Development and performance evaluation of calf diarrhea pathogen nucleic acid purification and detection workflow

Experimental co-infection of calves with SARS-CoV-2 Delta and Omicron variants of concern

Since emerging in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has repeatedly crossed the species barrier with natural infections reported in various domestic and wild animal species. The emergence and global spread of SARS-CoV-2 variants of concern (VOCs) has expanded the range of susceptible host species. Previous experimental infection studies in cattle using Wuhan-like SARS-CoV-2 isolates suggested that cattle were not likely amplifying hosts for SARS-CoV-2. However, SARS-CoV-2 sero- and RNA-positive cattle have since been identified in Europe, India, and Africa. Here, we investigated the susceptibility and transmission of the Delta and Omicron SARS-CoV-2 VOCs in cattle. Eight Holstein calves were co-infected orally and intranasally with a mixed inoculum of SARS-CoV-2 VOCs Delta and Omicron BA.2. Twenty-four hours post-challenge, two sentinel calves were introduced to evaluate virus transmission. The co-infection resulted in a high proportion of calves shedding SARS-CoV-2 RNA at 1- and 2-days post-challenge (DPC). Extensive tissue distribution of SARS-CoV-2 RNA was observed at 3 and 7 DPC and infectious virus was recovered from two calves at 3 DPC. Next-generation sequencing revealed that only the SARS-CoV-2 Delta variant was detected in clinical samples and tissues. Similar to previous experimental infection studies in cattle, we observed only limited seroconversion and no clear evidence of transmission to sentinel calves. Together, our findings suggest that cattle are more permissive to infection with SARS-CoV-2 Delta than Omicron BA.2 and Wuhan-like isolates but, in the absence of horizontal transmission, are not likely to be reservoir hosts for currently circulating SARS-CoV-2 variants.

Strategies for Bovine Respiratory Disease (BRD) Diagnosis and Prognosis: A Comprehensive Overview

Despite significant advances in vaccination strategies and antibiotic therapy, bovine respiratory disease (BRD) continues to be the leading disease affecting the global cattle industry. The etiology of BRD is complex, often involving multiple microbial agents, which lead to intricate interactions between the host immune system and pathogens during various beef production stages. These interactions present environmental, social, and geographical challenges. Accurate diagnosis is essential for effective disease management. Nevertheless, correct identification of BRD cases remains a daunting challenge for animal health technicians in feedlots. In response to current regulations, there is a growing interest in refining clinical diagnoses of BRD to curb the overuse of antimicrobials. This shift marks a pivotal first step toward establishing a structured diagnostic framework for this disease. This review article provides an update on recent developments and future perspectives in clinical diagnostics and prognostic techniques for BRD, assessing their benefits and limitations. The methods discussed include the evaluation of clinical signs and animal behavior, biomarker analysis, molecular diagnostics, ultrasound imaging, and prognostic modeling. While some techniques show promise as standalone diagnostics, it is likely that a multifaceted approach-leveraging a combination of these methods-will yield the most accurate diagnosis of BRD.

Establishment and application of multiplex droplet digital polymerase chain reaction assay for bovine enterovirus, bovine coronavirus, and bovine rotavirus

Bovine enterovirus (BEV), bovine coronavirus (BCoV), and bovine rotavirus (BRV) are still the major worldwide concerns in the health care of cattle, causing serious economic losses in the livestock industry. It is urgent to establish specific and sensitive methods to detect viruses for the early control of diseases. Droplet digital PCR (ddPCR) has been proposed to effectively detect viral particles, and it does not involve Ct values or standard curves. In this study, we designed specific primers and probes, based on conserved regions of viral genomes, to optimize protocols for a dual ddPCR assay for detecting BCoV and BRV and a multiplex ddPCR assay for BEV, BCoV, and BRV. Sensitivity assays revealed that the lower limit of detection for qPCR was 1,000 copies/μL and for ddPCR for BEV, BCoV, and BRV, 2.7 copies/μL, 1 copy/μL and 2.4 copies/μL, respectively. Studying 82 samples collected from diarrheal calves on a farm, our dual ddPCR method detected BCoV, BRV, and co-infection at rates of 18.29%, 14.63%, and 6.1%, respectively. In contrast, conventional qPCR methods detected BCoV, BRV, and co-infection at rates of 10.98%, 12.2%, and 3.66%, respectively. On the other hand, studying 68 samples from another farm, qPCR detected BCoV, BRV, BEV, and co-infection of BCoV and BEV at rates of 14.49%, 1.45%, 5.80%, and 1.45%, respectively. Our multiplex ddPCR method detected BCoV, BRV, BEV, co-infection of BCoV and BEV, and co-infection of BRV and BEV. at rates of 14.49%, 2.9%, 8.7%, 2.9%, and 1.45%, respectively. Studying 93 samples from another farm, qPCR detected BCoV, BRV, BEV, and co-infection of BCoV and BEV was detected at rates of 5.38%, 1.08%, 18.28%, and 1.08%, respectively. Co-infection of BCoV, BRV, BEV, BCoV, and BEV, and co-infection of BRV and BEV, were detected by multiplex ddPCR methods at rates of 5.38%, 2.15%, 20.45%, 1.08%, and 1.08%, respectively. These results indicated that our optimized dual and multiplex ddPCR methods were more effective than conventional qPCR assays to detect these viral infections.

