Document Type : Original Article


1 Department of Microbiology, Karaj Branch, Islamic Azad University, Karaj, Iran

2 Foot and Mouth Disease Reference Laboratory, Razi Vaccine and Serum Research Institute, Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran

3 Department of Basic Sciences, School of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran


Despite widespread vaccination against foot-and-mouth disease, many outbreaks still occur in endemic areas. We attempted to determine the genetic and antigenic properties of the O/PanAsia-2/QOM-15 foot-and-mouth disease virus new vaccine strain. Thus, whole-genome sequencing was used to identify vulnerable pinpoint sites across the genome. The VP1 sequence (1D gene) of the O/PanAsia-2/QOM-15 viral genome was then compared to the VP1 sequences of two previously used vaccine strains, O/PanAsia (JQ321837) and O/PanAsia-2 (JN676146). The antigenic relationship of these three viruses was calculated by the two dimensional-virus neutralization test. At the nucleotide level, 47 single variants were identified, of which 19.00% were in the 5' untranslated region (UTR), 79.00% in the polyprotein region, and 2.00% in the 3' UTR region. Approximately half of the single nucleotide polymorphisms that have occurred in 1D gene resulted in amino acid (AA) substitutions in the VP1 structure. The single nucleotide polymorphisms also caused AA substitutions in other structural proteins, including VP2 and VP3, and some non-structural proteins (Lpro, 2C, and 3A). The O/PanAsia-2/QOM-15 shared higher sequence similarity with O/PanAsia-2 (91.00%) compared to O/PanAsia (87.30%). Evaluating r-value showed that the antigenic relationship of O/PanAsia-2/QOM-15 with O/PanAsia-2 (29.00%) was greater than that of the O/PanAsia (24.00%); however, all three viruses were immunologically distinct. After 10 years, the alteration of virus antigenicity and the lack of detectable adaptive pressure on VP1 sequence suggest that studying genetic dynamics beyond the VP1 region is necessary to evaluate FMDV pathogenicity and vaccine failure.


