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Provenance, classification, and abundance of RNA sequence fragments used to assess virus infections in honey bees, Apis mellifera

Dates

Publication Date
Time Period
2016-09-29

Citation

Cornman, R.S., 2017, Provenance, classification, and abundance of RNA sequence fragments used to assess virus infections in honey bees, Apis mellifera: U.S. Geological Survey data release, https://doi.org/10.5066/F7BK1B8P.

Summary

Deformed wing virus (DWV) is a major pathogen of concern to apiculture, and recent reports have indicated the local predominance and potential virulence of recombinants between DWV and a related virus, Varroa destructor virus 1 (VDV). However, little is known about the frequency and titer of VDV and recombinants relative to DWV generally. In this study, I assessed the relative occurrence and titer of DWV and VDV in public RNA-seq accessions of honey bee using a rapid, kmer-based approach. Three recombinant types were detectable graphically and corroborated by de novo assembly. Recombination breakpoints did not disrupt the capsid-encoding region, consistent with previous reports, and both VDV- and DWV-derived capsids were observed in [...]

Contacts

Point of Contact :
Robert S Cornman
Originator :
Robert S Cornman
Metadata Contact :
Robert S Cornman
Publisher :
U.S. Geological Survey
Distributor :
GS ScienceBase
USGS Mission Area :
Ecosystems
SDC Data Owner :
Fort Collins Science Center

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data-file.txt.xml
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Purpose

Deformed wing virus (DWV) is a pathogen of utmost concern for apiculture. Individual studies have reported that genetic recombinants of DWV and a related virus, VDV, are more virulent, yet there are ascertainment biases that could potentially exaggerate the significance of these reports. There has been no systematic, large-scale assessment of the distribution of different viral types, and thus no basis for assessing whether the distribution of genetic variants is in flux. This study mined a large repository of public data to provide such a baseline, and assess whether kmer-based classifications are efficient for this purpose.

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Communities

  • Fort Collins Science Center (FORT)
  • USGS Data Release Products

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Provenance

Additional Information

Identifiers

Type Scheme Key
DOI https://www.sciencebase.gov/vocab/category/item/identifier doi:10.5066/F7BK1B8P

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