Development of a novel real-time PCR multiplex assay for detection of Streptococcus equi subspecies equi and Streptococcus equi subspecies zooepidemicus

Strangles is a contagious bacterial disease of horses caused by Streptococcus equi subspecies equi (SEE) that occurs globally. Rapid and accurate identification of infected horses is essential for controlling strangles. Because of limitations of existing PCR assays for SEE, we sought to identify novel primers and probes that enable simultaneous detection and differentiation of infection with SEE and S. equi subsp. zooepidemicus (SEZ). Comparative genomics of U.S. strains of SEE and SEZ (n = 50 each) identified SE00768 from SEE and comB from SEZ as target genes. Primers and probes for real-time PCR (rtPCR) were designed for these genes and then aligned in silico with the genomes of strains of SEE (n = 725) and SEZ (n = 343). Additionally, the sensitivity and specificity relative to microbiologic culture were compared between 85 samples submitted to an accredited veterinary medical diagnostic laboratory. The respective primer and probe sets aligned with 99.7 % (723/725) isolates of SEE and 97.1 % (333/343) of SEZ. Of 85 diagnostic samples, 20 of 21 (95.2 %) SEE and 22 of 23 SEZ (95.6 %) culture-positive samples were positive by rtPCR for SEE and SEZ, respectively. Both SEE (n = 2) and SEZ (n = 3) were identified by rtPCR among 32 culture-negative samples. Results were rtPCR-positive for both SEE and SEZ in 21 of 44 (47.7 %) samples that were culture-positive for SEE or SEZ. The primers and probe sets reported here reliably detect SEE and SEZ from Europe and the U.S., and permit detection of concurrent infection with both subspecies.

Evaluation of a novel multiplex qPCR method for rapid detection and quantification of pathogens associated with calf diarrhoea

AIMS

Diarrhoea is a common health problem in calves and a main reason for use of antimicrobials. It is associated with several bacterial, viral and parasitic pathogens, most of which are commonly present in healthy animals. Methods, which quantify the causative agents, may therefore improve confidence in associating a pathogen to the disease. This study evaluated a novel commercially available, multiplex quantitative polymerase chain reaction (qPCR) assay (Enterit4Calves) for detection and quantification of pathogens associated with calf-diarrhoea.

METHODS AND RESULTS

Performance of the method was first evaluated under laboratory conditions. Then it was compared with current routine methods for detection of pathogens in faecal samples from 65 calves with diarrhoea and in 30 spiked faecal samples. The qPCR efficiencies were between 84%-103% and detection limits of 100-1000 copies of nucleic acids per sample were observed. Correct identification was obtained on 42 strains of cultured target bacteria, with only one false positive reaction from 135 nontarget bacteria. Kappa values for agreement between the novel assay and current routine methods varied between 0.38 and 0.83.

CONCLUSION

The novel qPCR method showed good performance under laboratory conditions and a fair to good agreement with current routine methods when used for testing of field samples.

SIGNIFICANCE AND IMPACT OF STUDY

In addition to having fair to good detection abilities, the novel qPCR method allowed quantification of pathogens. In the future, use of quantification may improve diagnosis and hence treatment of calf diarrhoea.

