only a small fraction accumulating in the cytoplasm despite being a major structural protein. Furthermore, we identified unique nucleocytoplasmic trafficking signals and demonstrated the importance of NLS/NoLS for virus growth. This study is the first to undertake an in-depth investigation of the subcellular localization and intracellular trafficking signals of BToN. Our findings additionally suggest that the NLS/NoLS-mediated nuclear accumulation of BToN is important for virus replication. An understanding of the unique features of BToV may provide novel insights into the assembly mechanisms of not only ToVs but also other positive-stranded RNA viruses.

The effect of Cryptosporidiumparvum, rotavirus, and coronavirus infection on the health and performance of male dairy calves

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

Molecular-based cross-species evaluation of bovine coronavirus infection in cattle, sheep and goats in Ghana

Background

Apart from the huge worldwide economic losses often occasioned by bovine coronavirus (BCoV) to the livestock industry, particularly with respect to cattle rearing, continuous surveillance of the virus in cattle and small ruminants is essential in monitoring variations in the virus that could enhance host switching. In this study, we collected rectal swabs from a total of 1,498 cattle, sheep and goats. BCoV detection was based on reverse transcriptase polymerase chain reaction. Sanger sequencing of the partial RNA-dependent RNA polymerase (RdRp) region for postive samples were done and nucleotide sequences were compared with homologous sequences from the GenBank.

Results

The study reports a BCoV prevalence of 0.3%, consisting of 4 positive cases; 3 goats and 1 cattle. Less than 10% of all the animals sampled showed clinical signs such as diarrhea and respiratory distress except for high temperature which occurred in > 1000 of the animals. However, none of the 4 BCoV positive animals manifested any clinical signs of the infection at the time of sample collection. Bayesian majority-rule cladogram comparing partial and full length BCoV RdRp genes obtained in the study to data from the GenBank revealed that the sequences obtained from this study formed one large monophyletic group with those from different species and countries. The goat sequences were similar to each other and clustered within the same clade. No major variations were thus observed between our isolates and those from elsewhere.

Conclusions

Given that Ghana predominantly practices the extensive and semi-intensive systems of animal rearing, our study highlights the potential for spillover of BCoV to small ruminants in settings with mixed husbandry and limited separation between species.

First report and genetic characterization of bovine torovirus in diarrhoeic calves in China

Background

Coronaviruses are notorious pathogens that cause diarrheic and respiratory diseases in humans and animals. Although the epidemiology and pathogenicity of coronaviruses have gained substantial attention, little is known about bovine coronavirus in cattle, which possesses a close relationship with human coronavirus. Bovine torovirus (BToV) is a newly identified relevant pathogen associated with cattle diarrhoea and respiratory diseases, and its epidemiology in the Chinese cattle industry remains unknown.

Results

In this study, a total of 461 diarrhoeic faecal samples were collected from 38 different farms in three intensive cattle farming regions and analysed. Our results demonstrated that BToV is present in China, with a low prevalence rate of 1.74% (8/461). The full-length spike genes were further cloned from eight clinical samples (five farms in Henan Province). Phylogenetic analysis showed that two different subclades of BToV strains are circulating in China. Meanwhile, the three BToV strains identified from dairy calves, 18,307, 2YY and 5YY, all contained the amino acid variants R614Q, I801T, N841S and Q885E.

Conclusions

This is the first report to confirm the presence of BToV in beef and dairy calves in China with diarrhea, which extend our understanding of the epidemiology of BToVs worldwide.

First detection and genomic characteristics of bovine torovirus in dairy calves in China

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

Bovine coronavirus in neonatal calf diarrhoea in Iran

Partial gene sequencing for the bovine coronavirus at the World Genebank is available for many countries, which are distributed unevenly in five continents, but so far, no sequencing of strains has been recorded in Iran. One hundred ninety‐four stool samples from calves with diarrhoea less than one‐month old were collected from five different geographical regions of country in order to detect coronavirus and characterize it if coronavirus was found. Samples were screened for the presence of BCoV by using a commercially available ELISA kit. Furthermore, RT‐PCR was carried out on positive samples for confirmation of the presence of N and S specific genes. Sequencing and phylogenetic analysis was carried out following RT‐PCR tests. 7.2% of samples, were positive for BCoV and all stool samples from the South‐West, Northeast and West regions of Iran were negative. The results showed that all the strains of coronavirus identified in Iran were completely in independent clusters and that they did not stand in the same cluster as any of the strains identified in other parts of the world. The strains from Iran were quite different from strains in other parts of the world but from the point of similarity these viruses showed some similarities to the European strains, such as those found in France, Croatia, Denmark and Sweden.

