TY - JOUR
T1 - Off-season circulation and characterization of enterovirus D68 with respiratory and neurological presentation using whole-genome sequencing
AU - Cassidy, Hayley
AU - Lizarazo-Forero, Erley
AU - Schuele, Leonard
AU - Van Leer-Buter, Coretta
AU - Niesters, Hubert G.M.
N1 - Funding Information:
Hayley Cassidy and Leonard Schuele received funding from the European Union’s Horizon 2020 research and innovation program, under the Marie Sklodowska-Curie grant agreement 713660 (MSCA-COFUND-2015-DP “Pronkjewail”). Erley Lizarazo-Forero was funded by Quality Control Molecular Diagnostics (QCMD, Glasgow, Scotland) under an unrestricted grant.
Publisher Copyright:
Copyright © 2023 Cassidy, Lizarazo-Forero, Schuele, Van Leer-Buter and Niesters.
PY - 2023/2/9
Y1 - 2023/2/9
N2 - To explore an off-season enterovirus D68 (EV-D68) upsurge in the winter season of 2019/2020, we adapted a whole-genome sequencing approach for Nanopore Sequencing for 20 hospitalized patients with accompanying respiratory or neurological presentation. Applying phylodynamic and evolutionary analysis on Nextstrain and Datamonkey respectively, we report a highly diverse virus with an evolutionary rate of 3.05 × 10−3 substitutions per year (entire EV-D68 genome) and a positive episodic/diversifying selection with persistent yet undetected circulation likely driving evolution. While the predominant B3 subclade was identified in 19 patients, one A2 subclade was identified in an infant presenting with meningitis. Exploring single nucleotide variations using CLC Genomics Server showed high levels of non-synonymous mutations, particularly in the surface proteins, possibly highlighting growing problems with routine Sanger sequencing for typing enteroviruses. Surveillance and molecular approaches to enhance current knowledge of infectious pathogens capable of pandemic potential are paramount to early warning in health care facilities.
AB - To explore an off-season enterovirus D68 (EV-D68) upsurge in the winter season of 2019/2020, we adapted a whole-genome sequencing approach for Nanopore Sequencing for 20 hospitalized patients with accompanying respiratory or neurological presentation. Applying phylodynamic and evolutionary analysis on Nextstrain and Datamonkey respectively, we report a highly diverse virus with an evolutionary rate of 3.05 × 10−3 substitutions per year (entire EV-D68 genome) and a positive episodic/diversifying selection with persistent yet undetected circulation likely driving evolution. While the predominant B3 subclade was identified in 19 patients, one A2 subclade was identified in an infant presenting with meningitis. Exploring single nucleotide variations using CLC Genomics Server showed high levels of non-synonymous mutations, particularly in the surface proteins, possibly highlighting growing problems with routine Sanger sequencing for typing enteroviruses. Surveillance and molecular approaches to enhance current knowledge of infectious pathogens capable of pandemic potential are paramount to early warning in health care facilities.
KW - enterovirus D68
KW - long-read sequencing
KW - neurological infection
KW - respiratory infection
KW - whole-genome sequencing
U2 - 10.3389/fmicb.2022.1088770
DO - 10.3389/fmicb.2022.1088770
M3 - Article
AN - SCOPUS:85148656252
SN - 1664-302X
VL - 13
JO - Frontiers in Microbiology
JF - Frontiers in Microbiology
M1 - 1088770
ER -