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Home / Equine Research Bank / BMC Genomics / Whole genome sequence analysis of equid gammaherpesvirus -2 ...
BMC genomics2022; 23(1); 622; doi: 10.1186/s12864-022-08789-x

Whole genome sequence analysis of equid gammaherpesvirus -2 field isolates reveals high levels of genomic diversity and recombination.

Abstract: 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.
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Publication Date: 2022-08-30 PubMed ID: 36042397PubMed Central: PMC9426266DOI: 10.1186/s12864-022-08789-xGoogle Scholar: Lookup
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  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The study focuses on equid gammaherpesvirus 2 (EHV2), a disease that is globally common in horses and occasionally results in upper respiratory tract issues in foals. By analyzing the genome sequencing of 18 EHV2 isolates, the study provides an in-depth look at the genetic diversity and viral recombination of EHV2.

Objectives of the Study

  • The primary aim was to investigate any possible recombination and diversity in the genomes of EHV2 field isolates.
  • The researchers intended to gain a deeper understanding of herpesvirus evolution patterns, especially concerning EHV2.

Methodology

  • The team conducted whole genome sequencing analysis on 18 EHV2 isolates, coupled with the analysis of two publicly available EHV2 genomes.
  • They noted variations in genome sizes, guanine plus cytosine content, and the size of terminal repeat regions.
  • They also evaluated the nucleotide sequence identity among the genomes.
  • Further, individual gene sequences were analyzed to identify varying levels of nucleotide diversity.
  • The researchers utilized the recombination detection program (RDP4) and SplitsTree for recombination analyses of the 20 EHV2 genome sequences.

Findings

  • The researchers discovered that genome sizes varied from 173.7 to 184.8 kbp, guanine plus cytosine content ranged from 56.7 to 57.8%, and the size of terminal repeat regions ranged between 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 among the 20 EHV2 genomes was determined to be 2.9%.
  • Individual gene sequences revealed varying levels of nucleotide diversity, with a range between 0 and 38.1%.
  • Over 50% of EHV2 genes are undergoing diversifying selection, as suggested by the ratio of nonsynonymous substitutions, Ka, to synonymous substitutions, Ks, (Ka/Ks).
  • Significant evidence of viral recombination was found through the recombination analyses.

Conclusion

  • The analysis of 18 fresh EHV2 genomes and 2 previously sequenced ones revealed a high degree of genetic diversity and extensive recombination networks.
  • It was observed that recombination can be a key mechanism driving herpesvirus genome diversification and virus evolution, consistent with the researchers’ findings.

Cite This Article

APA
Onasanya AE, El-Hage C, Diaz-Méndez A, Vaz PK, Legione AR, Browning GF, Devlin JM, Hartley CA. (2022). Whole genome sequence analysis of equid gammaherpesvirus -2 field isolates reveals high levels of genomic diversity and recombination. BMC Genomics, 23(1), 622. https://doi.org/10.1186/s12864-022-08789-x

Publication

BMC genomics
ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 23
Issue: 1
Pages: 622
PII: 622

Researcher Affiliations

Onasanya, Adepeju E
  • Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The Asia-Pacific Centre for Animal Health, The University of Melbourne, Parkville, VIC, 3010, Australia.
El-Hage, Charles
  • Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The Asia-Pacific Centre for Animal Health, The University of Melbourne, Parkville, VIC, 3010, Australia.
  • Centre for Equine Infectious Diseases, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
Diaz-Méndez, Andrés
  • Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The Asia-Pacific Centre for Animal Health, The University of Melbourne, Parkville, VIC, 3010, Australia.
Vaz, Paola K
  • Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The Asia-Pacific Centre for Animal Health, The University of Melbourne, Parkville, VIC, 3010, Australia.
Legione, Alistair R
  • Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The Asia-Pacific Centre for Animal Health, The University of Melbourne, Parkville, VIC, 3010, Australia.
Browning, Glenn F
  • Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The Asia-Pacific Centre for Animal Health, The University of Melbourne, Parkville, VIC, 3010, Australia.
Devlin, Joanne M
  • Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The Asia-Pacific Centre for Animal Health, The University of Melbourne, Parkville, VIC, 3010, Australia. devlinj@unimelb.edu.au.
Hartley, Carol A
  • Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The Asia-Pacific Centre for Animal Health, The University of Melbourne, Parkville, VIC, 3010, Australia.

MeSH Terms

  • Animals
  • Genetic Variation
  • Genome, Viral
  • Genomics
  • Horses
  • Nucleotides
  • Phylogeny
  • Recombination, Genetic
  • Sequence Analysis

Conflict of Interest Statement

The Authors declares that there are no competing interests as defined by BMC, or other interests that might be perceived to influence the reults and/or discussion reported in this paper.

