Genome Sequence of Enterovirus D68 from St. Louis, Missouri, USA

Wylie, Kristine M.; Wylie, Todd; Orvedahl, Anthony; Buller, Richard S.; Herter, Brandi; Magrini, Vincent; Wilson, Richard K.; Storch, Gregory A.

doi:10.3201/eid2101.141605

Cited by 34 publications

(35 citation statements)

References 10 publications

(8 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…One of the most striking features of the 2014 outbreak was that most EV-D68 infections were associated with severe respiratory diseases in children (36,40,41,(60)(61)(62)(63)(64)(65)69). However, we found no association between age, gender, or clinical symptoms and different viral subclades in our Kansas City population.…”

Section: Discussioncontrasting

confidence: 53%

“…In line with our subclade definition, subclades A1 and B2 were endemic and found in many countries before the (16,19,30). During the 2014 outbreak, a novel subclade, B1, seems to have rapidly emerged and was dominant during the U.S. outbreak (38,60,61). During the same period, subclades A1 and B2 continued to be isolated in European countries (40,41,(62)(63)(64)(65).…”

Section: Discussionmentioning

confidence: 61%

“…During the same period, subclades A1 and B2 continued to be isolated in European countries (40,41,(62)(63)(64)(65). In addition, we found multiple viral introductions from other localities into the single locality of Kansas City during the 2014 U.S. outbreak despite the relatively small number of sequences collected (60), indicating that EV-D68 exhibits relatively fluid spatial dynamics within the United States.…”

Section: Discussionmentioning

confidence: 85%

See 2 more Smart Citations

Molecular Evolution and Intraclade Recombination of Enterovirus D68 during the 2014 Outbreak in the United States

Tan

Hassan

Schuster

et al. 2016

J Virol

View full text Add to dashboard Cite

In August 2014, an outbreak of enterovirus D68 (EV-D68) occurred in North America, causing severe respiratory disease in children. Due to a lack of complete genome sequence data, there is only a limited understanding of the molecular evolution and epidemiology of EV-D68 during this outbreak, and it is uncertain whether the differing clinical manifestations of EV-D68 infection are associated with specific viral lineages. We developed a high-throughput complete genome sequencing pipeline for EV-D68 that produced a total of 59 complete genomes from respiratory samples with a 95% success rate, including 57 genomes from Kansas City, MO, collected during the 2014 outbreak. With these data in hand, we performed phylogenetic analyses of complete genome and VP1 capsid protein sequences. Notably, we observed considerable genetic diversity among EV-D68 isolates in Kansas City, manifest as phylogenetically distinct lineages, indicative of multiple introductions of this virus into the city. In addition, we identified an intersubclade recombination event within EV-D68, the first recombinant in this virus reported to date. Finally, we found no significant association between EV-D68 genetic variation, either lineages or individual mutations, and a variety of demographic and clinical variables, suggesting that host factors likely play a major role in determining disease severity. Overall, our study revealed the complex pattern of viral evolution within a single geographic locality during a single outbreak, which has implications for the design of effective intervention and prevention strategies. IMPORTANCEUntil recently, EV-D68 was considered to be an uncommon human pathogen, associated with mild respiratory illness. However, in 2014 EV-D68 was responsible for more than 1,000 disease cases in North America, including severe respiratory illness in children and acute flaccid myelitis, raising concerns about its potential impact on public health. Despite the emergence of EV-D68, a lack of full-length genome sequences means that little is known about the molecular evolution of this virus within a single geographic locality during a single outbreak. Here, we doubled the number of publicly available complete genome sequences of EV-D68 by performing high-throughput next-generation sequencing, characterized the evolutionary history of this outbreak in detail, identified a recombination event, and investigated whether there was any correlation between the demographic and clinical characteristics of the patients and the viral variant that infected them. Overall, these results will help inform the design of intervention strategies for EV-D68.

