FREE SHIPPING over $40
OVER 9000 FIVE-STAR REVIEWS
5% OFF ALL SUBSCRIPTIONS
100% HAPPINESS GUARANTEE
Analyze Diet
0
Home / Equine Research Bank / Virol J / Phylogenomic assessment of 23 equid alphaherpesvirus 1 isola...
Virology journal2023; 20(1); 278; doi: 10.1186/s12985-023-02248-z

Phylogenomic assessment of 23 equid alphaherpesvirus 1 isolates obtained from USA-based equids.

Abstract: Equid alphaherpesvirus 1 (EHV-1) is a global viral pathogen of domestic equids which causes reproductive, respiratory and neurological disease. Few isolates acquired from naturally infected USA-based hosts have been fully sequenced and analyzed to date. An ORF 30 (DNA polymerase) variant (A2254G) has previously been associated with neurological disease in host animals. The purpose of this study was to perform phylogenomic analysis of EHV-1 isolates acquired from USA-based hosts and compare these isolates to previously sequenced global isolates. EHV-1 was isolated from 23 naturally infected USA-based equids (6 different states, 15 disease outbreaks) with reproductive (22/23) or neurological disease (1/23). Following virus isolation, EHV-1 DNA was extracted for sequencing using Illumina MiSeq. Following reference-based assembly, whole viral genomes were annotated and assessed. Previously sequenced EHV-1 isolates (n = 114) obtained from global host equids were included in phylogenomic analyses. The overall average genomic distance was 0.0828% (SE 0.004%) for the 23 newly sequenced USA isolates and 0.0705% (SE 0.003%) when all 137 isolates were included. Clade structure was predominantly based on geographic origin. Numerous nucleotide substitutions (mean [range], 179 [114-297] synonymous and 81 [38-120] non-synonymous substitutions per isolate) were identified throughout the genome of the newly sequenced USA isolates. The previously described ORF 30 A2254G substitution (associated with neurological disease) was found in only one isolate obtained from a host with non-neurological clinical signs (reproductive disease), six additional, unique, non-synonymous ORF 30 substitutions were detected in 22/23 USA isolates. Evidence of recombination was present in most (22/23) of the newly sequenced USA isolates. Overall, the genomes of the 23 newly sequenced EHV-1 isolates obtained from USA-based hosts were broadly similar to global isolates. The previously described ORF 30 A2254G neurological substitution was infrequently detected in the newly sequenced USA isolates, most of which were obtained from host animals with reproductive disease. Recombination was likely to be partially responsible for genomic diversity in the newly sequenced USA isolates.
© 2023. The Author(s).
Get Full Text
Publication Date: 2023-11-29 PubMed ID: 38031153PubMed Central: PMC10688130DOI: 10.1186/s12985-023-02248-zGoogle Scholar: Lookup
The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
LinkedInCopy
  • 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.

This research focuses on analyzing various isolates of Equid alphaherpesvirus 1 (EHV-1), a virus that impacts horses and causes reproductive, respiratory, and neurological diseases. It’s a comprehensive study that maps the genetic material of 23 EHV-1 isolates from the United States and measures them against previously sequenced global isolates for comparative analysis.

Methods Employed

  • The study focused on EHV-1 isolates extracted from 23 US-based horses that suffered from either reproductive (22) or neurological disease (1).
  • Viral DNA was extracted and its genome sequenced through a technology named Illumina MiSeq.
  • The genomes were then fully annotated and assessed.
  • For the comparative analysis, sequences of 114 previously isolated and sequenced EHV-1 from across the world were included.