Multiplexed serotype-specific real time PCR assays - a valuable tool to support large scale surveillance for bluetongue virus infection

In the last decade, real time PCR has been increasingly adopted for bluetongue diagnosis with both broadly reactive and serotype-specific assays widely used. The use of these assays and nucleic acid sequencing technologies have enhanced bluetongue virus detection, resulting in the identification of a number of new serotypes. As a result, 27 different serotypes are officially recognised and at least 3 more are proposed. Rapid identification of the virus serotype is essential for matching of antigens used in vaccines and to undertake surveillance and epidemiological studies to assist risk management. However, it is not uncommon for multiple serotypes to circulate in a region either concurrently or in successive years. It is therefore necessary to have a large suite of assays available to ensure that the full spectrum of viruses is detected. Nevertheless, covering a large range of virus serotypes is demanding from both a time and resource perspective. To overcome these challenges, real time PCR assays were optimised to match local virus strains and then combined in a panel of quadriplex assays, resulting in 3 assays to detect 12 serotypes directly from blood samples from cattle and sheep. These multiplex assays have been used extensively for bluetongue surveillance in both sentinel animals and opportunistically collected samples. A protocol to adapt these assays to capture variations in local strains of bluetongue virus and to expand the panel is described. Collectively these assays provide powerful tools for surveillance and the rapid identification of bluetongue virus serotypes directly from animal blood samples. This article is protected by copyright. All rights reserved.

Diarrhea outbreak associated with coronavirus infection in adult dairy goats

Background

Infection by coronaviruses cause gastrointestinal disease in many species. Little is known about its prevalence and importance in goats.

Objective

Identify the etiology, demographics, and clinical features of an outbreak of diarrhea in adult goats.

Hypothesis

Bovine coronavirus (BCoV) PCR would detect viral material in feces of goats in the herds involved in the diarrhea outbreak.

Animals

Twelve herds with 4 to 230 adult goats were affected. Goats sampled for fecal PCR were ≥1‐year‐old: 25 from affected herds and 6 from a control herd.

Methods

This is a cross‐sectional descriptive study of an outbreak of diarrheal disease in adult goats. BCoV PCR primers for the spike (S) or nucleocapsid (N) proteins were used to test fecal material from affected goats. The N protein sequencing and phylogenetic analysis was performed. Herd records and owner surveys were used to characterize morbidity, clinical signs, and treatment.

Results

In 2 affected herds 18/25 of animals had at least 1 positive BCoV PCR test. Goats from affected herds were significantly more likely to be PCR positive than the control herd (OR 8.75, 95% CI 1.11‐104, P = .05). The most common clinical signs were change in fecal consistency (19/20) and decreased milk production (14/15). Phylogenetic analysis of the N protein showed this virus was closely related to a bovine‐like coronavirus isolated from a giraffe.

Conclusions and Clinical Importance

Bovine coronavirus primers detected nucleic acids of the N and S proteins in feces of goats in affected herds. Coronavirus shedding frequency was temporally associated with the outbreak.

A Systematic Review of Automatic Health Monitoring in Calves: Glimpsing the Future From Current Practice

Infectious diseases, particularly bovine respiratory disease (BRD) and neonatal calf diarrhea (NCD), are prevalent in calves. Efficient health-monitoring tools to identify such diseases on time are lacking. Common practice (i.e., health checks) often identifies sick calves at a late stage of disease or not at all. Sensor technology enables the automatic and continuous monitoring of calf physiology or behavior, potentially offering timely and precise detection of sick calves. A systematic overview of automated disease detection in calves is still lacking. The objectives of this literature review were hence: to investigate previously applied sensor validation methods used in the context of calf health, to identify sensors used on calves, the parameters these sensors monitor, and the statistical tools applied to identify diseases, to explore potential research gaps and to point to future research opportunities. To achieve these objectives, systematic literature searches were conducted. We defined four stages in the development of health-monitoring systems: (1) sensor technique, (2) data interpretation, (3) information integration, and (4) decision support. Fifty-four articles were included (stage one: 26; stage two: 19; stage three: 9; and stage four: 0). Common parameters that assess the performance of these systems are sensitivity, specificity, accuracy, precision, and negative predictive value. Gold standards that typically assess these parameters include manual measurement and manual health-assessment protocols. At stage one, automatic feeding stations, accelerometers, infrared thermography cameras, microphones, and 3-D cameras are accurate in screening behavior and physiology in calves. At stage two, changes in feeding behaviors, lying, activity, or body temperature corresponded to changes in health status, and point to health issues earlier than manual health checks. At stage three, accelerometers, thermometers, and automatic feeding stations have been integrated into one system that was shown to be able to successfully detect diseases in calves, including BRD and NCD. We discuss these findings, look into potentials at stage four, and touch upon the topic of resilience, whereby health-monitoring system might be used to detect low resilience (i.e., prone to disease but clinically healthy calves), promoting further improvements in calf health and welfare.

