Enterovirus D68 Genome Sequenced

In recent months, the rare Enterovirus D68 (EV-D68) has spread rapidly across North America and caused severe respiratory illness in young children, with some requiring hospitalization.

Routine laboratory tests cannot identify specific Enterovirus and most hospitals and clinics can only perform tests to determine if a patient has a virus that fits broadly into the Enterovirus/rhinovirus category. As only specialized laboratories can identify the virus, merely 594 cases of EV-D68 infection have been officially confirmed in 43 US states and the District of Columbia.


Scientists at the Washington University School of Medicine (St. Louis, MO, USA) analyzed 14 patient samples testing positive for Enterovirus/rhinovirus. They determined the complete coding sequence of one strain from St. Louis by using high-throughput sequencing of nucleic acid from a clinical sample. To evaluate the sequence diversity in EV-D68 strains circulating in the St. Louis metropolitan area, they also generated partial-genome sequences from eight more EV-D68–positive clinical samples from the immediate area.

Residual material from a subset of nasopharyngeal specimens positive for Enterovirus/rhinovirus that had been tested by the BioFire FilmArray Respiratory Panel (BioFire Diagnostics; Salt Lake City, UT, USA) were selected for high-throughput sequencing. Total nucleic acid was extracted from clinical samples by using NucliSENS easyMAG (bioMérieux; Marcy l'Etoile, France) and used to make dual-indexed sequencing libraries. Enterovirus/rhinovirus sequences were enriched by using a NimbleGen custom sequence capture reagent (Roche/NimbleGen; Madison, WI, USA), which as of February 2014 was selective for all complete Enterovirus and rhinovirus genomes in the GenBank. Sequence data were generated on a HiSeq 2500 (Illumina; San Diego, CA, USA).

Of the 14 patient samples tested, nine were identified as infected with EV-D68 and the remaining five samples were other respiratory viruses. Seven of the nine patients with the EV-D68 strain had severe disease that required admission to the pediatric intensive care unit. The remaining two had moderate symptoms resulting in general hospital admission. Of the five patients with other viruses, three were classified with severe disease. The only two patients discharged home with mild disease did not have the EV-D68 strain.

Gregory A. Storch, MD, a professor of Pediatrics and senior author of the study said, “Having the DNA sequence of this virus enables additional investigative studies. It can be used to create better diagnostic tests. It also may help us understand why this epidemic seems to be producing severe and unusual disease, and why it's spreading more extensively than in the past." The study was published on October 28, 2014, in the journal Emerging Infectious Diseases.

Related Links:
Washington University School of Medicine
BioFire Diagnostics
BioMérieux