References

This article includes 103 references
  1. Ackermann M. Pathogenesis of gammaherpesvirus infections.. Vet Microbiol 2006 Mar 31;113(3-4):211-22.
    doi: 10.1016/j.vetmic.2005.11.008pubmed: 16332416google scholar: lookup
  2. Agius CT, Nagesha HS, Studdert MJ. Equine herpesvirus 5: comparisons with EHV2 (equine cytomegalovirus), cloning, and mapping of a new equine herpesvirus with a novel genome structure.. Virology 1992 Nov;191(1):176-86.
    pubmed: 1329316doi: 10.1016/0042-6822(92)90179-sgoogle scholar: lookup
  3. Andrews S. FastQC: a quality control tool for high throughput sequence data. .
  4. Arenas M, Araujo NM, Branco C, Castelhano N, Castro-Nallar E, Pérez-Losada M. Mutation and recombination in pathogen evolution: Relevance, methods and controversies.. Infect Genet Evol 2018 Sep;63:295-306.
    doi: 10.1016/j.meegid.2017.09.029pubmed: 28951202google scholar: lookup
  5. Ataseven VS, Bilge-Dagalp S, Oguzoglu TC, Karapinar Z, Güzel M, Tan MT. Detection and sequence analysis of equine gammaherpesviruses from horses with respiratory tract disease in Turkey.. Transbound Emerg Dis 2010 Aug 1;57(4):271-6.
    doi: 10.1111/j.1865-1682.2010.01146.xpubmed: 20553426google scholar: lookup
  6. Aydin I, Schelhaas M. Viral Genome Tethering to Host Cell Chromatin: Cause and Consequences.. Traffic 2016 Apr;17(4):327-40.
    doi: 10.1111/tra.12378pubmed: 26787361google scholar: lookup
  7. Bell SA, Balasuriya UB, Gardner IA, Barry PA, Wilson WD, Ferraro GL, MacLachlan NJ. Temporal detection of equine herpesvirus infections of a cohort of mares and their foals.. Vet Microbiol 2006 Sep 10;116(4):249-57.
    doi: 10.1016/j.vetmic.2006.05.002pubmed: 16774810google scholar: lookup
  8. Berenstein AJ, Lorenzetti MA, Preciado MV. Recombination rates along the entire Epstein Barr virus genome display a highly heterogeneous landscape.. Infect Genet Evol 2018 Nov;65:96-103.
    doi: 10.1016/j.meegid.2018.07.022pubmed: 30031929google scholar: lookup
  9. Borchers K, Ebert M, Fetsch A, Hammond T, Sterner-Kock A. Prevalence of equine herpesvirus type 2 (EHV-2) DNA in ocular swabs and its cell tropism in equine conjunctiva.. Vet Microbiol 2006 Dec 20;118(3-4):260-6.
    doi: 10.1016/j.vetmic.2006.07.024pubmed: 16996233google scholar: lookup
  10. Bowden R, Sakaoka H, Donnelly P, Ward R. High recombination rate in herpes simplex virus type 1 natural populations suggests significant co-infection.. Infect Genet Evol 2004 Jun;4(2):115-23.
    doi: 10.1016/j.meegid.2004.01.009pubmed: 15157629google scholar: lookup
  11. Brault SA, Bird BH, Balasuriya UB, MacLachlan NJ. Genetic heterogeneity and variation in viral load during equid herpesvirus-2 infection of foals.. Vet Microbiol 2011 Jan 27;147(3-4):253-61.
    doi: 10.1016/j.vetmic.2010.06.031pubmed: 20655670google scholar: lookup
  12. Browning GF, Studdert MJ. Epidemiology of equine herpesvirus 2 (equine cytomegalovirus).. J Clin Microbiol 1987 Jan;25(1):13-6.
    pmc: PMC265802pubmed: 3025249doi: 10.1128/jcm.25.1.13-16.1987google scholar: lookup
  13. Browning GF, Studdert MJ. Genomic heterogeneity of equine betaherpesviruses.. J Gen Virol 1987 May;68 ( Pt 5):1441-7.
    pubmed: 2883251doi: 10.1099/0022-1317-68-5-1441google scholar: lookup
  14. Browning GF, Studdert MJ. Physical mapping of the genomic heterogeneity of isolates of equine herpesvirus 2 (equine cytomegalovirus).. Arch Virol 1989;104(1-2):87-94.
    pubmed: 2564271doi: 10.1007/bf01313810google scholar: lookup
  15. Bruen TC, Philippe H, Bryant D. A simple and robust statistical test for detecting the presence of recombination.. Genetics 2006 Apr;172(4):2665-81.
    doi: 10.1534/genetics.105.048975pmc: PMC1456386pubmed: 16489234google scholar: lookup
  16. Burger M, Hartmann T, Burger JA, Schraufstatter I. KSHV-GPCR and CXCR2 transforming capacity and angiogenic responses are mediated through a JAK2-STAT3-dependent pathway.. Oncogene 2005 Mar 17;24(12):2067-75.
    doi: 10.1038/sj.onc.1208442pubmed: 15688008google scholar: lookup
