Bootscan analysis showed possible recombination between genotypes B and C from nucleotide positions 11500 to 13000, corresponding to the nsp6/nsp7 junction, giving rise to genotype A; and between genotypes A and B from nucleotide positions 21500 to 22500, corresponding to the nsp16/HE junction, giving rise to genotype C. Multiple alignments further narrowed the sites of cross-over to a 143-bp region between nucleotide positions 11750 and 11892, and a 29-bp region between nucleotide positions 21502 and 21530.