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Journal of Virology, May 2005, p. 6487-6504, Vol. 79, No. 10
0022-538X/05/$08.00+0     doi:10.1128/JVI.79.10.6487-6504.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Comparative Genomics of Foot-and-Mouth Disease Virus{dagger}

C. Carrillo,1 E. R. Tulman,1,3,4 G. Delhon,1,2 Z. Lu,1 A. Carreno,1 A. Vagnozzi,1,3,4 G. F. Kutish,1,3,4 and D. L. Rock1,3,4*

Plum Island Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Greenport, New York 11944,1 Area of Virology, School of Veterinary Sciences, University of Buenos Aires, 1427 Buenos Aires, Argentina,2 Department of Pathobiology and Veterinary Science,3 Center of Excellence for Vaccine Research, University of Connecticut, Storrs, Connecticut 062694

Received 4 August 2004/ Accepted 18 January 2005

Here we present complete genome sequences, including a comparative analysis, of 103 isolates of foot-and-mouth disease virus (FMDV) representing all seven serotypes and including the first complete sequences of the SAT1 and SAT3 genomes. The data reveal novel highly conserved genomic regions, indicating functional constraints for variability as well as novel viral genomic motifs with likely biological relevance. Previously undescribed invariant motifs were identified in the 5' and 3' untranslated regions (UTR), as was tolerance for insertions/deletions in the 5' UTR. Fifty-eight percent of the amino acids encoded by FMDV isolates are invariant, suggesting that these residues are critical for virus biology. Novel, conserved sequence motifs with likely functional significance were identified within proteins Lpro, 1B, 1D, and 3C. An analysis of the complete FMDV genomes indicated phylogenetic incongruities between different genomic regions which were suggestive of interserotypic recombination. Additionally, a novel SAT virus lineage containing nonstructural protein-encoding regions distinct from other SAT and Euroasiatic lineages was identified. Insights into viral RNA sequence conservation and variability and genetic diversity in nature will likely impact our understanding of FMDV infections, host range, and transmission.

* Corresponding author. Mailing address: Department of Pathobiology and Veterinary Science, University of Connecticut, 61 N. Eagleville Road, Unit-3089, Storrs, CT 06269-3089. Phone: (860) 486-2845. Fax: (860) 486-2794. E-mail: drock{at}cshore.com.

{dagger} Supplemental material for this article may be found at http://jvi.asm.org/.

Journal of Virology, May 2005, p. 6487-6504, Vol. 79, No. 10
0022-538X/05/$08.00+0     doi:10.1128/JVI.79.10.6487-6504.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



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