  17. Chiara M, Manzari C, Lionetti C, Mechelli R, Anastasiadou E, Chiara Buscarinu M, Ristori G, Salvetti M, Picardi E, D'Erchia AM, Pesole G, Horner DS. Geographic Population Structure in Epstein-Barr Virus Revealed by Comparative Genomics.. Genome Biol Evol 2016 Dec 14;8(11):3284-3291.
    pmc: PMC5203774pubmed: 27635051doi: 10.1093/gbe/evw226google scholar: lookup
  18. Correia S, Bridges R, Wegner F, Venturini C, Palser A, Middeldorp JM, Cohen JI, Lorenzetti MA, Bassano I, White RE, Kellam P, Breuer J, Farrell PJ. Sequence Variation of Epstein-Barr Virus: Viral Types, Geography, Codon Usage, and Diseases.. J Virol 2018 Nov 15;92(22).
    pmc: PMC6206488pubmed: 30111570doi: 10.1128/jvi.01132-18google scholar: lookup
  19. Craig MI, Barrandeguy ME, Fernández FM. Equine herpesvirus 2 (EHV-2) infection in thoroughbred horses in Argentina.. BMC Vet Res 2005 Nov 9;1:9.
    doi: 10.1186/1746-6148-1-9pmc: PMC1308826pubmed: 16281971google scholar: lookup
  20. Davison AJ. Evolution of the herpesviruses.. Vet Microbiol 2002 Apr 22;86(1-2):69-88.
    doi: 10.1016/s0378-1135(01)00492-8pubmed: 11888691google scholar: lookup
  21. Davison AJ, Eberle R, Ehlers B, Hayward GS, McGeoch DJ, Minson AC, Pellett PE, Roizman B, Studdert MJ, Thiry E. The order Herpesvirales.. Arch Virol 2009;154(1):171-7.
    doi: 10.1007/s00705-008-0278-4pmc: PMC3552636pubmed: 19066710google scholar: lookup
  22. de Munnik SM, Smit MJ, Leurs R, Vischer HF. Modulation of cellular signaling by herpesvirus-encoded G protein-coupled receptors.. Front Pharmacol 2015;6:40.
    doi: 10.3389/fphar.2015.00040pmc: PMC4353375pubmed: 25805993google scholar: lookup
  23. Drummer HE, Reubel GH, Studdert MJ. Equine gammaherpesvirus 2 (EHV2) is latent in B lymphocytes.. Arch Virol 1996;141(3-4):495-504.
    pubmed: 8645091doi: 10.1007/bf01718313google scholar: lookup
  24. Duarte M, Wang L, Calderwood MA, Adelmant G, Ohashi M, Roecklein-Canfield J, Marto JA, Hill DE, Deng H, Johannsen E. An RS motif within the Epstein-Barr virus BLRF2 tegument protein is phosphorylated by SRPK2 and is important for viral replication.. PLoS One 2013;8(1):e53512.
    doi: 10.1371/journal.pone.0053512pmc: PMC3541133pubmed: 23326445google scholar: lookup
  25. Dunowska M, Howe L, Hanlon D, Stevenson M. Kinetics of Equid herpesvirus type 2 infections in a group of Thoroughbred foals.. Vet Microbiol 2011 Aug 26;152(1-2):176-80.
    doi: 10.1016/j.vetmic.2011.04.017pubmed: 21616610google scholar: lookup
  26. Dunowska M, Wilks CR, Studdert MJ, Meers J. Viruses associated with outbreaks of equine respiratory disease in New Zealand.. N Z Vet J 2002 Aug;50(4):132-9.
    doi: 10.1080/00480169.2002.36299pubmed: 16032259google scholar: lookup
  27. Dynon K, Varrasso A, Ficorilli N, Holloway S, Reubel G, Li F, Hartley C, Studdert M, Drummer H. Identification of equine herpesvirus 3 (equine coital exanthema virus), equine gammaherpesviruses 2 and 5, equine adenoviruses 1 and 2, equine arteritis virus and equine rhinitis A virus by polymerase chain reaction.. Aust Vet J 2001 Oct;79(10):695-702.
    pubmed: 11712710doi: 10.1111/j.1751-0813.2001.tb10674.xgoogle scholar: lookup
  28. Edington N, Welch HM, Griffiths L. The prevalence of latent Equid herpesviruses in the tissues of 40 abattoir horses.. Equine Vet J 1994 Mar;26(2):140-2.
    doi: 10.1111/j.2042-3306.1994.tb04353.xpubmed: 8575377google scholar: lookup
  29. Fortier G, Richard E, Hue E, Fortier C, Pronost S, Pottier D, Lemaitre L, Lekeux P, Borchers K, Thiry E. Long-lasting airway inflammation associated with equid herpesvirus-2 in experimentally challenged horses.. Vet J 2013 Aug;197(2):492-5.
    doi: 10.1016/j.tvjl.2012.12.027pubmed: 23433569google scholar: lookup
  30. Fortier G, van Erck E, Fortier C, Richard E, Pottier D, Pronost S, Miszczak F, Thiry E, Lekeux P. Herpesviruses in respiratory liquids of horses: putative implication in airway inflammation and association with cytological features.. Vet Microbiol 2009 Oct 20;139(1-2):34-41.
