Detection and Genomic Characterization of Enterovirus D68 in Respiratory Samples Isolated in the United States in 2016

Ng, Terry Fei Fan; Montmayeur, Anna; Castro, Christina J.; Cone, Marshall; Stringer, Joey; Lamson, Daryl M.; Rogers, Shannon; Chern, Shur-Wern Wang; Valladares, Laura Magaña; Marine, Rachel L.; Rubino, Heather; Serinaldi, Daniel; George, Kirsten St.; Nix, W. Allan

doi:10.1128/genomea.01350-16

Cited by 13 publications

(15 citation statements)

References 6 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A representative subset of ten EV-D68 specimens from CHCO in 2016 all belonged to clade B3, which was similar to other circulating strains in the US in 2016 and did not contain significant amino acid changes in the capsid compared to 2014 clade B strains (personal communication, W. Allan Nix, Centers for Disease Control and Prevention Picornavirus Laboratory) (12, 13). …”

Section: Resultsmentioning

confidence: 87%

Surveillance for enterovirus D68 in colorado children reveals continued circulation

Messacar

Robinson

Pretty

et al. 2017

Journal of Clinical Virology

View full text Add to dashboard Cite

Background The largest, most widespread outbreak of enterovirus D68 respiratory disease occurred from August to December of 2014 in the United States with 1,153 confirmed infections in 49 states. The epidemiology of enterovirus D68 following the 2014 outbreak is unknown. Objectives This study seeks to describe the epidemiology of enterovirus D68 circulation amongst Colorado children from 2014–2016. Study Design This is a prospective observational surveillance study of enterovirus D68 infection amongst children tested for respiratory pathogens from July–October 2014–2016 at Children’s Hospital Colorado (CHCO), a quaternary care children’s hospital in Aurora, CO. Results Amongst rhinovirus/enterovirus positive respiratory specimens from intensive care unit patients, ninety-eight of 314 (31.2%) in 2014, none of 307 (0%) specimens in 2015, and 19 of 240 (7.9%) specimens in 2016 were identified as enterovirus D68. Amongst respiratory specimens from all patients during the prospective active surveillance period, none of 1469 (0%) in 2015 and 46 of 1403 (3.3%) were positive for enterovirus D68. Conclusions Surveillance for enterovirus D68 amongst respiratory specimens at a quaternary care children’s hospital revealed a seasonal pattern of circulation in the late summer to early fall of 2014 and 2016. Continued surveillance of respiratory specimens is necessary to define the circulation pattern and understand the epidemiology of this emerging pathogen.

show abstract

Section: Resultsmentioning

confidence: 87%

Surveillance for enterovirus D68 in colorado children reveals continued circulation

Messacar

Robinson

Pretty

et al. 2017

Journal of Clinical Virology

View full text Add to dashboard Cite

show abstract

“…Reports of acute flaccid myelitis (AFM) occurring coincident to the outbreak of EV-D68 respiratory disease raised the possibility that EV-D68 might be a causative agent of AFM ( 7 ). EV-D68 infection within a subset of these AFM cases was confirmed in several independent epidemiological clusters in the United States ( 9 – 14 ), France ( 15 ), Norway ( 16 ), Canada ( 17 ), and Australia ( 18 ). Statistical analyses of the AFM cases in Colorado ( 12 ) and California ( 19 ) have supported the association between EV-D68 and AFM, and viral nucleic acid detection studies of patient samples have failed to reveal an alternative etiology ( 7 , 10 ).…”

Section: Introductionmentioning

confidence: 77%

Contemporary Circulating Enterovirus D68 Strains Have Acquired the Capacity for Viral Entry and Replication in Human Neuronal Cells

Brown

Hixon

Oldfield

et al. 2018

mBio

View full text Add to dashboard Cite

Since the EV-D68 outbreak during the summer of 2014, evidence of a causal link to a type of limb paralysis (AFM) has been mounting. In this article, we describe a neuronal cell culture model (SH-SY5Y cells) in which a subset of contemporary 2014 outbreak strains of EV-D68 show infectivity in neuronal cells, or neurotropism. We confirmed the difference in neurotropism in vitro using primary human neuron cell cultures and in vivo with a mouse paralysis model. Using the SH-SY5Y cell model, we determined that a barrier to viral entry is at least partly responsible for neurotropism. SH-SY5Y cells may be useful in determining if specific EV-D68 genetic determinants are associated with neuropathogenesis, and replication in this cell line could be used as rapid screening tool for identification of neurotropic EV-D68 strains. This may assist with better understanding of pathogenesis and epidemiology and with the development of potential therapies.

