Whole genome sequence analysis of equid gammaherpesvirus -2 field isolates reveals high levels of genomic diversity and recombination
Abstract Background Equid gammaherpesvirus 2 (EHV2) is a gammaherpesvirus with a widespread distribution in horse populations globally. Although its pathogenic significance can be unclear in most cases of infection, EHV2 infection can cause upper respiratory tract disease in foals. Co-infection of d...
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| Format: | Article |
| Language: | English |
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BMC
2022-08-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-022-08789-x |
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| author | Adepeju E. Onasanya Charles El-Hage Andrés Diaz-Méndez Paola K. Vaz Alistair R. Legione Glenn F. Browning Joanne M. Devlin Carol A. Hartley |
| author_facet | Adepeju E. Onasanya Charles El-Hage Andrés Diaz-Méndez Paola K. Vaz Alistair R. Legione Glenn F. Browning Joanne M. Devlin Carol A. Hartley |
| author_sort | Adepeju E. Onasanya |
| collection | DOAJ |
| description | Abstract Background Equid gammaherpesvirus 2 (EHV2) is a gammaherpesvirus with a widespread distribution in horse populations globally. Although its pathogenic significance can be unclear in most cases of infection, EHV2 infection can cause upper respiratory tract disease in foals. Co-infection of different strains of EHV2 in an individual horse is common. Small regions of the EHV2 genome have shown considerable genetic heterogeneity. This could suggest genomic recombination between different strains of EHV2, similar to the extensive recombination networks that have been demonstrated for some alphaherpesviruses. This study examined natural recombination and genome diversity of EHV2 field isolates. Results Whole genome sequencing analysis of 18 EHV2 isolates, along with analysis of two publicly available EHV2 genomes, revealed variation in genomes sizes (from 173.7 to 184.8 kbp), guanine plus cytosine content (from 56.7 to 57.8%) and the size of the terminal repeat regions (from 17,196 to 17,551 bp). The nucleotide sequence identity between the genomes ranged from 86.2 to 99.7%. The estimated average inter-strain nucleotide diversity between the 20 EHV2 genomes was 2.9%. Individual gene sequences showed varying levels of nucleotide diversity and ranged between 0 and 38.1%. The ratio of nonsynonymous substitutions, Ka, to synonymous substitutions, Ks, (Ka/Ks) suggests that over 50% of EHV2 genes are undergoing diversifying selection. Recombination analyses of the 20 EHV2 genome sequences using the recombination detection program (RDP4) and SplitsTree revealed evidence of viral recombination. Conclusions Analysis of the 18 new EHV2 genomes alongside the 2 previously sequenced genomes revealed a high degree of genetic diversity and extensive recombination networks. Herpesvirus genome diversification and virus evolution can be driven by recombination, and our findings are consistent with recombination being a key mechanism by which EHV2 genomes may vary and evolve. |
| first_indexed | 2024-04-14T01:46:37Z |
| format | Article |
| id | doaj.art-1c91af8f6fa746ef993d00f8199daf3b |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-14T01:46:37Z |
| publishDate | 2022-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-1c91af8f6fa746ef993d00f8199daf3b2022-12-22T02:19:31ZengBMCBMC Genomics1471-21642022-08-0123111910.1186/s12864-022-08789-xWhole genome sequence analysis of equid gammaherpesvirus -2 field isolates reveals high levels of genomic diversity and recombinationAdepeju E. Onasanya0Charles El-Hage1Andrés Diaz-Méndez2Paola K. Vaz3Alistair R. Legione4Glenn F. Browning5Joanne M. Devlin6Carol A. Hartley7Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The Asia-Pacific Centre for Animal Health, The University of MelbourneMelbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The Asia-Pacific Centre for Animal Health, The University of MelbourneMelbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The Asia-Pacific Centre for Animal Health, The University of MelbourneMelbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The Asia-Pacific Centre for Animal Health, The University of MelbourneMelbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The Asia-Pacific Centre for Animal Health, The University of MelbourneMelbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The Asia-Pacific Centre for Animal Health, The University of MelbourneMelbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The Asia-Pacific Centre for Animal Health, The University of MelbourneMelbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The Asia-Pacific Centre for Animal Health, The University of MelbourneAbstract Background Equid gammaherpesvirus 2 (EHV2) is a gammaherpesvirus with a widespread distribution in horse populations globally. Although its pathogenic significance can be unclear in most cases of infection, EHV2 infection can cause upper respiratory tract disease in foals. Co-infection of different strains of EHV2 in an individual horse is common. Small regions of the EHV2 genome have shown considerable genetic heterogeneity. This could suggest genomic recombination between different strains of EHV2, similar to the extensive recombination networks that have been demonstrated for some alphaherpesviruses. This study examined natural recombination and genome diversity of EHV2 field isolates. Results Whole genome sequencing analysis of 18 EHV2 isolates, along with analysis of two publicly available EHV2 genomes, revealed variation in genomes sizes (from 173.7 to 184.8 kbp), guanine plus cytosine content (from 56.7 to 57.8%) and the size of the terminal repeat regions (from 17,196 to 17,551 bp). The nucleotide sequence identity between the genomes ranged from 86.2 to 99.7%. The estimated average inter-strain nucleotide diversity between the 20 EHV2 genomes was 2.9%. Individual gene sequences showed varying levels of nucleotide diversity and ranged between 0 and 38.1%. The ratio of nonsynonymous substitutions, Ka, to synonymous substitutions, Ks, (Ka/Ks) suggests that over 50% of EHV2 genes are undergoing diversifying selection. Recombination analyses of the 20 EHV2 genome sequences using the recombination detection program (RDP4) and SplitsTree revealed evidence of viral recombination. Conclusions Analysis of the 18 new EHV2 genomes alongside the 2 previously sequenced genomes revealed a high degree of genetic diversity and extensive recombination networks. Herpesvirus genome diversification and virus evolution can be driven by recombination, and our findings are consistent with recombination being a key mechanism by which EHV2 genomes may vary and evolve.https://doi.org/10.1186/s12864-022-08789-xEquid gammaherpesvirus 2EHV2RecombinationGenome sequenceDiversity |
| spellingShingle | Adepeju E. Onasanya Charles El-Hage Andrés Diaz-Méndez Paola K. Vaz Alistair R. Legione Glenn F. Browning Joanne M. Devlin Carol A. Hartley Whole genome sequence analysis of equid gammaherpesvirus -2 field isolates reveals high levels of genomic diversity and recombination BMC Genomics Equid gammaherpesvirus 2 EHV2 Recombination Genome sequence Diversity |
| title | Whole genome sequence analysis of equid gammaherpesvirus -2 field isolates reveals high levels of genomic diversity and recombination |
| title_full | Whole genome sequence analysis of equid gammaherpesvirus -2 field isolates reveals high levels of genomic diversity and recombination |
| title_fullStr | Whole genome sequence analysis of equid gammaherpesvirus -2 field isolates reveals high levels of genomic diversity and recombination |
| title_full_unstemmed | Whole genome sequence analysis of equid gammaherpesvirus -2 field isolates reveals high levels of genomic diversity and recombination |
| title_short | Whole genome sequence analysis of equid gammaherpesvirus -2 field isolates reveals high levels of genomic diversity and recombination |
| title_sort | whole genome sequence analysis of equid gammaherpesvirus 2 field isolates reveals high levels of genomic diversity and recombination |
| topic | Equid gammaherpesvirus 2 EHV2 Recombination Genome sequence Diversity |
| url | https://doi.org/10.1186/s12864-022-08789-x |
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