Sequence variation divides Equine rhinitis B virus into three distinct phylogenetic groups that correlate with serotype and acid stability

Characterization of Equine Rhinitis B Virus Infection in Clinically Ill Horses in the United States during the Period 2012-2023

Equine rhinitis B virus is a lesser-known equine respiratory pathogen that is being detected with increasing frequency via a voluntary upper respiratory biosurveillance program in the United States. This program received 8684 nasal swab submissions during the years 2012-2023. The nasal swabs were submitted for qPCR testing for six common upper respiratory pathogens: Streptococcus equi subspecies equi (S. equi), equine influenza virus (EIV), equine herpesvirus type 1 (EHV-1), equine herpesvirus type 4 (EHV-4), equine rhinitis A virus (ERAV), and equine rhinitis B virus (ERBV). The overall ERBV qPCR-positivity rate was 5.08% (441/8684). ERBV was detected as a single pathogen in 291 cases (65.99% of positives, 291/441) and was detected as a coinfection with at least one other respiratory pathogen in 150 cases (34.01%, 150/441). Young horses, less than a year of age, with acute onset of fever and respiratory signs and horses used for competition are more likely to test qPCR-positive for ERBV. Horses with ERBV may present with fever, nasal discharge, ocular discharge, and/or cough. Coinfection is a common feature of ERBV infection and S. equi, EHV-4 and EIV were the most common pathogens coinfected with ERBV. This report provides important information regarding the clinical relevance of ERBV in the horse and begins investigating the impact of coinfection on clinical disease.

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.

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.

Genomic analysis of a Canadian equine rhinitis A virus reveals low diversity among field isolates

Equine rhinitis A virus (ERAV) is an ubiquitous virus, routinely identified in equine respiratory infections; however, its role in disease and genetic features are not well defined due to a lack of genomic characterization of the recovered isolates. Therefore, we sequenced the full-length genome of a Canadian ERAV (ERAV/ON/05) and compared it with other ERAV sequences currently available in GenBank. The ERAV/ON/05 genome is 7,839 nucleotides (nts) in length with a variable 5'UTR and a more conserved 3'UTR. When ERAV/ON/05 was compared to other reported ERAV isolates, an insertion of 13 nt in the 5'UTR was identified. Further phylogenetic analysis demonstrated that ERAV/ON/05 is closely related to the ERAV/PERV isolate, which was isolated in 1962 in the United Kingdom. The polyprotein of ERAV/ON/05 had a 96 % nucleotide and amino acid sequence identity to reported ERAVs, and it appears that, despite the high error rate of RNA-dependent RNA polymerase, this isolate has retained high sequence identity to the strain first described by Plummer in 1962.

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.

Mapping B-cell epitopes in equine rhinitis B viruses and identification of a neutralising site in the VP1 C-terminus

Erbovirus is a genus of the family Picornaviridae and equine rhinitis B virus (ERBV) is the sole species. Erboviruses infect horses causing acute respiratory disease and sub-clinical and persistent infections. Despite the high seroprevalence and worldwide distribution of these viruses, the pathogenesis and antigenic structure of the three ERBV serotypes (ERBV1, 2 and 3) is poorly understood. To characterise linear epitopes on ERBV structural proteins, a set of fusion proteins were expressed in Escherichia coli. These proteins were tested in Western blot and ELISA and reactive proteins were also used to identify neutralisation epitopes. VP1 contained serotype specific epitopes whereas VP2 was highly cross-reactive across the serotypes. The C-terminus of VP1 accounted for most of the reactivity of full-length VP1 and was also the location of a neutralising site in each serotype.

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

REASONS FOR PERFORMING STUDY

Equine rhinitis viruses (ERV) cause respiratory disease and loss of performance in horses. It has been suggested that the economic significance of these viruses may have been underestimated due to insensitive methods of detection.

OBJECTIVES

To develop a sensitive, rapid, real-time RT-PCR (rRT-PCR) assay suitable for the routine diagnosis and epidemiological surveillance of the A and B variants of ERV.

