Identification of optimal regions for phylogenetic studies on VP1 gene of foot-and-mouth disease virus: analysis of types A and O Argentinean viruses

An analysis of the informative content of sequence stretches on the foot-an d-mouth disease virus (FMDV) VP1 gene was applied to two important viral se rotypes: A and O. Several sequence regions were identified to allow the rec onstruction of phylogenetic trees equivalent to those derived from the whol e VP1 gene. The optimal informative regions for sequence windows of 150 to 250 nt were predicted between positions 250 and 550 of the gene. The sequen ces spanning the 250 nt of the 3' end (positions 400 to 650), extensively u sed for FMDV phylogenetic analyses, showed a lower informative content. In spite of this, the use of sequences from this region allowed the derivation of phylogenetic trees for type A and type O FMDVs which showed topologies similar to those previously reported for the whole VP1 gene. When the seque nces determined for viruses isolated in Argentina, between 1990 and 1993, w ere included in these analyses, the results obtained revealed features of t he circulation of type A and type O viruses in the field, in the months tha t preceded the eradication of the disease in this country. Type A viruses w ere closely related to an Argentinean vaccine strain, and defined an indepe ndent cluster within this serotype. Among the type O viruses analysed, two groups were distinguished; one was closely related to the South American va ccine strains, while the other was grouped with viruses of the O3 subtype. In addition, a detailed phylogeny for type A FMDV is presented.