Fig. 1.

Alignment of primer hybridization sequences within 192 N ORFs available in May 2014 (A and B). Alignment of primer hybridization sequences within 56 N ORFs of the S-INDEL and S-non-INDEL PEDV strains circulating in Europe (C and D). Nucleotide probabilities at each position are shown as coloured text above the alignments. Red text in the alignment sequences represent a mismatch. Sequences of primers are shown above the alignment (PEDNF, mPEDNF or PEDNR). PEDNR is shown as reverse complement. Each line represents a hybridization sequence, the number of strains presenting this sequence is indicated to the left of the sequence (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.).