Molecular detection of canine respiratory pathogens between 2017 and 2018 in Japan

Development of one-step multiplex real-time PCR for the detection of CHV-1, CAdV-2, and CDV

Canine Infectious Respiratory Disease Complex (CIRDC) is a highly contagious disease that frequently affects canine populations and has emerged as a global epidemic. It has been reported that CIRDC can have a serious impact on related life. Therefore, the rapid detection and differentiation of common viruses that cause CIRDC are essential. It is generally believed that CIRDC is mainly caused by infection of three pathogens: canine herpesvirus-1 (CHV-1), canine adenovirus-2 (CAdV-2), and canine distemper virus (CDV). In this study, we developed and validated a TaqMan probe-based multiplex real-time PCR method to detect and identify these three viruses simultaneously. We designed specific primers and probes, and optimized the concentrations of each reactant in the system. The method was found to have good sensitivity, specificity and stability, and had a limit of detection of 102 copies/μL, 101 copies/μL and 101 copies/μL for CHV-1, CAdV-2, and CDV, respectively. In addition, co-infection simulation experiments confirmed that the method worked effectively, even if the concentrations of multiple viruses in the sample were close to the limit of detection or the concentrations of different viruses were different. The method was used to detect 122 clinical samples, and the results showed that it was more sensitive and reliable than conventional singleplex PCR. Thus, the method developed in this study is suitable for the clinical monitoring of CIRDC and is of great significance for the prevention and management of respiratory diseases in canine populations.

Coding-complete genome sequences of two strains of canine pneumovirus derived from dogs with upper respiratory disease in the United States

Canine pneumovirus was detected by RT-qPCR in 2022 from nasal swabs collected from two dogs with upper respiratory disease in a shelter in Louisiana, United States. The genomes from the designated strains CPnV USA/LA/2022/124423 and USA/LA/2022/123696 were sequenced and show the closest similarity to the pneumonia virus of mice J3666.

Validation of a real-time PCR panel for detection and quantification of nine pathogens commonly associated with canine infectious respiratory disease

Canine infectious respiratory disease (CIRD) is a complicated respiratory syndrome in dogs [1], [2], [3]. A panel PCR was developed [4] to detect nine pathogens commonly associated with CIRD: Mycoplasma cynos, Mycoplasma canis, Bordetella bronchiseptica; canine adenovirus type 2, canine herpesvirus 1, canine parainfluenza virus, canine distemper virus, canine influenza virus and canine respiratory coronavirus [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16]. To evaluate diagnostic performance of the assay, 740 nasal swab and lung tissue samples were collected and tested with the new assay, and compared to an older version of the assay detecting the same pathogens except that it does not differentiate the two Mycoplasma species. Results indicated that the new assay had the same level of specificity, but with higher diagnostic sensitivity and had identified additional samples with potential co-infections. To confirm the new assay is detecting the correct pathogens, samples with discrepant results between the two assays were sequence-confirmed. Spiking a high concertation target to samples carrying lower concentrations of other targets was carried out and the results demonstrated that there was no apparent interference among targets in the same PCR reaction. Another spike-in experiment was used to determine detection sensitivity between nasal swab and lung tissue samples, and similar results were obtained.•A nine-pathogen CIRD PCR panel assay had identified 139 positives from 740 clinical samples with 60 co-infections;•High-concentration target does not have apparent effect on detecting low-concentration targets;•Detection sensitivity were similar between nasal swab and lung tissue samples.

