First report and genomic characterization of a bovine-like coronavirus causing enteric infection in an odd-toed non-ruminant species (Indonesian tapir, Acrocodia indica) during an outbreak of winter dysentery in a zoo

Disease dynamics and mortality risk in tapirs (Perissodactyla: Tapiridae) through a systematic literature review: Implications for preventive medicine and conservation

The impact of diseases on tapir mortality and potential implications for preventive medicine and conservation remain unclear. A systematic literature review was conducted using seven databases and grey literature to address these gaps. The PRISMA statement was adopted to report results, and boosted regression tree models were employed for data analysis. After screening 5323 records and removing duplicates, the title and abstract of 2484 records were assessed. Out of 502 eligible studies, only 206 met all inclusion criteria. These were published between 1924 and 2023 in ten languages, comprising mainly case reports (45.1 %) and cross-sectional studies (41.3 %). Infectious diseases were found in 72.9 % of the reports, and 27.2 % presented clinical signs. The most affected systems were gastroenteric (22.7 %), integumentary (22.1 %), and respiratory (17.5 %). Respiratory diseases were associated with increased mortality. Factors affecting tapir mortality included species (relative influence 41.5 %), followed by geographic location (23.5 %) and captivity (16.8 %). Clinical signs were the least important variable (4 %). While infectious diseases were associated with higher mortality risk, tapirs were more likely to become ill from non-infectious than infectious diseases. Captive individuals were also more likely to present with illness than their wild counterparts. When considering external causes, vehicle collisions represented the most significant cause of death (52.2 %), followed by hunting (38.2 %). Diseases (8.7 %) were the third most important, with bacterial infections the leading cause of death. This review represents the most comprehensive overview on tapir health to date and provides novel ways to collate epidemiological data from disparate study designs.

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.

Frequency of Bovine Respiratory Disease Complex Bacterial and Viral Agents Using Multiplex Real-Time qPCR in Quebec, Canada, from 2019 to 2023

The bovine respiratory disease complex (BRD) is a multifactorial disease caused by various bacterial and viral pathogens. Using rapid pathogen detection techniques is helpful for tailoring therapeutic and preventive strategies in affected animals and herds. The objective of this study was to report the frequency of 10 pathogens by multiplex RT-qPCR on samples submitted for BRD diagnosis to a diagnostic laboratory (Biovet Inc., QC, Canada) in the Province of Quebec, Eastern Canada. From the 1st of January 2019 to the 31st of December 2023, a total of 1875 samples were analyzed. Most samples collected were individual samples (1547 of 1860 samples for which information was available (83.17%)), and the rest were from pooled samples of 2 (8.55%, n = 159) or ≥3 specimens (8.28%, n = 154). In 19.3% of the samples (n = 362), no pathogen was found, whereas 54.1% of samples had two or more different pathogens. Among the viruses, bovine coronavirus (BCV) was the most commonly found (27.5% of samples, n = 516), followed by bovine respiratory syncytial virus (BRSV) (17.7%, n = 332), whereas, for bacteria, Pasteurella multocida (50.1%, n = 940) and Mannheimia haemolytica (26.9%, n = 505) were the most common. The frequency of samples positive for Histophilus somni, Mycoplasmopsis bovis, influenza type D virus (IDV), bovine parainfluenza virus type 3 (BPI3V), bovine herpesvirus type 1 (BHV1), and bovine viral diarrhea virus (BVDV) was 22.6%, 22.4%, 4.6%, 4.3%, 2.7%, and 0.9%, respectively. In the multivariable Poisson regression model, the total number of pathogens increased with the number of animals in the pool, with an incidence risk ratio (IRR) of 1.15 (95% CI 1.02-1.29) and 1.32 (1.18-1.47) for 2 individuals in the pool and ≥3 individuals vs. individual samples, respectively. An increased number of pathogens were isolated in the winter season (IRR = 1.28 (95% CI 1.17-1.40)) compared to fall, and a lower number of pathogens were isolated in the summer compared to fall (IRR = 0.82 (95% CI 0.73-0.92)). These seasonal differences were mostly driven by the number of viruses isolated. This study gives interesting insights on the circulation of BRD pathogens in cattle from Eastern Canada.

Prevalence of coronaviruses in European bison (Bison bonasus) in Poland

Coronaviruses have been confirmed to infect a variety of species, but only one case of associated winter dysentery of European bison has been described. The study aimed to analyze the prevalence, and define the impact on the species conservation, the source of coronavirus infection, and the role of the European bison in the transmission of the pathogen in Poland. Molecular and serological screening was performed on 409 European bison from 6 free-ranging and 14 captive herds over the period of 6 years (2017-2023). Presence of coronavirus was confirmed in one nasal swab by pancoronavirus RT-PCR and in 3 nasal swab samples by bovine coronavirus (BCoV) specific real time RT-PCR. The detected virus showed high (> 98%) homology in both RdRp and Spike genes to BCoV strains characterised recently in Polish cattle and strains isolated from wild cervids in Italy. Antibodies specific to BCoV were found in 6.4% of tested samples, all originating from free-ranging animals. Seroprevalence was higher in adult animals over 5 years of age (p = 0.0015) and in females (p = 0.09). Our results suggest that European bison play only a limited role as reservoirs of bovine-like coronaviruses. Although the most probable source of infections in the European bison population in Poland is cattle, other wild ruminants could also be involved. In addition, the zoonotic potential of bovine coronaviruses is quite low.