Findings

  • The average genomic distance for the newly sequenced US isolates was 0.0828%, extending to 0.0705% when all the 137 isolates (including global ones) were considered.
  • Isolates were largely segmented into groups or clades based on their geographical origin.
  • Significant variations in the form of nucleotide substitutions were discovered throughout the genomes of these newly sequenced isolates. The range was between 114-297 synonymous substitutions and 38-120 non-synonymous substitutions per isolate.
  • The previously documented ORF 30 A2254G polymorphism, which has been associated with neurological disease, was found in only one isolate that had been linked to non-neurological clinical signs.
  • Another six unique ORF 30 substitutions were found in 22 out of the 23 USA isolates.
  • A major observation was that most of the newly sequenced USA isolates (22 out of 23) demonstrated evidence of genetic recombination.

Conclusions

  • The findings indicate a broad similarity between the genomes of the new US EHV-1 isolates and those at the global level.
  • Interestingly, the ORF 30 A2254G substitution, generally associated with neurological disease, was rarely detected in the newly sequenced isolates. These were mostly derived from hosts suffering from reproductive disease.
  • Another significant insight was regarding the likely role of genetic recombination in contributing to the genomic diversity of the new isolates sourced from the USA.

Cite This Article

APA
Emelogu U, Lewin AC, Balasuriya UBR, Liu CC, Wilkes RP, Zhang J, Mills EP, Carter RT. (2023). Phylogenomic assessment of 23 equid alphaherpesvirus 1 isolates obtained from USA-based equids. Virol J, 20(1), 278. https://doi.org/10.1186/s12985-023-02248-z

Publication

Virology journal
ISSN: 1743-422X
NlmUniqueID: 101231645
Country: England
Language: English
Volume: 20
Issue: 1
Pages: 278

Researcher Affiliations

Emelogu, Ugochi
  • Veterinary Clinical Sciences, School of Veterinary Medicine, Department of Veterinary Clinical Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
Lewin, Andrew C
  • Veterinary Clinical Sciences, School of Veterinary Medicine, Department of Veterinary Clinical Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA. alewin1@lsu.edu.
Balasuriya, Udeni B R
  • School of Veterinary Medicine, Louisiana Animal Disease Diagnostic Laboratory, Baton Rouge, LA, USA.
Liu, Chin-Chi
  • Veterinary Clinical Sciences, School of Veterinary Medicine, Department of Veterinary Clinical Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
Wilkes, Rebecca P
  • Purdue University, Animal Disease Diagnostic Laboratory, West Lafayette, IN, USA.
Zhang, Jianqiang
  • Iowa State University, Veterinary Diagnostic Laboratory, Ames, IA, USA.
Mills, Erinn P
  • Veterinary Clinical Sciences, School of Veterinary Medicine, Department of Veterinary Clinical Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
Carter, Renee T
  • Veterinary Clinical Sciences, School of Veterinary Medicine, Department of Veterinary Clinical Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.

MeSH Terms

  • Animals
  • Horses
  • Herpesvirus 1, Equid
  • Phylogeny
  • Herpesviridae Infections / epidemiology
  • Herpesviridae Infections / veterinary
  • Herpesviridae Infections / genetics
  • Genome, Viral
  • Base Sequence
  • Nervous System Diseases
  • Horse Diseases / epidemiology

Grant Funding

  • (2021-2022) / LSU SVM Charles V. Cusimano grant
  • (2021-2022) / LSU SVM Charles V. Cusimano grant

Conflict of Interest Statement

The authors declare that they have no competing interests.

