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Transboundary and emerging diseases2021; 69(3); 1010-1019; doi: 10.1111/tbed.14056

Use of nanopore sequencing to characterize african horse sickness virus (AHSV) from the African horse sickness outbreak in thailand in 2020.

Abstract: African horse sickness (AHS) is a highly infectious and deadly disease despite availability of vaccines. Molecular characterization of African horse sickness virus (AHSV) detected from the March 2020 Thailand outbreak was carried out by whole-genome sequencing using Nanopore with a Sequence-Independent Single Primer Amplification (SISPA) approach. Nucleotide sequence of the whole genome was compared with closest matching AHSV strains using phylogenetic analyses and the AHSV-1 virus shared high sequence identity with isolates from the same outbreak. Substitution analysis revealed non-synonymous and synonymous substitutions in the VP2 gene as compared to circulating South African strains. The use of sequencing technologies, such as Nanopore with SISPA, has enabled rapid detection, identification and detailed genetic characterization of the AHS virus for informed decision-making and implementation of disease control measures. Active genetic information sharing has also allowed emergence of AHSV to be better monitored on a global basis.
© 2021 The Authors. Transboundary and Emerging Diseases published by Wiley-VCH GmbH.
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Publication Date: 2021-03-30 PubMed ID: 33682298DOI: 10.1111/tbed.14056Google 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.

This research study investigates African horse sickness, a severe disease, by using advanced genomic sequencing techniques. The study offers a detailed genetic analysis of the virus that caused the 2020 outbreak in Thailand, providing critical insights for future disease control measures.

Research Study Overview

  • The research focuses on African horse sickness (AHS), a highly lethal and contagious disease that affects horses. Despite the availability of vaccines, the disease remains a significant threat.
  • The researchers used advanced genomic sequencing techniques to analyze samples from a 2020 outbreak of AHS in Thailand.
  • Nanopore sequencing and a method called Sequence-Independent Single Primer Amplification (SISPA) were used to carry out whole-genome sequencing of the African horse sickness virus (AHSV).

Findings of the Study

  • The whole-genome sequencing allowed the researchers to compare the nucleotide sequence of the entire genome of the AHSV identified in Thailand with existing strains of the virus.
  • Phylogenetic analysis, a method used to depict the evolutionary relationships between species, revealed that AHSV-1 virus from the Thailand outbreak shared a high level of genetic similarity with other isolates from the same breakout.
  • A detailed substitution analysis, which studied changes in the genetic code, showed both non-synonymous and synonymous substitutions in a critical gene called VP2 when compared to the strains common in South Africa. Non-synonymous substitutions are changes that affect protein sequence, while synonymous substitutions do not.

Implications of the Research

  • This study provided detailed genetic characterization of the AHSV responsible for the recent outbreak in Thailand, which is crucial information for the development and implementation of disease control measures.
  • The use of advanced sequencing technologies like Nanopore with SISPA has made it possible to quickly identify and examine the genetics of the virus in detail.
  • Sharing the genetic information of AHSV can improve global monitoring of the virus. It can help in predicting and responding to future outbreaks by understanding the changes and trends in the disease’s evolution.

Cite This Article

APA
Toh X, Wang Y, Rajapakse MP, Lee B, Songkasupa T, Suwankitwat N, Kamlangdee A, Judith Fernandez C, Huangfu T. (2021). Use of nanopore sequencing to characterize african horse sickness virus (AHSV) from the African horse sickness outbreak in thailand in 2020. Transbound Emerg Dis, 69(3), 1010-1019. https://doi.org/10.1111/tbed.14056

Publication

Transboundary and emerging diseases
ISSN: 1865-1682
NlmUniqueID: 101319538
Country: Germany
Language: English
Volume: 69
Issue: 3
Pages: 1010-1019

Researcher Affiliations

Toh, Xinyu
  • Center for Animal & Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), Singapore.
Wang, Yifan
  • Center for Animal & Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), Singapore.
Rajapakse, Menaka Priyadharsani
  • Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore.
Lee, Bernett
  • Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore.
Songkasupa, Tapanut
  • Virology section, Department of Livestock Development, National Institute of Animal Health, Bangkok, Thailand.
Suwankitwat, Nutthakarn
  • Virology section, Department of Livestock Development, National Institute of Animal Health, Bangkok, Thailand.
Kamlangdee, Attapon
  • Faculty of Veterinary Medicine, Kasetsart university, Kamphaengsean, Thailand.
Judith Fernandez, Charlene
  • Center for Animal & Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), Singapore.
Huangfu, Taoqi
  • Center for Animal & Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), Singapore.

