Real Time RT-PCR for the detection and quantitation of bovine respiratory syncytial virus

Phylogenetic Analysis of Bovine Respiratory Syncytial Virus (BRSV) Subgroups in Wallonia Region of Belgium in Relation to Current Vaccination Strategies

Background: Bovine respiratory syncytial virus (BRSV) is a major pathogen of the bovine respiratory disease complex and causes regular severe winter outbreaks of respiratory disease in cattle. It is therefore responsible for important economic losses for the farming industry. In this study, the genetic diversity of the circulating BRSV strains in Belgium, which has not been assessed since the end of the 1990s, was investigated. Methods: We analyzed 51 BRSV-positive samples collected from 2015 to 2023. This study is the first report on the circulation of BRSV subgroup VIII in Belgium. Furthermore, co-circulation of subgroups II and III was recorded in the same period. Four commercially available vaccine strains marketed in Belgium were also included in the analysis and they clustered with subgroup II or III. Results: Our findings indicate that different strains of BRSV are circulating in Belgium, including those from subgroups II and VIII, with the subgroup VIII strains being particularly distant from the commercially available vaccine strains. Conclusions: These results highlight the importance of ensuring that the available vaccines efficiently protect against strains from circulating subgroups and assessing the potential circulation of attenuated vaccine strains.

A surrogate in vitro experimental model for off-label drug repurposing: inhibitory effect of montelukast on bovine respiratory syncytial virus replication

BACKGROUND

Repurposing off-label drugs during epidemics or pandemics with unknown/known pathogens, particularly when their side effects and complications are already known, can be a strategic approach, as seen during the COVID-19 pandemic. Developing surrogate in vitro experimental models (passage-to-passage), which mimic epidemic/pandemic-like transmission (human-to-human), may enhance this repurposing process. This study evaluates montelukast sodium (MLS), a US FDA-approved leukotriene receptor antagonist for asthma, to explore its potential repurposing antiviral effects against bovine respiratory syncytial virus (BRSV), which has basic similarities to human respiratory syncytial virus (HRSV) as both belong to the Pneumoviridae family.

METHODS

An in vitro serial passage model was developed using MDBK cells infected with a local wild-type strain of BRSV (43TR2018). The cytotoxicity of MLS was assessed via the trypan blue exclusion method, identifying non-toxic concentrations. The impact of MLS on viral spread and infectivity was measured through TCID50 values over 10 passages. Viral loads were confirmed by nested RT-PCR and quantified using qPCR, while apoptosis, necrosis, and nitric oxide production were evaluated through staining and nitrite assays. Data were analyzed using ANOVA and Tukey's test (p < 0.05).

RESULTS

Control cells exhibited 97.16% viability, with 10 µM and 20 µM MLS concentrations maintaining viabilities of 89.2% and 87.3%, respectively. Viral titers significantly decreased at higher concentrations of MLS (up to 99.94% inhibition). Apoptosis rates decreased in MLS-treated cells, and live cell percentages improved, especially at 20 µM. Nitric oxide levels showed no significant differences across groups.

CONCLUSION

MLS demonstrated a dose-dependent antiviral effect against BRSV, achieving 99% viral inhibition properties in MDBK cells. These promising results warrant further investigation into the antiviral mechanisms of MLS.

Environmental Dissemination of SARS-CoV-2: An Analysis Employing Crassphage and Next-Generation Sequencing Protocols

This study aimed to investigate the dissemination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in water samples obtained during the coronavirus disease 2019 pandemic period, employing cross-assembly phage (crAssphage) as a fecal contamination biomarker and next-generation sequencing protocols to characterize SARS-CoV-2 variants. Raw wastewater and surface water (stream and sea) samples were collected for over a month in Rio de Janeiro, Brazil. Ultracentrifugation and negatively charged membrane filtration were employed for viral concentration of the wastewater and surface water samples, respectively. Viruses were detected and quantified by (RT-)qPCR applying TaqMan® system protocols. SARS-CoV-2 RNA signals were detected in 92.5% (37/40) of the wastewater samples and in 31.25% (10/32) of the stream water samples, but not in seawater samples. CrAssphage was detected in 100% of the wastewater samples, 93.75% (30/32) of the stream samples, and in 2/4 of the seawater samples. CrAssphage detection and high concentrations in stream surface waters (median 8.95 log10 gc/L) revealed diffuse contamination by domestic wastewater in a region with high sanitary coverage. The correlations detected between SARS-CoV-2 data and the moving averages of clinical cases per capita over the sampling period were moderate to strong when applying a 13-day offset, regardless of normalization by crAssphage data or not. Sequencing of the receptor-binding domain of the spike protein confirmed the detection of SARS-CoV-2, but did not characterize the circulating variant. On the other hand, the whole genome sequencing protocol identified circulation of the Gamma variant, corroborating the sampling period clinical data.

Establishment of a Real-Time Reverse Transcription Recombinase-Aided Isothermal Amplification (qRT-RAA) Assay for the Rapid Detection of Bovine Respiratory Syncytial Virus

BACKGROUND

Bovine respiratory syncytial virus (BRSV) is a significant cause of bovine respiratory disease, resulting in significant losses to the cattle industry. For rapid detection of BRSV, a real-time recombinase-aided isothermal amplification assay (qRT-RAA) based on the F gene of BRSV was developed in this study.

RESULTS

The developed qRT-RAA assay showed good exponential amplification of the target fragment in 20 min at a constant temperature of 39 °C. And this assay displayed a high specificity for BRSV, without cross-reactions with Infectious Bovine Rhinotracheitis Virus (IBRV), Bovine Parainfluenza Virus Type 3 (BPIV3), Bovine Viral Diarrhea Virus (BVDV), and Bovine Coronavirus (BCoV). With the standard RNA of BRSV serving as a template, the limit of detection for qRT-RAA was 102 copies/μL. We examined ninety-seven clinical samples from cattle with respiratory disease using this method and determined a positive rate of 7.2% (7/97), consistent with results using the classical PCR method reported previously.

CONCLUSIONS

A qRT-RAA assay for BRSV detection was established in this study. The method is specific and sensitive and can be completed within 20 min at 39 °C. These works demonstrate that the generated qRT-RAA assay is an effective diagnostic tool for rapidly detecting BRSV in resource-limited settings, which may be applied for the clinical detection of BRSV.

Identification of Mycoplasma Species in Cattle Associated with Bovine Respiratory Disease Mortality

Approximately 30 distinct Mycoplasma species have been isolated from cattle, but only a few are pathogenic and can cause serious respiratory diseases. Consequently, this study aimed to identify Mycoplasma spp. infections in cattle with bovine respiratory disease (BRD), considering factors such as animal demographics, concurrent infections with other pathogens, post-mortem clinical findings and histological examinations, and seasonality. A total of 326 samples were collected from 322 cattle that had died from BRD in Northwestern Italy. A total of 54 animals (16.8%) tested positive for Mycoplasma spp., and Mycoplasma bovis (n = 22, 40.7%) and Mycoplasma dispar (n = 13, 24.1%) were the most frequently detected species among the examined cattle. Among positive cattle, those aged five months or younger were approximately five times more likely to be infected by Mycoplasma dispar than by Mycoplasma bovis compared to those older than five months (proportional incidence ratio: 5.1, 95% CI 1.2-21.2). The main bacterial pathogens identified in cattle exhibiting co-infection was Pasteurella multocida, whereas the main viral pathogens were BRSV and BoHV-1. Histopathological investigations predominantly revealed catarrhal bronchopneumonia or purulent catarrhal bronchopneumonia among the examined cattle. Finally, Mycoplasma hyopharyngis, a species isolated from the pharyngeal and nasal cavities of pigs so far, was detected for the first time in the pneumonic lung of a bovine infected with BRD. Further investigations are necessary to thoroughly characterize its host range and pathogenic potential.

Wastewater Surveillance of US Coast Guard Installations and Seagoing Military Vessels to Mitigate the Risk of COVID-19 Outbreaks, March 2021-August 2022

OBJECTIVES

Military training centers and seagoing vessels are often environments at high risk for the spread of COVID-19 and other contagious diseases, because military trainees and personnel arrive after traveling from many parts of the country and live in congregate settings. We examined whether levels of SARS-CoV-2 genetic material in wastewater correlated with SARS-CoV-2 infections among military personnel living in communal barracks and vessels at US Coast Guard training centers in the United States.

METHODS

The Coast Guard developed and established 3 laboratories with wastewater testing capability at Coast Guard training centers from March 2021 through August 2022. We analyzed wastewater from barracks housing trainees and from 4 Coast Guard vessels for the presence of SARS-CoV-2 genes N and E and quantified the results relative to levels of a fecal indicator virus, pepper mild mottle virus. We compared quantified data with the timing of medically diagnosed COVID-19 infection among (1) military personnel who had presented with symptoms or had been discovered through contact tracing and had medical tests and (2) military personnel who had been discovered through routine surveillance by positive SARS-CoV-2 antigen or polymerase chain reaction test results.

RESULTS

Levels of viral genes in wastewater at Coast Guard locations were best correlated with diagnosed COVID-19 cases when wastewater testing was performed twice weekly with passive samplers deployed for the entire week; such testing detected ≥1 COVID-19 case 69.8% of the time and ≥3 cases 88.3% of the time. Wastewater assessment in vessels did not continue because of logistical constraints.

CONCLUSION

Wastewater testing is an effective tool for measuring the presence and patterns of SARS-CoV-2 infections among military populations. Success with wastewater testing for SARS-CoV-2 infections suggests that other diseases may be assessed with similar approaches.