References

This article includes 51 references
  1. Damiani AM, de Vries M, Reimers G, Winkler S, Osterrieder N. A severe equine herpesvirus type 1 (EHV-1) abortion outbreak caused by a neuropathogenic strain at a breeding farm in northern Germany.. Vet Microbiol 2014;172(3–4):555–562.
    doi: 10.1016/j.vetmic.2014.06.023pubmed: 25042527google scholar: lookup
  2. Negussie H, Gizaw D, Tessema TS, Nauwynck HJ. Equine herpesvirus-1 myeloencephalopathy, an emerging threat of working equids in Ethiopia.. Transbound Emerg Dis 2017;64(2):389–397.
    doi: 10.1111/tbed.12377pubmed: 26010868google scholar: lookup
  3. Schulman ML, Becker A, van der Merwe BD, Guthrie AJ, Stout TA. Epidemiology and reproductive outcomes of EHV-1 abortion epizootics in unvaccinated Thoroughbred mares in South Africa.. Equine Vet J 2015;47(2):155–159.
    doi: 10.1111/evj.12264pubmed: 24617603google scholar: lookup
  4. Hussey GS, Goehring LS, Lunn DP, Hussey SB, Huang T, Osterrieder N. Experimental infection with equine herpesvirus type 1 (EHV-1) induces chorioretinal lesions.. Vet Res 2013;44(1):118.
    doi: 10.1186/1297-9716-44-118pmc: PMC4028784pubmed: 24308772google scholar: lookup
  5. Vandekerckhove AP, Glorieux S, Gryspeerdt AC, Steukers L, Van Doorsselaere J, Osterrieder N. Equine alphaherpesviruses (EHV-1 and EHV-4) differ in their efficiency to infect mononuclear cells during early steps of infection in nasal mucosal explants.. Vet Microbiol 2011;152(1–2):21–28.
    doi: 10.1016/j.vetmic.2011.03.038pubmed: 21536394google scholar: lookup
  6. Dimock WW, Edwards PR. Is there a filterable virus of abortion in mares?. Ky Agric Exp Stn Bull 1933;333(9):297–301.
  7. Ma G, Azab W, Osterrieder N. Equine herpesviruses type 1 (EHV-1) and 4 (EHV-4)-masters of co-evolution and a constant threat to equids and beyond.. Vet Microbiol 2013;167(1–2):123–134.
    doi: 10.1016/j.vetmic.2013.06.018pubmed: 23890672google scholar: lookup
  8. Fritsche AK, Borchers K. Detection of neuropathogenic strains of Equid Herpesvirus 1 (EHV-1) associated with abortions in Germany.. Vet Microbiol 2011;147(1–2):176–180.
    doi: 10.1016/j.vetmic.2010.06.014pubmed: 20619972google scholar: lookup
  9. Pronost S, Léon A, Legrand L, Fortier C, Miszczak F, Freymuth F. Neuropathogenic and non-neuropathogenic variants of equine herpesvirus 1 in France.. Vet Microbiol 2010;145(3–4):329–333.
    doi: 10.1016/j.vetmic.2010.03.031pubmed: 20427133google scholar: lookup
  10. Stasiak K, Rola J, Ploszay G, Socha W, Zmudzinski JF. Detection of the neuropathogenic variant of equine herpesvirus 1 associated with abortions in mares in Poland.. BMC Vet Res 2015;11:102.
    doi: 10.1186/s12917-015-0416-7pmc: PMC4416348pubmed: 25929692google scholar: lookup
  11. Tsujimura K, Oyama T, Katayama Y, Muranaka M, Bannai H, Nemoto M. Prevalence of equine herpesvirus type 1 strains of neuropathogenic genotype in a major breeding area of Japan.. J Vet Med Sci 2011;73(12):1663–1667.
    doi: 10.1292/jvms.11-0140pubmed: 21828961google scholar: lookup
  12. Telford EA, Watson MS, McBride K, Davison AJ. The DNA sequence of equine herpesvirus-1.. Virology 1992;189(1):304–316.
    doi: 10.1016/0042-6822(92)90706-Upubmed: 1318606google scholar: lookup