METHODS

TaqMan primer probe sets for ERAV and ERBV were designed from conserved regions of the 5' UTR of the ERV genome. Over 400 samples from both clinically affected and asymptomatic horses were employed for validation of the assays. ERAV samples positive by rRT-PCR were verified by virus isolation and ERBV positive samples were verified by rRT-PCR using a different set of primers.

RESULTS

The detection limit of the rRT-PCR for both viruses was 10-100 genome copies. Of 250 archival nasal swabs submitted for diagnostic testing over a 7 year period, 29 were ERAV positive and 3 were ERBV positive with an average incidence rate per year of 10 and 1.5%, respectively. There was evidence of co-circulation of ERAV and ERBV with equine influenza virus (EIV). Of 100 post race urine samples tested, 29 were ERAV positive by rRT-PCR. Partial sequencing of 2 ERBV positive samples demonstrated that one was 100% identical to ERBV1 from a 270 bp sequence and the other was more closely related to ERBV2 than ERBV1 (95% compared to 90% nucleotide identity in 178 bp).

CONCLUSIONS

The rRT-PCR assays described here are specific and more sensitive than virus isolation. They have good reproducibility and are suitable for the routine diagnosis of ERAV and ERBV.

POTENTIAL RELEVANCE

These assays should be useful for investigating the temporal association between clinical signs and rhinitis virus shedding.

Virion associated proteins of equine rhinitis B virus 1 (ERBV1): the non-structural protein 3C(pro) co-purifies with virions

Equine rhinitis B virus (ERBV), genus Erbovirus, is most closely related to the Cardiovirus genus in the family Picornaviridae. The structural proteins (VP1-4) of erboviruses are not well described, but are predicted by sequence to be 35, 29, 26 and 7 kDa. Methods for the purification of cardioviruses (polyethylene glycol, trypsin treatment) were used to characterise the structural proteins of ERBV1. Only one of the virus proteins detected was an expected molecular mass, and this 26 kDa protein was identified as VP3 by N-terminal amino acid sequencing. N-terminal sequencing of the 56 and a 29 kDa protein identified sequences consistent with VP2 and VP1 respectively, despite these being 27 kDa larger and 6 kDa smaller than predicted. Virus purified without trypsin showed proteins more consistent with masses predicted for VP1, VP2 and VP3 at 35, 29 and 26 kDa respectively. These proteins were further identified with antibodies affinity purified to recombinant VP1, VP2, VP3 produced in E. coli. Interestingly, antibodies affinity purified to the non-structural protein 3C(pro), produced in insect cells, strongly detected a 27 kDa protein in western blots of virus purified with and without trypsin treatment, suggesting the non-structural 27 kDa 3C(pro) co-purifies with ERBV1 virions.

Development of a real-time duplex TaqMan-PCR for the detection of Equine rhinitis A and B viruses in clinical specimens

Equine rhinitis A and B viruses (ERAV and ERBV) are respiratory viruses of horses belonging to the family Picornaviridae. Although these viruses are considered to cause respiratory disease in horses and are potentially infectious for humans, little is known about their prevalence and pathogenesis. Virus isolation is often unsuccessful due to their inefficient growth and lack of cytopathic effect in cell cultures. Therefore, molecular assays should be considered as the method of choice to detect infection in symptomatic or apparently healthy horses. In the present study, a novel real-time duplex PCR was developed for the detection and differentiation of both ERAV and ERBV. The method was evaluated for its ability to detect viral RNA in cell culture supernatants and nasal swabs, and lung and urine spiked with known quantities of virus. The assay demonstrated high analytical specificity, sensitivity and good reproducibility, with coefficients of variation (CV%) ranging from 1% to 7.4% and from 1.2% to 12% for intra- and inter-assay variability respectively. The assay detected ERBV in 14 of 86 nasal swabs collected from horses with respiratory disease. The real-time duplex PCR is a useful new diagnostic method for the rapid detection and differentiation of ERAV and ERBV.