Nidoviruses in Reptiles: A Review

Since their discovery in 2014, reptile nidoviruses (also known as serpentoviruses) have emerged as significant pathogens worldwide. They are known for causing severe and often fatal respiratory disease in various captive snake species, especially pythons. Related viruses have been detected in other reptiles with and without respiratory disease, including captive and wild populations of lizards, and wild populations of freshwater turtles. There are many opportunities to better understand the viral diversity, species susceptibility, and clinical presentation in different species in this relatively new field of research. In captive snake collections, reptile nidoviruses can spread quickly and be associated with high morbidity and mortality, yet the potential disease risk to wild reptile populations remains largely unknown, despite reptile species declining on a global scale. Experimental studies or investigations of disease outbreaks in wild reptile populations are scarce, leaving the available literature limited mostly to exploring findings of naturally infected animals in captivity. Further studies into the pathogenesis of different reptile nidoviruses in a variety of reptile species is required to explore the complexity of disease and routes of transmission. This review focuses on the biology of these viruses, hosts and geographic distribution, clinical signs and pathology, laboratory diagnosis and management of reptile nidovirus infections to better understand nidovirus infections in reptiles.

Suggested guidelines for validation of real-time PCR assays in veterinary diagnostic laboratories

This consensus document presents the suggested guidelines developed by the Laboratory Technology Committee (LTC) of the American Association of Veterinary Laboratory Diagnosticians (AAVLD) for development, validation, and modification (methods comparability) of real-time PCR (rtPCR) assays. These suggested guidelines are presented with reference to the World Organisation for Animal Health (OIE) guidelines for validation of nucleic acid detection assays used in veterinary diagnostic laboratories. Additionally, our proposed practices are compared to the guidelines from the Foods Program Regulatory Subdivision of the U.S. Food and Drug Administration (FDA) and from the American Society for Veterinary Clinical Pathology (ASVCP). The LTC suggestions are closely aligned with those from the OIE and comply with version 2021-01 of the AAVLD Requirements for an Accredited Veterinary Medical Diagnostic Laboratory, although some LTC recommendations are more stringent and extend beyond the AAVLD requirements. LTC suggested guidelines are substantially different than the guidelines recently published by the U.S. FDA for validation and modification of regulated tests used for detection of pathogens in pet food and animal-derived products, such as dairy. Veterinary diagnostic laboratories that perform assays from the FDA Bacteriological Analytical Method (BAM) manual must be aware of the different standard.

Inhibition monitoring in veterinary molecular testing

Many of the sample matrices typically used for veterinary molecular testing contain inhibitory factors that can potentially reduce analytic sensitivity or produce false-negative results by masking the signal produced by the nucleic acid target. Inclusion of internal controls in PCR-based assays is a valuable strategy not only for monitoring for PCR inhibitors, but also for monitoring nucleic acid extraction efficiency, and for identifying technology errors that may interfere with the ability of an assay to detect the intended target. The Laboratory Technology Committee of the American Association of Veterinary Laboratory Diagnosticians reviewed the different types of internal controls related to monitoring inhibition of PCR-based assays, and provides information here to encourage veterinary diagnostic laboratories to incorporate PCR internal control strategies as a routine quality management component of their molecular testing.

Detection and Cellular Tropism of Porcine Astrovirus Type 3 on Breeding Farms

Astroviruses cause disease in a variety of species. Yet, little is known about the epidemiology of a majority of astroviruses including porcine astrovirus type 3 (PoAstV3), which is a putative cause of polioencephalomyelitis in swine. Accordingly, a cross-sectional study was conducted on sow farms with or without reported PoAstV3-associated neurologic disease in growing pigs weaned from those farms. Additionally, a conveniently selected subset of piglets from one farm was selected for gross and histologic evaluation. The distribution of PoAstV3 in the enteric system was evaluated through in situ hybridization. PoAstV3, as detected by RT-qPCR on fecal samples, was frequently detected across sows and piglets (66–90%) on all farms (65–85%). PoAstV3 was detected subsequently at a similar detection frequency (77% vs 85%) on one farm after three months. Viral shedding, as determined by the cycle quantification value, suggests that piglets shed higher quantities of virus than adult swine. No link between gastrointestinal disease and PoAstV3 was found. However, PoAstV3 was detected by in situ in myenteric plexus neurons of piglets elucidating a possible route of spread of the virus from the gastrointestinal tract to the central nervous system. These data suggest PoAstV3 has endemic potential, is shed in the feces at greater quantities by suckling piglets when compared to sows, and infection is widespread on farms in which it is detected.

