Abstract
Complete genome sequences of nine enterovirus D68 (EV-D68) strains from patients in New York were obtained in 2016 by metagenomic next-generation sequencing. Comparative genomic analysis suggests that a new subclade B3, with ~4.5% nucleotide divergence from subclade B1 strains causing the 2014 outbreak, is circulating in the United States in 2016.
Highlights
Complete genome sequences of nine enterovirus D68 (EV-D68) strains from patients in New York were obtained in 2016 by metagenomic next-generation sequencing
During the 2014 U.S outbreak, we identified 95 children with EV-D68 infection from September and October 2014 using an EV-D68-specific real-time reverse transcriptionPCR [5] and a shotgun next-generation sequencing assay [6]
From 1 June to 30 September 2016, 358 of 1,219 (29.4%) NP specimens were positive for rhinovirus/enterovirus (RhV/EV) by the FilmArray Respiratory Panel (BioFire, Salt Lake City, UT, USA)
Summary
Complete genome sequences of nine enterovirus D68 (EV-D68) strains from patients in New York were obtained in 2016 by metagenomic next-generation sequencing. Enterovirus D68 (EV-D68) was first recovered from patients with respiratory illness in California in 1962 [1] and was infrequently reported until its recent emergence worldwide [2]. In August 2014, a nationwide outbreak of EV-D68-associated severe respiratory illness with at least 1,153 confirmed cases was reported from 49 U.S states [3, 4].
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