Longitudinal fecal shedding of SARS-CoV-2, pepper mild mottle virus, and human mitochondrial DNA in COVID-19 patients

Since the coronavirus disease 2019 (COVID-19) pandemic, wastewater-based epidemiology (WBE) has been widely applied in many countries and regions for monitoring COVID-19 transmission in the population through testing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater. However, the amount of virus shed by individuals over time based on the stage of infection and accurate number of infections in the community creates challenges in predicting COVID-19 prevalence in the population and interpreting WBE results. In this study, we measured SARS-CoV-2, pepper mild mottle virus (PMMoV), and human mitochondrial DNA (mtDNA) in longitudinal fecal samples collected from 42 COVID-19 patients for up to 42 days after diagnosis. SARS-CoV-2 RNA was detected in 73.1% (19/26) of inpatient study participants in at least one of the collected fecal specimens during the sampling period. Most participants shed the virus within 3 weeks after diagnosis, but five inpatient participants still shed the virus between 20 and 60 days after diagnosis. The median concentration of SARS-CoV-2 in positive fecal samples was 1.08 × 105 genome copies (GC)/gram dry fecal material. PMMoV and mtDNA were detected in 99.4% (154/155) and 100% (155/155) of all fecal samples, respectively. The median concentrations of PMMoV RNA and mtDNA in fecal samples were 1.73 × 107 and 2.49 × 108 GC/dry gram, respectively. These results provide important information about the dynamics of fecal shedding of SARS-CoV-2 and two human fecal indicators in COVID-19 patients. mtDNA showed higher positive rates, higher concentrations, and less variability between and within individuals than PMMoV, suggesting that mtDNA could be a better normalization factor for WBE results than PMMoV.

Assessment of crAssphage as a biological variable for SARS-CoV-2 data normalization in wastewater surveillance

AIMS

This study aimed to assess the use of cross-assembled phage (crAssphage) as an endogenous control employing a multivariate normalization analysis and its application as a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) data normalizer.

METHODS AND RESULTS

A total of 188 twelve-hour composite raw sewage samples were obtained from eight wastewater treatment plants (WWTP) during a 1-year monitoring period. Employing the N1 and N2 target regions, SARS-CoV-2 RNA was detected in 94% (177) and 90% (170) of the samples, respectively, with a global median of 5 log10 genomic copies per liter (GC l-1). CrAssphage was detected in 100% of the samples, ranging from 8.29 to 10.43 log10 GC l-1, with a median of 9.46 ± 0.40 log10 GC l-1, presenting both spatial and temporal variabilities.

CONCLUSIONS

Although SARS-CoV-2 data normalization employing crAssphage revealed a correlation with clinical cases occurring during the study period, crAssphage normalization by the flow per capita per day of each WWTP increased this correlation, corroborating the importance of normalizing wastewater surveillance data in disease trend monitoring.

Molecular Characterisation and Antibody Response to Bovine Respiratory Syncytial Virus in Vaccinated and Infected Cattle in Turkey

Bovine respiratory syncytial virus (BRSV) is one of the most important respiratory pathogens of cattle. In this study, frequency of infection, analysis of variants, and the immune status of vaccinated and non-vaccinated cattle were studied. Blood (n = 162) and nasal/oropharyngeal (n = 277) swabs were collected from 62 cattle herds in Turkey. Lung samples (n = 37) were also taken from dead animals and abattoirs. Antibodies to BRSV were detected in 76 (46%) out of 162 sera. The antibody levels in the vaccinated and non-vaccinated groups were statistically significant. Among 277 nasal/oropharyngeal swabs and 37 lungs, ten nasal/oropharyngeal and four lung samples were positive for BRSV-RNA. BRSV-G gene sequences of 5 out of 14 RT-PCR positive samples showed that all viruses clustered as Group-III in phylogenetic analysis with 88-100% homology. Similarity with previous Turkish BRSVs was 89-98%, and that with BRSVs detected in the USA and Czechia was 89.47-93.12%. BRSV continues to circulate in Turkish cattle, and vaccination seems beneficial in preventing BRSV. The diversity of the BRSVs found in this study needs be considered in vaccination strategies.

Incomplete sanitation in the Metropolitan Region of São Paulo results in detection of SARS-CoV-2 in headwater streams

Among the largest metropolitan regions in the world, the Metropolitan Region of São Paulo (MRSP) represents an important case study for the COVID-19 respiratory disease pandemic because it is home to >20 million people, making it one of the largest metropolitan regions in the global south. Besides the high population density, the MRSP has several problems related to social and economic aspects, which may reflect in the dynamics of SARS-CoV-2 virus, such as low income, lack of sanitation and social vulnerability in the peripheral regions of MRSP. In these regions, the input of untreated sewage on the streams and rivers can be frequently observed, which may represent an indicator of poor sewer system. Therefore, this study aimed to identify if streams draining urbanized regions without appropriate sanitation are prone to receive higher loads of detectable SARS-CoV-2 in its waters. For this, we collected water samples from 45 headwater streams distributed across an urbanization gradient (0-100 % of urbanization) in the MRSP, with three replicates in each stream and analyzed the concentrations of SARS-CoV-2 RNA targeting the nucleocapsid N1 and N2 genomic regions. In addition, we analyzed the relationship between the concentrations of SARS-CoV-2 RNA and sanitation and social variables. Our results showed that the concentrations of SARS-CoV-2 RNA were higher in the streams draining medium to high urbanized catchments, especially because of the lack of sanitation and the higher probabilities to detect SARS-CoV-2 RNA in the stream water was associated with households without a septic tank or sewage system within the catchment, followed by per capita household income. These results reflect the lack of urbanization planning and the lack of sanitation, especially in the poor regions from the MRSP, adding another risk for the already vulnerable population in a metropolitan region from the global south during a pandemic disease.

Analyzing community wastewater in sub-sewersheds for the small-scale detection of SARS-CoV-2 variants in a German metropolitan area

Wastewater surveillance of SARS-CoV-2 proved useful, including for identifying the local appearance of newly identified virus variants. Previous studies focused on wastewater treatment plants (WWTP) with sewersheds of several hundred thousand people or at single building level, representing only a small number of people. Both approaches may prove inadequate for small-scale intra-urban inferences for early detection of emerging or novel virus variants. Our study aims (i) to analyze SARS-CoV-2 single nucleotide variants (SNVs) in wastewater of sub-sewersheds and WWTP using whole genome sequencing in order to (ii) investigate the potential of small-scale detection of novel known SARS-CoV-2 variants of concern (VOC) within a metropolitan wastewater system. We selected three sub-sewershed sampling sites, based on estimated population- and built environment-related indicators, and the inlet of the receiving WWTP in the Ruhr region, Germany. Untreated wastewater was sampled weekly between October and December 2021, with a total of 22 samples collected. SARS-CoV-2 RNA was analyzed by RT-qPCR and whole genome sequencing. For all samples, genome sequences were obtained, while only 13 samples were positive for RT-qPCR. We identified multiple specific SARS-CoV-2 SNVs in the wastewater samples of the sub-sewersheds and the WWTP. Identified SNVs reflected the dominance of VOC Delta at the time of sampling. Interestingly, we could identify an Omicron-specific SNV in one sub-sewershed. A concurrent wastewater study sampling the same WWTP detected the VOC Omicron one week later. Our observations suggest that the small-scale approach may prove particularly useful for the detection and description of spatially confined emerging or existing virus variants circulating in populations. Future studies applying small-scale sampling strategies taking into account the specific features of the wastewater system will be useful to analyze temporal and spatial variance in more detail.

The Effect of Copper and Zinc Sources on Liver Copper and Zinc Concentrations and Performance of Beef Cows and Suckling Calves

To determine the influence of the source of gestational and postnatal Cu and Zn supplementation on cow and calf performance, cows (n = 287) were assigned to one of the following two treatments: (1) inorganic (INORG) treatment, in which cows were supplemented with 15 mg of Cu (as CuSO4) and 15 mg of Zn (as ZnSO4) per kg of diet DM, or (2) organic (ORG) treatment, in which cows were supplemented with 15 mg of Cu (as Cu proteinate; Bioplex Cu, Alltech, Inc., Nicholasville, KY, USA) and 15 mg of Zn (as Zn proteinate; Bioplex Zn, Alltech, Inc., Nicholasville, KY, USA) per kg of diet DM. The treatments were initiated prior to breeding and continued throughout gestation until weaning. Liver biopsies were collected for analysis of mineral content. Cow body condition score (BCS), body weight (BW), pregnancy data, calf weaning weight (WW), and antibody response of the calves were recorded. The cows receiving the INORG treatment had a greater BW (p < 0.05) and BCS (p < 0.01) at breeding in Year 2, while the cows on the ORG treatment had a greater (p < 0.05) BW at weaning in Year 2. The cows that received the ORG mineral had improved (p < 0.05) conception rates in Year 1. The calves receiving the ORG treatment had heavier (p < 0.05) 205-day adjusted WWs.

Wastewater-based epidemiology: the crucial role of viral shedding dynamics in small communities

Background

Wastewater surveillance (WWS) of pathogens is a rapidly evolving field owing to the 2019 coronavirus disease pandemic, which brought about a paradigm shift in public health authorities for the management of pathogen outbreaks. However, the interpretation of WWS in terms of clinical cases remains a challenge, particularly in small communities where large variations in pathogen concentrations are routinely observed without a clear relation to clinical incident cases.

Methods

Results are presented for WWS from six municipalities in the eastern part of Canada during the spring of 2021. We developed a numerical model based on viral kinetics reduction functions to consider both prevalent and incident cases to interpret the WWS data in light of the reported clinical cases in the six surveyed communities.

