Journal of Veterinary Science

The Korean Society of Veterinary Science (대한수의학회)
권호 표지
DOI QR코드

DOI QR Code

Novel pan-lineage VP1 specific degenerate primers for precise genetic characterization of serotype O foot and mouth disease virus circulating in India

  • Received : 2022.12.12
  • Accepted : 2023.02.14
  • Published : 2023.05.31
Download PDF
⟨ Previous Next ⟩

Abstract

Analysis of the VP1 gene sequence of the foot and mouth disease virus (FMDV) is critical to understanding viral evolution and disease epidemiology. A standard set of primers have been used for the detection and sequence analysis of the VP1 gene of FMDV directly from suspected clinical samples with limited success. The study validated VP1-specific degenerate primer-based reverse transcription polymerase chain reaction (RT-PCR) for the qualitative detection and sequencing of serotype O FMDV lineages circulating in India. The novel degenerate primer-based RT-PCR amplifying the VP1 gene can circumvent the genetic heterogeneity observed in viruses after cell culture adaptation and facilitate precise viral gene sequence analysis from clinical samples.

Keywords

Acknowledgement

Infrastructure and funding provided to carry out the study by the Indian Council of Agriculture Research, New Delhi, and the National Animal Disease Control Program- FMD, Department of Animal Husbandry and Dairying, Government of India, is duly acknowledged.

References

  1. Knight-Jones TJ, Rushton J. The economic impacts of foot and mouth disease - what are they, how big are they and where do they occur? Prev Vet Med. 2013;112(3-4):161-173. https://doi.org/10.1016/j.prevetmed.2013.07.013
  2. Knowles NJ, Samuel AR. Molecular epidemiology of foot-and-mouth disease virus. Virus Res. 2003;91(1):65-80. https://doi.org/10.1016/S0168-1702(02)00260-5
  3. Hemadri D, Tosh C, Sanyal A, Venkataramanan R. Emergence of a new strain of type O foot-and-mouth disease virus: its phylogenetic and evolutionary relationship with the PanAsia pandemic strain. Virus Genes. 2002;25(1):23-34.
  4. Subramaniam S, Sanyal A, Mohapatra JK, Sharma GK, Biswal JK, Ranjan R, et al. Emergence of a novel lineage genetically divergent from the predominant Ind2001 lineage of serotype O foot-and-mouth disease virus in India. Infect Genet Evol. 2013;18:1-7. https://doi.org/10.1016/j.meegid.2013.04.027
  5. Subramaniam S, Mohapatra JK, Sharma GK, Biswal JK, Ranjan R, Rout M, et al. Evolutionary dynamics of foot-and-mouth disease virus O/ME-SA/Ind2001 lineage. Vet Microbiol. 2015;178(3-4):181-189. https://doi.org/10.1016/j.vetmic.2015.05.015
  6. Dahiya SS, Subramaniam S, Biswal JK, Das B, Prusty BR, Ali SZ, et al. Genetic characterization of foot-and-mouth disease virus serotype O isolates collected during 2014-2018 revealed dominance of O/ME-SA/Ind2001e and the emergence of a novel lineage in India. Transbound Emerg Dis. 2021;68(6):3498-3508. https://doi.org/10.1111/tbed.13954
  7. Davie J. The classification of subtype variants of the virus of foot-and-mouth disease. Bull Off Int Epizoot. 1962;17:34.
  8. Samuel AR, Knowles NJ. Foot-and-mouth disease type O viruses exhibit genetically and geographically distinct evolutionary lineages (topotypes). J Gen Virol. 2001;82(Pt 3):609-621. https://doi.org/10.1099/0022-1317-82-3-609
  9. Giridharan P, Hemadri D, Tosh C, Sanyal A, Bandyopadhyay SK. Development and evaluation of a multiplex PCR for differentiation of foot-and-mouth disease virus strains native to India. J Virol Methods. 2005;126(1-2):1-11. https://doi.org/10.1016/j.jviromet.2005.01.015
  10. Knowles NJ, Wadsworth J, Bachanek-Bankowska K, King DP. VP1 sequencing protocol for foot and mouth disease virus molecular epidemiology. Rev Sci Tech. 2016;35(3):741-755. https://doi.org/10.20506/rst.35.3.2565
  11. Beck E, Strohmaier K. Subtyping of European foot-and-mouth disease virus strains by nucleotide sequence determination. J Virol. 1987;61(5):1621-1629. https://doi.org/10.1128/jvi.61.5.1621-1629.1987
  12. Meyer RF, Pacciarini M, Hilyard EJ, Ferrari S, Vakharia VN, Donini G, et al. Genetic variation of foot-and-mouth disease virus from field outbreaks to laboratory isolation. Virus Res. 1994;32(3):299-312. https://doi.org/10.1016/0168-1702(94)90079-5
  13. Reid SM, Ferris NP, Hutchings GH, Samuel AR, Knowles NJ. Primary diagnosis of foot-and-mouth disease by reverse transcription polymerase chain reaction. J Virol Methods. 2000;89(1-2):167-176. https://doi.org/10.1016/S0166-0934(00)00213-5
  14. Saeed A, Khan QM, Waheed U, Arshad M, Asif M, Farooq M. RT-PCR evaluation for identification and sequence analysis of foot-and-mouth disease serotype O from 2006 to 2007 in Punjab, Pakistan. Comp Immunol Microbiol Infect Dis. 2011;34(2):95-101. https://doi.org/10.1016/j.cimid.2009.10.004
  15. Korevaar DA, Cohen JF, Reitsma JB, Bruns DE, Gatsonis CA, Glasziou PP, et al. Updating standards for reporting diagnostic accuracy: the development of STARD 2015. Res Integr Peer Rev. 2016;1(1):7.