show abstract

Section: Discussioncontrasting

confidence: 53%

Section: Discussionmentioning

confidence: 61%

Section: Discussionmentioning

confidence: 85%

See 1 more Smart Citation

Molecular Evolution and Intraclade Recombination of Enterovirus D68 during the 2014 Outbreak in the United States

Tan

Hassan

Schuster

et al. 2016

J Virol

View full text Add to dashboard Cite

show abstract

“…Cold Wylie et al 2015), and in that work, the extensive sequence data that we obtained allowed us carry out detailed comparative analysis of closely related strains that differed at a limited number of nucleotide positions. Second, the use of ViroCap can reduce the depth of sequencing needed to detect viruses in samples.…”

Section: Discussionmentioning

confidence: 99%

Enhanced virome sequencing using targeted sequence capture

et al. 2015

Self Cite

View full text Add to dashboard Cite

Metagenomic shotgun sequencing (MSS) is an important tool for characterizing viral populations. It is culture independent, requires no a priori knowledge of the viruses in the sample, and may provide useful genomic information. However, MSS can lack sensitivity and may yield insufficient data for detailed analysis. We have created a targeted sequence capture panel, ViroCap, designed to enrich nucleic acid from DNA and RNA viruses from 34 families that infect vertebrate hosts. A computational approach condensed ∼1 billion bp of viral reference sequence into <200 million bp of unique, representative sequence suitable for targeted sequence capture. We compared the effectiveness of detecting viruses in standard MSS versus MSS following targeted sequence capture. First, we analyzed two sets of samples, one derived from samples submitted to a diagnostic virology laboratory and one derived from samples collected in a study of fever in children. We detected 14 and 18 viruses in the two sets, comprising 19 genera from 10 families, with dramatic enhancement of genome representation following capture enrichment. The median fold-increases in percentage viral reads post-capture were 674 and 296. Median breadth of coverage increased from 2.1% to 83.2% post-capture in the first set and from 2.0% to 75.6% in the second set. Next, we analyzed samples containing a set of diverse anellovirus sequences and demonstrated that ViroCap could be used to detect viral sequences with up to 58% variation from the references used to select capture probes. ViroCap substantially enhances MSS for a comprehensive set of viruses and has utility for research and clinical applications.

show abstract

“…One limitation of this study was that all clinical samples were collected from patients with respiratory illness in the lower Hud- (20,21), and patients in California (22) suggests that this EV-D68 real-time RT-PCR assay was able to detect other EV-D68 strains associated with a national outbreak of EV-D68 infections in 2014. This is further confirmed by a CDC internal validation study in which 100% sensitivity and 96% specificity were achieved when 134 respiratory specimens from several U.S. states were analyzed (16).…”

Section: Discussionmentioning

confidence: 99%

Evaluation of a Real-Time Reverse Transcription-PCR Assay for Detection of Enterovirus D68 in Clinical Samples from an Outbreak in New York State in 2014

et al. 2015

View full text Add to dashboard Cite

An outbreak of severe respiratory illness associated with enterovirus D68 (EV-D68) infection was reported in mid-The EV-D68 rRT-PCR showed diagnostic sensitivity and specificity of 98.6% and 97.5%, respectively. Our data suggest that the EV-D68 rRT-PCR is a reliable assay for detection of EV-D68 in clinical samples and has a potential to be used as a tool for rapid diagnosis and outbreak investigation of EV-D68-associated infections in clinical and public health laboratories.

show abstract

Genome Sequence of Enterovirus D68 from St. Louis, Missouri, USA

Cited by 34 publications

References 10 publications

Molecular Evolution and Intraclade Recombination of Enterovirus D68 during the 2014 Outbreak in the United States

Molecular Evolution and Intraclade Recombination of Enterovirus D68 during the 2014 Outbreak in the United States

Enhanced virome sequencing using targeted sequence capture

Evaluation of a Real-Time Reverse Transcription-PCR Assay for Detection of Enterovirus D68 in Clinical Samples from an Outbreak in New York State in 2014

Contact Info

Product

Resources

About