    doi: 10.1016/j.vetmic.2009.04.021pubmed: 19427139google scholar: lookup
  31. Fowler P, Marques S, Simas JP, Efstathiou S. ORF73 of murine herpesvirus-68 is critical for the establishment and maintenance of latency.. J Gen Virol 2003 Dec;84(Pt 12):3405-3416.
    doi: 10.1099/vir.0.19594-0pubmed: 14645921google scholar: lookup
  32. Frappier L. The Epstein-Barr Virus EBNA1 Protein.. Scientifica (Cairo) 2012;2012:438204.
    doi: 10.6064/2012/438204pmc: PMC3820569pubmed: 24278697google scholar: lookup
  33. Gascuel O. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.. Mol Biol Evol 1997 Jul;14(7):685-95.
    doi: 10.1093/oxfordjournals.molbev.a025808pubmed: 9254330google scholar: lookup
  34. Goltz M, Broll H, Mankertz A, Weigelt W, Ludwig H, Buhk HJ, Borchers K. Glycoprotein B of bovine herpesvirus type 4: its phylogenetic relationship to gB equivalents of the herpesviruses.. Virus Genes 1994 Sep;9(1):53-9.
    doi: 10.1007/BF01703435pubmed: 7871762google scholar: lookup
  35. Hartley CA, Dynon KJ, Mekuria ZH, El-Hage CM, Holloway SA, Gilkerson JR. Equine gammaherpesviruses: perfect parasites?. Vet Microbiol 2013 Nov 29;167(1-2):86-92.
    doi: 10.1016/j.vetmic.2013.05.031pubmed: 23845734google scholar: lookup
  36. Holloway SA, Lindquester GJ, Studdert MJ, Drummer HE. Analysis of equine herpesvirus 2 strain variation using monoclonal antibodies to glyucoprotein B.. Arch Virol 2000;145(8):1699-713.
    doi: 10.1007/s007050070085pubmed: 11003478google scholar: lookup
  37. Hue ES, Fortier GD, Fortier CI, Leon AM, Richard EA, Legrand LJ, Pronost SL. Detection and quantitation of equid gammaherpesviruses (EHV-2, EHV-5) in nasal swabs using an accredited standardised quantitative PCR method.. J Virol Methods 2014 Mar;198:18-25.
    doi: 10.1016/j.jviromet.2013.12.008pubmed: 24370678google scholar: lookup
  38. Huson DH. SplitsTree: analyzing and visualizing evolutionary data.. Bioinformatics 1998;14(1):68-73.
    doi: 10.1093/bioinformatics/14.1.68pubmed: 9520503google scholar: lookup
  39. Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies.. Mol Biol Evol 2006 Feb;23(2):254-67.
    doi: 10.1093/molbev/msj030pubmed: 16221896google scholar: lookup
  40. Kasolo FC, Spinks J, Bima H, Bates M, Gompels UA. Diverse genotypes of Kaposi's sarcoma associated herpesvirus (KSHV) identified in infant blood infections in African childhood-KS and HIV/AIDS endemic region.. J Med Virol 2007 Oct;79(10):1555-61.
    pmc: PMC2683451pubmed: 17705172doi: 10.1002/jmv.20952google scholar: lookup
  41. Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.. Nucleic Acids Res 2002 Jul 15;30(14):3059-66.
    doi: 10.1093/nar/gkf436pmc: PMC135756pubmed: 12136088google scholar: lookup
  42. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability.. Mol Biol Evol 2013 Apr;30(4):772-80.
    doi: 10.1093/molbev/mst010pmc: PMC3603318pubmed: 23329690google scholar: lookup
  43. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.. Bioinformatics 2012 Jun 15;28(12):1647-9.
    doi: 10.1093/bioinformatics/bts199pmc: PMC3371832pubmed: 22543367google scholar: lookup
  44. Kershaw O, von Oppen T, Glitz F, Deegen E, Ludwig H, Borchers K. Detection of equine herpesvirus type 2 (EHV-2) in horses with keratoconjunctivitis.. Virus Res 2001 Nov 28;80(1-2):93-9.
    pubmed: 11597754doi: 10.1016/s0168-1702(01)00299-4google scholar: lookup
  45. Knerr JM, Kledal TN, Rosenkilde MM. Molecular Properties and Therapeutic Targeting of the EBV-Encoded Receptor BILF1.. Cancers (Basel) 2021 Aug 13;13(16).
    pmc: PMC8392491pubmed: 34439235doi: 10.3390/cancers13164079google scholar: lookup
  46. Kryazhimskiy S, Plotkin JB. The population genetics of dN/dS.. PLoS Genet 2008 Dec;4(12):e1000304.
    doi: 10.1371/journal.pgen.1000304pmc: PMC2596312pubmed: 19081788google scholar: lookup
  47. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.. Mol Biol Evol 2016 Jul;33(7):1870-4.
    pmc: PMC8210823pubmed: 27004904doi: 10.1093/molbev/msw054google scholar: lookup