Main Subjects

  1. Zell R, Delwart E, Gorbalenya AE, et al. ICTV virus taxonomy profile: Picornaviridae. J Gen Virol 2017; 98(10): 2421-2422.
  2. Foot‐and‐mouth disease (infection with foot and mouth disease virus). Paris, France: World Organization for Animal Health; 2022.
  3. Compston P, Limon G, Häsler B. A systematic review of the methods used to analyze the economic impact of endemic foot‐and‐mouth disease. Transbound Emerg Dis 2022; 69(5): e2249-e2260.
  4. Belsham GJ. Towards improvements in foot-and-mouth disease vaccine performance. Acta Vet Scand 2020; 62(1): 20. doi: 10.1186/s13028-020-00519-1.
  5. Dong H, Liu P, Bai M, et al. Structural and molecular basis for foot-and-mouth disease virus neutralization by two potent protective antibodies. Protein Cell 2022; 13(6): 446-453.
  6. Brito BP, Rodriguez LL, Hammond JM, et al. Review of the global distribution of foot‐and‐mouth disease virus from 2007 to 2014. Transbound Emerg Dis 2017; 64(2): 316-332.
  7. Upadhyaya S, Mahapatra M, Mioulet V, et al. Molecular basis of antigenic drift in serotype O foot-and-mouth disease viruses (2013–2018) from Southeast Asia. Viruses 2021; 13(9): 1886. doi: 10.3390/v13091886.
  8. Dill V, Eschbaumer M. Cell culture propagation of foot-and-mouth disease virus: adaptive amino acid substitutions in structural proteins and their functional implications. Virus Genes 2020; 56(1): 1-15.
  9. Brown E, Freimanis G, Shaw AE, et al. Characterising foot-and-mouth disease virus in clinical samples using nanopore sequencing. Front Vet Sci 2021; 8: 656256. doi: 10.3389/fvets.2021.656256.
  10. Emami SJ, Bahonar AR, Mehrabadi MHF, et al. Evaluation of foot and mouth disease (FMD) vaccine using registered surveillance data. Trop Anim Health Prod 2022; 54(4): 215. doi: 10.1007/s11250-022-03204-9.
  11. Knowles NJ, Samuel AR. RT-PCR and sequencing protocols for the molecular epidemiology of exotic virus diseases of animals. Institute of Animal Health, Pirbright Laboratory, Surry, UK. 1998 6; 37.
  12. Sutton TDS, Clooney AG, Ryan FJ, et al. Choice of assembly software has a critical impact on virome characterisation. Microbiome 2019; 7(1): 12. doi: 10.1186/s40168-019-0626-5.
  13. Ghorbani A, Samarfard S, Eskandarzade N, et al. Comparative phylogenetic analysis of SARS-CoV-2 spike protein - possibility effect on virus spillover. Brief Bioinform 2021; 22(5): bbab144. doi: 10.1093/ bib/bbab144.
  14. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33(7): 1870-1874.
  15. Lukas SS. Molecular characterization of foot-and-mouth disease Virus recently recovered in Zambezi region, Namibia. PhD Thesis. Sokoine University of Agriculture. Morogoro, Tanzania: 2020.
  16. Mahravani H, Deljoo M. Assessment of foot and mouth virus subtype O2016 genetic alterations during successive passages in BHK monolayer. Iran J Virol 2019; 13(2): 1-10.
  17. Li K, Wang C, Yang F, et al. Virus - host interactions in foot-and-mouth disease virus infection. Front Immunol 2021; 12: 571509. doi: 10.3389/fimmu.2021.571509.
  18. Dill V, Hoffmann B, Zimmer A, et al. Adaption of FMDV Asia-1 to suspension culture: cell resistance is overcome by virus capsid alterations. Viruses 2017; 9(8): 231. doi: 10.3390/v9080231
  19. Han SC, Guo HC, Sun SQ. Three-dimensional structure of foot-and-mouth disease virus and its biological functions. Arch Virol 2015; 160(1): 1-16.
  20. Harmsen MM, Li H, Sun S, et al. Mapping of foot-and-mouth disease virus antigenic sites recognized by single-domain antibodies reveals different 146S particle specific sites and particle flexibility. Front Vet Sci 2023; 9: 1040802. doi: 10.3389/fvets.2022.1040802.
  21. Sarangi LN, Mohapatra JK, Subramaniam S, et al. Antigenic site variation in foot-and-mouth disease virus serotype O grown under vaccinal serum antibodies in vitro. Virus Res 2013; 176(1-2): 273-279.
  22. Lee HW, Yang CY, Lee MC, et al. The use of distinctive monoclonal antibodies in FMD VLP- and P1-based blocking ELISA for the seromonitoring of vaccinated swine. Int J Mol Sci 2022; 23(15): 8542. doi: 10.3390/ijms23158542.
  23. Li K, Wang S, Cao Y, et al. Development of foot-and-mouth disease virus-neutralizing monoclonal anti-bodies derived from plasmablasts of infected cattle and their germline gene usage. Front Immunol 2019; 10: 2870. doi: 10.3389/fimmu.2019.02870.
  24. Mahapatra M, Yuvaraj S, Madhanmohan M, et al. Antigenic and genetic comparison of foot-and-mouth disease virus serotype O Indian vaccine strain, O/IND/R2/75 against currently circulating viruses. Vaccine 2015; 33(5): 693-700.
  25. Lee G, Hwang JH, Kim A, et al. Analysis of amino acid mutations of the foot-and-mouth disease virus serotype O using both heparan sulfate and JMJD6 receptors. Viruses 2020; 12(9): 1012. doi: 10.3390/ v12091012.
  26. Mishu ID, Akter S, Alam ASMRU, et al. In silico evolutionary divergence analysis suggests the potentiality of capsid protein VP2 in serotype-independent foot-and-mouth disease virus detection. Front Vet Sci 2020; 7: 592. doi: 10.3389/fvets. 2020.00592.
  27. Fish I, Stenfeldt C, Palinski RM, et al. Into the deep (Sequence) of the foot-and-mouth disease virus gene pool: Bottlenecks and adaptation during infection in Naïve and vaccinated cattle. Pathogens 2020; 9(3): 208. doi: 10.3390/pathogens9030208.
  28. Asfor AS, Upadhyaya S, Knowles NJ, et al. Novel antibody binding determinants on the capsid surface of serotype O foot-and-mouth disease virus. J Gen Virol 2014; 95(Pt 5): 1104-1116.
  29. Pacheco JM, Gladue DP, Holinka LG, et al. A partial deletion in non-structural protein 3A can attenuate foot-and-mouth disease virus in cattle. Virology 2013; 446(1-2): 260-267.
  30. Pierce DM, Hayward C, Rowlands D, et al. Insights into polyprotein processing and RNA-protein interactions in foot-and-mouth disease virus genome replication. J Virol 2023: 97(5): e0017123. doi: 10.1128/ jvi.00171-23.
  31. Yang F, Zhu Z, Cao W, et al. Genetic determinants of altered virulence of type O foot-and-mouth disease virus. J Virol 2020; 94(7): e01657-19. doi: 10.1128/ JVI.01657-19.