All 180 complete EV-D68 VP1 sequences available in GenBank as of Dec 2014, including the 17 new EV-D68 VP1 gene sequences in this study (boldface), were aligned using MUSCLE29, and phylogenetic trees were constructed using the MrBayes algorithm30. EV-D68 strains from AFM patients are grouped together in a novel clade (clade B1) and include sequences from patients with severe respiratory illness from the 2014 outbreak. AFM cases are marked in red text, encephalitis in orange text, and respiratory illness only in blue text. Abbreviations: nt, nucleotide.