Genetic diversity of BCoV in Brazilian cattle herds

Bovine coronavirus (BCoV) is one of the main aetiological agents of gastroenteritis in calves, causing significant economic damage to livestock. This study aims to characterise BCoV genetically on the basis of the N gene. A total of 114 faecal samples from beef and dairy calves with or without clinical symptoms of diarrhoea from five Brazilian states (São Paulo, Minas Gerais, Santa Catarina, Mato Grosso and Bahia) were evaluated between 2008 and 2015 by technique of Semi-nested RT-PCR for gene N and genealogical analysis. Of the 114 samples analysed, 14.91% (17/114) were positive. BCoV was detected in 22.72% (10/44) of the animals with diarrhoea and in 10% (7/70) of asymptomatic animals. BCoV was identified in calves from rural properties located in all of the regions sampled. Genealogical analysis showed that the Brazilian sequences of BCoV for the gene which codes for the N protein can be broken down into two distinct clusters, and the samples from this study were closely linked to Asian strains. These results contribute to the molecular characterization of BCoV in Brazil and are the first report of the circulation of BCoV in the states of Santa Catarina and Bahia.

Viral enteritis in calves

A complex community of bacteria, viruses, fungi, protists, and other microorganisms inhabit the gastrointestinal tract of calves and play important roles in gut health and disease. The viral component of the microbiome (the virome) is receiving increasing attention for its role in neonatal calf diarrhea (NCD). Rotavirus and coronavirus have for a long time been associated with NCD and commercial vaccines have been produced against these agents. Recently, several other viruses which may play a role in diarrhea have been discovered in calf fecal samples, mostly by sequence-based methods. These viruses include torovirus, norovirus, nebovirus, astrovirus, kobuvirus, and enterovirus. Most studies have involved epidemiologic investigations seeking to show association with diarrhea for each virus alone or in combination with potential pathogens. However, determining the contribution of these viruses to calf diarrhea has been challenging and much uncertainty remains concerning their roles as primary pathogens, co-infection agents, or commensals.

Detection of Bovine Coronavirus in Healthy and Diarrheic Dairy Calves

Background

BCoV is identified in both healthy and diarrheic calves, complicating its assessment as a primary pathogen.

Objectives

To investigate the detection rates of bovine coronavirus (BCoV) in feces of healthy and diarrheic calves and to describe the usefulness of a pancoronavirus reverse transcriptase (RT) PCR (PanCoV‐RT‐PCR) assay to identify BCoV in samples of diarrheic calves.

Animals

Two hundred and eighty‐six calves <21 days. Calves with liquid or semiliquid feces, temperature >39.5°C, and inappetence were considered as cases, and those that had pasty or firm feces and normal physical examination were designated as controls.

Methods

Prospective case–control study. A specific BCoV‐RT‐PCR assay was used to detect BCoV in fecal samples. Association between BCoV and health status was evaluated by exact and random effect logistic regression. Fecal (n = 28) and nasal (n = 8) samples from diarrheic calves were tested for the presence of BCoV by both the PanCoV‐RT‐PCR and a specific BCoV‐RT‐PCR assays. A Kappa coefficient test was used to assess the level of agreement of both assays.

Results

BCoV was detected in 55% (157/286) of calves; 46% (66/143), and 64% (91/143) of healthy and diarrheic calves, respectively. Diarrheic calves had higher odds of BCoV presence than healthy calves (OR: 2.16, 95% CI: 1.26 to 3.83, P = 0.004). A good agreement between PanCoV‐RT‐PCR and BCoV‐RT‐PCR to detect BCoV was identified (κ = 0.68, 95% CI: 0.392 to 0.967; P < 0.001).

Conclusions and Clinical Importance

BCoV was more likely to be detected in diarrheic than healthy calves. The PanCoV‐RT‐PCR assay can be a useful tool to detect CoV samples from diarrheic calves.

Molecular detection of enteric viruses from diarrheic calves in Egypt

Neonatal calf diarrhea (NCD) is a major cause of morbidity, mortality and economic losses in the beef and dairy industries. This study was conducted to investigate the existence of enteric viruses in two Egyptian farms with a history of recurrent diarrhea. Fecal samples were collected from 25 diarrheic calves. RNA was extracted and tested by reverse transcription polymerase chain reaction (RT-PCR) for the presence of rotavirus, norovirus, astrovirus, torovirus, coronavirus and bovine viral diarrhea virus. Overall, 76 % (19/25) of samples tested positive for one or more viruses. Rota-, noro- and astroviruses were detected in 48 %, 24 % and 32 % of tested samples, respectively. About 37 % (7/19) of positive samples had two different viruses. One-month-old calves were the group most vulnerable to infections. Based on phylogenetic analysis, bovine rotaviruses were of genotypes G6 and G10, bovine noroviruses were in GIII.2, and bovine astroviruses were in the BAstV lineage 1. Astrovirus sequences showed a high level nucleotide sequence similarity with the Brazilian BAstV sequences available in GenBank. We believe this is the first report of bovine norovirus and bovine astrovirus circulating among calves in Egypt. Further epidemiological studies are recommended to investigate their presence on a wider scale, to predict their association with NCD, and to design appropriate diagnostic and control methods.