MeSH Terms

  • African Horse Sickness
  • African Horse Sickness Virus
  • Animals
  • Disease Outbreaks / veterinary
  • Horse Diseases / epidemiology
  • Horses
  • Nanopore Sequencing / veterinary
  • Phylogeny
  • Thailand / epidemiology
  • Viral Vaccines

Grant Funding

  • National Parks Board - Singapore

References

This article includes 40 references
  1. Agüero M, Gómez-Tejedor C, Angeles Cubillo M, Rubio C, Romero E, Jiménez-Clavero A. Real-time fluorogenic reverse transcription polymerase chain reaction assay for detection of African horse sickness virus. Journal of Veterinary Diagnostic Investigation 20, 325-328.
  2. Barnard B J. Epidemiology of African horse sickness and the role of the zebra in South Africa. Archives of Virology. Supplementum 14, 13-19.
  3. Bryans, J. T., & H. Gerber (Eds.) (1978). Veterinary Publications: Princeton. NJ. (pp. 401-403).
  4. Burrage T G, Laegreid W W. African horsesickness: Pathogenesis and immunity. Comparative Immunology, Microbiology and Infectious Diseases 17, 275-285.
    doi: 10.1016/0147-9571(94)90047-7google scholar: lookup
  5. Chrzastek K, Lee D H, Smith D, Sharma P, Suarez D L, Pantin-Jackwood M, Kapczynski D R. Use of Sequence-Independent, Single-Primer-Amplification (SISPA) for rapid detection, identification, and characterization of avian RNA viruses. Virology 509, 159-166.
    doi: 10.1016/j.virol.2017.06.019google scholar: lookup
  6. Coetzer J A W, Erasmus B J. African horse sickness. In J. A. W. Coetzer, G. R. Thomson, & R. C. Tustin (Eds.), Infectious diseases of live-stock with special reference to southern Africa, Vol. 1 (pp. 460-475).
  7. Coetzer J A W, Guthrie A J. African horse sickness. In J. A. W. Coetzer, R. C. Tustin (Eds.), Infectious Diseases of Livestock, Africa. 2nd ed. : Oxford University Press, 1231-1246.
  8. Crafford J E, Lourens C W, Smit T K, Gardner I A, MacLachlan N J, Guthrie A J. Serological response of foals to polyvalent and monovalent live-attenuated African horse sickness virus vaccines. Vaccine 32, 3611-3616.
    doi: 10.1016/j.vaccine.2014.04.087google scholar: lookup
  9. Erasmus B A. New Approach to Polyvalent Immunization Against African Horsesickness. In Proceedings of the 4th International Conference on Equine Infectious DiseasesLyonFrance, 24-27 September 1976.
  10. Fernández-Pinero J, Fernández-Pacheco P, Rodríguez B, Sotelo E, Robles A, Arias M, Sánchez-Vizcaíno J M. Rapid and sensitive detection of African horse sickness virus by real-time PCR. Research in Veterinary Science 86, 353-358.
    doi: 10.1016/j.rvsc.2008.07.015google scholar: lookup
  11. Gohre D S, Khot J B, Paranjpe V L, Manjrekar S L. Observations on the outbreak of South African horse sickness in India during 1960-1961. Bombay Vet Coll Meg 5-15.
  12. Goodwin S, Gurtowski J, Ethe-Sayers S, Deshpande P, Schatz M C, McCombie W R. Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome. Genome Research 25, 1750-1756.
    doi: 10.1101/gr.191395.115google scholar: lookup
  13. Greninger A L, Chen E C, Sittler T, Scheinerman A, Roubinian N, Yu G, Kim E, Pillai D R, Guyard C, Mazzulli T, Isa P, Arias C F, Hackett J, Schochetman G, Miller S, Tang P, Chiu C Y. A metagenomic analysis of pandemic influenza A (2009 H1N1) infection in patients from North America. PLoS One 5(10):e13381.
    doi: 10.1371/journal.pone.0013381google scholar: lookup
