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Pathogens (Basel, Switzerland)2019; 8(2); doi: 10.3390/pathogens8020062

Whole Genome Sequencing of the First H3N8 Equine Influenza Virus Identified in Malaysia.

Abstract: In August 2015, Malaysia experienced an outbreak of acute respiratory disease in racehorses. Clinical signs observed were consistent with equine influenza (EI) infection. The index cases were horses recently imported from New Zealand. Rapid control measures, including temporary cancellation of racing, were implemented to minimize the impact of the outbreak. By November, the disease outbreak was resolved, and movement restrictions were lifted. The aim of this study was to confirm the clinical diagnosis and characterize the causal virus. A pan-reactive influenza type A real-time RT-PCR was used for confirmatory diagnosis. Antigenic characterization by haemagglutinin inhibition using a panel of specific ferret antisera indicated that the causal virus belonged to clade 1 of the H3N8 Florida sub-lineage. The genetic characterization was achieved by the whole genome sequencing of positive nasal swabs from clinically affected animals. Pylogenetic analysis of the haemagglutinin (HA) and neuraminidase (NA) genes demonstrated ≥99% homology with several EI strains that had recently circulated in the USA and Japan. The antigenic and genetic characterization did not indicate that the current World Organisation for Animal Health (OIE) recommendations for EI vaccine composition required modification.
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Publication Date: 2019-05-10 PubMed ID: 31083430PubMed Central: PMC6630255DOI: 10.3390/pathogens8020062Google Scholar: Lookup
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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 research explores an outbreak of equine influenza in racehorses in Malaysia in 2015 and uses genetic sequencing to identify the virus strain responsible, which was consistent with the H3N8 subtype normally associated with equine influenza.

Background of the Research

  • In 2015, Malaysia experienced a significant outbreak of acute respiratory disease amongst racehorses, characterized by symptoms indicative of equine influenza (EI) infection.
  • The initial cases were discovered in horses that had been recently imported from New Zealand.
  • Several control measures were immediately implemented, which included the temporary halt of racing activities. By November, the disease outbreak had been successfully contained and restrictions were lifted.

Aim and Approach of the Study

  • The objective of this study was to confirm the clinical diagnosis of equine influenza following the outbreak and characterize the virus responsible for the infection.
  • The researchers carried out a confirmatory diagnosis using an influenza type A real-time RT-PCR, which is a method used to detect and quantify specific genetic material in a sample.
  • The antigenic characterization of the virus was done using haemagglutinin inhibition along with a panel of ferret antisera.
  • The genetic characterization was attained by sequencing the entire genome from nasal swabs taken from the clinically affected animals.

Findings and Implications

  • The research identified the virus to belong to clade 1 of the H3N8 Florida sub-lineage, implicating this as the strain responsible for the equine influenza outbreak.
  • The phylogenetic analysis of haemagglutinin (HA) and neuraminidase (NA) genes showed high homology (≥99%) to several EI strains recently identified in the USA and Japan.
  • The study’s findings suggest that despite the outbreak and virus identification, there was no need for revision to the existing World Organisation for Animal Health’s recommendations for equine influenza vaccine composition.

The results of this study hold important implications for equine influenza surveillance and control measures, especially regarding international equine trade. Future monitoring efforts can be improved by utilizing the genetic information provided in this study.

Cite This Article

APA
Gahan J, Garvey M, Asmah Abd Samad R, Cullinane A. (2019). Whole Genome Sequencing of the First H3N8 Equine Influenza Virus Identified in Malaysia. Pathogens, 8(2). https://doi.org/10.3390/pathogens8020062

Publication

Pathogens (Basel, Switzerland)
ISSN: 2076-0817
NlmUniqueID: 101596317
Country: Switzerland
Language: English
Volume: 8
Issue: 2

Researcher Affiliations

Gahan, Jacinta
  • Virology Unit, The Irish Equine Centre, Johnstown, Naas, Co. Kildare W91 RH93, Ireland. JGahan@irishequinecentre.ie.
Garvey, Marie
  • Virology Unit, The Irish Equine Centre, Johnstown, Naas, Co. Kildare W91 RH93, Ireland. MGarvey@irishequinecentre.ie.
Asmah Abd Samad, Rozanah
  • Department of Veterinary Services, Federal Government Administration Centre, 62630 Putrajaya, Malaysia. rozanah@dvs.gov.my.
Cullinane, Ann
  • Virology Unit, The Irish Equine Centre, Johnstown, Naas, Co. Kildare W91 RH93, Ireland. ACullinane@irishequinecentre.ie.

