Real-time RT-PCR for the detection and quantitative analysis of equine rhinitis viruses

What have we learned from 7 years of equine rhinitis B virus qPCR testing in nasal secretions from horses with respiratory signs

BACKGROUND

Equine rhinitis B virus (ERBV) has been given little attention by practitioners compared to other respiratory viruses, mainly because of the lack of diagnostic modalities and association with clinical disease. The objective of the study was to determine the frequency of detection of ERBV in nasal secretions from 6568 horses with acute onset of respiratory signs.

METHODS

ERBV-positive qPCR results from nasal secretions submitted to a molecular diagnostic laboratory from 2013 to 2019 were reviewed.

RESULTS

A total of 333 ERBV qPCR-positive samples (5.1%) were detected with increasing yearly frequency since the introduction of the assay in 2013. In comparison, only three of 356 (0.8%) healthy horses tested qPCR-positive for ERBV. Median age for ERBV qPCR-positive horses was 3 years of age, and fever, coughing and nasal discharge were the most common signs reported. Further, co-infections with other respiratory pathogens were reported in 73 (21.9%) of ERBV qPCR-positive samples.

CONCLUSION

ERBV is a commonly detected respiratory virus from nasal secretions of young horses presenting with fever, nasal discharge and coughing.

Equine Rhinitis A Virus Infection in Thoroughbred Racehorses-A Putative Role in Poor Performance?

The aim of this study was to identify respiratory viruses circulating amongst elite racehorses in a training yard by serological testing of serial samples and to determine their impact on health status and ability to race. A six-month longitudinal study was conducted in 30 Thoroughbred racehorses (21 two-year-olds, five three-year-olds and four four-year-olds) during the Flat racing season. Sera were tested for the presence of antibodies against equine herpesvirus 1 and 4 (EHV-1 and EHV-4) and equine rhinitis viruses A and B (ERAV and ERBV) by complement fixation (CF) and equine arteritis virus (EAV) by ELISA. Antibodies against equine influenza (EI) were measured by haemagglutination inhibition (HI). Only ERAV was circulating in the yard throughout the six-month study period. Seroconversion to ERAV frequently correlated with clinical respiratory disease and was significantly associated with subsequent failure to race (p = 0.0009). Over 55% of the two-year-olds in the study seroconverted to ERAV in May and June. In contrast, only one seroconversion to ERAV was observed in the older horses. They remained free of any signs of respiratory disease and raced successfully throughout the study period. The importance of ERAV as a contributory factor in the interruption of training programmes for young horses may be underestimated.

Multiple molecular detection of respiratory viruses and associated signs of airway inflammation in racehorses

Background

The potential involvement of viruses in inflammatory airway disease (IAD) was previously investigated through either serology or PCR from nasopharyngeal swabs (NS). The aims of this study were to determine the prevalence and incidence of viral genome detection by qPCR in the equine airways, and their association with respiratory clinical signs.

Methods

Both NS and tracheal washes (TW) were collected monthly on 52 Standardbred racehorses at training, over 27 consecutive months (581 samples). Equid herpesviruses (EHV)-1, −4, −2 and −5, equine rhinitis virus-A and -B (ERBV), equine adenovirus-1 and −2, equine coronavirus and equine influenza virus were systematically investigated in both NS and TW. Nasal discharge, coughing, tracheal mucus score and TW neutrophil proportions were simultaneously recorded.

Results

Genome for 7/10 viruses were detected at least once throughout the study; up to 4 different viruses being also concomitantly detected. Monthly incidence in TW was respectively 27.9% (EHV-5), 24.8% (EHV-2), 7.1% (ERBV), 3.8% (EHV-4), 1.9% (EAdV1) and 0.2% (EHV-1; ERAV). Neither agreement nor correlation between NS and TW was found for respectively genome detection and viral loads. Detection of viral genome in NS was not associated with any clinical sign. Coughing was significantly associated with TW detection of EHV-2 DNA (OR 3.1; P = 0.01) and ERBV RNA (OR 5.3; P < 0.001). Detection of EHV-2 DNA in TW was also significantly associated with excess tracheal mucus (OR 2.1; P = 0.02).

Conclusions

Detection and quantification of EHV-2 and ERBV by qPCR in TW, but not in NS, should be considered when investigating horses with IAD.

Electronic supplementary material

The online version of this article (doi:10.1186/s12985-016-0657-5) contains supplementary material, which is available to authorized users.