  14. Greninger A L, Naccache S N, Federman S, Yu G, Mbala P, Bres V, Stryke D, Bouquet J, Somasekar S, Linnen J M, Dodd R, Mulembakani P, Schneider B S, Muyembe-Tamfum J J, Stramer S L, Chiu C Y. Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genome Medicine 7, 99.
    doi: 10.1186/s13073-015-0220-9google scholar: lookup
  15. Guthrie A J, Maclachlan N J, Joone C, Lourens C W, Weyer C T, Quan M, Monyai M S, Gardner I A. Diagnostic accuracy of a duplex real-time reverse transcription quantitative PCR assay for detection of African horse sickness virus. Journal of Virological Methods 189, 30-35.
    doi: 10.1016/j.jviromet.2012.12.014google scholar: lookup
  16. Guthrie A J, Weyer C T. African horse sickness. In K. A. Sprayberry, & N. E. Robinson (Eds.), Robinson’s Current Therapy in Equine Medicine, 7th ed. (pp. 150-151).
  17. Hasnaoui H, el Harrak M, Zientara S, Laviada M, Hamblin C. Serological and virological responses in mules and donkeys following inoculation with African horse sickness virus serotype 4. Archives of Virology Supplementum 14, 29-36.
  18. Hassan S S, Roy P. Expression and functional characterization of bluetongue virus VP2 protein: Role in cell entry. Journal of Virology 73, 9832-9842.
    doi: 10.1128/jvi.73.12.9832-9842.1999google scholar: lookup
  19. Hazrati A. Identification and typing of horse-sickness virus strains isolated in the recent epizootic of the disease in Morocco, Tunisia, and Algeria. Archives of Razi Institute 19, 131-143.
  20. King S, Rajko-Nenow P, Ashby M, Frost L, Carpenter S, Batten C. Outbreak of African horse sickness in Thailand. Transboundary and Emerging Diseases .
    doi: 10.1111/tbed.13701google scholar: lookup
  21. Lubroth J. African Horsesickness and the epizootic in Spain 1987. Equine Pract 10, 26-33.
  22. Martínez-Torrecuadrada J L, Langeveld J, Meloen R H, Casal J I. Definition of neutralizing sites on African horse sickness virus serotype 4 VP2 at the level of peptides. Journal of General Virology 82, 2415-2424.
    doi: 10.1099/0022-1317-82-10-2415google scholar: lookup
  23. Meiswinkel R, Paweska J T. Evidence for a new field Culicoides vector of African horse sickness in South Africa. Preventive Veterinary Medicine 60, 243-253.
    doi: 10.1016/s0167-5877(02)00231-3google scholar: lookup
  24. Meiswinkel R, Venter G J, Nevill E M. Vectors: Culicoides spp.. In J. A. W. Coetzer, & R. C. Tustin (Eds.), South Africa: (Infectious Diseases of Livestock with Special Reference to South Africa), Vol. 1, 2nd ed. (pp. 93-136).
  25. Mellor P S. African horse sickness: Transmission and epidemiology. Veterinary Research 24, 199-212.
  26. Mellor P S, Boorman J. The transmission and geographical spread of African horse sickness and bluetongue viruses. Annals of Tropical Medicine and Parasitology 89, 1-15.
    doi: 10.1080/00034983.1995.11812923google scholar: lookup
  27. Naccache S N, Federman S, Veeraraghavan N, Zaharia M, Lee D, Samayoa E, Bouquet J, Greninger A L, Luk K-C, Enge B, Wadford D A, Messenger S L, Genrich G L, Pellegrino K, Grard G, Leroy E, Schneider B S, Fair J N, Martinez M A, Chiu C Y. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Research 24, 1180-1192.
    doi: 10.1101/gr.171934.113google scholar: lookup