Denatured virion protein 1 of equine rhinitis B virus 1 contains authentic B-cell epitopes recognised in an enzyme-linked immunosorbent assay--short communication

Equine rhinitis B virus 1 (ERBV1), genus Erbovirus, family Picornaviridae, is a pathogen of horses which causes clinical and subclinical infection of the upper respiratory tract in horses. The virus is widespread in European horse populations and the current standard method for the detection of antibody against ERBV1 is by virus neutralisation (VN). VN tests, however, are labour-intensive and time-consuming, require tissue culture facilities, and generally do not provide same-day results. In this study, a protocol for the high-level expression and purification of recombinant virion protein 1 (rVP1) was established using metal-chelate affinity chromatography under denaturing condition. When used as a coating antigen in a prototype enzyme-linked immunosorbent assay (ELISA), denatured rVP1 was recognised by ERBV1 antibody present in horse serum. This finding suggests that denatured rVP1 is a promising candidate for the development of an ELISA to be used in the routine laboratory diagnosis of ERBV1 infection in horses.

Sequence analysis of a duck picornavirus isolate indicates that it together with porcine enterovirus type 8 and simian picornavirus type 2 should be assigned to a new picornavirus genus

In a 1990 outbreak, a virus isolated in Taiwan from the intestines of ducks showing signs of hepatitis was tentatively classified as a picornavirus on the basis of physical, chemical, and morphological characteristics. The virus was cloned and then found not to be type 1 duck hepatitis virus (DHV-1) or a new serotype of duck hepatitis virus (N-DHV) by serum neutralization. Complete genome sequencing indicated that the virus genome had 8351 nucleotides and the typical picornavirus genome organization (i.e., 5' untranslated region (UTR)-L-P1 (VP 4-2-3-1)-P2 (2A-B-C)-P3 (3A-B-C-D)-3' UTR-poly A). One open reading frame encoded 2521 amino acids, which makes this virus one of the largest picornaviruses, second only to equine rhinitis B virus of the genus Erbovirus. Its L protein was the largest within the family Picornaviridae (451 amino acids) and suspected to be a trypsin-like protease. The 235-nucleotide 3' UTR region was of intermediate size, quite long compared to other picornaviruses but shorter than other picornaviruses of duck-origin (DHV-1 and N-DHV) and had four regions of secondary structure. The 2A protein was composed of only 12 amino acids, which is the shortest of any member of the family Picornaviridae. Phylogenetic analysis of the polyprotein and 3D sequences indicated that this virus (named duck picornavirus [DPV]) together with porcine enterovirus type 8 virus and several simian picornaviruses form a distinct branch of the family Picornaviridae and should be assigned to a new picornavirus genus.

Detection of viruses in nasal swab samples from horses with acute, febrile, respiratory disease using virus isolation, polymerase chain reaction and serology

OBJECTIVE

To examine the association of viruses with acute febrile respiratory disease in horses. Design Nasal swab and serum samples were collected from 20 horses with acute febrile upper respiratory disease that was clinically assessed to have a viral origin.

METHODS

Each of the samples was inoculated onto equine fetal kidney, RK13 and Vero cell cultures, and viral nucleic acid was extracted for polymerase chain reaction (PCR) or reverse transcription PCR. PCR primers were designed to amplify nucleic acid from viruses known to cause or be associated with acute febrile respiratory disease in horses in Australia. A type specific ELISA was used to measure equine herpesvirus (EHV1 and EHV4) antibody, and serum neutralisation assays were used to measure equine rhinitis A virus (ERAV) and equine rhinitis B virus 1 and 2 (ERBV1 and ERBV2) antibody titres in serum samples.

RESULTS

Virus was isolated from 4 of 20 nasal swab samples. There were three isolations of EHV4 and one of ERBV2. By PCR, virus was identified in the nasal swab samples of 12 of the 20 horses. Of the 12 horses [corrected] that were positive, 17 viruses were detected as follows: there was [corrected] one triple positive (EHV4, EHV2, and EHV5), three double positives (EHV4, ERBV and EHV5, ERBV (2 horses)) and 8 [corrected] single positives (EHV4 (2 horses), EHV5 (3 horses) and ERBV (3 [corrected] horses).

CONCLUSION

By virus isolation and PCR, 17 viruses were identified in nasal swab samples from 12 of 20 horses that had acute febrile respiratory disease consistent with a diagnosis of virus infection. Initial PCR identification and subsequent virus isolation led to the isolation of ERBV2 for the first time in Australia and the second time anywhere of ERBV2.