show abstract

“…Even lower multiplexing levels (or sequencing kits with greater output) would be necessary for sequencing of EV-D68 from nasal swabs. In these situations, a targeted NGS method, such as generating EV-D68 amplicons prior to library preparation and sequencing, is likely the most cost-effective option (42, 43). Ideally, researchers should strive to sequence as many samples as possible on a run, as multiplexing dramatically decreases the cost per sample.…”

Section: Discussionmentioning

confidence: 99%

Comparison of Illumina MiSeq and the Ion Torrent PGM and S5 platforms for whole-genome sequencing of picornaviruses and caliciviruses

Marine¹,

Valladares

Castro

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

28Next-generation sequencing is a powerful tool for virological surveillance. While 29 Illumina® and Ion Torrent® sequencing platforms are used extensively for generating 30 viral RNA genome sequences, there is limited data comparing different platforms. We 31 evaluated the Illumina MiSeq, Ion Torrent PGM and Ion Torrent S5 platforms using a 32 panel of sixteen specimens containing picornaviruses and human caliciviruses 33 (noroviruses and sapoviruses). The specimens were processed, using combinations of 34 three library preparation and five sequencing kits, to assess the quality and 35 completeness of assembled viral genomes, and an estimation of cost per sample to 36 generate the data was calculated. The choice of library preparation kit and sequencing 37 platform was found to impact the breadth of genome coverage and accuracy of 38 consensus viral genomes. The Ion Torrent S5 outperformed the older Ion Torrent PGM 39 platform in data quality and cost, and generated the highest proportion of reads for 40 enterovirus D68 samples. However, indels at homopolymer regions impacted the 41 accuracy of consensus genome sequences. For lower throughput sequencing runs (i.e., 42 Ion Torrent 510 or Illumina MiSeq Nano V2), the cost per sample was lower on the 43 MiSeq platform, whereas with higher throughput runs (Ion Torrent 530 or Illumina MiSeq 44 V2) the cost per sample was comparable. These findings suggest that the Ion Torrent 45 S5 and Illumina MiSeq platforms are both viable options for genomic sequencing of 46 RNA viruses, each with specific advantages and tradeoffs.47 48Conventional Sanger sequencing has been the gold standard for genomic analysis of 49 pathogens in public health laboratories for over three decades. However, the expansion 50 of next-generation sequencing (NGS) technologies has increased demand for high-51 throughput sequencing of genomes at a lower cost (1). NGS has been used extensively 52 for routine surveillance and outbreak investigation of numerous viral RNA pathogens. 53The exponential growth of genomic information generated for important pathogens has 54 provided increased resolution for molecular epidemiology, as well as information 55 necessary for the design of clinical assays and therapeutics (2-5). NGS methods are 56 also useful for identifying pathogens in syndromes where etiologies often remain 57 unknown (e.g., encephalitis, febrile illness), complementing or even replacing current 58 diagnostic methods (2, 6, 7). 60Over the past several years, the suppliers of high-capacity short-read sequencers have 61 been reduced to two manufacturers: Illumina (sequencing-by-synthesis technology) and 62 Thermo Fisher Scientific (Ion Torrent semi-conductor sequencing technology) (3). 63 Illumina platforms have been used to generate nearly 90% of NGS data worldwide 64 (https://www.wired.com/2016/02/gene-sequencing-goliath-wants-get-bigger-still/). 65Illumina produces several benchtop and production-scale sequencers with data outputs 66 varying from 1.2 gigabases (Gb) to 6 terabases (Tb). In mic...

show abstract

Detection and Genomic Characterization of Enterovirus D68 in Respiratory Samples Isolated in the United States in 2016

Cited by 13 publications

References 6 publications

Surveillance for enterovirus D68 in colorado children reveals continued circulation

Surveillance for enterovirus D68 in colorado children reveals continued circulation

Contemporary Circulating Enterovirus D68 Strains Have Acquired the Capacity for Viral Entry and Replication in Human Neuronal Cells

Comparison of Illumina MiSeq and the Ion Torrent PGM and S5 platforms for whole-genome sequencing of picornaviruses and caliciviruses

Contact Info

Product

Resources

About