  28. Quan M, Lourens C W, MacLachlan N J, Gardner I A, Guthrie A J. Development and optimisation of a duplex real-time reverse transcription quantitative PCR assay targeting the VP7 and NS2 genes of African horse sickness virus. Journal of Virological Methods 167, 45-52.
    doi: 10.1016/j.jviromet.2010.03.009google scholar: lookup
  29. Rodriguez M, Hooghuis H, Castano M. African horse sickness in Spain. Veterinary Microbiology 33, 129-142.
    doi: 10.1016/0378-1135(92)90041-qgoogle scholar: lookup
  30. Roy P, Merten P P, Casal I. African horse sickness virus structure. Comparative Immunology, Microbiology and Infectious Diseases 17, 243-273.
    doi: 10.1016/0147-9571(94)90046-9google scholar: lookup
  31. Stecher G, Tamura K, Kumar S. Molecular Evolutionary Genetics Analysis (MEGA) for macOS. Molecular Biology and Evolution 37, 1237-1239.
    doi: 10.1093/molbev/msz312google scholar: lookup
  32. Vilsker M, Moosa Y, Nooij S, Fonseca V, Ghysens Y, Dumon K, Pauwels R, Alcantara L C, Vanden Eynden E, Vandamme A M, Deforche K, de Oliveira T. Genome Detective: An automated system for virus identification from high-throughput sequencing data. Bioinformatics 35, 871-873.
    doi: 10.1093/bioinformatics/bty695google scholar: lookup
  33. Von Teichman B F, Dungu B, Smit T K. In vivo cross-protection to African horse sickness Serotypes 5 and 9 after vaccination with Serotypes 8 and 6. Vaccine 28, 6505-6517.
    doi: 10.1016/j.vaccine.2010.06.105google scholar: lookup
  34. Weyer C T, Grewar J D, Burger P, Rossouw E, Lourens C, Joone C, le Grange M, Coetzer P, Venter E, Martin D P, MacLachlan N J, Guthrie A J. African horse sickness caused by genome reassortment and reversion to virulence of live, attenuated vaccine viruses, South Africa, 2004-2014. Emerging Infectious Diseases 22, 2087-2096.
    doi: 10.3201/eid2212.160718google scholar: lookup
  35. Weyer C T, Joone C, Lourens C W, Monyai M S, Koekemoer O, Grewar J D, van Schalkwyk A, Majiwa P O, MacLachlan N J, Guthrie A J. Development of three triplex real-time reverse transcription PCR assays for the qualitative molecular typing of the nine serotypes of African horse sickness virus. Journal of Virological Methods 223, 69-74.
    doi: 10.1016/j.jviromet.2015.07.015google scholar: lookup
  36. World Organization for Animal Health. Infection with African horse sickness virus. Terrestrial Animal Health Code .
  37. Zhang X, Boyce M, Bhattacharya B, Zhang X, Schein S, Roy P, Zhou Z H. Bluetongue virus coat protein VP2 contains sialic acid-binding domains, and VP5 resembles enveloped virus fusion proteins. Proceedings of the National Academy of Sciences of the United States of America 107, 6292-6297.
    doi: 10.1073/pnas.0913403107google scholar: lookup
  38. Zientara S, Sailleau C, Moulay S, Plateau E, Crucière C. Diagnosis and molecular epidemiology of the African horsesickness virus by the polymerase chain reaction and restriction patterns. Veterinary Research 24, 385-395.
  39. Zientara S, Sailleau C, Moulay S, Wade-Evans A, Cruciere C. Application of the polymerase chain reaction to the detection of African horse sickness viruses. Journal of Virological Methods 53, 47-54.
    doi: 10.1016/0166-0934(94)00175-ggoogle scholar: lookup
  40. Zientara S, Weyer C T, Lecollinet S. African horse sickness. Revue Scientifique Et Technique (International Office of Epizootics) 34(2), 315-327.
    doi: 10.20506/rst.34.2.2359google scholar: lookup