Results

The use of the proposed numerical model with a viral kinetics reduction function drastically increased the interpretability of the WWS data in terms of the clinical cases reported for the surveyed community. In line with our working hypothesis, the effects of viral kinetics reduction modeling were more important in small communities than in larger communities. In all but one of the community cases (where it had no effect), the use of the proposed numerical model led to a change from a +1.5% (for the larger urban center, Quebec City) to a +48.8% increase in the case of a smaller community (Drummondville).

Conclusion

Consideration of prevalent and incident cases through the proposed numerical model increases the correlation between clinical cases and WWS data. This is particularly the case in small communities. Because the proposed model is based on a biological mechanism, we believe it is an inherent part of any wastewater system and, hence, that it should be used in any WWS analysis where the aim is to relate WWS measurement to clinical cases.

Zika virus RNA persistence and recovery in water and wastewater: An approach for Zika virus surveillance in resource-constrained settings

During the 2015-2016 Zika virus (ZIKV) epidemic in the Americas, serological cross-reactivity with other flaviviruses and relatively high costs of nucleic acid testing in the region hindered the capacity for widespread diagnostic testing. In such cases where individual testing is not feasible, wastewater monitoring approaches may offer a means of community-level public health surveillance. To inform such approaches, we characterized the persistence and recovery of ZIKV RNA in experiments where we spiked cultured ZIKV into surface water, wastewater, and a combination of both to examine the potential for detection in open sewers serving communities most affected by the ZIKV outbreak, such as those in Salvador, Bahia, Brazil. We used reverse transcription droplet digital PCR to quantify ZIKV RNA. In our persistence experiments, we found that the persistence of ZIKV RNA decreased with increasing temperature, significantly decreased in surface water versus wastewater, and significantly decreased when the initial concentration of virus was lowered by one order of magnitude. In our recovery experiments, we found higher percent recovery of ZIKV RNA in pellets versus supernatants from the same sample, higher recoveries in pellets using skimmed milk flocculation, lower recoveries of ZIKV RNA in surface water versus wastewater, and lower recoveries from a freeze thaw. We also analyzed samples collected from Salvador, Brazil during the ZIKV outbreak (2015-2016) that consisted of archived samples obtained from open sewers or environmental waters thought to be contaminated by sewage. Although we did not detect any ZIKV RNA in the archived Brazil samples, results from these persistence and recovery experiments serve to inform future wastewater monitoring efforts in open sewers, an understudied and important application of wastewater monitoring.

Evaluation of low-cost SARS-CoV-2 RNA purification methods for viral quantification by RT-qPCR and next-generation sequencing analysis: Implications for wider wastewater-based epidemiology adoption

Based Epidemiology (WBE) consists of quantifying biomarkers in sewerage systems to derive real-time information on the health and/or lifestyle of the contributing population. WBE usefulness was vastly demonstrated in the context of the COVID-19 pandemic. Many methods for SARS-CoV-2 RNA determination in wastewater were devised, which vary in cost, infrastructure requirements and sensitivity. For most developing countries, implementing WBE for viral outbreaks, such as that of SARS-CoV-2, proved challenging due to budget, reagent availability and infrastructure constraints. In this study, we assessed low-cost methods for SARS-CoV-2 RNA quantification by RT-qPCR, and performed variant identification by NGS in wastewater samples. Results showed that the effect of adjusting pH to 4 and/or adding MgCl2 (25 mM) was negligible when using the adsorption-elution method, as well as basal physicochemical parameters in the sample. In addition, results supported the standardized use of linear rather than plasmid DNA for a more accurate viral RT-qPCR estimation. The modified TRIzol-based purification method in this study yielded comparable RT-qPCR estimation to a column-based approach, but provided better NGS results, suggesting that column-based purification for viral analysis should be revised. Overall, this work provides evaluation of a robust, sensitive and cost-effective method for SARS-CoV-2 RNA analysis that could be implemented for other viruses, for a wider WEB adoption.

Assessment of virus concentration methods for detecting SARS-CoV-2 IN wastewater

Wastewater-based epidemiology has been described as a valuable tool for monitoring the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a community. However, there is no consensus on the best concentration method to allow reliable detection of SARS-CoV-2 in this matrix, considering different laboratory facilities. This study compares two viral concentration methods, ultracentrifugation (ULT) and skimmed-milk flocculation (SMF), for detecting SARS-CoV-2 in wastewater samples. The analytical sensitivity (limits of detection and quantification [LoD/LoQ]) of both methods was evaluated using a bovine respiratory syncytial virus (BRSV) as a surrogate. Three different approaches were conducted to establish LoD of each method based on the assays on the standard curve (ALoDsc), on the dilution of internal control (ALoDiC), and the processing steps (PLoD). For PLoD, ULT method had the lowest value (1.86 × 103 genome copy/microliter [GC/µL]) when compared to the SMF method (1.26 × 107 GC/µL). The LoQ determination showed a mean value of 1.55 × 105 GC/µL and 3.56 × 108 GC/µL to ULT and SMF, respectively. The detection of SARSCoV-2 in naturally contaminated wastewater revealed 100% (12/12) and 25% (3/12) of detection using ULT and SMF with quantification ranging from 5.2 to 7.2 log10 genome copy/liter (GC/L) and 5.06 to 5.46 log10 GC/L, respectively. The detection success rate of BRSV used as an internal control process was 100% (12/12) for ULT and 67% (8/12) for SMF, with an efficiency recovery rate ranging from 12 to 38% and 0.1 to 5%, respectively. Our data consolidates the importance of assessing the methods used; however, further analysis should be carried out to improve low-cost concentration methodologies, essential for use in low-income and developing countries.

Highly socially vulnerable communities exhibit disproportionately increased viral loads as measured in community wastewater

Wastewater surveillance has proven to be a useful tool for evidence-based epidemiology in the fight against the SARS-CoV-2 virus. It is particularly useful at the population level where acquisition of individual test samples may be time or cost-prohibitive. Wastewater surveillance for SARS-CoV-2 has typically been performed at wastewater treatment plants; however, this study was designed to sample on a local level to monitor the spread of the virus among three communities with distinct social vulnerability indices in Shreveport, Louisiana, located in a socially vulnerable region of the United States. Twice-monthly grab samples were collected from September 30, 2020, to March 23, 2021, during the Beta wave of the pandemic. The goals of the study were to examine whether: 1) concentrations of SARS-CoV-2 RNA in wastewater varied with social vulnerability indices and, 2) the time lag of spikes differed during wastewater monitoring in the distinct communities. The size of the population contributing to each sample was assessed via the quantification of the pepper mild mottle virus (PMMoV), which was significantly higher in the less socially vulnerable community. We found that the communities with higher social vulnerability exhibited greater viral loads as assessed by wastewater when normalized with PMMoV (Kruskal-Wallis, p < 0.05). The timing of the spread of the virus through the three communities appeared to be similar. These results suggest that interconnected communities within a municipality experienced the spread of the SARS-CoV-2 virus at similar times, but areas of high social vulnerability experienced more intense wastewater viral loads.

Genetic characterization of bovine respiratory syncytial viruses in Japan between 2017 and 2019

Bovine respiratory syncytial virus (BRSV) strains that were detected in Kagoshima prefecture and isolated in Hokkaido between 2017 and 2019, together with a BRSV vaccine strain, were subjected to full-genome sequencing. The BRSV strains identified in Japan were found to be genetically close to each other but distant from the vaccine strains. The deduced amino acids at positions 206 and 208 of the glycoprotein (G protein), which form one of the major epitopes of the recent Japanese BRSV strains, were different from those of the vaccine strains. Therefore, the recent Japanese BRSV strains might be antigenically different from the BRSV vaccine strains.

Reduction in Mortality of Calves with Bovine Respiratory Disease in Detection with Influenza C and D Virus

Both influenza C (ICV) and influenza D (IDV) viruses were recently included as bovine respiratory disease (BRD) causes, but their role in BRD has not been evaluated. Therefore, the mortality and reproductive performances of BRD calves with different isolated viruses were determined in this study. Data on 152 BRD calves with bovine viral diarrhoea virus (BVDV), bovine respiratory syncytial virus (BRSV), bovine coronavirus (BCoV), bovine parainfluenza virus 3 (BPIV-3), ICV, or IDV from nasal swab samples using real-time rt-PCR were used. The general data and respiratory signs were recorded immediately, and thereafter, the data on dead or culling calves due to BRD and reproductive performance were collected. The percentages of the BRD calves were 71.7%, 52.6%, 40.8%, 10.5%, 68.4%, and 65.8% for BVDV, BRSV, BCoV, BPIV-3, ICV, and IDV, respectively. Mucous secretion (OR = 4.27) and age ≤ 6 months (OR =14.97) had higher risks of mortality than those with serous secretion and older age. The calves with IDV had lower risks of culling than those without IDV (OR = 0.19). This study shows that most viral infections in BRD calves are a combination of viruses with BVDV, ICV, and IDV. In addition, IDV might have a role in reducing the severity of BRD calves.