Physiological and behavioral responses as indicators for early disease detection in dairy calves

This study investigated physiological and behavioral responses associated with the onset of neonatal calf diarrhea (NCD) in calves experimentally infected with rotavirus and assessed the suitability of these responses as early disease indicators. The suitability of infrared thermography (IRT) as a noninvasive, automated method for early disease detection was also assessed. Forty-three calves either (1) were experimentally infected with rotavirus (n = 20) or (2) acted as uninfected controls (n = 23). Health checks were conducted on a daily basis to identify when calves presented overt clinical signs of disease. In addition, fecal samples were collected to verify NCD as the cause of illness. Feeding behavior was recorded continuously as calves fed from an automated calf feeder, and IRT temperatures were recorded once per day across 5 anatomical locations using a hand-held IRT camera. Lying behavior was recorded continuously using accelerometers. Drinking behavior at the water trough was filmed continuously to determine the number and duration of visits. Respiration rate was recorded once per day by observing flank movements. The effectiveness of inoculating calves with rotavirus was limited because not all calves in the infected group contracted the virus; further, an unexpected outbreak of Salmonella during the trial led to all calves developing NCD, including those in the healthy control group. Therefore, treatment was ignored and instead each calf was analyzed as its own control, with data analyzed with respect to when each calf displayed clinical signs of disease regardless of the causative pathogen. Milk consumption decreased before clinical signs of disease appeared. The IRT temperatures were also found to change before clinical signs of disease appeared, with a decrease in shoulder temperature and an increase in side temperature. There were no changes in respiration rate or lying time before clinical signs of disease appeared. However, the number of lying bouts decreased and lying bout duration increased before and following clinical signs of disease. There was no change in the number of visits to the water trough, but visit duration increased before clinical signs of disease appeared. Results indicate that milk consumption, IRT temperatures of the side and shoulder, number and duration of lying bouts, and duration of time spent at the water trough show potential as suitable early indicators of disease.

Measurement of dairy calf behavior prior to onset of clinical disease and in response to disbudding using automated calf feeders and accelerometers

We determined if feeding and lying behavior, recorded by automatic calf feeding systems (ACFS) and accelerometers, could be used to detect changes in behavior before onset of neonatal calf diarrhea (NCD) or in response to disbudding pain in dairy calves. At 4 d of age, 112 calves had accelerometers attached to their hind leg and were housed in pens with ACFS. Calves were examined daily for signs of illness or injury. Of the 112 calves monitored, 18 were diagnosed with NCD; activities of calves with NCD were then compared with those of 18 healthy controls (calves that had no symptoms of NCD, other illnesses, or injury). Feeding (milk consumption and the number of rewarded and unrewarded visits to the feeder) and lying behavior during the 5 d leading up to calves displaying clinical signs of NCD were analyzed. Calves with NCD performed fewer unrewarded visits and consumed less milk than healthy calves during the 2- and 4-d periods before diagnosis with NCD, respectively. Calves with NCD tended to perform fewer lying bouts than healthy calves over the 5-d period before diagnosis with NCD. At 3 wk of age, a subset of 51 healthy calves were allocated to 1 of 5 treatment groups: (1) sham handling (SHAM, n = 10), (2) cautery disbudding (DB, n = 11), (3) administration of local anesthetic (LA) and DB (LA+DB, n = 11), 4) administration of a nonsteroidal anti-inflammatory drug (NSAID) and DB (NSAID+DB, n = 9), and (5) administration of LA, NSAID and DB (LA+NSAID+DB, n = 10). Feeding and lying behavior were recorded continuously for 24 h pre- and postdisbudding. We found no effect of treatment on the number of rewarded or unrewarded visits to the feeder and milk volume consumed 24 h before administration of treatments. During the 24-h postdisbudding period, SHAM calves performed more unrewarded visits than DB, LA+DB, and NSAID+DB calves, but the number of unrewarded visits did not differ between SHAM and LA+NSAID+DB calves. During the first hour of the posttreatment period we noted a difference in lying times among treatments, with DB and NSAID+DB calves spending less time lying than SHAM calves and lying times being similar between SHAM, LA+DB, and LA+NSAID+DB calves. The ACFS and accelerometers have the potential to automatically gather valuable information regarding health status and pain in calves. Therefore, it may be advantageous to combine both of these measures (ACFS and accelerometers) when evaluating NCD on farm or pain in calves in future research.