Grant Funding

  • 2016 OIE / Department of Agriculture, Food and the Marine

Conflict of Interest Statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

References

This article includes 34 references
  1. Cullinane A, Newton J.R. Equine influenza-A global perspective.. Vet. Microbiol. 2013;167:205–214.
    doi: 10.1016/j.vetmic.2013.03.029pubmed: 23680107google scholar: lookup
  2. Cowled B, Ward M.P, Hamilton S, Garner G. The equine influenza epidemic in Australia: Spatial and temporal descriptive analyses of a large propagating epidemic.. Prev. Vet. Med. 2009;92:60–70.
    doi: 10.1016/j.prevetmed.2009.08.006pubmed: 19748691google scholar: lookup
  3. Woodward A.L, Rash A.S, Blinman D, Bowman S, Chambers T.M, Daly J.M, Damiani A, Joseph S, Lewis N, McCauley J.W. Development of a surveillance scheme for equine influenza in the UK and characterisation of viruses isolated in Europe, Dubai and the USA from 2010–2012.. Vet. Microbiol. 2014;169:113–127.
    doi: 10.1016/j.vetmic.2013.11.039pubmed: 24480583google scholar: lookup
  4. Lewis N, Daly J, Russell C, Horton D, Skepner E, Bryant N, Burke D, Rash A, Wood J, Chambers T. Antigenic and genetic evolution of equine influenza A (H3N8) virus from 1968 to 2007.. J. Virol. 2011;85:12742–12749.
    doi: 10.1128/JVI.05319-11pmc: PMC3209411pubmed: 21937642google scholar: lookup
  5. Bryant N.A, Rash A.S, Russell C.A, Ross J, Cooke A, Bowman S, MacRae S, Lewis N.S, Paillot R, Zanoni R. Antigenic and genetic variations in European and North American equine influenza virus strains (H3N8) isolated from 2006 to 2007.. Vet. Microbiol. 2009;138:41–52.
    doi: 10.1016/j.vetmic.2009.03.004pubmed: 19346084google scholar: lookup
  6. Daly J.M, Lai A.C.K, Binns M.M, Chambers T.M, Barrandeguy M, Mumford J.A. Antigenic and genetic evolution of equine H3N8 influenza A viruses.. J. Gen. Virol. 1996;77:661–671.
    doi: 10.1099/0022-1317-77-4-661pubmed: 8627254google scholar: lookup
  7. Lai A, Chambers T, Holland R, Morley P, Haines D, Townsend H, Barrandeguy M. Diverged evolution of recent equine-2 influenza (H3N8) viruses in the Western Hemisphere.. Arch. Virol. 2001;146:1063–1074.
    doi: 10.1007/s007050170106pubmed: 11504416google scholar: lookup
  8. Cullinane A. Equine influenza and air transport.. Equine Vet. Educ. 2014;26:456–457.
    doi: 10.1111/eve.12215pmc: PMC7163656pubmed: 32313389google scholar: lookup
  9. King E, Macdonald D. Report of the Board of Inquiry appointed by the Board of the National Horseracing Authority to conduct enquiry into the causes of the equine influenza which started in the Western cape in early December 2003 and spread to the Eastern Cape and Gauteng.. Aust. Equine Vet. 2004;23:139–142.
  10. Yamanaka T, Niwa H, Tsujimura K, Kondo T, Matsumura T. Epidemic of equine influenza among vaccinated racehorses in Japan in 2007.. J. Vet. Med. Sci. 2008;70:623–625.
    doi: 10.1292/jvms.70.623pubmed: 18628606google scholar: lookup
  11. Watson J, Daniels P, Kirkland P, Carroll A, Jeggo M. The 2007 outbreak of equine influenza in Australia: Lessons learned for international trade in horses.. Rev. Sci. Et Tech.-OIE. 2011;30:87–93.
    doi: 10.20506/rst.30.1.2021pubmed: 21809755google scholar: lookup
  12. Gildea S, Quinlivan M, Arkins S, Cullinane A. The molecular epidemiology of equine influenza in Ireland from 2007–2010 and its international significance.. Equine Vet. J. 2012;44:387–392.
    doi: 10.1111/j.2042-3306.2011.00472.xpubmed: 21978127google scholar: lookup
  13. Qi T, Guo W, Huang W, Dai L, Zhao L, Li H, Li X, Zhang X, Wang Y, Yan Y. Isolation and genetic characterization of H3N8 equine influenza virus from donkeys in China.. Vet. Microbiol. 2010;144:455–460.
    doi: 10.1016/j.vetmic.2010.01.006pubmed: 20153940google scholar: lookup
  14. Yondon M, Heil G.L, Burks J.P, Zayat B, Waltzek T.B, Jamiyan B.O, McKenzie P.P, Krueger W.S, Friary J.A, Gray G.C. Isolation and characterization of H3N8 equine influenza A virus associated with the 2011 epizootic in Mongolia.. Influenza Other Respir. Viruses. 2013;7:659–665.
    doi: 10.1111/irv.12069pmc: PMC3626732pubmed: 23289427google scholar: lookup
  15. Virmani N, Bera B, Singh B, Shanmugasundaram K, Gulati B, Barua S, Vaid R, Gupta A, Singh R. Equine influenza outbreak in India (2008–09): Virus isolation, sero-epidemiology and phylogenetic analysis of HA gene.. Vet. Microbiol. 2010;143:224–237.
    doi: 10.1016/j.vetmic.2009.12.007pubmed: 20053509google scholar: lookup
  16. Padalino B. Effects of the different transport phases on equine health status, behavior, and welfare: A review.. J. Vet. Behav. 2015;10:272–282.
    doi: 10.1016/j.jveb.2015.02.002google scholar: lookup