Spatiotemporal Surveillance of SARS-CoV-2 in the Sewage of Three Major Urban Areas in Peru: Generating Valuable Data Where Clinical Testing Is Extremely Limited

Peru has been severely affected by the COVID-19 pandemic. By January 2022, Peru had surpassed 200 000 COVID-19 deaths, constituting the highest death rate per capita worldwide. Peru has had several limitations during the pandemic: insufficient testing access, limited contact tracing, a strained medical infrastructure, and many economic hurdles. These limitations hindered the gathering of accurate information about infected individuals with spatial resolution in real time, a critical aspect of effectively controlling the pandemic. Wastewater monitoring for SARS-CoV-2 RNA offered a promising alternative for providing needed population-wide information to complement health care indicators. In this study, we demonstrate the feasibility and value of implementing a decentralized SARS-CoV-2 RNA wastewater monitoring system to assess the spatiotemporal distribution of COVID-19 in three major cities in Peru: Lima, Callao, and Arequipa. Our data on viral loads showed the same trends as health indicators such as incidence and mortality. Furthermore, we were able to identify hot spots of contagion within the surveyed urban areas to guide the efforts of health authorities. Viral decay in the sewage network of the cities studied was found to be negligible (<2%). Overall, our results support wastewater monitoring for SARS-CoV-2 as a valuable and cost-effective tool for monitoring the COVID-19 pandemic in the Peruvian context.

Relationship between SARS-CoV-2 in wastewater and clinical data from five wastewater sheds

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has resulted in a global pandemic starting in 2019 with nearly 500 million confirmed cases as of April 2022. Infection with SARS-CoV-2 is accompanied by shedding of virus in stool, and its presence in wastewater samples has been documented globally. Therefore, monitoring of SARS-CoV-2 in wastewater offers a promising approach to assess the pandemic situation covering pre-symptomatic and asymptomatic cases in areas with limited clinical testing. In this study, the presence of SARS-CoV-2 RNA in wastewater from five wastewater resource recovery facilities (WRRFs), located in two adjacent counties, was investigated and compared with the number of clinical COVID-19 cases during a 2020-2021 outbreak in United States. Statistical correlation analyses of SARS-CoV-2 viral abundance in wastewater and COVID-19 daily vs weekly clinical cases was performed. While a weak correlation on a daily basis was observed, this correlation improved when weekly clinical case data were applied. The viral fecal indicator Pepper Mild Mottle Virus (PMMoV) was furthermore used to assess the effects of normalization and the impact of dilution due to infiltration in the wastewater sheds. Normalization did not improve the correlations with clinical data. However, PMMoV provided important information about infiltration and presence of industrial wastewater discharge in the wastewater sheds. This study showed the utility of WBE to assist in public health responses to COVID-19, emphasizing that routine monitoring of large WRRFs could provide sufficient information for large-scale dynamics.

Wastewater-based epidemiology: A Brazilian SARS-COV-2 surveillance experience

Since 2020, developed countries have rapidly shared both publicly and academically relevant wastewater surveillance information. Data on SARS-CoV-2 circulation is pivotal for guiding public health policies and improving the COVID-19 pandemic response. Conversely, low- and middle-income countries, such as Latin America and the Caribbean, showed timid activities in the Wastewater-Based Epidemiology (WBE) context. In these countries, isolated groups perform viral wastewater monitoring, and the data are unevenly shared or accessible to health agencies and the scientific community. This manuscript aims to highlight the relevance of a multiparty effort involving research, public health, and governmental agencies to support usage of WBE methodology to its full potential during the COVID-19 pandemic as part of a joint One Health surveillance approach. Thus, in this study, we explored the results obtained from wastewater surveillance in different regions of Brazil as a part of the COVID-19 Wastewater Monitoring Network ANA (National Water Agency), MCTI (Ministry of Science, Technology, and Innovations) and MS (Ministry of Health). Over the epidemiological weeks of 2021 and early 2022, viral RNA concentrations in wastewater followed epidemiological trends and variations. The highest viral loads in wastewater samples were detected during the second Brazilian wave of COVID-19. Corroborating international reports, our experience demonstrated usefulness of the WBE approach in viral surveillance. Wastewater surveillance allows hotspot identification, and therefore, early public health interventions. In addition, this methodology allows tracking of asymptomatic and oligosymptomatic individuals, who are generally underreported, especially in emerging countries with limited clinical testing capacity. Therefore, WBE undoubtedly contributes to improving public health responses in the context of this pandemic, as well as other sanitary emergencies.

First case of SARS-CoV-2 RNA detection in municipal solid waste leachate from Brazil

This work presents the first case of SARS-CoV-2 RNA detection in leachate collected from a transfer station in the city of São Paulo, Brazil. After calibration of the viral detection method already used for wastewater samples with a pilot leachate sample and virus fragments in laboratory, twelve polyethylene glycol concentrated leachates samples were tested by RT-qPCR. The results confirmed the presence of N1 gene in 9 of the 12 analyzed samples between epidemiological weeks 33 and 38 of the year 2021 (08/15/2021 to 09/19/2021). The occurrence of the N2 gene was only observed in 5 of the 12 samples. The concentration values for N1 and N2 genes varied between 3.1 and 4.6 log10.GC·L-1, which are values close to those measured in sanitary wastewater. This method showed to be a promising procedure to verify the presence of viral RNA in municipal solid waste leachate, being especially useful where there is no treatment system and sanitation infrastructure, which makes the conventional wastewater surveillance unfeasible.

Sampling strategies for wastewater surveillance: Evaluating the variability of SARS-COV-2 RNA concentration in composite and grab samples

The shedding of SARS-CoV-2 RNA titers by infected individuals, even asymptomatic and oligosymptomatic ones, allows the use of wastewater monitoring to track the COVID-19 spread in a community. This approach is interesting especially for emerging countries with limited clinical testing capabilities. However, there are still important methodological aspects that need validation so that wastewater monitoring data become more representative and useful for public health. This study evaluated the between-day and within-day variability of SARS-CoV-2 RNA concentrations in 24-hour composite and grab samples from three different sampling points, including two wastewater treatment plants (WTTP) and a sewer manhole. In the between-day evaluation (17 weeks of monitoring), a good agreement between the SARS-CoV-2 RNA concentration of each sampling method was observed. There were no significant differences between the mean concentrations of the grab and composite samples (p-value > 0.05), considering N1 and N2 gene assays. The strong relationship between composite and grab samples was proven by correlation coefficients: Pearson's r of 0.83 and Spearman's rho of 0.78 (p-value < 0.05). In within-day evaluation, 24-hour cycles were analyzed and low variability in hourly viral concentrations was observed for three sampling points. The coefficient of variation (CV) values ranged from 3.0% to 11.5%. Overall, 24-hour profiles showed that viral RNA concentrations had less variability and greater agreement with the mean values between 8 a.m. and 10 a.m, the recommended time for grab sampling. Therefore, this study provides important information on wastewater sampling techniques for COVID-19 surveillance. Wastewater monitoring information will only be useful to public health and decision-makers if we ensure data quality through best practices.

Evaluation of multiple analytical methods for SARS-CoV-2 surveillance in wastewater samples

In this study, 14 virus concentration protocols based on centrifugation, filtration, polyethylene glycol (PEG) precipitation and ultrafiltration were tested for their efficacy for the quantification of SARS-CoV-2 in wastewater samples. These protocols were paired with four RNA extraction procedures resulting in a combination of 50 unique approaches. Bovine respiratory syncytial virus (BRSV) was used as a process control and seeded in each wastewater sample subjected to all 50 protocols. The recovery of BRSV obtained through the application of 50 unique approaches ranged from <0.03 to 64.7% (±1.6%). Combination of centrifugation as the solid removal step, ultrafiltration (Amicon-UF-15; 100 kDa cut-off; protocol 9) as the primary virus concentration method, and Zymo Quick-RNA extraction kit provided the highest BRSV recovery (64.7 ± 1.6%). To determine the impact of prolonged storage of large wastewater sample volume (900 mL) at -20 °C on enveloped virus decay, the BRSV seeded wastewaters samples were stored at -20 °C up to 110 days and analyzed using the most efficient concentration (protocol 9) and extraction (Zymo Quick-RNA kit) methods. BRSV RNA followed a first-order decay rate (k = 0.04/h with r2 = 0.99) in wastewater. Finally, 21 wastewater influent samples from five wastewater treatment plants (WWTPs) in southern Maryland, USA were analyzed between May to August 2020 to determine SARS-CoV-2 RNA concentrations. SARS-CoV-2 RNA was quantifiable in 17/21 (81%) of the influent wastewater samples with concentration ranging from 1.10 (±0.10) × 104 to 2.38 (±0.16) × 106 gene copies/L. Among the RT-qPCR assays tested, US CDC N1 assay was the most sensitive followed by US CDC N2, E_Sarbeco, and RdRp assays. Data presented in this study may enhance our understanding on the effective concentration and extraction of SARS-CoV-2 from wastewater.

A sensitive, simple, and low-cost method for COVID-19 wastewater surveillance at an institutional level

SARS-CoV-2 is a respiratory virus, but it is also detected in a significant proportion of fecal samples from COVID-19 cases. Recent studies have shown that wastewater surveillance can be a low-cost tool compared to massive diagnostic testing for tracking COVID-19 outbreaks in communities, but most studies have focused on sampling from wastewater treatment plants. Institutional level wastewater surveillance may serve well for early warning purposes because specific geographic areas/populations with emerging cases can be tracked and immediate action can be executed in the event of a positive wastewater signal. In this study, a novel Moore swab method was developed and used for wastewater surveillance of COVID-19 at an institutional level. Of the 442 swab samples tested, 148 (33.5%) swabs collected from the three campuses and two buildings were positive for SARS-CoV-2 RNA. Further study of the quarantine building with a known number of cases indicated that this method was sensitive enough to detect few cases in the building. In addition, comparison between grab samples and Moore swab samples from the hospital sewage line indicated that Moore swabs were more sensitive than grab samples and offer a simple, inexpensive method for obtaining a composite sample of virus in wastewater over a 24-48 h period. These results suggest that collection and analyses of Moore swabs for SARS-CoV-2 RNA detection is a sensitive, low-cost, and easy to use tool for COVID-19 surveillance that is useful for institutional settings and could be deployed in low-resource settings to identify emerging COVID-19 clusters in communities.