Equine rhinitis B viruses in horse fecal samples from the Middle East

Background

Among all known picornaviruses, only two species, equine rhinitis A virus and equine rhinitis B virus (ERBV) are known to infect horses, causing respiratory infections. No reports have described the detection of ERBV in fecal samples of horses and no complete genome sequences of ERBV3 are available.

Methods

We performed a molecular epidemiology study to detect ERBVs in horses from Dubai and Hong Kong. Complete genome sequencing of the ERBVs as well as viral loads and genome, phylogenetic and evolutionary analysis were performed on the positive samples.

Results

ERBV was detected in four (13.8 %) of the 29 fecal samples in horses from Dubai, with viral loads 8.28 × 10³ to 5.83 × 10⁴ copies per ml, but none of the 47 fecal samples in horses from Hong Kong by RT-PCR. Complete genome sequencing and phylogenetic analysis showed that three of the four strains were ERBV3 and one was ERBV2. The major difference between the genomes of ERBV3 and those of ERBV1 and ERBV2 lied in the amino acid sequences of their VP1 proteins. The Ka/Ks ratios of all the coding regions in the ERBV3 genomes were all <0.1, suggesting that ERBV3 were stably evolving in horses. Using the uncorrelated lognormal distributed relaxed clock model on VP1 gene, the date of the most recent common ancestor (MRCA) of ERBV3 was estimated to be 1785 (HPDs, 1176 to 1937) and the MRCA dates of ERBV1 and ERBV2 were estimated to be 1848 (HPDs, 1466 to 1949) respectively.

Conclusions

Both acid stable (ERBV3) and acid labile (ERBV2) ERBVs could be found in fecal samples of horses. Detection of ERBVs in fecal samples would have implications for their transmission and potential role in gastrointestinal diseases as well as fecal sampling as an alternative method of identifying infected horses.

Association between inflammatory airway disease of horses and exposure to respiratory viruses: a case control study

Background

Inflammatory airway disease (IAD) in horses, similar to asthma in humans, is a common cause of chronic poor respiratory health and exercise intolerance due to airway inflammation and exaggerated airway constrictive responses. Human rhinovirus is an important trigger for the development of asthma; a similar role for viral respiratory disease in equine IAD has not been established yet.

Methods

In a case–control study, horses with IAD (n = 24) were compared to control animals from comparable stabling environments (n = 14). Horses were classified using pulmonary function testing and bronchoalveolar lavage. PCR for equine rhinitis virus A and B (ERAV, ERBV), influenza virus (EIV), and herpesviruses 2, 4, and 5 (EHV-2, EHV-4, EHV-5) was performed on nasal swab, buffy coat from whole blood, and cells from BAL fluid (BALF), and serology were performed. Categorical variables were compared between IAD and control using Fisher’s exact test; continuous variables were compared with an independent t-test. For all analyses, a value of P <0.05 was considered significant.

Results

There was a significant association between diagnosis of IAD and history of cough (P = 0.001) and exercise intolerance (P = 0.003) but not between nasal discharge and IAD. Horses with IAD were significantly more likely to have a positive titer to ERAV (68 %) vs. control horses (32 %). Horses with IAD had higher log-transformed titers to ERAV than did controls (2.28 ± 0.18 v.1.50 ± 0.25, P = 0.038). There was a significant association between nasal shedding (positive PCR) of EHV-2 and diagnosis of IAD (P = 0.002).

Conclusions

IAD remains a persistent problem in the equine population and has strong similarities to the human disease, asthma, for which viral infection is an important trigger. The association between viral respiratory infection and development or exacerbation of IAD in this study suggests that viral infection may contribute to IAD susceptibility; there is, therefore, merit in further investigation into the relationship between respiratory virus exposure and development of IAD.

Seroprevalence study of Equine rhinitis B virus (ERBV) in Australian weanling horses using serotype-specific ERBV enzyme-linked immunosorbent assays

Respiratory infections are a major burden in the performance horse industry. Equine rhinitis B virus (ERBV) has been isolated from horses displaying clinical respiratory disease, and ERBV-neutralizing antibodies have been detected in 50-80% of horses in reported surveys. Current ERBV isolation and detection methods may underestimate the number of ERBV-positive animals and do not identify multiple serotype infections. The aim of the current study was to develop a serotyping ERBV antibody-detection enzyme-linked immunosorbent assay (ELISA) and examine the seroprevalence of ERBV in a group of Australian weanling horses. ELISAs with high sensitivity and specificity were developed. The seroprevalence of ERBV in the weanling horses was high (74-86%); ERBV-3 antibodies were most prevalent (58-62%) and ERBV-2 antibodies were least prevalent (10-16%). Many horses were seropositive to 2 or more serotypes. All 3 serotypes of ERBV were detected, and concurrent positivity to multiple serotypes was common.

