A PROCEDURE FOR DETECTING SELECTION IN HIGHLY VARIABLE VIRAL GENOMES - EVIDENCE OF POSITIVE SELECTION IN ANTIGENIC REGIONS OF CAPSID PROTEIN VP1 OF FOOT-AND-MOUTH-DISEASE VIRUS

A new procedure is described for the detection of positive selection a mong sequences of viral proteins from highly variable viruses. The app roach is based on the estimation of the rates of nonsynonymous to syno nymous (ns/s) mutations to the overall genetic distances amongst the s equences compared. Rates of ns/s substitutions were calculated, and th e individual profiles were arranged as a function of the genetic dista nce observed between the complete sequences. The resulting surfaces al lowed identification of protein regions whose rates of ns/s substituti ons were consistent with the existence of positive selection. This pro cedure has been applied to the study of a highly variable antigenic pr otein, VP1, a protein present in foot-and-mouth disease virus (FMDV). The analysis of groups of VP1 sequences corresponding to FMDV serotype s A, O and C, resulted in the identification of two regions, which con tribute to an important antigenic site, where positive selection appea rs to operate. (C) 1998 Elsevier Science B.V. All rights reserved.