  13. Castro ER, Arbiza J. Detection and genotyping of equid herpesvirus 1 in Uruguay.. Rev Sci Tech 2017;36(3):799–806.
    doi: 10.20506/rst.36.3.2715pubmed: 30160700google scholar: lookup
  14. Goodman LB, Loregian A, Perkins GA, Nugent J, Buckles EL, Mercorelli B. A point mutation in a herpesvirus polymerase determines neuropathogenicity.. PLoS Pathog 2007;3(11):e160.
    doi: 10.1371/journal.ppat.0030160pmc: PMC2065875pubmed: 17997600google scholar: lookup
  15. Khusro A, Aarti C, Rivas-Caceres RR, Barbabosa-Pliego A. Equine herpesvirus-I infection in horses: recent updates on its pathogenicity, vaccination, and preventive management strategies.. J Equine Vet Sci 2020;87:102923.
    doi: 10.1016/j.jevs.2020.102923pubmed: 32172913google scholar: lookup
  16. Allen GP, Breathnach CC. Quantification by real-time PCR of the magnitude and duration of leucocyte-associated viraemia in horses infected with neuropathogenic vs. non-neuropathogenic strains of EHV-1.. Equine Vet J 2006;38(3):252–257.
    doi: 10.2746/042516406776866453pubmed: 16706281google scholar: lookup
  17. Bryant NA, Wilkie GS, Russell CA, Compston L, Grafham D, Clissold L. Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks.. Transbound Emerg Dis 2018;65(3):817–832.
    doi: 10.1111/tbed.12809pmc: PMC5947664pubmed: 29423949google scholar: lookup
  18. Mumford J, Hannant D, Jesset D, O'Neill T, Smith K, Ostlund E. Abortigenic and neurological disease caused by experimental infection with equid herpesvirus-1.. In: Nakajima H, Plowright W, editors. International conference on equine infectious diseases: Newmarket. R&W Publications; 1994. pp. 261–275.
  19. Gardiner DW, Lunn DP, Goehring LS, Chiang YW, Cook C, Osterrieder N. Strain impact on equine herpesvirus type 1 (EHV-1) abortion models: viral loads in fetal and placental tissues and foals.. Vaccine 2012;30(46):6564–6572.
    doi: 10.1016/j.vaccine.2012.08.046pubmed: 22944628google scholar: lookup
  20. Nugent J, Birch-Machin I, Smith KC, Mumford JA, Swann Z, Newton JR. Analysis of equid herpesvirus 1 strain variation reveals a point mutation of the DNA polymerase strongly associated with neuropathogenic versus nonneuropathogenic disease outbreaks.. J Virol 2006;80(8):4047–4060.
    doi: 10.1128/JVI.80.8.4047-4060.2006pmc: PMC1440451pubmed: 16571821google scholar: lookup
  21. Kolb AW, Lewin AC, Moeller Trane R, McLellan GJ, Brandt CR. Phylogenetic and recombination analysis of the herpesvirus genus varicellovirus.. BMC Genom 2017;18(1):887.
    doi: 10.1186/s12864-017-4283-4pmc: PMC5697016pubmed: 29157201google scholar: lookup
  22. Vaz PK, Horsington J, Hartley CA, Browning GF, Ficorilli NP, Studdert MJ. 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;97(3):747–755.
    doi: 10.1099/jgv.0.000378pmc: PMC5381393pubmed: 26691326google scholar: lookup
  23. Diallo IS, Hewitson G, Wright L, Rodwell BJ, Corney BG. Detection of equine herpesvirus type 1 using a real-time polymerase chain reaction.. J Virol Methods 2006;131(1):92–98.
    doi: 10.1016/j.jviromet.2005.07.010pubmed: 16137772google scholar: lookup
  24. Lewin AC, Coghill LM, Mironovich M, Liu CC, Carter RT, Ledbetter EC. Phylogenomic analysis of global isolates of canid alphaherpesvirus 1.. Viruses 2020;12(12):1421.
    doi: 10.3390/v12121421pmc: PMC7764265pubmed: 33322040google scholar: lookup