Citations

This article has been cited 12 times.
  1. Chaves M, Hashish A, Goraichuk IV, Casserta LC, Mears MC, Gadu E, Bakre A, Alexander Morris ER, Shelkamy MMS, Nadendla S, Perez DR, El-Gazzar M. Nanopore sequencing in veterinary medicine: from concepts to clinical applications. Front Cell Infect Microbiol 2025;15:1701570.
    doi: 10.3389/fcimb.2025.1701570pubmed: 41341958google scholar: lookup
  2. Pipitpornsirikul P, Thangthamniyom N, Laikul A, Songkasupa T, Pathomsakulwong W, Apichaimongkonkun T, Kasemsuwan S, E-Kobon T, Lekcharoensuk P. The Viremic Phase and Humoral Immune Response Against African Horse Sickness Virus That Emerged in Thailand in 2020. Vet Sci 2025 Sep 11;12(9).
    doi: 10.3390/vetsci12090878pubmed: 41012803google scholar: lookup
  3. Li H, Gao J, Xiong H, Yishake D, Liu L, Kong J, Chen Q, Fang X, Weng W. Electrostatically Adjustable AuNR-Mediated Thermal-Start Isothermal Nucleic Acid Amplification. ACS Omega 2025 Sep 16;10(36):41524-41531.
    doi: 10.1021/acsomega.5c05097pubmed: 40978397google scholar: lookup
  4. Ripoll L, Iserte J, Cerrudo CS, Presti D, Serrat JH, Poma R, Mangione FAJ, Micheloud GA, Gioria VV, Berrón CI, Zago MP, Borio C, Bilen M. Insect-specific RNA viruses detection in Field-Caught Aedes aegypti mosquitoes from Argentina using NGS technology. PLoS Negl Trop Dis 2025 Jan;19(1):e0012792.
    doi: 10.1371/journal.pntd.0012792pubmed: 39792957google scholar: lookup
  5. Ashby M, Moore R, King S, Newbrook K, Flannery J, Batten C. Designing a Multiplex PCR-xMAP Assay for the Detection and Differentiation of African Horse Sickness Virus, Serotypes 1-9. Microorganisms 2024 May 3;12(5).
    doi: 10.3390/microorganisms12050932pubmed: 38792762google scholar: lookup
  6. Zheng P, Zhou C, Ding Y, Liu B, Lu L, Zhu F, Duan S. Nanopore sequencing technology and its applications. MedComm (2020) 2023 Aug;4(4):e316.
    doi: 10.1002/mco2.316pubmed: 37441463google scholar: lookup
  7. Schulz A, Sadeghi B, Stoek F, King J, Fischer K, Pohlmann A, Eiden M, Groschup MH. Whole-Genome Sequencing of Six Neglected Arboviruses Circulating in Africa Using Sequence-Independent Single Primer Amplification (SISPA) and MinION Nanopore Technologies. Pathogens 2022 Dec 8;11(12).
    doi: 10.3390/pathogens11121502pubmed: 36558837google scholar: lookup
  8. Wang Y, Ong J, Ng OW, Songkasupa T, Koh EY, Wong JPS, Puangjinda K, Fernandez CJ, Huangfu T, Ng LC, Chang SF, Yap HH. Development of Differentiating Infected from Vaccinated Animals (DIVA) Real-Time PCR for African Horse Sickness Virus Serotype 1. Emerg Infect Dis 2022 Dec;28(12):2446-2454.
    doi: 10.3201/eid2812.220594pubmed: 36417933google scholar: lookup
  9. Dotto-Maurel A, Pelletier C, Morga B, Jacquot M, Faury N, Dégremont L, Bereszczynki M, Delmotte J, Escoubas JM, Chevignon G. Evaluation of tangential flow filtration coupled to long-read sequencing for ostreid herpesvirus type 1 genome assembly. Microb Genom 2022 Nov;8(11).
    doi: 10.1099/mgen.0.000895pubmed: 36355418google scholar: lookup
  10. Huggins LG, Colella V, Atapattu U, Koehler AV, Traub RJ. Nanopore Sequencing Using the Full-Length 16S rRNA Gene for Detection of Blood-Borne Bacteria in Dogs Reveals a Novel Species of Hemotropic Mycoplasma. Microbiol Spectr 2022 Dec 21;10(6):e0308822.
    doi: 10.1128/spectrum.03088-22pubmed: 36250862google scholar: lookup
  11. Plangsangmas T, Rattanathanya H, Tipkantha W, Sanannu S, Maikaew U, Thaeonoen J, Sangkharak B, Chinson P, Hin-On W, Kanatiyanont N, Siriaroonrat B, Chansue N, Ratanakorn P. Immobilization of captive plains zebras (Equus quagga) with a combination of etorphine hydrochloride, acepromazine, and xylazine hydrochloride. J Vet Med Sci 2022 Jan 24;84(1):181-185.
    doi: 10.1292/jvms.21-0458pubmed: 34866094google scholar: lookup
  12. Clemmons EA, Alfson KJ, Dutton JW 3rd. Transboundary Animal Diseases, an Overview of 17 Diseases with Potential for Global Spread and Serious Consequences. Animals (Basel) 2021 Jul 8;11(7).
    doi: 10.3390/ani11072039pubmed: 34359167google scholar: lookup
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