  48. Loesing JB, Di Fiore S, Ritter K, Fischer R, Kleines M. Epstein-Barr virus BDLF2-BMRF2 complex affects cellular morphology.. J Gen Virol 2009 Jun;90(Pt 6):1440-1449.
    doi: 10.1099/vir.0.009571-0pubmed: 19264620google scholar: lookup
  49. Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination.. J Virol 1999 Jan;73(1):152-60.
    doi: 10.1128/JVI.73.1.152-160.1999pmc: PMC103818pubmed: 9847317google scholar: lookup
  50. Loncoman CA, Hartley CA, Coppo MJC, Vaz PK, Diaz-Méndez A, Browning GF, García M, Spatz S, Devlin JM. Genetic Diversity of Infectious Laryngotracheitis Virus during In Vivo Coinfection Parallels Viral Replication and Arises from Recombination Hot Spots within the Genome.. Appl Environ Microbiol 2017 Dec 1;83(23).
    pmc: PMC5691407pubmed: 28939604doi: 10.1128/aem.01532-17google scholar: lookup
  51. Martin DP, Murrell B, Golden M, Khoosal A, Muhire B. RDP4: Detection and analysis of recombination patterns in virus genomes.. Virus Evol 2015;1(1):vev003.
    pmc: PMC5014473pubmed: 27774277doi: 10.1093/ve/vev003google scholar: lookup
  52. Martin DP, Murrell B, Khoosal A, Muhire B. Detecting and Analyzing Genetic Recombination Using RDP4.. Methods Mol Biol 2017;1525:433-460.
    doi: 10.1007/978-1-4939-6622-6_17pubmed: 27896731google scholar: lookup
  53. Mayer C. Phobos 3.3.12. .
  54. McGeoch DJ. Molecular evolution of the gamma-Herpesvirinae.. Philos Trans R Soc Lond B Biol Sci 2001 Apr 29;356(1408):421-35.
    pmc: PMC1088436pubmed: 11313003doi: 10.1098/rstb.2000.0775google scholar: lookup
  55. Mekuria ZH, El-Hage C, Ficorilli NP, Washington EA, Gilkerson JR, Hartley CA. Mapping B lymphocytes as major reservoirs of naturally occurring latent equine herpesvirus 5 infection.. J Gen Virol 2017 Mar;98(3):461-470.
    pubmed: 27902371doi: 10.1099/jgv.0.000668google scholar: lookup
  56. Mutsvunguma LZ, Rodriguez E, Escalante GM, Muniraju M, Williams JC, Warden C, Qin H, Wang J, Wu X, Barasa A, Mulama DH, Mwangi W, Ogembo JG. Identification of multiple potent neutralizing and non-neutralizing antibodies against Epstein-Barr virus gp350 protein with potential for clinical application and as reagents for mapping immunodominant epitopes.. Virology 2019 Oct;536:1-15.
    doi: 10.1016/j.virol.2019.07.026pmc: PMC6733660pubmed: 31377598google scholar: lookup
  57. Muylkens B, Farnir F, Meurens F, Schynts F, Vanderplasschen A, Georges M, Thiry E. Coinfection with two closely related alphaherpesviruses results in a highly diversified recombination mosaic displaying negative genetic interference.. J Virol 2009 Apr;83(7):3127-37.
    doi: 10.1128/JVI.02474-08pmc: PMC2655596pubmed: 19153224google scholar: lookup
  58. Negussie H, Gizaw D, Tesfaw L, Li Y, Oguma K, Sentsui H, Tessema TS, Nauwynck HJ. Detection of Equine Herpesvirus (EHV) -1, -2, -4 and -5 in Ethiopian Equids with and without Respiratory Problems and Genetic Characterization of EHV-2 and EHV-5 Strains.. Transbound Emerg Dis 2017 Dec;64(6):1970-1978.
    doi: 10.1111/tbed.12601pubmed: 28102009google scholar: lookup
  59. Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.. Mol Biol Evol 2015 Jan;32(1):268-74.
    doi: 10.1093/molbev/msu300pmc: PMC4271533pubmed: 25371430google scholar: lookup
  60. Nicholas J. Human gammaherpesvirus cytokines and chemokine receptors.. J Interferon Cytokine Res 2005 Jul;25(7):373-83.
    doi: 10.1089/jir.2005.25.373pubmed: 16022582google scholar: lookup
  61. Nordengrahn A, Merza M, Ros C, Lindholmc A, Palfl V, Hannant D, Belák S. Prevalence of equine herpesvirus types 2 and 5 in horse populations by using type-specific PCR assays.. Vet Res 2002 May-Jun;33(3):251-9.
    doi: 10.1051/vetres:2002013pubmed: 12056476google scholar: lookup
  62. Nordengrahn A, Rusvai M, Merza M, Ekström J, Morein B, Belák S. Equine herpesvirus type 2 (EHV-2) as a predisposing factor for Rhodococcus equi pneumonia in foals: prevention of the bifactorial disease with EHV-2 immunostimulating complexes.. Vet Microbiol 1996 Jul;51(1-2):55-68.
