Genomic Analyses of Acute Flaccid Myelitis Cases among a Cluster in Arizona Provide Further Evidence of Enterovirus D68 Role

FIG 1. Results of microbiomic analysis by 16S rRNA partial gene sequencing after removing background taxa present in the 91 reads of a reagent-only negative-control sample, showing normal flora carriage in the NP swabs in all of the patients regardless of their neurologic disease diagnosis and probable contaminants in the CSF samples. The sample size is too small to detect differences in NP bacterial communities. ?, unknown.

FIG 2. EV-D68 genome map with locations of the real-time PCR/amplicon sequencing assay and the metagenomic read alignments of two NP swab samples, 48136 and 48145, from children diagnosed with AFM. The unpaired reads from 48136 cover 132 bases of the p3D gene and overlap for 48 bases. The sequence was a perfect match to several 2016 genomes from an outbreak in the Lower Hudson Valley, New York in 2016 (18), including NY230_16 (accession no. KY385890, positions 6862 to 6993), NY172_16, NY141_16, and NY135_16, and other genomes, including NY75_16 (85) and USA/TX/2016-19506, and USA/FL/2016-19504 (52). These latter two genomes were isolated from confirmed AFM cases (52). For the paired reads from 48145, the forward read aligns to the p2A protease gene for 35 bases and the p2B polypeptide gene for 58 bases (accession no. KY385890, positions 3665 to 3757 with two SNPs). The best BLAST hit is to three 2015 genomes from Osaka City, Japan (accession no. LC107898, LC107899, and LC107901) (86), with one SNP. The reverse read aligns to the p2B polypeptide gene (accession no. KY385890, positions 3799 to 3891 with one SNP). Best BLAST hits include many genomes, all with one SNP.