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Whole-Genome Sequence Analysis Reveals the Enterovirus D68 Isolates during the United States 2014 Outbreak Mainly Belong to a Novel Clade.
- Source :
-
Scientific reports [Sci Rep] 2015 Oct 15; Vol. 5, pp. 15223. Date of Electronic Publication: 2015 Oct 15. - Publication Year :
- 2015
-
Abstract
- In the late summer and the fall of 2014, the United States experienced an unprecedented outbreak of enterovirus D68 (EV-D68) infections. During the outbreak, we collected nasopharyngeal swab specimens from patients in the Lower Hudson Valley of New York. Here, we conduct a retrospective study on the genomic diversity of EV-D68 strains. We first employ a metagenomic shotgun sequencing protocol on a total of 93 clinical samples, including 21 negative controls, the results of which allow assembly of 20 EV-D68 genomes, six complete and 14 near-complete. We then investigate their genetic relationships, along with additional 20 EV-D68 strains having whole-genome sequences publicly available. Our comparative genomic analysis uncovers that the majority (26/29) of EV-D68 strains circulating in the 2014 outbreak differ significantly from prior ones, have a main feature of three variables, C1817T, C3277A, and A4020G, and belong to a new clade. C3277A causes amino acid substitution T860N in the protease 2A(pro) cleavage site between VP1 and 2A, whereas A4020G causes S1108G in a 3C(pro) cleavage site between 2B and 2C. The two functional mutations may alter the proteases' cleavage efficiency, leading to increased rate of viral replication and transmission. These provide insights into the evolution of epidemic EV-D68 strains.
- Subjects :
- Base Sequence
Cluster Analysis
Discriminant Analysis
Disease Outbreaks
Enterovirus D, Human isolation & purification
Enterovirus Infections epidemiology
Female
High-Throughput Nucleotide Sequencing
Humans
Male
Molecular Sequence Data
Nasopharynx virology
Principal Component Analysis
RNA, Viral analysis
RNA, Viral metabolism
Real-Time Polymerase Chain Reaction
Respiratory Tract Infections epidemiology
Retrospective Studies
Seasons
Sequence Alignment
Sequence Analysis, RNA
United States epidemiology
Enterovirus D, Human genetics
Enterovirus Infections virology
Respiratory Tract Infections virology
Subjects
Details
- Language :
- English
- ISSN :
- 2045-2322
- Volume :
- 5
- Database :
- MEDLINE
- Journal :
- Scientific reports
- Publication Type :
- Academic Journal
- Accession number :
- 26469882
- Full Text :
- https://doi.org/10.1038/srep15223