    pubmed: 8828122doi: 10.1016/0378-1135(96)00032-6google scholar: lookup
  63. Olp LN, Jeanniard A, Marimo C, West JT, Wood C. Whole-Genome Sequencing of Kaposi's Sarcoma-Associated Herpesvirus from Zambian Kaposi's Sarcoma Biopsy Specimens Reveals Unique Viral Diversity.. J Virol 2015 Dec;89(24):12299-308.
    pmc: PMC4665246pubmed: 26423952doi: 10.1128/jvi.01712-15google scholar: lookup
  64. Palser AL, Grayson NE, White RE, Corton C, Correia S, Ba Abdullah MM, Watson SJ, Cotten M, Arrand JR, Murray PG, Allday MJ, Rickinson AB, Young LS, Farrell PJ, Kellam P. Genome diversity of Epstein-Barr virus from multiple tumor types and normal infection.. J Virol 2015 May;89(10):5222-37.
    doi: 10.1128/JVI.03614-14pmc: PMC4442510pubmed: 25787276google scholar: lookup
  65. Pennington MR, Cossic BGA, Perkins GA, Duffy C, Duhamel GE, Van de Walle GR. First demonstration of equid gammaherpesviruses within the gastric mucosal epithelium of horses.. Virus Res 2017 Oct 15;242:30-36.
    doi: 10.1016/j.virusres.2017.09.002pubmed: 28870469google scholar: lookup
  66. Pérez-Losada M, Arenas M, Galán JC, Palero F, González-Candelas F. Recombination in viruses: mechanisms, methods of study, and evolutionary consequences.. Infect Genet Evol 2015 Mar;30:296-307.
    doi: 10.1016/j.meegid.2014.12.022pmc: PMC7106159pubmed: 25541518google scholar: lookup
  67. Plummer G, Goodheart CR, Studdert MJ. Equine herpesviruses: antigenic relationships and deoxyribonucleic acid densities.. Infect Immun 1973 Oct;8(4):621-7.
    pmc: PMC422900pubmed: 4742974doi: 10.1128/iai.8.4.621-627.1973google scholar: lookup
  68. Purushothaman P, Dabral P, Gupta N, Sarkar R, Verma SC. KSHV Genome Replication and Maintenance.. Front Microbiol 2016;7:54.
    doi: 10.3389/fmicb.2016.00054pmc: PMC4740845pubmed: 26870016google scholar: lookup
  69. Renner DW, Szpara ML. Impacts of Genome-Wide Analyses on Our Understanding of Human Herpesvirus Diversity and Evolution.. J Virol 2018 Jan 1;92(1).
    pmc: PMC5730764pubmed: 29046445doi: 10.1128/jvi.00908-17google scholar: lookup
  70. Renzette N, Pokalyuk C, Gibson L, Bhattacharjee B, Schleiss MR, Hamprecht K, Yamamoto AY, Mussi-Pinhata MM, Britt WJ, Jensen JD, Kowalik TF. Limits and patterns of cytomegalovirus genomic diversity in humans.. Proc Natl Acad Sci U S A 2015 Jul 28;112(30):E4120-8.
    doi: 10.1073/pnas.1501880112pmc: PMC4522815pubmed: 26150505google scholar: lookup
  71. Roizmann B, Desrosiers RC, Fleckenstein B, Lopez C, Minson AC, Studdert MJ. The family Herpesviridae: an update. The Herpesvirus Study Group of the International Committee on Taxonomy of Viruses.. Arch Virol 1992;123(3-4):425-49.
    pubmed: 1562239doi: 10.1007/bf01317276google scholar: lookup
  72. Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sánchez-Gracia A. DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets.. Mol Biol Evol 2017 Dec 1;34(12):3299-3302.
    doi: 10.1093/molbev/msx248pubmed: 29029172google scholar: lookup
  73. Rushton JO, Kolodziejek J, Nell B, Weissenböck H, Nowotny N. Keratoconjunctivitis in a group of Icelandic horses with suspected γ-herpesvirus involvement.. Equine Vet J 2016 Jul;48(4):427-9.
    doi: 10.1111/evj.12465pubmed: 26032576google scholar: lookup
  74. Sallah N, Palser AL, Watson SJ, Labo N, Asiki G, Marshall V, Newton R, Whitby D, Kellam P, Barroso I. Genome-Wide Sequence Analysis of Kaposi Sarcoma-Associated Herpesvirus Shows Diversification Driven by Recombination.. J Infect Dis 2018 Oct 20;218(11):1700-1710.
    doi: 10.1093/infdis/jiy427pmc: PMC6195662pubmed: 30010810google scholar: lookup
  75. Sharp EL, Farrell HE, Borchers K, Holmes EC, Davis-Poynter NJ. Sequence analysis of the equid herpesvirus 2 chemokine receptor homologues E1, ORF74 and E6 demonstrates high sequence divergence between field isolates.. J Gen Virol 2007 Sep;88(Pt 9):2450-2462.
    doi: 10.1099/vir.0.82942-0pubmed: 17698654google scholar: lookup
