Metagenomic detection and reconstruction of Lake Sinai Virus from honey bee sequence data
Dates
Publication Date
2019-03-14
Time Period
2018-04-01
Citation
Cornman, R.S., 2019, Metagenomic detection and reconstruction of Lake Sinai Virus from honey bee sequence data: U.S. Geological Survey data release, https://doi.org/10.5066/P9F4YR6P.
Summary
A survey of public honey bee sequence data was performed to detect infections by Lake Sinai Virus (LSV). The Sequence Read Archive of the National Center for Biotechnology Information (NCBI) was queried to identify accessions of RNA sequence data derived from honey bee. These were filtered as described below and then up to 50 million reads or read pairs were downloaded and searched against a reference database of conserved LSV sequence. Accessions with matches above a specified threshold were downloaded in their entirety and assembled into longer contiguous sequences (contigs). The result contigs were searched against each open reading frame (ORF) of the reference LSV genome present in the NCBI database (accession NC_032433.1) and [...]
Summary
A survey of public honey bee sequence data was performed to detect infections by Lake Sinai Virus (LSV). The Sequence Read Archive of the National Center for Biotechnology Information (NCBI) was queried to identify accessions of RNA sequence data derived from honey bee. These were filtered as described below and then up to 50 million reads or read pairs were downloaded and searched against a reference database of conserved LSV sequence. Accessions with matches above a specified threshold were downloaded in their entirety and assembled into longer contiguous sequences (contigs). The result contigs were searched against each open reading frame (ORF) of the reference LSV genome present in the NCBI database (accession NC_032433.1) and matching regions from each contig. These ORF sequences were aligned with additional sequences identified in NCBI databases through the BLAST web service. These alignments provide the basis for computing phylogenetic trees, rates of nucleotide substitution, codon usage bias, and other evolutionary parameters.
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Metagenomic_scan_for_Lake_Sinai_Virus_infecting_honey_bees.xml Original FGDC Metadata
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FinalData.zip
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Related External Resources
Type: Related Primary Publication
Cornman R.S., 2019, Relative abundance and molecular evolution of Lake Sinai Virus (Sinaivirus) clades: PeerJ, v. 7, p. e6305, https://doi.org/10.7717/peerj.6305.
The data were collected to evaluate the diversity, phylogeny, and molecular evolution of Lake Sinai Viruses infecting honey bees. This recently described clade of viruses is known only from sequence data, as there are no described disease phenotypes in honey bees or any other arthropod, despite the high titer and high prevalence often observed from molecular assays.