  17. Domingo E, Baranowski E, Ruiz-Jarabo C.M, Martín-Hernández A.M, Sáiz J.C, Escarmís C. Quasispecies structure and persistence of RNA viruses.. Emerg. Infect. Dis. 1998;4:521.
    doi: 10.3201/eid0404.980402pmc: PMC2640251pubmed: 9866728google scholar: lookup
  18. Murcia P.R, Wood J.L, Holmes E.C. Genome-scale evolution and phylodynamics of equine H3N8 influenza A virus.. J. Virol. 2011;85:5312–5322.
    doi: 10.1128/JVI.02619-10pmc: PMC3094979pubmed: 21430049google scholar: lookup
  19. Baz M, Paskel M, Matsuoka Y, Zengel J, Cheng X, Jin H, Subbarao K. Replication and immunogenicity of swine, equine and avian H3 subtype influenza viruses in mice and ferrets.. J. Virol. 2013;87:6901–6910.
    doi: 10.1128/JVI.03520-12pmc: PMC3676140pubmed: 23576512google scholar: lookup
  20. Dominguez M, Münstermann S, Guindos I, Timoney P. Equine disease events resulting from international horse movements: Systematic review and lessons learned.. Equine Vet. J. 2016;48:641–653.
    doi: 10.1111/evj.12523pubmed: 26509734google scholar: lookup
  21. Callinan I. Equine Influenza: The August 2007 Outbreak in Australia. Report of the Equine Influenza Enquiry.. 2008.
  22. Beuttemmüller E.A, Woodward A, Rash A, dos Santos Ferraz L.E, Alfieri A.F, Alfieri A.A, Elton D. Characterisation of the epidemic strain of H3N8 equine influenza virus responsible for outbreaks in South America in 2012.. Virol. J. 2016;13:45.
    doi: 10.1186/s12985-016-0503-9pmc: PMC4799594pubmed: 26993620google scholar: lookup
  23. Favaro P.F, Fernandes W.R, Reischak D, Brandão P.E, de Souza Silva S.O, Richtzenhain L.J. Evolution of equine influenza viruses (H3N8) during a Brazilian outbreak, 2015.. Braz. J. Microbiol. 2017;49:336–346.
    doi: 10.1016/j.bjm.2017.07.003pmc: PMC5913825pubmed: 29100932google scholar: lookup
  24. Sreenivasan C.C, Jandhyala S.S, Luo S, Hause B.M, Thomas M, Knudsen D.E, Leslie-Steen P, Clement T, Reedy S.E, Chambers T.M. Phylogenetic Analysis and Characterization of a Sporadic Isolate of Equine Influenza A H3N8 from an Unvaccinated Horse in 2015.. Viruses. 2018;10:31.
    doi: 10.3390/v10010031pmc: PMC5795444pubmed: 29324680google scholar: lookup
  25. Khan A, Mushtaq M.H, Ahmad M.U.D, Nazir J, Farooqi S.H, Khan A. Molecular Epidemiology of a novel re-assorted epidemic strain of equine influenza virus in Pakistan in 2015–16.. Virus Res. 2017;240:56–63.
    doi: 10.1016/j.virusres.2017.07.022pubmed: 28757141google scholar: lookup
  26. Cullinane A, Elton D, Mumford J. Equine influenza—Surveillance and control.. Influenza Other Respir. Viruses. 2010;4:339–344.
    doi: 10.1111/j.1750-2659.2010.00176.xpmc: PMC4634605pubmed: 20958927google scholar: lookup
  27. Woodward A, Rash A.S, Medcalf E, Bryant N.A, Elton D.M. Using epidemics to map H3 equine influenza virus determinants of antigenicity.. Virology. 2015;481:187–198.
    doi: 10.1016/j.virol.2015.02.027pubmed: 25797606google scholar: lookup
  28. Gahan J, Garvey M, Gildea S, Gür G, Kagankaya A, Cullinane A. Whole genome sequencing and antigenic analysis of the first equine influenza virus identified in Turkey.. Influenza Other Respir. Viruses. 2017;12:374–382.
    doi: 10.1111/irv.12485pmc: PMC5907808pubmed: 28940727google scholar: lookup
  29. Heine H, Trinidad L, Selleck P, Lowther S. Rapid detection of highly pathogenic avian influenza H5N1 virus by Taqman reverse transcriptase–polymerase chain reaction.. Avian Dis. 2007;51:370–372.
    doi: 10.1637/7587-040206R.1pubmed: 17494586google scholar: lookup
  30. Rash A, Woodward A, Bryant N, McCauley J, Elton D. An efficient genome sequencing method for equine influenza [H3N8] virus reveals a new polymorphism in the PA-X protein.. Virology Journal. 2014;11:1–9.
    doi: 10.1186/1743-422X-11-159pmc: PMC4161859pubmed: 25183201google scholar: lookup
  31. Larkin M.A, Blackshields G, Brown N, Chenna R, McGettigan P.A, McWilliam H, Valentin F, Wallace I.M, Wilm A, Lopez R. Clustal W and Clustal X version 2.0.. Bioinformatics. 2007;23:2947–2948.
    doi: 10.1093/bioinformatics/btm404pubmed: 17846036google scholar: lookup
  32. Hall. BioEdit: A user-friendly sequence alignment editor and analysis program for Windows 95/98/NT.. Nucleic Acids Symp. 1999;41:95–98.
  33. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets.. Mol. Boil. Evol. 2016;33:1870–1874.
    doi: 10.1093/molbev/msw054pmc: PMC8210823pubmed: 27004904google scholar: lookup
  34. Shu Y, McCauley J. GISAID: Global initiative on sharing all influenza data–from vision to reality.. Eurosurveillance. 2017;22:30494.
    doi: 10.2807/1560-7917.ES.2017.22.13.30494pmc: PMC5388101pubmed: 28382917google scholar: lookup