Co-Circulation of Multiple Coronavirus Genera and Subgenera during an Epizootic of Lethal Respiratory Disease in Newborn Alpacas (Vicugna pacos) in Peru: First Report of Bat-like Coronaviruses in Alpacas

Coronaviruses (CoVs) infect a wide range of hosts, including humans, domestic animals, and wildlife, typically causing mild-to-severe respiratory or enteric disease. The main objective of this study was to identify CoV genera and subgenera detected in Peruvian alpacas. Lung lavage specimens were collected from 32 animals aged 1 to 6 weeks. CoVs were identified by using RT-PCR to amplify a pan-CoV conserved region of the RNA-dependent RNA polymerase-encoding gene. A nested PCR was performed to identify β-CoVs. Then, β-CoV-positive samples were subjected to RT-PCR using specific primers to identify the Embecovirus subgenus. Out of 32 analyzed samples, 30 (93.8%) tested positive for at least one CoV genus. β-, α-, or unclassified CoVs were identified in 24 (80%), 1 (3.3%), and 1 (3.3%) of the positive samples, respectively. A CoV genus could not be identified in two (6.7%) samples. A mixture of different CoV genera was detected in two (6.7%) samples: one was co-infected with β- and α-CoVs, and the other contained a β- and an unclassified CoV. A sequence analysis of the amplicons generated by the PCR identified 17 β-CoV strains belonging to the subgenus Embecovirus and two α-CoV strains belonging to Decacovirus. A phylogenetic analysis of two strains revealed a relationship with an unclassified Megaderma BatCoV strain. A subgenus could not be identified in nine β-CoV samples. Our data show a high prevalence and a high genetic diversity of CoV genera and subgenera that infect alpacas, in which the β-CoV subgenus Embecovirus predominated. Our data also suggest a new role for bats in the dissemination and transmission of uncommon CoVs to alpacas raised in rural Peru.

Presence of Equine and Bovine Coronaviruses, Endoparasites, and Bacteria in Fecal Samples of Horses with Colic

Acute abdominal pain (colic) is one of the major equine health threats worldwide and often necessitates intensive veterinary medical care and surgical intervention. Equine coronavirus (ECoV) infections can cause colic in horses but are rarely considered as a differential diagnosis. To determine the frequency of otherwise undetected ECoV infections in horses with acute colic, fresh fecal samples of 105 horses with acute colic and 36 healthy control horses were screened for viruses belonging to the Betacoronavirus 1 species by RT-PCR as well as for gastrointestinal helminths and bacteria commonly associated with colic. Horses with colic excreted significantly fewer strongyle eggs than horses without colic. The prevalence of anaerobic, spore-forming, gram-positive bacteria (Clostridium perfringens and Clostridioides difficile) was significantly higher in the feces of horses with colic. Six horses with colic (5.7%) and one horse from the control group (2.8%) tested positive for Betacoronaviruses. Coronavirus-positive samples were sequenced to classify the virus by molecular phylogeny (N gene). Interestingly, in three out of six coronavirus-positive horses with colic, sequences closely related to bovine coronaviruses (BCoV) were found. The pathogenic potential of BCoV in horses remains unclear and warrants further investigation.

Diagnostics for Viral Pathogens in Veterinary Diagnostic Laboratories

Laboratory testing is one part of clinical diagnosis, and quick and reliable testing results provide important data to support treatment decision and develop control strategies. Clinical viral testing has been shifting from traditional virus isolation and electron microscopy to molecular polymerase chain reaction and point-of-care antigen tests. This shift in diagnostic methodology also means change from looking for infectious virions or viral particles to hunting viral antigens and genomes. With technological development, it is predicted that metagenomic sequencing will be commonly used in veterinary clinical diagnosis for unveiling the whole picture of microbes involved in diseases in the future.

Seroprevalence and Risk Factors for Bovine Coronavirus Infection among Dairy Cattle and Water Buffalo in Campania Region, Southern Italy

Cattle and water buffalo are the main livestock species that are raised in the Campania region, southern Italy, and they contribute significantly to the regional rural economy. Currently there are limited data on the prevalence of relevant impact infections, such as bovine coronavirus (BCov), an RNA virus that causes acute enteric and respiratory disease. Although these diseases are described primarily in cattle, there have been reports of spillovers to other ruminants, including water buffalo. Here, we determined the seroprevalence of BCoV in cattle and water buffalo in the Campania region of southern Italy. An overall seroprevalence of 30.8% was determined after testing 720 sampled animals with a commercial enzyme-linked immunosorbent assay. A risk factor analysis revealed that the seropositivity rates in cattle (49.2%) were higher than in water buffalo (5.3%). In addition, higher seroprevalence rates were observed in older and purchased animals. In cattle, housing type and location were not associated with higher seroprevalence. The presence of BCoV antibodies in water buffalo was associated with the practice of co-inhabiting with cattle, demonstrating that this practice is incorrect and promotes the transmission of pathogens between different species. Our study found a considerable seroprevalence, which is consistent with previous research from other countries. Our results provide information on the widespread distribution of this pathogen as well as the risk factors that are involved in its transmission. This information could be useful in the control and surveillance of this infection.