Genetic evolution of Swine Vesicular Disease viruses circulating in Italy from 1992 to the eradication in 2015 and emergence of a recent recombinant strain

Swine vesicular disease virus (SVDV) was considered endemic in Italy until 2015, when eradication was achieved. From 1992, when the most recent antigenic-genomic variant of SVDV was identified, to 2015, about 685 SVD outbreaks occurred. In order to understand the evolutionary drivers of SVDV in Italy, 152 viral strains were selected and whole genome sequencing performed. Comparison of the polyprotein coding region revealed a minimum pairwise identity of 85% and 98% at the nucleotide and amino acid levels, respectively, consistent with the antigenic homogeneity of the analysed strains. Phylogenetic analysis confirmed the presence of two sub-lineages: sub-lineage 1, which evolved and circulated specifically in Italy since 1995, and sub-lineage 2, which also includes strains circulating in both Spain and Portugal in 1993 and in Portugal during 2003. Recombination analysis revealed a breakpoint site within the 2B coding region resulting in a recombination strain originated from viruses belonging to the two sub-lineages, which was dated to beginning of 2008. This single recombination event gave rise to at least 20 recombinant strains, which circulated together with their parental strains until 2010 and from then on circulated on their own until eradication in 2015. Our data showed that, apart from the recombination event, SVDV, which has been present on Italian territory for more than 20 years, has not been subject to positive selective pressures that would have conferred a possible evolutionary advantage.