Evaluation of a duplex reverse-transcription real-time PCR assay for the detection of encephalomyocarditis virus

We evaluated a fluorogenic probe-based assay for the detection of encephalomyocarditis virus (EMCV) by comparing a set of published primers and probe to a new set of primers and probe. The published reagents failed to amplify a range of Australian isolates and an Italian reference strain of EMCV. In contrast, an assay based on 2 new sets of primers and probes that were run in a duplex reverse-transcription real-time PCR (RT-rtPCR) worked well, with high amplification efficiency. The analytical sensitivity was ~100-fold higher than virus isolation in cell culture. The intra-assay variation was 0.21-4.90%. No cross-reactivity was observed with a range of other porcine viruses. One hundred and twenty-two clinical specimens were tested simultaneously by RT-rtPCR and virus isolation in cell culture; 72 specimens gave positive results by RT-rtPCR, and 63 of these were also positive by virus isolation. Of 245 archived cell culture isolates of EMCV that were tested in the RT-rtPCR, 242 samples were positive. The new duplex RT-rtPCR assay is a reliable tool for the detection of EMCV in clinical specimens and for use in epidemiologic investigations.

Pathogenicity and teratogenicity of Schmallenberg virus and Akabane virus in experimentally infected chicken embryos

Schmallenberg virus (SBV) and Akabane virus (AKAV) are teratogenic Simbu serogroup Orthobunyaviruses. Embryonated chicken egg models (ECE) have been used to study the pathogenicity and teratogenicity of Simbu viruses previously, however to date no such studies have been reported for SBV. Hence, the aims of this study were to investigate if ECE are susceptible to experimental SBV infection, and to evaluate the pathogenicity and teratogenicity of SBV and AKAV in ECE models. Two studies were conducted. In Study A, SBV (10^6.4 TCID₅₀) was inoculated into the yolk-sac of 6-day-old and 8-day-old ECEs. In Study B, SBV and AKAV were inoculated into 7-day-old ECEs at a range of doses (10^2.0-10^6.0 TCID₅₀). ECE were incubated at 37 °C until day 19, when they were submitted for pathological and virological examination. SBV infection in ECE at 6, 7 and 8 days of incubation resulted in stunted growth and musculoskeletal malformations (arthrogryposis, skeletal muscle atrophy, contracted toes, distorted and twisted legs). Mortality was greater in embryos inoculated with SBV (31%) compared to AKAV (19%), (P < 0.01), suggesting that SBV was more embryo-lethal. However, embryos infected with AKAV had a significantly higher prevalence of stunted growth (P < 0.05) and musculoskeletal malformations (P < 0.01), suggesting that AKAV was more teratogenic in this model. These studies demonstrate for the first time that the ECE model is a suitable in vivo small animal model to study SBV. Furthermore, these results are consistent with the clinico-pathological findings of natural SBV and AKAV infection in ruminants.

Genome-wide analysis of codon usage bias in Bovine Coronavirus

BACKGROUND

Bovine coronavirus (BCoV) belong to the genus Betacoronavirus of the family Coronaviridae. BCoV are widespread around the world and cause enteric or respiratory infections among cattle, leading to important economic losses to the beef and dairy industry worldwide. To study the relation of codon usage among viruses and their hosts is essential to understand host-pathogen interaction, evasion from host's immune system and evolution.

METHODS

We performed a comprehensive analysis of codon usage and composition of BCoV.

RESULTS

The global codon usage among BCoV strains is similar. Significant differences of codon preferences in BCoV genes in relation to codon usage of Bos taurus host genes were found. Most of the highly frequent codons are U-ending. G + C compositional constraint and dinucleotide composition also plays a role in the overall pattern of BCoV codon usage.

CONCLUSIONS

The results of these studies revealed that mutational bias is a leading force shaping codon usage in this virus. Additionally, relative dinucleotide frequencies, geographical distribution, and evolutionary processes also influenced the codon usage pattern.

Surveillance of diarrhea-causing pathogens in dairy and beef cows in Yamagata Prefecture, Japan from 2002 to 2011

The economic consequences of bovine diarrhea are serious. Few long‐term epidemiological data are available concerning the causative pathogens of bovine diarrhea in Japan. From 2002 to 2011, surveillance of enteric pathogens was performed in cows of various breed and age from 302 farms in which diarrhea had occurred in Yamagata Prefecture, Japan. Differences between dairy and beef cows in the number of cases of diarrhea and rates of infection by Salmonella spp. and Eimeria spp. were found. Clinical symptoms (duration of epidemic, hematochezia and complications) caused by bovine rotavirus infection were milder than those caused by bovine coronavirus infection.

