Phylogenetics analysis

All complete Enterovirus A protein sequences were downloaded from NCBI virus, then clustered at 98% by cd-hit yielding 107 sequence clusters. The representative sequences derived from this clustering were then aligned by MAFFT. Next, the aligned sequences were indexed to the EV-A71 strain Tainan/4643/98 and the starting position of all gaps was recorded. These gap positions were then graphically mapped onto the experimental InDel screen results in R. A second MAFFT alignment was performed using the same 107 Enterovirus A clusters and the ICTV Enterovirus B exemplar isolate sequence (GenBank: {"type":"entrez-protein","attrs":{"text":"AAB59927.1","term_id":"323433","term_text":"AAB59927.1"}}AAB59927.1) as an outgroup. A phylogenetic tree was produced from this alignment using the maximum-likelihood method in RAxML with 100 bootstrap replications. The PROTGAMMAWAG option was selected in RAxML which is for amino acids with a gamma rate heterogeneity model using a WAG substitution matrix. FigTree was used for phylogenetic tree visualization and customization. AliView was used for visualization and representation of the multiple sequence alignment.