Abstract
Here, we report 17 nearly complete genome sequences of enterovirus D68 (EV-D68) isolated from Kansas City, MO, in 2018. Phylogenetic analysis suggests that these strains belong to subclade B3, similar to the ones that caused the 2016 epidemics in the United States but different from the 2014 outbreak B1 strains.
Highlights
Enterovirus D68 (EV-D68) belongs to the genus Enterovirus in the family Picornaviridae, with a single positive-strand RNA genome of ϳ7.5 kb in length coding for 4 structural proteins (VP1 to VP4) and 7 nonstructural proteins (2A to 2C and 3A to 3D) [1]
BLASTN searches of the resulting contigs identified an EV-D68 isolate from 2016, with GenBank accession number KY385889, as the closest match
GϩC contents vary between 41.6% and 41.9%. They were annotated using the VAPiD annotation pipeline (v 1.6.2) [16] and submitted to GenBank. These 17 2018 EV-D68 isolates from Kansas City belonged to the B3 subclade, phylogenetic analysis shows that they did not cluster with the strains that caused the 2016 epidemics in the United States and Europe (ϳ98.21% similarity) or the strains reported in Europe (France) in 2018 (ϳ97.93% similarity), which are in subclade B3 (Fig. 1)
Summary
Enterovirus D68 (EV-D68) belongs to the genus Enterovirus in the family Picornaviridae, with a single positive-strand RNA genome of ϳ7.5 kb in length coding for 4 structural proteins (VP1 to VP4) and 7 nonstructural proteins (2A to 2C and 3A to 3D) [1]. The median number of reads generated per sample was 376,488 (interquartile range [IQR], 326,864 to 421,360 reads). Sequencing reads were binned by barcode, adapters were trimmed with Cutadapt (v 1.18) [13], and low-quality bases were removed with Trimmomatic (v 0.36) [14]. BLASTN searches of the resulting contigs identified an EV-D68 isolate from 2016, with GenBank accession number KY385889 (enterovirus D68 isolate NY212_16, complete genome), as the closest match.
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