Development and Validation of a Panel of One-Step Four-Plex qPCR/RT-qPCR Assays for Simultaneous Detection of SARS-CoV-2 and Other Pathogens Associated with Canine Infectious Respiratory Disease Complex

Canine infectious respiratory disease complex (CIRDC) is the primary cause of respiratory disease in the canine population and is caused by a wide array of viruses and bacterial pathogens with coinfections being common. Since its recognition in late 2019, Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has been reported to cause respiratory disease in dogs. Therefore, the rapid detection and differentiation of SARS-CoV-2 from other common viral and bacterial agents is critical from a public health standpoint. Here, we developed and validated a panel of four one-step multiplex qPCR/RT-qPCR assays for the detection and identification of twelve pathogens associated with CIRDC (canine adenovirus-2, canine distemper virus, canine herpesvirus-1, canine influenza A virus, canine parainfluenza virus, canine pneumovirus, canine respiratory coronavirus, SARS-CoV-2, Bordetella bronchiseptica, Streptococcus equi subsp. zooepidemicus, Mycoplasma cynos, and M. canis), as well as the identification of three main CIV subtypes (i.e., H3N2, H3N8, and H1N1). All developed assays demonstrated high specificity and analytical sensitivity. This panel was used to test clinical specimens (n = 76) from CIRDC-suspected dogs. M. canis, M. cynos, and CRCoV were the most frequently identified pathogens (30.3%, 25.0%, and 19.7% of samples, respectively). The newly emerging pathogens CPnV and SARS-CoV-2 were detected in 5.3% of samples and coinfections were identified in 30.3%. This new multiplex qPCR/RT-qPCR panel is the most comprehensive panel developed thus far for identifying CIRDC pathogens, along with SARS-CoV-2.

An Improved Duplex Real-Time Quantitative RT-PCR Assay with a Canine Endogenous Internal Positive Control for More Sensitive and Reliable Detection of Canine Parainfluenza Virus 5

A duplex real-time quantitative reverse transcription-polymerase chain reaction (dqRT-PCR) assay was successfully developed to simultaneously detect canine parainfluenza virus 5 (CPIV5) and a canine endogenous internal positive control (EIPC) in canine clinical samples. Two sets of primers and probes for the CPIV5 L and canine 16S rRNA genes were included in the dqRT-PCR assay to detect CPIV and monitor invalid results throughout the qRT-PCR process. The developed dqRT-PCR assay specifically detected CPIV5 but no other canine pathogens. Furthermore, 16S rRNA was stably amplified by dqRT-PCR assay in all samples containing canine cellular materials. The assay's sensitivity was determined as below ten RNA copies per reaction, with CPIV5 L gene standard RNA and 1 TCID₅₀/mL with the CPIV5 D008 vaccine strain, which was 10-fold higher than that of the previous HN gene-specific qRT-PCR (HN-qRT-PCR) assays and was equivalent to that of the previous N gene-specific qRT-PCR (N-qRT-PCR) assays, respectively. Moreover, the Ct values of the CPIV5-positive samples obtained using the dqRT-PCR assay were lower than those obtained using the previous HN- and N-qRT-PCR assays, indicating that the diagnostic performance of the dqRT-PCR assay was superior to those of previous HN- and N-qRT-PCR assays. The calculated Cohen's kappa coefficient values (95% confidence interval) between dqRT-PCR and the HN- or N-specific qRT-PCR assays were 0.97 (0.90-1.03) or 1.00 (1.00-1.00), respectively. In conclusion, the newly developed dqRT-PCR assay with high sensitivity, specificity, and reliability will be a promising diagnostic tool for the detection of CPIV5 in clinical samples and useful for etiological and epidemiological studies of CPIV5 infection in dogs.

Development of a three-panel multiplex real-time PCR assay for simultaneous detection of nine canine respiratory pathogens

