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Comparative complete genome analysis of Indian type A foot-and-mouth disease virus field isolates

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Abstract

Comparative complete genome analysis of 17 serotype A Indian field isolates representing different genotypes and sub-lineages is presented in this report. Overall 79% of amino acids were invariant in the coding region. Chunk deletion of nucleotide was observed in S and L fragment of 5′-UTR. More variability which is comparable to that of capsid coding region was found in L and 3A region. Functional motifs and residues critical for virus biology were conserved most. Polyprotein cleavage sites accepted few changes. Many sites were detected to be under positive selection in L, P1, 2C, 3A, 3C, and 3D region and of which some are functionally important and antigenically critical. Genotype/lineage specific signature residues could be identified which implies evolution under different selection pressure. Transmembrane domain could be predicted in 2B, 2C, 3A, and 3C proteins in agreement with their membrane binding properties. Phylogenetic analysis at complete coding region placed the isolates in genotype IV, VI, and VII and two broad clusters comprising VP359-deletion and non-deletion group within genotypes VII. The VP359-deletion group has diversified genetically with time giving rise to three lineages. Incongruence in tree topology observed for different non structural protein coding region and UTRs-based phylogeny indicate suspected recombination.

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Acknowledgments

Indian Council of Agricultural Research provided necessary facilities to carry out this work. We sincerely thank all the past and continuing scientists of PDFMD who have been instrumental in maintaining the ‘National FMD Virus Repository’.

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Authors and Affiliations

  1. Project Directorate on Foot-and-mouth disease, Mukteswar-Kumaon, Nainital, 263138, Uttarakhand, India

    Saravanan Subramaniam, Aniket Sanyal, Jajati K. Mohapatra & Bramhadev Pattnaik

  2. Project Directorate on Animal Disease Monitoring and Surveillance, Hebbal, 560024, Karnataka, India

    Divakar Hemadri

Authors
  1. Saravanan Subramaniam
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  2. Aniket Sanyal
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  3. Jajati K. Mohapatra
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  4. Divakar Hemadri
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  5. Bramhadev Pattnaik
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Correspondence to Bramhadev Pattnaik.

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Subramaniam, S., Sanyal, A., Mohapatra, J.K. et al. Comparative complete genome analysis of Indian type A foot-and-mouth disease virus field isolates. Virus Genes 43, 224–233 (2011). https://doi.org/10.1007/s11262-011-0622-8

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  • DOI: https://doi.org/10.1007/s11262-011-0622-8

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