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Comparative sequence analysis of representative foot-and-mouth disease virus genomes from Southeast Asia

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Abstract

Foot-and-mouth disease (FMD) is endemic in mainland Southeast Asia where up to seven genetically distinct viral lineages co-circulate (O/SEA/Mya-98, O/SEA/Cam-94, O/ME-SA/PanAsia, O/ME-SA/PanAsia-2, O/CATHAY, A/ASIA/Sea-97, and serotype Asia 1). The aim of this study was to analyse the sequence variability between representative complete genomes for these seven lineages. The genome sequences varied from 8130 to 8192 nucleotides in length and shared nucleotide identities ranging from 91.8 to 78.9%. Broad-scale differences such as block and codon deletions observed in these genomes paralleled features that have been reported previously for other FMDV sequences from Southeast Asia. Comparison between these sequences revealed the presence of 2501 variant sites which were more evident in regions encoding surface capsid proteins (VP2, VP3 and VP1) compared to regions encoding non-structural proteins. Specific comparisons between closely related O/ME-SA sequences showed that the distribution of variant sites was focussed particularly at the 5′ end of the genome indicating that recombination may have occurred during the evolution of the O/ME-SA/PanAsia-2 lineage. These sequences provide insights into the evolutionary mechanisms by which new lineages generate genetic and antigenic novelty in the region and will form the basis of studies to define the spatio-temporal epidemiology of FMDV.

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Acknowledgments

This study was carried out at Institute for Animal Health, Pirbright Laboratory, UK, and was sponsored by Department of Public Services of the Malaysian Government and supported by the Department for Environment, Food and Rural Affairs, UK (project number SE2938) and Food and Agriculture Organisation of the United Nations (Project PR 41764). The authors thank staff within the WRLFMD at IAH, particularly Nigel Ferris and Geoff Hutchings for help preparing the samples.

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Authors and Affiliations

  1. Institute for Animal Health, Pirbright Laboratory, Ash Road, Pirbright, Woking, Surrey, GU24 0NF, UK

    Nor Faizah Abdul-Hamid, Nick J. Knowles & Donald P. King

  2. Institute of Infection and Global Health, University of Liverpool, Chester High Road, Neston, South Wirral, CH64 7TE, UK

    Nor Faizah Abdul-Hamid, Alan D. Radford & Donald P. King

  3. Department of Veterinary Services, Federal Government Administration Centre, Wisma Tani, Block Podium, Lot 4G1, Precinct 4, 62630, Putrajaya, Malaysia

    Nor Faizah Abdul-Hamid

  4. SAP Foot-and-Mouth Disease Institute, Ulus, Ankara, Turkey

    Müge Fırat-Saraç

Authors
  1. Nor Faizah Abdul-Hamid
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  2. Müge Fırat-Saraç
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  3. Alan D. Radford
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  4. Nick J. Knowles
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  5. Donald P. King
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Corresponding author

Correspondence to Donald P. King.

Additional information

The FMDV genome sequences described in this paper have been submitted to GenBank and assigned the following accession numbers: HQ632768 (O/MAY/3/2000); HQ632769 (O/MAY/7/2001); HQ632770 (O/MAY/1/2004); HQ632771 (O/MAY/8/2005); HQ632772 (O/MAY/7/2007); HQ632773 (A/MAY/3/2007) and HQ632774 (Asia 1/MAY/9/99).

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Abdul-Hamid, N.F., Fırat-Saraç, M., Radford, A.D. et al. Comparative sequence analysis of representative foot-and-mouth disease virus genomes from Southeast Asia. Virus Genes 43, 41–45 (2011). https://doi.org/10.1007/s11262-011-0599-3

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  • DOI: https://doi.org/10.1007/s11262-011-0599-3

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