  76. Shukla D, Spear PG. Herpesviruses and heparan sulfate: an intimate relationship in aid of viral entry.. J Clin Invest 2001 Aug;108(4):503-10.
    doi: 10.1172/JCI13799pmc: PMC209412pubmed: 11518721google scholar: lookup
  77. Sijmons S, Thys K, Mbong Ngwese M, Van Damme E, Dvorak J, Van Loock M, Li G, Tachezy R, Busson L, Aerssens J, Van Ranst M, Maes P. High-throughput analysis of human cytomegalovirus genome diversity highlights the widespread occurrence of gene-disrupting mutations and pervasive recombination.. J Virol 2015 Aug 1;89(15):7673-7695.
    pmc: PMC4505652pubmed: 25972543doi: 10.1128/jvi.00578-15google scholar: lookup
  78. Simbiri KO, Smith NA, Otieno R, Wohlford EE, Daud II, Odada SP, Middleton F, Rochford R. Epstein-Barr virus genetic variation in lymphoblastoid cell lines derived from Kenyan pediatric population.. PLoS One 2015;10(5):e0125420.
    doi: 10.1371/journal.pone.0125420pmc: PMC4416826pubmed: 25933165google scholar: lookup
  79. Smith LM, McWhorter AR, Shellam GR, Redwood AJ. The genome of murine cytomegalovirus is shaped by purifying selection and extensive recombination.. Virology 2013 Jan 20;435(2):258-68.
    doi: 10.1016/j.virol.2012.08.041pubmed: 23107009google scholar: lookup
  80. Sorel O, Dewals BG. The Critical Role of Genome Maintenance Proteins in Immune Evasion During Gammaherpesvirus Latency.. Front Microbiol 2018;9:3315.
    doi: 10.3389/fmicb.2018.03315pmc: PMC6333680pubmed: 30687291google scholar: lookup
  81. Sorem J, Longnecker R. Cleavage of Epstein-Barr virus glycoprotein B is required for full function in cell-cell fusion with both epithelial and B cells.. J Gen Virol 2009 Mar;90(Pt 3):591-595.
    doi: 10.1099/vir.0.007237-0pmc: PMC2768059pubmed: 19218203google scholar: lookup
  82. Stampfer SD, Heldwein EE. Stuck in the middle: structural insights into the role of the gH/gL heterodimer in herpesvirus entry.. Curr Opin Virol 2013 Feb;3(1):13-9.
    doi: 10.1016/j.coviro.2012.10.005pmc: PMC3562363pubmed: 23107819google scholar: lookup
  83. Stasiak K, Dunowska M, Rola J. Prevalence and sequence analysis of equid herpesviruses from the respiratory tract of Polish horses.. Virol J 2018 Jul 11;15(1):106.
    doi: 10.1186/s12985-018-1018-3pmc: PMC6042439pubmed: 29996858google scholar: lookup
  84. Stebbing J, Powles T, Nelson M, Bower M. Significance of variation within HIV, EBV, and KSHV subtypes.. J Int Assoc Physicians AIDS Care (Chic) 2006 Sep;5(3):93-102.
    doi: 10.1177/1545109706290171pubmed: 16928877google scholar: lookup
  85. Studdert MJ, Gleeson LJ. Isolation of equine rhinovirus type 1.. Aust Vet J 1977 Sep;53(9):452.
    doi: 10.1111/j.1751-0813.1977.tb05504.xpubmed: 201238google scholar: lookup
  86. Szpara ML, Gatherer D, Ochoa A, Greenbaum B, Dolan A, Bowden RJ, Enquist LW, Legendre M, Davison AJ. Evolution and diversity in human herpes simplex virus genomes.. J Virol 2014 Jan;88(2):1209-27.
    doi: 10.1128/JVI.01987-13pmc: PMC3911644pubmed: 24227835google scholar: lookup
  87. Telford EA, Watson MS, Aird HC, Perry J, Davison AJ. The DNA sequence of equine herpesvirus 2.. J Mol Biol 1995 Jun 9;249(3):520-8.
    doi: 10.1006/jmbi.1995.0314pubmed: 7783207google scholar: lookup
  88. Telford M, Hughes DA, Juan D, Stoneking M, Navarro A, Santpere G. Expanding the Geographic Characterisation of Epstein-Barr Virus Variation through Gene-Based Approaches.. Microorganisms 2020 Oct 29;8(11).
    pmc: PMC7692309pubmed: 33138327doi: 10.3390/microorganisms8111686google scholar: lookup
  89. Thiry E, Meurens F, Muylkens B, McVoy M, Gogev S, Thiry J, Vanderplasschen A, Epstein A, Keil G, Schynts F. Recombination in alphaherpesviruses.. Rev Med Virol 2005 Mar-Apr;15(2):89-103.
    doi: 10.1002/rmv.451pubmed: 15546129google scholar: lookup
  90. Thorley-Lawson DA, Poodry CA. Identification and isolation of the main component (gp350-gp220) of Epstein-Barr virus responsible for generating neutralizing antibodies in vivo.. J Virol 1982 Aug;43(2):730-6.