Efficacy of oleandrin and PBI-05204 against bovine viruses of importance to commercial cattle health

Background

Bovine viral diarrhea virus (BVDV), bovine respiratory syncytial virus (BRSV). and bovine coronavirus (BCV) threaten the productivity of cattle worldwide. Development of therapeutics that can control the spread of these viruses is an unmet need. The present research was designed to explore the in vitro antiviral activity of the Nerium oleander derived cardiac glycoside oleandrin and a defined N. oleander plant extract (PBI-05204) containing oleandrin.

Methods

Madin Darby Bovine Kidney (MDBK) cells, Bovine Turbinate (BT) cells, and Human Rectal Tumor-18 (HRT-18) cells were used as in vitro culture systems for BVDV, BRSV and BCV, respectively. Cytotoxicity was established using serial dilutions of oleandrin or PBI-05204. Noncytotoxic concentrations of each drug were used either prior to or at 12 h and 24 h following virus exposure to corresponding viruses. Infectious virus titers were determined following each treatment.

Results

Both oleandrin as well as PBI-05204 demonstrated strong antiviral activity against BVDV, BRSV, and BCV, in a dose-dependent manner, when added prior to or following infection of host cells. Determination of viral loads by PCR demonstrated a concentration dependent decline in virus replication. Importantly, the relative ability of virus produced from treated cultures to infect new host cells was reduced by as much as 10,000-fold at noncytotoxic concentrations of oleandrin or PBI-05204.

Conclusions

The research demonstrates the potency of oleandrin and PBI-05204 to inhibit infectivity of three important enveloped bovine viruses in vitro. These data showing non-toxic concentrations of oleandrin inhibiting infectivity of three bovine viruses support further investigation of in vivo antiviral efficacy.

Etiology and risk factors for bovine respiratory disease in pre-weaned calves on California dairies and calf ranches

Our study objective was to estimate the magnitude of association of BRD risk factors including failure of passive immunity transfer, sex, age, and the detection of suspected BRD etiological pathogens in pre-weaned dairy calves in California. A conditional logistic regression model and a mixed-effects logistic regression model were used to estimate the association of these potential risk factors with BRD from a matched and nested case-control studies, respectively. For each exposure covariate, the odds ratio (OR) is the ratio of odds of an exposure in a BRD calf (case) to that in a non-BRD calf (control). In the matched case-control study, an interaction term between failure of transfer of passive immunity and sex of calf showed that female calves were more negatively impacted by failure of transfer of passive immunity compared to male calves. The odds ratios comparing failure of transfer of passive immunity in BRD score positive calves versus controls for male calves was 1.34 (95 % CI: 0.87, 2.06) and was 2.47 (95 % CI: 1.54, 3.96) for female calves. The model odds ratios varied from 1.74 (95 % CI: 1.26, 2.42) for Mycoplasma spp. to 9.18 (95 % CI: 2.60, 32.40) for Histophilus somni, with Mannheimia haemolytica and Pasteurella multocida having an OR of 6.64 (95 % CI: 4.39, 10.03) and 6.53 (95 % CI: 4.44, 9.59), respectively. For bovine respiratory syncytial virus positive calves, the OR was 4.60 (95 % CI: 3.04, 6.97). Findings from the nested case-control study showed that based on thoracic ultrasonography findings consistent with BRD, the odds of a calf being 1 day older compared to a day younger were 1.01 (95 % CI: 1.00, 1.02) among BRD cases. For the bacterial and viral pathogens, the OR for Mycoplasma spp. and Pasteurella multocida were 1.85 (95 % CI: 1.24, 2.75) and 1.86 (95 % CI: 1.28, 2.71), respectively. The OR values for these pathogens were similar when both thoracic auscultation and ultrasound findings were used to detect cases of BRD. Based on positive scores for BRD using the California BRD scoring system, the OR for facility type, calf ranch versus dairy farm, was 3.17 (95 % CI: 1.43, 7.01), Mannheimia haemolytica was 3.50 (95 % CI: 2.00, 6.11), Pasteurella multocida was 1.78 (95 % CI: 1.21, 2.60), and bovine coronavirus was 2.61 (95 % CI: 1.85, 3.70). Results from both study designs showed the difference in relative contributions of age, sex, immune status, and pathogens in BRD occurrence between cases and controls in pre-weaned dairy calves.

Long-term monitoring of SARS-COV-2 RNA in wastewater in Brazil: A more responsive and economical approach

SARS-CoV-2, the novel Coronavirus, was first detected in Wuhan, China, in December 2019, and has since spread rapidly, causing millions of deaths worldwide. As in most countries of the world, in Brazil, the consequences of the COVID-19 pandemic have been catastrophic. Several studies have reported the fecal shedding of SARS-CoV-2 RNA titers from infected symptomatic and asymptomatic individuals. Therefore, the quantification of SARS-CoV-2 in wastewater can be used to track the virus spread in a population. In this study, samples of untreated wastewater were collected for 44 weeks at five sampling sites in the ABC Region (São Paulo, Brazil), in order to evaluate the SARS-CoV-2 occurrence in the sewerage system. SARS-CoV-2 RNA titers were detected throughout the period, and the concentration ranged from 2.7 to 7.7 log10 genome copies.L-1, with peaks in the last weeks of monitoring. Furthermore, we observed a positive correlation between the viral load in wastewater and the epidemiological/clinical data, with the former preceding the latter by approximately two weeks. The COVID-19 prevalence for each sampling site was estimated via Monte-Carlo simulation using the wastewater viral load. The mean predicted prevalence ranged 0.05 to 0.38%, slightly higher than reported (0.016 ± 0.005%) in the ABC Region for the same period. These results highlight the viability of the wastewater surveillance for COVID-19 infection monitoring in the largest urban agglomeration in South America. This approach can be especially useful for health agencies and public decision-makers in predicting SARS-CoV-2 outbreaks, as well as in local tracing of infection clusters.

Prevalence of BRD-Related Viral Pathogens in the Upper Respiratory Tract of Swiss Veal Calves

The prevention of bovine respiratory disease is important, as it may lead to impaired welfare, economic losses, and considerable antimicrobial use, which can be associated with antimicrobial resistance. The aim of this study was to describe the prevalence of respiratory viruses and to identify risk factors for their occurrence. A convenience sample of 764 deep nasopharyngeal swab samples from veal calves was screened by PCR for bovine respiratory syncytial virus (BRSV), bovine parainfluenza-3 virus (BPI3V), bovine coronavirus (BCoV), influenza D virus (IDV), and influenza C virus (ICV). The following prevalence rates were observed: BRSV, 2.1%; BPI3V, 3.3%; BCoV, 53.5%; IDV, 4.1%; ICV, 0%. Logistic mixed regression models were built for BCoV to explore associations with calf management and housing. Positive swab samples were more frequent in younger calves than older calves (>100 days; p < 0.001). The probability of detecting BCoV increased with increasing group size in young calves. Findings from this study suggested that young calves should be fattened in small groups to limit the risk of occurrence of BCoV, although an extended spectrum of risk factors for viral associated respiratory disorders such as nutritional aspects should be considered in future studies.

Indoor Dust as a Matrix for Surveillance of COVID-19

Ongoing disease surveillance is a critical tool to mitigate viral outbreaks, especially during a pandemic. Environmental monitoring has significant promise even following widespread vaccination among high-risk populations. The goal of this work is to demonstrate molecular severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) monitoring in bulk floor dust and related samples as a proof of concept of a noninvasive environmental surveillance methodology for coronavirus disease 2019 (COVID-19) and potentially other viral diseases. Surface swab, passive sampler, and bulk floor dust samples were collected from the rooms of individuals positive for COVID-19, and SARS-CoV-2 was measured with quantitative reverse transcription-PCR (RT-qPCR) and two digital PCR (dPCR) methods. Bulk dust samples had a geometric mean concentration of 163 copies/mg of dust and ranged from nondetects to 23,049 copies/mg of dust detected using droplet digital PCR (ddPCR). An average of 89% of bulk dust samples were positive for the virus by the detection methods compared to 55% of surface swabs and fewer on the passive sampler (19% carpet, 29% polystyrene). In bulk dust, SARS-CoV-2 was detected in 76%, 93%, and 97% of samples measured by qPCR, chip-based dPCR, and droplet dPCR, respectively. Detectable viral RNA in the bulk vacuum bags did not measurably decay over 4 weeks, despite the application of a disinfectant before room cleaning. Future monitoring efforts should further evaluate RNA persistence and heterogeneity in dust. This study did not measure virus infectivity in dust or potential transmission associated with dust. Overall, this work demonstrates that bulk floor dust is a potentially useful matrix for long-term monitoring of viral disease in high-risk populations and buildings.

IMPORTANCE Environmental surveillance to assess pathogen presence within a community is proving to be a critical tool to protect public health, and it is especially relevant during the ongoing COVID-19 pandemic. Importantly, environmental surveillance tools also allow for the detection of asymptomatic disease carriers and for routine monitoring of a large number of people as has been shown for SARS-CoV-2 wastewater monitoring. However, additional monitoring techniques are needed to screen for outbreaks in high-risk settings such as congregate care facilities. Here, we demonstrate that SARS-CoV-2 can be detected in bulk floor dust collected from rooms housing infected individuals. This analysis suggests that dust may be a useful and efficient matrix for routine surveillance of viral disease.

