Abstract
The full-length nucleotide sequence of the foot-and-mouth disease virus O/BY/CHA/2010 strain, Mya-98 lineage of Southeast Asia (SEA) topotype, was determined and compared with O/HKN/20/2010 and other known FMDV strains. Homology analysis indicated >98.0% nucleotide identity between O/BY/CHA/2010 and the epidemic strains, O/HKN/20/2010, and O/VN/2009. However, with the exception of the VP4, 2A, and 3BCD regions, O/BY/CHA/2010 showed a lower similarity with SEA topotype strains, O/VN/2006, and HLJOC12/03. A comparison of O/BY/CHA/2010 with non-SEA topotype strains showed the highest level of homology (97.4–100%) with UKG/7B/2007, Akesu/58, and the PanAsia strains in the 2A, P2, and 3CD regions, which suggested the presence of similar characteristics among these strains. Phylogenetic analysis revealed that O/BY/CHA/2010 is clustered in the Mya-98 lineage of the SEA topotype and is linked to four other isolates: HKN/20/2010, O/VN/2009, O/VN/2006, and HLJOC12/03. The VP1-based phylogenetic tree was divided into distinct clusters according to the different topotypes, while other gene-based phylogenetic trees exhibited some degree of intercrossing among topotypes. Furthermore, sequence analysis of the Lpro gene revealed a single amino acid insertion in O/HKN/20/2010 and a single amino acid deletion in O/BY/CHA/2010, in addition to a 70-nucleotide deletion within the 5′-untranslated region of O/HKN/20/2010. The majority of strains were shown to be homologous in the pseudoknots region although some exceptions were noted. This study provides a comprehensive genetic characterization of a novel FMDV isolate of the Mya-98 lineage.
Similar content being viewed by others
References
M.J. Grubman et al., Biochemical map of polypeptides specified by foot-and-mouth disease virus. J. Virol. 50(2), 579–586 (1984)
T. Jackson et al., Structure and receptor binding. Virus Res. 91(1), 33–46 (2003)
V.I. Agol, A.V. Paul, E. Wimmer, Paradoxes of the replication of picornaviral genomes. Virus Res. 62(2), 129–147 (1999)
E. Domingo et al., Evolution of foot-and-mouth disease virus. Virus Res. 91(1), 47–63 (2003)
N.J. Knowles, A.R. Samuel, Molecular epidemiology of foot-and-mouth disease virus. Virus Res. 91(1), 65–80 (2003)
J. Davie, A complement fixation technique for the quantitative measurement of antigenic differences between strains of the virus of foot-and-mouth disease. J. Hyg. (Lond.) 62, 401–411 (1964)
A.R. Samuel, N.J. Knowles, Foot-and-mouth disease virus: cause of the recent crisis for the UK livestock industry. Trends Genet. 17(8), 421–424 (2001)
D.J. Paton et al., Recent spread of foot-and-mouth disease in the Far East. Vet. Rec. 166(18), 569–570 (2010)
N.J. Knowles et al., Outbreak of foot-and-mouth disease virus serotype O in the UK caused by a pandemic strain. Vet. Rec. 148(9), 258–259 (2001)
N.J. Knowles et al., Pandemic strain of foot-and-mouth disease virus serotype O. Emerg. Infect. Dis. 11(12), 1887–1893 (2005)
C. Carrillo et al., Comparative genomics of foot-and-mouth disease virus. J. Virol. 79(10), 6487–6504 (2005)
J.D. Thompson, D.G. Higgins, T.J. Gibson, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting. Position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22(22), 4673–4680 (1994)
K. Tamura et al., MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24(8), 1596–1599 (2007)
D. Hemadri et al., 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 25(1), 23–34 (2002)
T. Kanno et al., The complete nucleotide sequence of the PanAsia strain of foot-and-mouth disease virus isolated in Japan. Virus Genes 25(2), 119–125 (2002)
N.J. Savill et al., Effect of data quality on estimates of farm infectiousness trends in the UK 2001 foot-and-mouth disease epidemic. J. R. Soc. Interface 4(13), 235–241 (2007)
B.E. Clarke, D.V. Sangar, Processing and assembly of foot-and-mouth disease virus proteins using subgenomic RNA. J. Gen. Virol. 69, 2313–2325 (1988)
V.N. Vakharia et al., Proteolytic processing of foot-and-mouth disease virus polyproteins expressed in a cell-free system from clone-derived transcripts. J. Virol. 61(10), 3199–3207 (1987)
E. Kuehnel et al., Foot-and-mouth disease virus leader proteinase: specificity at the P2 and P3 positions and comparison with other papain-like enzymes. Biochemistry 43(36), 11482–11490 (2004)
C.S. Dunn, A.I. Donaldson, Natural adaption to pigs of a Taiwanese isolate of foot-and-mouth disease virus. Vet. Rec. 141(7), 174–175 (1997)
P.C. Yang et al., Epidemiological characteristics and financial costs of the 1997 foot-and-mouth disease epidemic in Taiwan. Vet. Rec. 145(25), 731–734 (1999)
A.T. Giraudo et al., Identification of a nucleotide deletion in parts of polypeptide 3A in two independent attenuated aphthovirus strains. Virology 177(2), 780–783 (1990)
J. Graff et al., Mutational events in consecutive passages of hepatitis A virus strain GBM during cell culture adaptation. Virology 204(1), 60–68 (1994)
A.T. Giraudo et al., Isolation and characterization of recombinants between attenuated and virulent aphthovirus strains. J. Virol. 61(2), 419–425 (1987)
A. Sagedahl et al., Biochemical characterization of an aphthovirus type C3 strain Resende attenuated for cattle by serial passages in chicken embryos. Virology 157(2), 366–374 (1987)
C.W. Beard, P.W. Mason, Genetic determinants of altered virulence of Taiwanese foot-and-mouth disease virus. J. Virol. 74(2), 987–991 (2000)
P.W. Mason et al., Comparisons of the complete genomes of Asian, African and European isolates of a recent foot-and-mouth disease virus type O pandemic strain (PanAsia). J. Gen. Virol. 84(Pt 6), 1583–1593 (2003)
M. George et al., The non-structural leader protein gene of foot-and-mouth disease virus is highly variable between serotypes. Virus Genes 22(3), 271–278 (2001)
Acknowledgments
This study was supported by Gansu J (1013JHTA008), IAEA (16025/R0) and EPIZON projects.
Note added to the proof
The sequence data for O/BY/CHA/2010 and O/GZ/CHA/2010 have been submitted to GenBank and are available under GenBank IDs JN998085 and JN998086, respectively.
Author information
Authors and Affiliations
Corresponding author
Additional information
Haixue Zheng and Jijun He contributed equally to this study.
Rights and permissions
About this article
Cite this article
Zheng, H., He, J., Guo, J. et al. Genetic characterization of a new pandemic Southeast Asia topotype strain of serotype O foot-and-mouth disease virus isolated in China during 2010. Virus Genes 44, 80–88 (2012). https://doi.org/10.1007/s11262-011-0670-0
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11262-011-0670-0