Biennial Upsurge and Molecular Epidemiology of Enterovirus D68 Infection in New York, USA, 2014 to 2018

Abstract

Enterovirus D68 (EV-D68) infection has been associated with outbreaks of severe respiratory illness and increased cases of nonpolio acute flaccid myelitis. The patterns of EV-D68 circulation and molecular epidemiology are not fully understood. In this study, nasopharyngeal (NP) specimens collected from patients in the Lower Hudson Valley, New York, from 2014 to 2018 were examined for rhinovirus/enterovirus (RhV/EV) by the FilmArray respiratory panel. Selected RhV/EV-positive NP specimens were analyzed using two EV-D68-specific real-time RT-PCR assays, Sanger sequencing and metatranscriptomic next-generation sequencing. A total of 2,398 NP specimens were examined. EV-D68 was detected in 348 patients with NP specimens collected in 2014 (n = 94), 2015 (n = 0), 2016 (n = 160), 2017 (n = 5), and 2018 (n = 89), demonstrating a biennial upsurge of EV-D68 infection in the study area. Ninety-one complete or nearly complete EV-D68 genome sequences were obtained. Genomic analysis of these EV-D68 strains revealed dynamics and evolution of circulating EV-D68 strains since 2014. The dominant EV-D68 strains causing the 2014 outbreak belonged to subclade B1, with a few belonging to subclade B2. New EV-D68 subclade B3 strains emerged in 2016 and continued in circulation in 2018. Clade D strains that are rarely detected in the United States also arose and spread in 2018. The establishment of distinct viral strains and their variable circulation patterns provide essential information for future surveillance, diagnosis, vaccine development, and prediction of EV-D68-associated disease prevalence and potential outbreaks.

Keywords: enterovirus; enterovirus D68; molecular epidemiology; next-generation sequencing; outbreak investigation; real-time RT-PCR; viral evolution.

FIG 1

Temporal and geographic distributions of enterovirus D68 in the Lower Hudson Valley, NY, 2014 to 2018. (A) Monthly distribution of nasopharyngeal (NP) specimens that were positive for rhinovirus/enterovirus (RhV/EV) (left y axis) and EV-D68 (right y axis) from January 2014 to December 2018. (B) Map of the seven counties in the Lower Hudson Valley and distribution of the number of patients with enterovirus D68 detected from respiratory specimens between 2014 and 2018. Three hundred twenty-three of 348 (92.8%) confirmed cases were from this region. The map was adapted from the New York State Department of Environmental Conservation website (http://www.dec.ny.gov/outdoor/7804.html) with permission.

FIG 2

Phylogenetic tree of enterovirus D68 strains from the Lower Hudson Valley from 2014 to 2018 (n = 91). Strains representing each clade (A, C, D, and prototype) were included for comparison. The numbers at the branch nodes are percent nucleotide sequence identity. CHN, China; HKG, Hong Kong, China.

FIG 3

Alignment of amino acid sequences at the cleavage sites of proteases 2A^pro and 3C^pro of 27 representative EV-D68 strains. Two amino acid substitutions, T860N in 2A^pro at the position between VP1 and 2A and S1108G in 3C^pro between 2B and 2C, were observed only in the subclade B1 strains from the 2014 outbreak. The gaps are indicated by dashes and the conserved amino acid residues by dots. Asterisks indicate EV-D68 strains from the Lower Hudson Valley.