Identification of a novel equine rhinitis B virus detected in horse from Japan.

Overview

• This study discovered a novel and genetically distinct strain of equine rhinitis B virus (ERBV) in a horse from Japan through metagenomic analysis.
• The research highlights the genetic uniqueness of this ERBV strain and the development of updated molecular diagnostic tools for improved detection and epidemiological monitoring.

Background on Equine Rhinitis B Virus (ERBV)

• ERBV is a member of the Picornaviridae virus family, known to cause mild to moderate respiratory illness in horses.
• The virus’s genomic diversity and the full scope of its variants are not yet fully characterized, which limits understanding of its epidemiology and pathogenicity.

Research Methods

• Metagenomic analysis was performed on a rectal swab sample from a diarrheic foal already diagnosed with rotavirus A infection.
• The goal was to explore possible co-infections or unknown pathogens present in the sample.

Key Findings

• A novel and highly divergent ERBV strain was identified unexpectedly, which had a genome size of 9,448 nucleotides encoding a polyprotein of 2,721 amino acids.
• Comparative sequence analysis revealed:
  • Only 62.5-63.1% nucleotide identity in the polyprotein region compared to known ERBV serotypes.
  • Only 47.1-49.8% identity in the VP1 region, a key viral capsid protein, indicating it is genetically distinct and likely represents a new genotype.
• The genome showed typical picornavirus elements, such as a type II internal ribosome entry site (IRES), which is important for viral protein translation.
• Unique genomic features included:
  • An 87-amino-acid insertion in the leader proteinase (Lpro) region, which is uncommon in known ERBV strains.
  • Atypical cleavage motifs that differ from previously described ERBVs, which may affect how the viral polyprotein is processed.

Development of Diagnostic Tools

• A strain-specific real-time quantitative PCR (RT-qPCR) assay was developed to detect this novel ERBV strain precisely.
• Additionally, a broad-range assay targeting known ERBV types 1–3 was created for comparison.
• These assays were used to screen 37 rectal swab samples from horses:
• 10.8% of samples tested positive with the newly developed specific assay.
• Infections clustered temporally and spatially, particularly among horses from the same farm in 2022, with a recurring positive case identified in 2024.
• No positives were identified using the broad-range primers, suggesting that the existing broad assays may miss some genetically divergent ERBV strains.

Significance and Implications

• The discovery of a new ERBV genotype expands knowledge of the genetic diversity and evolution of equine picornaviruses.
• Metagenomics proved to be a powerful approach for pathogen discovery, revealing viral sequences that standard targeted tests could miss.
• The findings highlight gaps in current molecular surveillance tools, which may fail to detect novel or divergent strains of ERBV circulating in horse populations.
• Improved diagnostic assays enable better monitoring of ERBV infections, which is important for understanding clinical impacts, controlling outbreaks, and guiding equine health management.

Conclusions

• This study successfully identified and characterized a previously unrecognized ERBV strain with distinct genetic features.
• It calls for ongoing genomic surveillance using advanced molecular techniques to detect and monitor emerging viral variants in horses.
• Updated diagnostic assays tailored to novel genotypes are essential for accurate detection and epidemiological assessment in veterinary medicine.