Citations

This article has been cited 6 times.
  1. Yang Y, Guo K, Xu L, Guo W, Dong M, Liu W, Li S, Zhang Z, Chu X, Wang Y, Zhang Z, Hu Z, Wang X. Development and application of a NP-cELISA for the detection of nucleoprotein antibodies of equine influenza virus. Microbiol Spectr 2025 Oct 7;13(10):e0093925.
    doi: 10.1128/spectrum.00939-25pubmed: 40853243google scholar: lookup
  2. Wasik BR, Rothschild E, Voorhees IEH, Reedy SE, Murcia PR, Pusterla N, Chambers TM, Goodman LB, Holmes EC, Kile JC, Parrish CR. Understanding the divergent evolution and epidemiology of H3N8 influenza viruses in dogs and horses. Virus Evol 2023;9(2):vead052.
    doi: 10.1093/ve/vead052pubmed: 37692894google scholar: lookup
  3. Ahmed BM, Bayoumi MM, Farrag MA, Elgamal MA, Daly JM, Amer HM. Emergence of equine influenza virus H3Nx Florida clade 2 in Arabian racehorses in Egypt. Virol J 2022 Nov 12;19(1):185.
    doi: 10.1186/s12985-022-01917-9pubmed: 36371185google scholar: lookup
  4. Oladunni FS, Oseni SO, Martinez-Sobrido L, Chambers TM. Equine Influenza Virus and Vaccines. Viruses 2021 Aug 20;13(8).
    doi: 10.3390/v13081657pubmed: 34452521google scholar: lookup
  5. Yongfeng Y, Xiaobo S, Nan X, Jingwen Z, Wenqiang L. Detection of the epidemic of the H3N8 subtype of the equine influenza virus in large-scale donkey farms. Int J Vet Sci Med 2020;8(1):26-30.
    doi: 10.1080/23144599.2020.1739844pubmed: 32341914google scholar: lookup
  6. Cullinane A, Gahan J, Walsh C, Nemoto M, Entenfellner J, Olguin-Perglione C, Garvey M, Huang Fu TQ, Venner M, Yamanaka T, Barrandeguy M, Fernandez CJ. Evaluation of Current Equine Influenza Vaccination Protocols Prior to Shipment, Guided by OIE Standards. Vaccines (Basel) 2020 Feb 29;8(1).
    doi: 10.3390/vaccines8010107pubmed: 32121419google scholar: lookup
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