Wastewater-based epidemiology as a useful tool to track SARS-CoV-2 and support public health policies at municipal level in Brazil

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) wastewater-based epidemiology (WBE) has been applied as a complementary approach for spatial tracking of coronavirus disease 2019 cases (COVID-19) as well as early warning of the occurrence of infected populations. The present study presents the result of the monitoring of sanitary sewerage in the municipality of Niterói, a metropolitan region of Rio de Janeiro (Brazil) and its use as a complementary indicator in the surveillance of COVID-19 cases, thus assisting actions of public health from local authorities. Twelve composite raw sewage samples were weekly collected from two wastewater treatment plants (WWTPs) and alternately from 17 sewer pipes (SP) from surrounding neighbourhoods and slums throughout 20 weeks (April 15th to August 25th, 2020). Two hundred twenty-three samples were concentrated using the ultracentrifugation-based method and SARS-CoV-2 RNA detected and quantified by RT-qPCR using primers and probe targeting the N2 genome. SARS-CoV-2 RNA was detected in 84.3% (188/223) of samples with a positive rate ranging from 42% (5/12) in the first week of monitoring to 100% during the peak of epidemic with viral concentration ranging from 3.1 to 7.1 log10 genome copies /100 mL throughout the studied period. Positive rates were higher in WWTPs when compared to SP, being useful tool for monitoring trends in the evolution of the COVID-19 curve, while SP data were more effective when health public interventions were needed. Whole-genome sequencing using Illumina MiSeq System confirmed the lineage of three genomes as B.1.1.33 (clade G) containing the nucleotide substitutions observed in strains that circulate in the Rio de Janeiro during the period of this study. In addition, geoprocessing tool was used to build heat maps based on SARS-CoV-2 data from sewage samples, which were weekly updated and available online to the general population as an indicator of the ongoing epidemic situation in Niterói city, raising public awareness.

NASYM, a live intranasal vaccine, protects young calves from bovine respiratory syncytial virus in the presence of maternal antibodies

BACKGROUND

Bovine respiratory syncytial virus (BRSV) is a major problem for cattle worldwide during their first year of life. The aim of the present study was to evaluate efficacy and longevity of immunity of a live vaccine (NASYM, HIPRA) in the presence of maternally derived antibodies (MDA).

METHOD

Calves (36) were distributed in four groups, based on MDA status and treatment. They received NASYM or a placebo at an early age (less than two weeks) by intranasal route. Eight weeks later, animals were challenged with the Asquith strain of BRSV. Efficacy was assessed by monitoring clinical signs and mortality, PaO₂ , virus shedding and lung lesions. The immunological response was evaluated by measuring IgG in serum and IgA in nasal secretions.

RESULTS

A reduction of mortality, lung lesions, shedding and a higher PaO₂ was achieved in NASYM vaccinated groups, independently of MDA status. An anamnestic IgG response was observed after challenge in vaccinated animals, both in MDA+ and MDA- groups. An IgA response was also observed in vaccinated animals after vaccination and challenge.

CONCLUSION

NASYM protected newborn calves with MDAs during the first 10 weeks of life, against a very virulent challenge that caused extensive pulmonary lesions and deaths in control animals, with just a single intranasal dose.

Developing and Testing a Real-Time Polymerase Chain Reaction to Identify and Quantify Bovine Respiratory Syncytial Viruses

The bovine respiratory syncytial virus (BRSV) known as Bovine orthopneumovirus according to the international classification is one of the most important etiological agents of respiratory diseases in calves. At present, rapid and reliable methods to detect and measure the concentrations of this pathogen are needed. The objectives of the survey are developing the real-time polymerase chain reaction (PCR) to identify and quantify the BRSV RNA and, based on it, determining the number of the virus genomes in the respiratory tract of sick animals during the disease outbreaks. The nucleocapsid (N) protein gene of the virus served as the target for amplification. Messenger RNA (mRNA) of bovine GAPDH was used as a reference gene. A panel of positive control samples at known concentrations was used to estimate the virus and GAPDH numbers. The concentration of viral RNA extracted from the biomaterial samples was quantified relative to the bovine GAPDH mRNA level. The analytical sensitivity of PCR demonstrating high specificity and reproducibility was 1 × 10³ genome equivalents per 1 cm³. All 273 samples of biological material taken from the animals with the respiratory diseases were analyzed. The virus genome was detected in 19.4% of samples. The viral RNA was more frequently detected in the lungs, which comprised 10.61% of positive samples. It was less frequently found in the mucous membranes of trachea and bronchi and the lymph nodes of the lungs, which comprised 0.73% of positive samples each. Concentrations of the virus in samples varied. The highest concentration was recorded in the lungs (1.3 ± 0.5—4.8 ± 0.47 log₁₀ copies of BRSV/GAPDH RNA). The developed test kit may be used to quantify the concentration of the bovine respiratory syncytial virus in disease pathogenesis and to estimate the efficiency of vaccine or antivirus preparations for animals.

Influenza C and D viral load in cattle correlates with bovine respiratory disease (BRD): Emerging role of orthomyxoviruses in the pathogenesis of BRD

Bovine respiratory disease (BRD) is the costliest disease affecting the cattle industry globally. Orthomyxoviruses, influenza C virus (ICV) and influenza D virus (IDV) have recently been implicated to play a role in BRD. However, there are contradicting reports about the association of IDV and ICV to BRD. Using the largest cohort study (cattle, n = 599) to date we investigated the association of influenza viruses in cattle with BRD. Cattle were scored for respiratory symptoms and pooled nasal and pharyngeal swabs were tested for bovine viral diarrhea virus, bovine herpesvirus 1, bovine respiratory syncytial virus, bovine coronavirus, ICV and IDV by real-time PCR. Cattle that have higher viral loads of IDV and ICV also have greater numbers of co-infecting viruses than controls. More strikingly, 2 logs higher IDV viral RNA in BRD-symptomatic cattle that are co-infected animals than those infected with IDV alone. Our results strongly suggest that ICV and IDV may be significant contributors to BRD.

Determination of the reference genes for qRT-PCR normalization and expression levels of MAT genes under various conditions in Ulocladium

The genus Ulocladium is thought to be strictly asexual. One of the possible reasons for the lack of sexuality in Ulocladium species is the absence of the stimulus of environmental factors. Sexual reproduction in ascomycetes is controlled by a specific region in the genome referred to as mating-type locus (MAT) that consists of two dissimilar DNA sequences in the mating partners, termed MAT1-1 and MAT1-2 idiomorphs. To identify the response of MAT loci to environmental conditions, the mRNA transcription level of MAT1-1-1 and MAT1-2-1 genes was tested using qRT-PCR under different temperatures (−20 °C, −10 °C, 0 °C, 10 °C, 20 °C, 30 °C and 40 °C), culture medias (CM, OA, HAY, PCA, PDA and V8), photoperiods (24 h light, 24 h dark, 12 h light/12 h dark, 10 h light/14 h dark and 8 h light/16 h dark), and CO₂ concentrations (0.03%, 0.5%, 1%, 5%, 10%, 15% and 20%). For obtaining reliable results from qRT-PCR, the most stable internal control gene and optimal number of reference genes for normalization were determined under different treatments. The results showed that there is no universal internal control gene that is expressed at a constant level under different experimental treatments. In comparison to various incubation conditions, the relative expression levels of both MAT genes were significantly increased when fungal mycelia were grown on HAY culture media at 0–10 °C with a light/dark cycle, indicating that temperature, culture media, and light might be the key environmental factors for regulating the sexuality in Ulocladium. Moreover, MAT1-1-1 and MAT1-2-1 genes showed similar expression patterns under different treatments, suggesting that the two MAT genes might play an equally important role in the sexual evolutionary process.

Circulation of Indigenous Bovine Respiratory Syncytial Virus Strains in Turkish Cattle: The First Isolation and Molecular Characterization

Bovine respiratory disease (BRD) is a huge economic burden on the livestock industries of countries worldwide. Bovine respiratory syncytial virus (BRSV) is one of the most important pathogens that contributes to BRD. In this study, we report the identification and first isolation, with molecular characterization, of a new BRSV strain from lung specimens of three beef cows in Turkey that died from respiratory distress. After the screening of lung tissues for BRD-associated viruses using a multiscreen antigen-ELISA, a BRSV antigen was detected. This was then confirmed by real-time RT-PCR specific for BRSV. Following confirmation, virus isolation was conducted in MDBK cell cultures and clear CPE, including syncytia compatible with BRSV, were detected. RT-nested PCR, using F gene-specific primers, was performed on the cultured isolates, and the products were sequenced and deposited to Genbank with accession numbers MT179304, MT024766, and MT0244767. Phylogenetic analysis of these sequences indicated that the cattle were infected with BRSV from subgroup III and were closely related to previously identified American and Turkish strains, but contained some amino acid and nucleotide differences. This research paves the way for further studies on the molecular characteristics of natural BRSV isolates, including full genome analysis and disease pathogenesis, and also contributes to the development of robust national strategies against this virus.

Design of a multiplex quantitative reverse transcription-PCR system to simultaneously detect 16 pathogens associated with bovine respiratory and enteric diseases

AIM

Bovine respiratory disease (BRD) and bovine enteric disease (BED) are two major diseases in cattle, resulting in severe economic losses in the dairy and beef industries. The two major diseases are associated with several factors such as viruses, bacteria, the health condition of the host and environmental factors. We aimed to design a new efficient diagnostic method, which rapidly detect causative pathogens, minimizing economic loss due to BRD and BED.