Detection of African swine fever, classical swine fever, and foot-and-mouth disease viruses in swine oral fluids by multiplex reverse transcription real-time polymerase chain reaction

African swine fever (ASF), classical swine fever (CSF), and foot-and-mouth disease (FMD) are highly contagious animal diseases of significant economic importance. Pigs infected with ASF and CSF viruses (ASFV and CSFV) develop clinical signs that may be indistinguishable from other diseases. Likewise, various causes of vesicular disease can mimic clinical signs caused by the FMD virus (FMDV). Early detection is critical to limiting the impact and spread of these disease outbreaks, and the ability to perform herd-level surveillance for all 3 diseases rapidly and cost effectively using a single diagnostic sample and test is highly desirable. This study assessed the feasibility of simultaneous ASFV, CSFV, and FMDV detection by multiplex reverse transcription real-time polymerase chain reaction (mRT-qPCR) in swine oral fluids collected through the use of chewing ropes. Animal groups were experimentally infected independently with each virus, observed for clinical signs, and oral fluids collected and tested throughout the course of infection. All animal groups chewed on the ropes readily before and after onset of clinical signs and before onset of lameness or serious clinical signs. ASFV was detected as early as 3 days postinoculation (dpi), 2–3 days before onset of clinical disease; CSFV was detected at 5 dpi, coincident with onset of clinical disease; and FMDV was detected as early as 1 dpi, 1 day before the onset of clinical disease. Equivalent results were observed in 4 independent studies and demonstrate the feasibility of oral fluids and mRT-qPCR for surveillance of ASF, CSF, and FMD in swine populations.

Molecular and serological in-herd prevalence of Anaplasma marginale infection in Texas cattle

Bovine anaplasmosis is an infectious, non-contagious disease caused by the rickettsial pathogen Anaplasma marginale (A. marginale). The organism has a global distribution and infects erythrocytes, resulting in anemia, jaundice, fever, abortions and death. Once infected, animals remain carriers for life. The carrier status provides immunity to clinical disease, but is problematic if infected and naïve cattle are comingled. Knowledge of infection prevalence and spatial distribution is important in disease management. The objective of this study was to assess A. marginale infection in-herd prevalence in Texas cattle using both molecular and serological methods. Blood samples from 11 cattle herds within Texas were collected and analyzed by reverse transcription quantitative real-time PCR (RT-qPCR) and a commercial competitive enzyme-linked immunosorbent assay (cELISA). Samples from experimentally infected animals were also analyzed and RT-qPCR detected A. marginale infection up to 15 days before cELISA, providing empirical data to support the interpretation of herd prevalence results. Herds with high prevalence were located in the north Texas Rolling Plains and west Trans-Pecos Desert, with RT-qPCR prevalence as high as 82% and cELISA prevalence as high as 88%. Overall prevalence was significantly higher in cattle in north and west Texas compared to cattle in east Texas (p<0.0001 for prevalence based on both RT-qPCR and cELISA). The overall RT-qPCR and cELISA results exhibited 90% agreement (kappa=0.79) and provide the first A. marginale infection prevalence study for Texas cattle using two diagnostic methods. Since cattle are the most important reservoir host for A. marginale and can serve as a source of infection for tick and mechanical transmission, information on infection prevalence is beneficial in the development of prevention and control strategies.

Characterization of Escherichia coli virulence genes, pathotypes and antibiotic resistance properties in diarrheic calves in Iran

Background

Calf diarrhea is a major economic concern in bovine industry all around the world. This study was carried out in order to investigate distribution of virulence genes, pathotypes, serogroups and antibiotic resistance properties of Escherichia coli isolated from diarrheic calves.

Results

Totally, 76.45% of 824 diarrheic fecal samples collected from Isfahan, Chaharmahal, Fars and Khuzestan provinces, Iran were positive for E. coli and all of them were also positive for cnf2, hlyA, cdtIII, f17c, lt, st, stx1, eae, ehly, stx2 and cnf1 virulence genes. Chaharmahal had the highest prevalence of STEC (84.61%), while Isfahan had the lowest (71.95%). E. coli serogroups had the highest frequency in 1–7 days old calves and winter season. Distribution of ETEC, EHEC, AEEC and NTEC pathotypes among E. coli isolates were 28.41%, 5.07%, 29.52% and 3.49%, respectively. Statistical analyses were significant for presence of bacteria between various seasons and ages. All isolates had the high resistance to penicillin (100%), streptomycin (98.25%) and tetracycline (98.09%) antibiotics. The most commonly detected resistance genes were aadA1, sul1, aac[3]-IV, CITM, and dfrA1. The most prevalent serogroup among STEC was O26.