Prevalence of serum neutralising antibody to equine rhinitis A virus (ERAV), equine rhinitis B virus 1 (ERBV1) and ERBV2

The objective of this study was to determine the incidence of serum neutralising (SN) antibody to ERAV, ERBV1 and ERBV2 in a population of horses from birth to 22 years of age. The prevalences of ERAV, ERBV1 and ERBV2 SN antibodies in 381 sera obtained from 291 horses were 37%, 83% and 66%, respectively. ERAV, ERBV1 and ERBV2 maternal antibody was present in foals 12 h postsuckling but by 10-12 months, ERAV SN antibody was not detected in any of the horses, while ERBV1 and ERBV2 SN antibodies were common (83% and 100%, respectively). Sera were obtained from 44 Thoroughbred horses when they were newly introduced into a training centre when their average age was 23 months and a second sample was obtained approximately 7 months later. ERAV SN antibody was present in 8 (18%) when first bled and in 27 (61%) when tested 7 months later. Accordingly 19 of the 44 horses (43%) seroconverted to ERAV within 7 months of entering the training stable. Among all the horses the average ERAV SN antibody titre was relatively high (3796) and in contrast, ERBV1 and ERBV2 titres were relatively low (average 84 and 45, respectively) and often fell to below detectable levels over time and at a rate comparable to new seroconversions in the same group of horses.

Reverse transcriptase-polymerase chain reaction for the detection equine rhinitis B viruses and cell culture isolation of the virus

Equine rhinitis B virus (ERBV), genus Erbovirus, family Picornaviridae occurs as two serotypes, ERBV1 and ERBV2. An ERBV-specific nested reverse transcriptase-polymerase chain reaction (RT-PCR) that amplified a product within the 3D(pol) and 3' non-translated region of the viral genome was developed. The RT-PCR detected all 24 available ERBV1 isolates and one available ERBV2 isolate. The limit of detection for the prototype strain ERBV1.1436/71 was 0.1 50% tissue culture infectious doses. The RT-PCR was used to detect viral RNA in six of 17 nasopharyngeal swab samples from horses that had clinical signs of acute febrile respiratory disease but from which ERBV was not initially isolated in cell culture. The sequences of these six ERBV RT-PCR positive samples had 93-96% nucleotide identity with six other partially sequenced ERBV1 isolates and one ERBV2. ERBV was isolated from one of the six samples at fourth cell culture passage when it was shown that the addition of 20 mg/mL MgCl(2) to the cell culture medium enhanced the growth of the virus. This isolated virus was antigenically similar to ERBV2.313/75. Determination of the nucleotide sequence of the P1 region of the genome also indicated that the isolate was ERBV2, and it was therefore designated ERBV2.1576/99. This is the first reported isolation of ERBV in Australia. The study highlights the utility of PCR for the identification of viruses in clinical samples that may initially be considered negative by conventional cell culture isolation.

Formerly unclassified, acid-stable equine picornaviruses are a third equine rhinitis B virus serotype in the genus Erbovirus

Acid-stable equine picornaviruses (ASPs) were identified as a distinct serotype of equine picornaviruses that were isolated from nasal swabs taken from horses with acute febrile respiratory disease in the UK and Japan, and were placed in the group of unclassified picornaviruses. The nucleotide sequence of the P1 region, encoding the capsid proteins, was determined for three ASP isolates from the UK and the sequences were aligned with published sequences of Equine rhinitis B virus (ERBV), genus Erbovirus, including acid-labile ERBV1 and ERBV2 and the recently identified acid-stable ERBV1. The ASPs belong to the same phylogenetic group, composed of five acid-stable ERBV1 isolates. ERBV1 rabbit antiserum neutralized the ASP isolates at approximately 1/10 titre relative to acid-stable and acid-labile ERBV1 isolates, supporting prior findings that ASPs are a distinct serotype, albeit cross-neutralizing weakly with ERBV1. The genus Erbovirus therefore presently comprises three serotypes: ERBV1, ERBV2 and the proposed ERBV3.