METHODS AND RESULTS

We designed a multiplex quantitative reverse transcription-PCR (qRT-PCR) system for the simultaneous diagnosis of 16 pathogens, including 12 viruses and 4 bacteria related to BRD and BED, based on single qRT-PCR assays in previous studies. The designed multiplex qRT-PCR was highly sensitive and has minimal detection levels which will be no different from those of single qRT-PCR. Moreover, the multiplex qRT-PCR could more efficiently detect the causative pathogens than conventional RT-PCR in test using a part of BRD and BED clinical samples. Furthermore, our data revealed that the multiplex qRT-PCR had high performance in its specificity and reproducibility tests.

CONCLUSIONS

Our system can effectively detect multiple BRD or BED related pathogens from each animal while testing several clinical samples via the multiplex qRT-PCR. It is more time-, cost- and labour-efficient than other diagnostic methods.

SIGNIFICANCE AND IMPACT OF THE STUDY

Rapid detection of infected animals from the herd using our system will greatly contribute to infection control and prompt treatment in field.

Bluetongue Serotype 3 in Israel 2013-2018: Clinical Manifestations of the Disease and Molecular Characterization of Israeli Strains

In this paper, the results of the diagnostic activities on Bluetongue virus serotype 3 (BTV-3) conducted at Kimron Veterinary Institute (Beit Dagan, Israel) between 2013 and 2018 are reported. Bluetongue virus is the causative agent of bluetongue (BT), a disease of ruminants, mostly transmitted by competent Culicoides species. In Israel, BTV-3 circulation was first detected in 2013 from a sheep showing classical BT clinical signs. It was also evidenced in 2016, and, since then, it has been regularly detected in Israeli livestock. Between 2013 and 2017, BTV-3 outbreaks were limited in sheep flocks located in the southern area only. In 2018, BTV-3 was instead found in the Israeli coastal area being one of the dominant BTV serotypes isolated from symptomatic sheep, cattle and goats. In Israeli sheep, BTV-3 was able to cause BT classical clinical manifestations and fatalities, while in cattle and goats infection ranged from asymptomatic forms to death cases, depending on either general welfare of the herds or on the occurrence of viral and bacterial co-infections. Three different BTV-3 strains were identified in Israel between 2013 and 2018: ISR-2019/13 isolated in 2013, ISR-2153/16 and ISR-2262/2/16 isolated in 2016. Sequencing and phylogenetic analysis of these strains showed more than 99% identity by segment (Seg) 2, 5, 6, 7, and 8 sequences. In contrast, a wide range of diversity among these strains was exhibited in other viral gene segments, implying the occurrence of genome reassortment between these local circulating strains and those originating from Africa. The genome sequences of the BTV-3 isolated in 2017 and 2018 were most closely related to those of the ISR-2153/16 strain suggesting their common ancestor. Comparison of BTV-3 Israeli strains with those recently detected in the Mediterranean region uncovered high percentage identity (98.19–98.28%) only between Seg-2 of all Israeli strains and the BTV-3 Zarzis/TUN2016 strain. A 98.93% identity was also observed between Seg-4 sequences of ISR-2019/13 and the BTV-3 Zarzis/TUN2016 strain. This study demonstrated that BTV-3 has been circulating in the Mediterranean region at least since 2013, but, unlike the other Mediterranean strains, Israeli BTV-3 were able to cause clinical signs also in cattle.

Seroprevalence and risk factors of bovine respiratory syncytial virus in cattle in the Nineveh Governorate, Iraq

Background and Aim

Bovine respiratory syncytial virus (BRSV) is one of the main causes of severe pneumonia, interstitial edema, and emphysema in cattle. The current study investigated the prevalence and risk factors of BRSV in cattle in the Nineveh Province, Iraq.

Materials and Methods

Between September 2017 and September 2018, 450 serum samples were collected from non-vaccinated cattle of different ages and breeds for BRSV testing. The epidemiological information of the animals was recorded. The prevalence of the disease was determined using an indirect enzyme-linked immunosorbent assay kit.

Results

The prevalence of BRSV was 83.11%, and it was significantly (p<0.05) higher in cattle aged greater than 7 months-1.5 years than in older animals; in imported cattle than in Native animals; and in animals originating from large herds (100 animals) than in those from smaller herds (40 animals). There was no significant difference between BRSV prevalence in male and female animals. When samples from different regions of the Nineveh Governorate were compared, the northern region was associated with the highest prevalence of the disease. Samples harvested in the winter displayed the highest BRSV titer, compared to those collected during the other seasons.

Conclusion

BRSV is prevalent in cattle from the Nineveh Governorate. Risk factors such as animal age, origin, herd size, and the herd's geographical location are associated with an increased prevalence of the disease in this region. Routine vaccination programs should be adopted to reduce the prevalence of BRSV.

Co-infection of epithelial cells established from the upper and lower bovine respiratory tract with bovine respiratory syncytial virus and bacteria

Bovine respiratory disease complex is a major disease affecting the global cattle industry. Multiple infections by viruses and bacteria increase disease severity. Previously, we reported that bovine respiratory syncytial virus (BRSV) infection increases adherence of Pasteurella multocida to human respiratory and bovine kidney epithelial cells. To examine the interaction between the virus and bacteria in bovine respiratory cells, we generated respiratory epithelial cell lines from bovine trachea (bTEC), bronchus (bBEC), and lung (bLEC). Although all established cell lines were infected by BRSV and P. multocida susceptibility differed according to site of origin. The cells derived from the lower respiratory tract (bBEC and bLEC) were significantly more susceptible to BRSV than those derived from the upper respiratory tract (bTEC). Pre-infection of bBEC and bLEC with BRSV increased adherence of P. multocida; this was not the case for bTEC. These results indicate that BRSV may reproduce better in the lower respiratory tract and encourage adherence of bacteria. Thus, we identify one possible mechanism underlying severe pneumonia.

Longitudinal study of humoral immunity to bovine coronavirus, virus shedding, and treatment for bovine respiratory disease in pre-weaned beef calves

Background

Bovine coronavirus (BCV) is associated with respiratory infections in cattle of all ages; however, a temporal study to evaluate the effect of BCV immunity on virus shedding and bovine respiratory disease (BRD) incidence in pre-weaned beef calves has not been reported. Thus, we report here a prospective study in three herds of crossbred beef calves (n = 817) with endemic BCV.

Serial blood samples for measurement of serum anti-BCV antibody titers and nasal swabs for detection of BCV and other common viral and bacterial BRD pathogens were collected from all calves or subsets of calves at predetermined times from birth through weaning. The calves were monitored for BRD and those that developed signs of respiratory disease were sampled for diagnostic testing. To discover additional risk factors that could have influenced BRD development, sequence analysis of the BCV strain(s) circulating in each herd, and the prevalence of common opportunistic bacterial pathogens in the upper respiratory tract of sick and apparently healthy cattle were also evaluated.

Results

Two hundred forty-eight of the 817 study calves (30.4%) were treated for BRD prior to weaning; 246 of those were from a single herd involved in two outbreaks of BRD leading to mass treatment of all calves in that group. Molecular diagnostic testing found BCV and Histophilus somni in nasal swabs taken at the time of BRD treatment. Between herd analyses revealed anti-BCV serum antibody abundance did not associate with the incidence of BRD or BCV shedding, though these measurements may have been hindered by the long periods between sample collections. Analysis of the BCV spike gene hypervariable region revealed four polymorphisms in 15 isolates from the three herds, making strain variation unlikely to account for differences in treatment rates between herds. Persistent or recurrent shedding episodes of BCV occurred in some animals treated for BRD.

Conclusion

Co-detection of BCV and H. somni at the time of the disease outbreak suggests that these pathogens contributed to disease pathogenesis. Developing appropriate control measures for respiratory BCV infections may help decrease the incidence of pre-weaning BRD. The role of antibodies in protection must still be further defined.

Electronic supplementary material

The online version of this article (10.1186/s12917-019-1887-8) contains supplementary material, which is available to authorized users.

Bovine respiratory syncytial virus in experimentally exposed and rechallenged calves; viral shedding related to clinical signs and the potential for transmission

Background

Bovine respiratory syncytial virus (BRSV) is an important respiratory pathogen worldwide, detrimentally affecting the economy and animal welfare. To prevent and control BRSV infection, further knowledge on virus shedding and transmission potential in individual animals is required. This study aimed to detect viral RNA and infective virions during BRSV infection to evaluate duration of the transmission period and correlation with clinical signs of disease. The outcome of BRSV re-exposure on calves, their housing environment and effect of introduction of sentinel calves was also investigated.

A live animal experiment including 10 calves was conducted over 61 days. Initially, two calves were inoculated with a non-passaged BRSV field isolate. Two days later, six naïve calves (EG: Exposed group) were introduced for commingling and four weeks later, another two naïve calves (SG: Sentinel group) were introduced. Seven weeks after commingling, EG animals were re-inoculated. Clinical examination was performed daily. Nasal swabs were collected regularly and analysed for viral RNA by RT-ddPCR, while virus isolation was performed in cell culture. BRSV serology was performed with ELISA.

Results

All the EG calves seroconverted and showed clinical signs of respiratory disease. Viral RNA was detected from days 1–27 after exposure, while the infective virus was isolated on day 6 and 13. On day 19, all animals were seropositive and virus could not be isolated. Total clinical score for respiratory signs corresponded well with the shedding of viral RNA. The SG animals, introduced 27 days after exposure, remained negative for BRSV RNA and stayed seronegative throughout the study. Inoculation of the EG calves seven weeks after primary infection did not lead to new shedding of viral RNA or clinical signs of disease.