Infectious respiratory disease is one of the most common diseases in dogs worldwide. Several bacterial and viral pathogens can serve as causative agents of canine infectious respiratory disease (CIRD), including Mycoplasma cynos, Mycoplasma canis, Bordetella bronchiseptica, canine adenovirus type 2 (CAdV-2), canine herpesvirus 1 (CHV-1), canine parainfluenza virus (CPIV), canine distemper virus (CDV), canine influenza virus (CIA) and canine respiratory coronavirus (CRCoV). Since these organisms cause similar clinical symptoms, disease diagnosis based on symptoms alone can be difficult. Therefore, a quick and accurate test is necessary to rapidly identify the presence and relative concentrations of causative CIRD agents. In this study, a multiplex real-time PCR panel assay was developed and composed of three subpanels for detection of the aforementioned pathogens. Correlation coefficients (R²) were >0.993 for all singleplex and multiplex real-time PCR assays with the exception of one that was 0.988; PCR amplification efficiencies (E) were between 92.1% and 107.8% for plasmid DNA, and 90.6-103.9% for RNA templates. In comparing singular and multiplex PCR assays, the three multiplex reactions generated similar R² and E values to those by corresponding singular reactions, suggesting that multiplexing did not interfere with the detection sensitivities. The limit of detection (LOD) of the multiplex real-time PCR for DNA templates was 5, 2, 3, 1, 1, 1, 4, 24 and 10 copies per microliter for M. cynos, M. canis, B. brochiseptica, CAdV-2, CHV-1, CPIV, CDV, CIA and CRCoV, respectively; and 3, 2, 6, 17, 4 and 8 copies per microliter for CAdV-2, CHV-1, CPIV, CDV, CIA and CRCoV, respectively, when RNA templates were used for the four RNA viruses. No cross-detection was observed among the nine pathogens. For the 740 clinical samples tested, the newly designed PCR assay showed higher diagnostic sensitivity compared to an older panel assay; pathogen identities from selected samples positive by the new assay but undetected by the older assay were confirmed by Sanger sequencing. Our data showed that the new assay has higher diagnostic sensitivity while maintaining the assay's specificity, as compared to the older version of the panel assay.

An emerging orthopneumovirus detected from dogs with canine infectious respiratory disease in China

Canine infectious respiratory disease (CIRD) is a major cause of morbidity in dogs and is associated with several viral pathogens. The viral diversity associated with CIRD was investigated by analyzing the viral communities from nine CIRD-affected dogs using metagenomics. The results identified 10 mammalian viruses, including canine parvovirus, canid alphaherpesvirus 1, canine kobuvirus, Felis catus papillomavirus 3, canine respiratory coronavirus, canine adenovirus 2, Canis familiaris polyomavirus (DogPyV), canine coronavirus, human papillomavirus and canine pneumovirus (CPnV). Interestingly, CPnV and DogPyV were first discovered in China. Further investigation in 107 samples in China using specific PCR found only two CPnV positive strains in 51 CIRD samples and none in 56 healthy samples. Furthermore, a complete nucleotide sequence of CPnV strain SMU-2020-CB19 and a partial nucleotide sequence of strain SMU-2020-CB14 were obtained. Sequence comparisons and phylogenetic analysis showed that both novel CPnV strains were a close match to the detected swine orthopneumovirus strain in USA, but distantly related to other CPnV strains. Here, the first discovery and characterization of orthopneumovirus in dogs with CIRD in China were reported, highlighting the need for further research on pathogenicity and transmission in China.

A molecular survey of canine respiratory viruses in New Zealand

AIMS

The aim of this study was to identify viruses associated with canine infectious respiratory disease syndrome (CIRDS) among a population of New Zealand dogs.

METHODS

Convenience samples of oropharyngeal swabs were collected from 116 dogs, including 56 CIRDS-affected and 60 healthy dogs from various locations in New Zealand between March 2014 and February 2016. Pooled samples from CIRDS-affected (n = 50) and from healthy (n = 50) dogs were tested for the presence of canine respiratory viruses using next generation sequencing (NGS). Individual samples (n = 116) were then tested by quantitative PCR (qPCR) and reverse transcriptase qPCR (RT-qPCR) for specific viruses. Groups were compared using Fisher's exact or χ² tests. The effect of explanatory variables (age, sex, type of household, presence of viral infection) on the response variable (CIRDS-affected or not) was tested using RR.