Conclusions

Our findings should raise awareness about antibiotic resistance in diarrheic calves in Iran. Clinicians should exercise caution when prescribing antibiotics.

Evaluation of lamb and calf responses to Rift Valley fever MP-12 vaccination

Rift Valley fever (RVF) is an important viral disease of animals and humans in Africa and the Middle East that is transmitted by mosquitoes. The disease is of concern to international agricultural and public health communities. The RVFV MP-12 strain has been the most safety tested attenuated vaccine strain; thus it is being considered as a potential vaccine for the US national veterinary stockpile. This study was designed to establish safety protocols for large animal research with virulent RVF viruses, establish a target host immune response baseline using RVF MP-12 strain, and independently evaluate this strain as a potential US emergency response vaccine. Ten, approximately four month-old lambs and calves were vaccinated with RVF MP-12 strain; two additional animals per species provided negative control specimens. The animals were monitored for clinical and immune response, fever, and viremia. Two animals per species were sacrificed on 2, 3, 4, 10 and 28 days post infection and full necropsies were performed for histopathological examination. No clinical or febrile responses were observed in this study. The onset and titer of the immune response is discussed. There was no significant histopathology in the lambs; however, 6 out of 10 vaccinated calves had multifocal, random areas of hepatocellular degeneration and necrosis. RVF MP12 antigen was detected in these areas of necrosis by immunohistochemistry in one calf. This study provides independent and baseline information on the RVF MP-12 attenuated vaccination in vaccine relevant age target species and indicates the importance of performing safety testing on vaccine relevant aged target animals.

Development and performance evaluation of a streamlined method for nucleic acid purification, denaturation, and multiplex detection of Bluetongue virus and Epizootic hemorrhagic disease virus

Bluetongue virus (BTV) and Epizootic hemorrhagic disease virus (EHDV) possess similar structural and molecular features, are transmitted by biting midges (genus Culicoides), and cause similar diseases in some susceptible ruminants. Generally, BTV causes subclinical disease in cattle, characterized by a prolonged viremia. EHDV-associated disease in cattle is less prominent; however, it has emerged as a major economic threat to the white-tailed deer (Odocoileus virginianus) industry in many areas of the United States. The recent emergence of multiple BTV and EHDV serotypes previously undetected in the United States demonstrates the need for robust detection of all known serotypes and differential diagnosis. For this purpose, a streamlined workflow consisting of an automated nucleic acid purification and denaturation method and a multiplex one-step reverse transcription quantitative polymerase chain reaction for the simultaneous detection of BTV serotypes 1-24 and EHDV serotypes 1-7 was developed using previously published BTV and EHDV assays. The denaturation of double-stranded (ds) BTV and EHDV RNA was incorporated into the automated nucleic acid purification process thus eliminating the commonly used separate step of dsRNA denaturation. The performance of this workflow was compared with the World Organization of Animal Health BTV reference laboratory (National Veterinary Services Laboratory, Ames, Iowa) workflow for BTV and EHDV detection, and high agreement was observed. Implementation of the workflow in routine diagnostic testing enables the detection of, and differentiation between, BTV and EHDV, and coinfections in bovine blood and cervine tissues, offering significant benefits in terms of differential disease diagnosis, herd health monitoring, and regulated testing.

Development of a Rift Valley fever real-time RT-PCR assay that can detect all three genome segments

Outbreaks of Rift Valley fever in Kenya, Madagascar, Mauritania, and South Africa had devastating effects on livestock and human health. In addition, this disease is a food security issue for endemic countries. There is growing concern for the potential introduction of RVF into non-endemic countries. A number of single-gene target amplification assays have been developed for the rapid detection of RVF viral RNA. This paper describes the development of an improved amplification assay that includes two confirmatory target RNA segments (L and M) and a third target gene, NSs, which is deleted in the Clone 13 commercial vaccine and other candidate vaccines. The assay also contains an exogenous RNA control added during the PCR setup for detection of amplification inhibitors. The assay was evaluated initially with samples from experimentally infected animals, after which clinical veterinary and human samples from endemic countries were tested for further evaluation. The assay has a sensitivity range of 66.7-100% and a specificity of 92.0-100% depending on the comparison. The assay has an overall sensitivity of 92.5%, specificity of 95% and a positive predictive value of 98.7%. The single-tube assay provides confirmation of the presence of RVFV RNA for improved confidence in diagnostic results and a "differentiate infected from vaccinated animals" (DIVA)--compatible marker for RVFV NSs--deleted vaccines, which is useful for RVF endemic countries, but especially important in non-endemic countries.