Porcine reproductive and respiratory syndrome virus diversity of Eastern Canada swine herds in a large sequence dataset reveals two hypervariable regions under positive selection

► A PRRSV ORF5 dataset of 1301 sequences collected between 1998 and 2009 was used. ► PRRSV diversity, glycotypes and amino acid under positive selection were investigated. ► The 12% regional pairwise diversity was comparable to the overall worldwide diversity. ► Thirty-eight GP5 glycotype patterns were observed with a newly described site at position N57. ► Two positively selected hypervariable regions flank a conserved neutralizing epitope.