RESULTS

Canine pneumovirus (CnPnV), canine respiratory coronavirus (CRCoV), canine herpesvirus-1 (CHV-1), canine picornavirus and influenza C virus sequences were identified by NGS in the pooled sample from CIRDS-affected but not healthy dogs. At least one virus was detected by qPCR/RT-qPCR in 20/56 (36%) samples from CIRDS dogs and in 23/60 (38%) samples from healthy dogs (p = 0.84). CIRDS-affected dogs were most commonly positive for CnPnV (14/56, 25%) followed by canine adenovirus-2 (CAdV-2, 5/56, 9%), canine parainfluenza virus (CpiV) and CHV-1 (2/56, 4% each), and CRCoV (1/56, 2%). Only CnPnV (17/60, 28%) and CAdV-2 (14/60, 23%) were identified in samples from healthy dogs, and CAdV-2 was more likely to be detected healthy than diseased dogs (RR 0.38; 95% CI = 0.15-0.99; p = 0.045).

CONCLUSIONS

The frequency of detection of viruses traditionally linked to CIRDS (CAdV-2 and CPiV) among diseased dogs was low. This suggests that other pathogens are likely to have contributed to development of CIRDS among sampled dogs. Our data represent the first detection of CnPnV in New Zealand, but the role of this virus in CIRDS remains unclear. On-going monitoring of canine respiratory pathogens by NGS would be beneficial, as it allows rapid detection of novel viruses that may be introduced to the New Zealand canine population in the future. Such monitoring could be done using pooled samples to minimise costs.

CLINICAL RELEVANCE

Testing for novel respiratory viruses such as CnPnV and CRCoV should be considered in all routine laboratory investigations of CIRDS cases, particularly in dogs vaccinated with currently available kennel cough vaccines.

Asymptomatic carriage of canine infectious respiratory disease complex pathogens among healthy dogs

OBJECTIVES

The objectives of this study were to determine the prevalence of canine infectious respiratory disease pathogens among asymptomatic client-owned dogs, and to compare the risks of asymptomatic pathogen carriage between client-owned dogs and dogs in an animal shelter.

MATERIALS AND METHODS

Pooled tonsillar, conjunctival and nasal cavity swabs from asymptomatic client-owned dogs (n=133) were tested using a real-time polymerase chain reaction canine respiratory panel. Identical samples from asymptomatic dogs in an animal shelter (n=295) were similarly tested for selected pathogens. Risk differences were calculated between client-owned dogs and shelter dogs for each of the respiratory pathogens included in the analyses.

RESULTS

A total of 15 of 133 (11.3%) asymptomatic client-owned dogs were positive for at least one pathogen in the complex. Seven dogs (6.1%) were positive for M. cynos, six (5.2%) were positive for B. bronchiseptica, two (1.7%) were positive for canine herpesvirus type 1 and two (1.7%) were positive for canine respiratory coronavirus. For all eight pathogens tested in both groups, the proportion of positive cases was higher among shelter dogs than among client-owned dogs. Shelter dogs had a higher risk for M. cynos (0.18, 95% confidence interval: 0.12 to 0.25), canine respiratory coronavirus (0.15, 95% confidence interval: 0.10 to 0.19), canine distemper virus (0.06, 95% confidence interval: 0.03 to 0.09), and canine pneumovirus (0.05, 95% confidence interval: 0.03 to 0.08) than client-owned dogs. Odds ratios for M. cynos (0.31, 95% confidence interval: 0.08 to 0.92) and canine respiratory coronavirus (0.05, 95% confidence interval: 0.01 to 0.18) were significantly different between client-owned and shelter dogs. In all cases except for canine herpesvirus type 1, dogs within the shelter population were observed to be at higher risk of exhibiting asymptomatic carriage of a respiratory pathogen as compared to client-owned dogs. The strength of this association was strongest for M. cynos and canine respiratory coronavirus.

CLINICAL SIGNIFICANCE

The risk of canine infectious respiratory disease pathogen exposure posed by asymptomatic client-owned dogs is poorly defined. This study also corroborates previous reports of high canine infectious respiratory disease prevalence among clinically healthy shelter dogs, and further determined that the overall prevalence of canine infectious respiratory disease pathogen carriage among clinically healthy client-owned dogs is low but is highest for the traditional pathogen B. bronchiseptica and the emerging pathogen M. cynos.