Genomic diversity and natural recombination of equid gammaherpesvirus 5 isolates

Adepeju E Onasanya; Charles El-Hage; Andrés Diaz-Méndez; Paola K Vaz; Alistair R Legione; Joanne M Devlin; Carol A Hartley

doi:10.1016/j.meegid.2023.105517

Genomic diversity and natural recombination of equid gammaherpesvirus 5 isolates

Infect Genet Evol. 2023 Nov:115:105517. doi: 10.1016/j.meegid.2023.105517. Epub 2023 Oct 23.

Authors

Adepeju E Onasanya¹, Charles El-Hage², Andrés Diaz-Méndez¹, Paola K Vaz¹, Alistair R Legione¹, Joanne M Devlin³, Carol A Hartley⁴

Affiliations

¹ The Asia-Pacific Centre for Animal Health, Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia.
² Centre for Equine Infectious Disease, Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia.
³ The Asia-Pacific Centre for Animal Health, Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia. Electronic address: devlinj@unimelb.edu.au.
⁴ The Asia-Pacific Centre for Animal Health, Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia; Centre for Equine Infectious Disease, Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia.

PMID: 37879385
DOI: 10.1016/j.meegid.2023.105517

Abstract

Background: Equid gammaherpesvirus 5 (EHV5) is closely related to equid gammaherpesvirus 2 (EHV2). Detection of EHV5 is frequent in horse populations worldwide, but it is often without a clear and significant clinical impact. Infection in horses can often present as subclinical disease; however, it has been associated with respiratory disease, including equine multinodular pulmonary fibrosis (EMPF). Genetic heterogeneity within small regions of the EHV5 glycoprotein B (gB) sequences have been reported and multiple genotypes of this virus have been identified within individual horses, but full genome sequence data for these viruses is limited. The primary focus of this study was to assess the genomic diversity and natural recombination among EHV5 isolates.

Results: The genome size of EHV5 prototype strain and the five EHV5 isolates cultured for this study, including four isolates from the same horse, ranged from 181,929 to 183,428 base pairs (bp), with the sizes of terminal repeat regions varying from 0 to 10 bp. The nucleotide sequence identity between the six EHV5 genomes ranged from 95.5 to 99.1%, and the estimated average nucleotide diversity between isolates was 1%. Individual genes displayed varying levels of nucleotide diversity that ranged from 0 to 19%. The analysis of nonsynonymous substitution (Ka > 0.025) revealed high diversity in eight genes. Genome analysis using RDP4 and SplitsTree programs detected evidence of past recombination events between EHV5 isolates.

Conclusion: Genomic diversity and recombination hotspots were identified among EHV5 strains. Recombination can drive genetic diversity, particularly in viruses that have a low rate of nucleotide substitutions. Therefore, the results from this study suggest that recombination is an important contributing factor to EHV5 genomic diversity. The findings from this study provide additional insights into the genetic heterogeneity of the EHV5 genome.

Keywords: Equid herpesvirus 5; Equine gammaherpesvirus; Full genome sequencing; Genetic diversity; Recombination.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Genomics
Herpesviridae Infections* / veterinary
Horse Diseases*
Horses
Nucleotides
Phylogeny
Recombination, Genetic

Substances

Nucleotides

Supplementary concepts

Equid gammaherpesvirus 5