A survey of respiratory viruses in New Zealand horses

AIMS

To determine which viruses circulate among selected populations of New Zealand horses and whether or not viral infections were associated with development of respiratory disease.

METHODS

Nasal swabs were collected from 33 healthy horses and 52 horses with respiratory disease and tested by virus isolation and/or PCR for the presence of equine herpesviruses (EHV) and equine rhinitis viruses.

RESULTS

Herpesviruses were the only viruses detected in nasal swab samples. When both the results of nasal swab PCR and virus isolation were considered together, a total of 41/52 (79%) horses with respiratory disease and 2/32 (6%) healthy horses were positive for at least one virus. As such, rates of virus detection were significantly higher (p<0.001) in samples from horses with respiratory disease than from healthy horses. More than half of the virus-positive horses were infected with multiple viruses. Infection with EHV-5 was most common (28 horses), followed by EHV-2 (27 horses), EHV-4 (21 horses) and EHV-1 (3 horses).

CONCLUSIONS

Herpesviruses were more commonly detected in nasal swabs from horses with respiratory disease than from healthy horses suggesting their aetiological involvement in the development of clinical signs among sampled horses. Further investigation to elucidate the exact relationships between these viruses and respiratory disease in horses is warranted.

CLINICAL RELEVANCE

Equine respiratory disease has been recognised as an important cause of wastage for the equine industry worldwide. It is likely multifactorial, involving complex interactions between different microorganisms, the environment and the host. Ability to control, or minimise, the adverse effects of equine respiratory disease is critically dependent on our understanding of microbial agents involved in these interactions. The results of the present study update our knowledge on the equine respiratory viruses currently circulating among selected populations of horses in New Zealand.

Development of one-step TaqMan® real-time reverse transcription-PCR and conventional reverse transcription-PCR assays for the detection of equine rhinitis A and B viruses

BACKGROUND

Equine rhinitis viruses A and B (ERAV and ERBV) are common equine respiratory viruses belonging to the family Picornaviridae. Sero-surveillance studies have shown that these two viral infections are prevalent in many countries. Currently, the diagnosis of ERAV and ERBV infections in horses is mainly based on virus isolation (VI). However, the sensitivity of VI testing varies between laboratories due to inefficient viral growth in cell culture and lack of cytopathic effect. Therefore, the objective of this study was to develop molecular diagnostic assays (real-time RT-PCR [rRT-PCR] and conventional RT-PCR [cRT-PCR] assays) to detect and distinguish ERAV from ERBV without the inherent problems traditionally associated with laboratory diagnosis of these infections.

RESULTS

Three rRT-PCR assays targeting the 5'-UTR of ERAV and ERBV were developed. One assay was specific for ERAV, with the two remaining assays specific for ERBV. Additionally, six cRT-PCR assays targeting the 5'-UTR and 3D polymerase regions of ERAV and ERBV were developed. Both rRT-PCR and cRT-PCR assays were evaluated using RNA extracted from 21 archived tissue culture fluid (TCF) samples previously confirmed to be positive for ERAV (n = 11) or ERBV (n = 10) with mono-specific rabbit antisera. The ERAV rRT-PCR and cRT-PCR assays could only detect ERAV isolates and not ERBV isolates. Similarly, the ERBV rRT-PCR and cRT-PCR assays could only detect ERBV isolates and not ERAV isolates. None of the rRT-PCR or cRT-PCR assays cross-reacted with any of the other common equine respiratory viruses. With the exception of one cRT-PCR assay, the detection limit of all of these assays was 1 plaque forming unit per ml (pfu/ml).

CONCLUSION

The newly developed rRT-PCR and cRT-PCR assays provide improved diagnostic capability for the detection and differentiation of ERAV and ERBV. However, a larger number of clinical specimens will need to be tested before each assay is adequately validated for the detection of ERAV and/or ERBV in suspect cases of either viral infection.