  25. Marino ME, Mironovich MA, Ineck NE, Citino SB, Emerson JA, Maggs DJ. Full viral genome sequencing and phylogenomic analysis of feline herpesvirus type 1 (FHV-1) in cheetahs (Acinonyx jubatus). Viruses 2021;13(11):2307.
    doi: 10.3390/v13112307pmc: PMC8625435pubmed: 34835113google scholar: lookup
  26. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability.. Mol Biol Evol 2013;30(4):772–780.
    doi: 10.1093/molbev/mst010pmc: PMC3603318pubmed: 23329690google scholar: lookup
  27. Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates.. Nat Methods 2017;14(6):587–589.
    doi: 10.1038/nmeth.4285pmc: PMC5453245pubmed: 28481363google scholar: lookup
  28. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era.. Mol Biol Evol 2020;37(5):1530–1534.
    doi: 10.1093/molbev/msaa015pmc: PMC7182206pubmed: 32011700google scholar: lookup
  29. Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies.. Mol Biol Evol 2006;23(2):254–267.
    doi: 10.1093/molbev/msj030pubmed: 16221896google scholar: lookup
  30. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms.. Mol Biol Evol 2018;35(6):1547–1549.
    doi: 10.1093/molbev/msy096pmc: PMC5967553pubmed: 29722887google scholar: lookup
  31. 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.
    doi: 10.1093/ve/vev003pmc: PMC5014473pubmed: 27774277google scholar: lookup
  32. Jin L, Nei M. Limitations of the evolutionary parsimony method of phylogenetic analysis.. Mol Biol Evol 1990;7(1):82–102.
    pubmed: 2299983
  33. Martin D, Rybicki E. RDP: detection of recombination amongst aligned sequences.. Bioinformatics 2000;16(6):562–563.
    doi: 10.1093/bioinformatics/16.6.562pubmed: 10980155google scholar: lookup
  34. Padidam M, Sawyer S, Fauquet CM. Possible emergence of new geminiviruses by frequent recombination.. Virology 1999;265(2):218–225.
    doi: 10.1006/viro.1999.0056pubmed: 10600594google scholar: lookup
  35. Smith JM. Analyzing the mosaic structure of genes.. J Mol Evol 1992;34(2):126–129.
    doi: 10.1007/BF00182389pubmed: 1556748google scholar: lookup
  36. Posada D, Crandall KA. Evaluation of methods for detecting recombination from DNA sequences: computer simulations.. Proc Natl Acad Sci U S A 2001;98(24):13757–13762.
    doi: 10.1073/pnas.241370698pmc: PMC61114pubmed: 11717435google scholar: lookup
  37. Gibbs MJ, Armstrong JS, Gibbs AJ. Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences.. Bioinformatics 2000;16(7):573–582.
    doi: 10.1093/bioinformatics/16.7.573pubmed: 11038328google scholar: lookup
  38. Lewin AC, Kolb AW, McLellan GJ, Bentley E, Bernard KA, Newbury SP. Genomic, recombinational and phylogenetic characterization of global feline herpesvirus 1 isolates.. Virology 2018;518:385–397.
    doi: 10.1016/j.virol.2018.03.018pmc: PMC5935452pubmed: 29605685google scholar: lookup
  39. Malik P, Bálint A, Dán A, Pálfi V. Molecular characterisation of the ORF68 region of equine herpesvirus-1 strains isolated from aborted fetuses in Hungary between 1977 and 2008.. Acta Vet Hung 2012;60(1):175–187.
    doi: 10.1556/avet.2012.015pubmed: 22366142google scholar: lookup
  40. Matczuk AK, Skarbek M, Jackulak NA, Bażanów BA. Molecular characterisation of equid alphaherpesvirus 1 strains isolated from aborted fetuses in Poland.. Virol J 2018;15(1):186.