Conclusion

Viral RNA was detected in nasal swabs from the calves up to four weeks after exposure. The detection and amount of viral RNA corresponded well with the degree of respiratory signs. The calves were shedding infective virions for a considerable shorter period, and naïve calves introduced after four weeks were not infected. Infected calves were protected from reinfection for at least seven weeks. This knowledge is useful to prevent spread of BRSV.

Development of a nanoparticle-assisted PCR assay for detection of bovine respiratory syncytial virus

Background

Bovine respiratory syncytial virus (BRSV) is a common pathogen causing respiratory disease in cattle and a significant contributor to the bovine respiratory disease (BRD) complex. BRSV is widely distributed around the world, causing severe economic losses. This study we established a new molecular detection method of BRSV pathogen NanoPCR attributed to the combination of nano-particles in traditional PCR (Polymerase chain reaction) technology.

Results

In this study, the BRSV NanoPCR assay was developed, and its specificity and sensitivity were investigated. The results showed that no cross-reactivity was observed for the NanoPCR assay for related viruses, including the infectious bovine rhinotracheitis virus (IBRV), bovine viral diarrhea virus (BVDV), and bovine parainfluenza virus type 3 (BPIV3), and the assay was more sensitive than the conventional PCR assay, with a detection limit of 1.43 × 10² copies recombinant plasmids per reaction, compared with 1.43 × 10³ copies for conventional PCR analysis. Moreover, thirty-nine clinical bovine samples collected from two provinces in North-Eastern China, 46.15% were determined BRSV positive by our NanoPCR assay, compared with 23.07% for conventional PCR.

Conclusions

This is the first report to demonstrate the application of a NanoPCR assay for the detection of BRSV. The sensitive and specific NanoPCR assay developed in this study can be applied widely in clinical diagnosis and field surveillance of BRSV infection.

Temporary carriage of bovine coronavirus and bovine respiratory syncytial virus by fomites and human nasal mucosa after exposure to infected calves

BACKGROUND

In order to prevent spread of the endemic pathogens bovine coronavirus (BCoV) and bovine respiratory syncytial virus (BRSV) between herds, knowledge of indirect transmission by personnel and fomites is fundamental. The aims of the study were to determine the duration of viral RNA carriage and the infectivity of viral particles on fomites and human nasal mucosa after exposure to BCoV and BRSV. During two animal infection experiments, swabs were collected from personnel (nasal mucosa) and their clothes, boots and equipment after contact with calves shedding either virus. Viral RNA was quantified by RT-qPCR or droplet digital RT-PCR (RT-ddPCR), and selected samples with high levels of viral RNA were tested by cell culture for infectivity.

RESULTS

For BCoV, 46% (n = 80) of the swabs from human nasal mucosa collected 30 min after exposure were positive by RT-qPCR. After two, four and six hours, 15%, 5% and 0% of the swabs were positive, respectively. Infective virions were not detected in mucosal swabs (n = 2). A high viral RNA load was detected on 97% (n = 44) of the fomites 24 h after exposure, and infective virions were detected in two of three swabs. For BRSV, 35% (n = 26) of the human nasal mucosa swabs collected 30 min after exposure, were positive by RT-ddPCR, but none were positive for infective virions. Of the fomites, 89% (n = 38) were positive for BRSV RNA 24 h after exposure, but all were negative for infective viruses.

CONCLUSIONS

The results indicate that human nasal mucosa can carry both BCoV and BRSV RNA after exposure to virus shedding calves, but the carriage seems short-lived and the transmission potential is likely limited. High viral loads on contaminates fomites 24 h after exposure to infected animals, and detection of infective BCoV, indicate that contaminated fomites represent a significant risk for indirect transmission between herds.

Dexamethasone treatment differentially alters viral shedding and the antibody and acute phase protein response after multivalent respiratory vaccination in beef steers

Our objective was to examine immunosuppression induced by dexamethasone (DEX) administration in cattle on immunological responses to a multivalent respiratory vaccine containing replicating and nonreplicating agents. Steers ( = 32; 209 ± 8 kg) seronegative to infectious bovine rhinotracheitis virus (IBRV), bovine viral diarrhea virus (BVDV), bovine respiratory syncytial virus (BRSV), and parainfluenza-3 virus (PI3V) were stratified by BW and randomly assigned to 1 of 3 treatments: 1) acute immunosuppression (ACU; 0.5 mg/kg BW DEX intravenously at 1000 h only on d 0), 2) chronic immunosuppression (CHR; 0.5 mg/kg BW DEX intravenously at 1000 h on d -3 to 0), or 3) a control (CON; no DEX). On d -4, steers were fitted with intravenous catheters in the jugular vein and placed into individual stanchions. At 1200 h on d 0, steers were administered a respiratory vaccine containing modified-live virus (MLV) isolates of IBRV, BVDV, BRSV, and PI3V and a (MH) toxoid. On d 4, cattle were transported (177 km) and housed in an isolated outdoor pen. Serum was harvested on d 0, 7, 14, 21, 28, 35, 42, and 56 to determine IBRV-, BVDV-, BRSV-, and PI3V-specific antibody titers and MH whole cell and leukotoxin antibody concentrations. Sera from d -2, 0, 1, 3, 7, and 14 were used to quantify haptoglobin (Hp) concentration and ceruloplasmin (Cp) activity. Nasal swab specimens were collected on d 0, 3, and 14 to determine the presence of IBRV, BVDV, BRSV, and PI3V via PCR analysis. There was a treatment × day interaction ( < 0.01) such that CHR steers had a greater ( ≤ 0.07) BVDV antibody titer on d 14, 21, and 28. Moreover, IBRV-specific antibodies increased beginning on d 14 for CHR and on d 28 for ACU and remained greater through d 56 compared with CON ( ≤ 0.03). Conversely, serum MH whole cell antibody concentration was least ( ≤ 0.06) for CHR from d 7 to 28 and greatest for CON ( ≤ 0.04) on d 56. Treatment altered Hp such that CON exhibited a greater ( < 0.01) Hp concentration than CHR but was not different from ACU ( = 0.16). On d 3, Cp was greatest for CON, intermediate for ACU, and least for CHR (treatment × day; ≤ 0.01). The prevalence of IBRV and BVDV in nasal swabs on d 14 was 67 and 56%, respectively, for CHR; 10 and 10%, respectively, for CON; and 9 and 0%, respectively, for ACU ( ≤ 0.006). Results suggest that CHR allowed increased replication of MLV vaccine agents. Conversely, DEX-induced immunosuppression blunted the acute phase protein and antibody response against the nonreplicating MH toxoid.

Type 2 BVDV Npro suppresses IFN-1 pathway signaling in bovine cells and augments BRSV replication

Bovine viral diarrhea virus (BVDV) infection induces immunosuppression and in conjunction with bovine respiratory syncytial virus (BRSV) contributes to the bovine respiratory disease complex. Bovine turbinate cells were single or co-infected with type 2 BVDV wild-type (BVDV2-wt), its dysfunctional N^pro mutant (BVDV2-E), and/or BRSV. BVDV2-E significantly up-regulated PKR, IRF-7, TBK-1, IRF-3, and IFN-β mRNAs based on real-time Q-RT-PCR. BRSV-infected cells expressed significantly up-regulated PKR, IRF-3, IRF-7, and IFN-β mRNAs, whereas BVDV2-wt, but not BVDV2-E, abolished this up-regulation in co-infection. No significant differences were observed in MAVS, NF-κB, and PIN-1 mRNAs. A dual-luciferase reporter assay showed that BVDV2-wt significantly increased NF-κB activity compared to BVDV2-E, while BVDV2-E significantly increased IFN-β activity compared to BVDV2-wt. The BRSV titer and RNA levels significantly increased in cells co-infected with BRSV/BVDV2-wt compared to cells co-infected with BRSV/BVDV2-E or infected with BRSV alone. This data supports the synergistic action of BVDV2-wt and BRSV inhibition of IFN-1.

Agreement Among 4 Sampling Methods to Identify Respiratory Pathogens in Dairy Calves with Acute Bovine Respiratory Disease

Background

Four sampling techniques commonly are used for antemortem identification of pathogens from cattle with bovine respiratory disease (BRD): the nasal swab (NS), guarded nasopharyngeal swab (NPS), bronchoalveolar lavage (BAL), and transtracheal wash (TTW). Agreement among these methods has not been well characterized.

Objective

To evaluate agreement among TTW and NS, NPS, or BAL for identification of viral and bacterial pathogens in dairy calves with BRD.

Animals

One hundred dairy calves with naturally acquired BRD.

Methods

Calves were sampled by all 4 methods. Viral agents were identified by real‐time RT‐PCR, bacteria were identified by aerobic culture, and Mycoplasma bovis (M. bovis) isolates were speciated by PCR. Agreement among TTW and NS, NPS, or BAL was evaluated by calculating the kappa statistic and percent positive agreement. McNemar's exact test was used to compare the proportions of positive results.

Results

Agreement among TTW and NS, TTW and NPS, and TTW and BAL, was very good for identification of P. multocida, M. haemolytica, and M. bovis. For bovine respiratory syncytial virus (BRSV), agreement with TTW was moderate for NS, good for NPS, and very good for BAL. For bovine coronavirus (BCV), agreement with TTW was moderate for NS and NPS, and good for BAL. McNemar's test was significant only for BCV, indicating that for this pathogen the proportion of positive results from NS and NPS could not be considered comparable to TTW.

Conclusions and Clinical Importance

This study provides guidance for veterinarians selecting diagnostic tests for antemortem identification of pathogens associated with BRD.