Abstract

Introduction: One of the most challenging aspects of foot-and-mouth disease (FMD) control is the understanding of the virus genetic variability, and the forces that impact such changes in virus evolution. Selection of specific sites within the FMD virus (FMDV) capsid structure may vary depending on the values observed of certain environmental factors, which are heterogeneous through different endemic settings. Serotype A FMDV is of special interest because of the variable nature of the virus, posing a major difficulty for selecting appropriate vaccine antigens in specific areas. Materials and Methods: FMDV serotype O VP1 sequences from Pakistan and Afghanistan (n=37, sampled between 07/2008-09/2009), Iran (n=38, sampled between 04/2005-10/2007) and Turkey (n=57 sampled between 11/2005-06/2008). Sequences were analyzed separately for each region for detection of evidence of positive selection by exploring the differences between synonymous (dS) and non-synonymous changes (dN). Three different statistical methods were used to identify individual codons under selection. Mean values of dN/dS (MdN/dS) were computed for each dataset. A site was considered under positive selection if evidence was detected by at least 1 statistical method. Results: The values of MdN/dS were similar for viruses from Iran and Turkey (1.60 and 1.61, respectively), whereas it was relatively higher (1.84) for Pakistan/Afghanistan sequences. The individual codon analysis yielded 18 positively selected sites for Iran sequences, 5 sites in Turkey and 3 in Pakistan/Afghanistan. One site (141), located close to the RGD motif, was the only codon consistently found under positive selection for all three datasets. Within Turkey and Iran sequences, additionally codons (45, 149, 149, and 196) were consistently under positive selection. Discussion: Characteristics of the animal population in different areas may have a different impact in selecting FMDV. These results will help to develop effective prevention and control strategies in the region.