    doi: 10.1128/JVI.43.2.730-736.1982pmc: PMC256176pubmed: 6287039google scholar: lookup
  91. Thorsteinsdóttir L, Torfason EG, Torsteinsdóttir S, Svansson V. Genetic diversity of equine gammaherpesviruses (γ-EHV) and isolation of a syncytium forming EHV-2 strain from a horse in Iceland.. Res Vet Sci 2013 Feb;94(1):170-7.
    doi: 10.1016/j.rvsc.2012.07.011pubmed: 22862856google scholar: lookup
  92. Torfason EG, Thorsteinsdóttir L, Torsteinsdóttir S, Svansson V. Study of equid herpesviruses 2 and 5 in Iceland with a type-specific polymerase chain reaction.. Res Vet Sci 2008 Dec;85(3):605-11.
    doi: 10.1016/j.rvsc.2008.01.003pubmed: 18336849google scholar: lookup
  93. Vallbracht M, Backovic M, Klupp BG, Rey FA, Mettenleiter TC. Common characteristics and unique features: A comparison of the fusion machinery of the alphaherpesviruses Pseudorabies virus and Herpes simplex virus.. Adv Virus Res 2019;104:225-281.
    doi: 10.1016/bs.aivir.2019.05.007pubmed: 31439150google scholar: lookup
  94. van Gent M, Braem SG, de Jong A, Delagic N, Peeters JG, Boer IG, Moynagh PN, Kremmer E, Wiertz EJ, Ovaa H, Griffin BD, Ressing ME. Epstein-Barr virus large tegument protein BPLF1 contributes to innate immune evasion through interference with toll-like receptor signaling.. PLoS Pathog 2014 Feb;10(2):e1003960.
    doi: 10.1371/journal.ppat.1003960pmc: PMC3930590pubmed: 24586164google scholar: lookup
  95. Vaz PK, Horsington J, Hartley CA, Browning GF, Ficorilli NP, Studdert MJ, Gilkerson JR, Devlin JM. Evidence of widespread natural recombination among field isolates of equine herpesvirus 4 but not among field isolates of equine herpesvirus 1.. J Gen Virol 2016 Mar;97(3):747-755.
    doi: 10.1099/jgv.0.000378pmc: PMC5381393pubmed: 26691326google scholar: lookup
  96. Waddell PJ, Steel MA. General time-reversible distances with unequal rates across sites: mixing gamma and inverse Gaussian distributions with invariant sites.. Mol Phylogenet Evol 1997 Dec;8(3):398-414.
    doi: 10.1006/mpev.1997.0452pubmed: 9417897google scholar: lookup
  97. Wang D, Liu F, Wang L, Huang S, Yu J. Nonsynonymous substitution rate (Ka) is a relatively consistent parameter for defining fast-evolving and slow-evolving protein-coding genes.. Biol Direct 2011 Feb 22;6:13.
    doi: 10.1186/1745-6150-6-13pmc: PMC3055854pubmed: 21342519google scholar: lookup
  98. Wang D, Zhang S, He F, Zhu J, Hu S, Yu J. How do variable substitution rates influence Ka and Ks calculations?. Genomics Proteomics Bioinformatics 2009 Sep;7(3):116-27.
    doi: 10.1016/S1672-0229(08)60040-6pmc: PMC5054415pubmed: 19944384google scholar: lookup
  99. Wang L, Raidal SL, Pizzirani A, Wilcox GE. Detection of respiratory herpesviruses in foals and adult horses determined by nested multiplex PCR.. Vet Microbiol 2007 Mar 31;121(1-2):18-28.
    doi: 10.1016/j.vetmic.2006.11.009pubmed: 17208393google scholar: lookup
  100. Wei F, Gan J, Wang C, Zhu C, Cai Q. Cell Cycle Regulatory Functions of the KSHV Oncoprotein LANA.. Front Microbiol 2016;7:334.
    doi: 10.3389/fmicb.2016.00334pmc: PMC4811921pubmed: 27065950google scholar: lookup
  101. Weiss ER, Lamers SL, Henderson JL, Melnikov A, Somasundaran M, Garber M, Selin L, Nusbaum C, Luzuriaga K. Early Epstein-Barr Virus Genomic Diversity and Convergence toward the B95.8 Genome in Primary Infection.. J Virol 2018 Jan 15;92(2).
    pmc: PMC5752928pubmed: 29093087doi: 10.1128/jvi.01466-17google scholar: lookup
  102. Wilkie GS, Kerr K, Stewart JP, Studdert MJ, Davison AJ. Genome sequences of equid herpesviruses 2 and 5.. Genome Announc 2015 Mar 12;3(2).
    pmc: PMC4357765pubmed: 25767243doi: 10.1128/genomea.00119-15google scholar: lookup
  103. Zanella L, Riquelme I, Buchegger K, Abanto M, Ili C, Brebi P. A reliable Epstein-Barr Virus classification based on phylogenomic and population analyses.. Sci Rep 2019 Jul 8;9(1):9829.
    doi: 10.1038/s41598-019-45986-3pmc: PMC6614506pubmed: 31285478google scholar: lookup

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