Off-season circulation and characterization of enterovirus D68 with respiratory and neurological presentation using whole-genome sequencing

Abstract

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.

Emergence of enterovirus D68 in a Norwegian paediatric population 2012-2022

“…Notably, our data from the 2016 season reveal an even higher incidence of EV-D68 compared to the 2014 outbreak, again primarily among hospitalised patients. This high incidence in 2016 aligns with reports of outbreaks from Sweden, France, Spain, the Netherlands and the United States (7,8,10,13,14). However, our 2018 findings deviate from reports from Cases of EV-D68 by age in years, per year.…”

Circulation, viral diversity and genomic rearrangement in mpox virus in the Netherlands during the 2022 outbreak and beyond

“…12,13 Due to continuous technical advancements and decreasing costs of sequencing techniques, whole genome sequencing (WGS) is increasingly being used as a tool to provide insight into the evolutionary dynamics, transmission and genomic diversity of RNA viruses during local and global outbreaks. [14][15][16] Additionally, the SARS-CoV-2 pandemic has greatly increased the capacity to perform viral WGS with data sharing platforms and practices. 17 These capabilities have resulted in an efficient global response to sequence hMPXV genomes associated with the 2022 outbreak to track viral evolution.…”