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Genetic characterization of a new pandemic Southeast Asia topotype strain of serotype O foot-and-mouth disease virus isolated in China during 2010

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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.

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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.

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Authors and Affiliations

  1. State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China

    Haixue Zheng, Jijun He, Jianhong Guo, Ye Jin, Fan Yang, Lv Lv & Xiangtao Liu

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  1. Haixue Zheng
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  2. Jijun He
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  3. Jianhong Guo
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  4. Ye Jin
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  5. Fan Yang
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  6. Lv Lv
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  7. Xiangtao Liu
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Corresponding author

Correspondence to Xiangtao Liu.

Additional information

Haixue Zheng and Jijun He contributed equally to this study.

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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

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  • DOI: https://doi.org/10.1007/s11262-011-0670-0

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