    doi: 10.1186/s12985-018-1093-5pmc: PMC6276253pubmed: 30509297google scholar: lookup
  41. Lunn DP, Davis-Poynter N, Flaminio MJ, Horohov DW, Osterrieder K, Pusterla N. Equine herpesvirus-1 consensus statement.. J Vet Intern Med 2009;23(3):450–461.
    doi: 10.1111/j.1939-1676.2009.0304.xpubmed: 19645832google scholar: lookup
  42. Mori E, Borges AS, Delfiol DJ, Oliveira Filho JP, Gonçalves RC, Cagnini DQ. First detection of the equine herpesvirus 1 neuropathogenic variant in Brazil.. Rev Sci Tech 2011;30(3):949–954.
    doi: 10.20506/rst.30.3.2090pubmed: 22435205google scholar: lookup
  43. Smith KL, Allen GP, Branscum AJ, Frank Cook R, Vickers ML, Timoney PJ. The increased prevalence of neuropathogenic strains of EHV-1 in equine abortions.. Vet Microbiol 2010;141(1–2):5–11.
    doi: 10.1016/j.vetmic.2009.07.030pubmed: 19733451google scholar: lookup
  44. Pusterla N, Barnum S, Lawton K, Wademan C, Corbin R, Hodzic E. Investigation of the EHV-1 genotype (N(752), D(752), and H(752)) in swabs collected from equids with respiratory and neurological disease and abortion from the United States (2019–2022). J Equine Vet Sci 2023;123:104244.
    doi: 10.1016/j.jevs.2023.104244pubmed: 36773852google scholar: lookup
  45. Pusterla N, Barnum S, Miller J, Varnell S, Dallap-Schaer B, Aceto H. Investigation of an EHV-1 outbreak in the United States Caused by a new H(752) genotype.. Pathogens 2021;10(6):747.
    doi: 10.3390/pathogens10060747pmc: PMC8231618pubmed: 34199153google scholar: lookup
  46. Sutton G, Thieulent C, Fortier C, Hue ES, Marcillaud-Pitel C, Pléau A. Identification of a new equid herpesvirus 1 DNA polymerase (ORF30) genotype with the isolation of a C(2254)/H(752) strain in French horses showing no major impact on the strain behaviour.. Viruses 2020;12(10):1160.
    doi: 10.3390/v12101160pmc: PMC7650556pubmed: 33066315google scholar: lookup
  47. Loncoman CA, Vaz PK, Coppo MJ, Hartley CA, Morera FJ, Browning GF. Natural recombination in alphaherpesviruses: Insights into viral evolution through full genome sequencing and sequence analysis.. Infect Genet Evol 2017;49:174–185.
    doi: 10.1016/j.meegid.2016.12.022pubmed: 28017915google scholar: lookup
  48. Burrel S, Boutolleau D, Ryu D, Agut H, Merkel K, Leendertz FH. Ancient recombination events between human herpes simplex viruses.. Mol Biol Evol 2017;34(7):1713–1721.
    doi: 10.1093/molbev/msx113pmc: PMC5455963pubmed: 28369565google scholar: lookup
  49. Kolb AW, Larsen IV, Cuellar JA, Brandt CR. Genomic, phylogenetic, and recombinational characterization of herpes simplex virus 2 strains.. J Virol 2015;89(12):6427–6434.
    doi: 10.1128/JVI.00416-15pmc: PMC4474301pubmed: 25855744google scholar: lookup
  50. Lee K, Kolb AW, Sverchkov Y, Cuellar JA, Craven M, Brandt CR. Recombination analysis of herpes simplex virus 1 reveals a bias toward GC content and the inverted repeat regions.. J Virol 2015;89(14):7214–7223.
    doi: 10.1128/JVI.00880-15pmc: PMC4473588pubmed: 25926637google scholar: lookup
  51. Kuny CV, Szpara ML. Alphaherpesvirus genomics: past, present and future.. Curr Issues Mol Biol 2021;42:41–80.
    pmc: PMC7946737pubmed: 33159012
Subscribe to our newsletter
Join 99,344 horse owners like you who receive our email updates on horse health and nutrition.