Metagenomic detection and reconstruction of Lake Sinai Virus from honey bee sequence data
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.
Citation Information
| Publication Year | 2019 |
|---|---|
| Title | Metagenomic detection and reconstruction of Lake Sinai Virus from honey bee sequence data |
| DOI | 10.5066/P9F4YR6P |
| Authors | Robert S Cornman |
| Product Type | Data Release |
| Record Source | USGS Digital Object Identifier Catalog |
| USGS Organization | Fort Collins Science Center |
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Relative abundance and molecular evolution of Lake Sinai Virus (Sinaivirus) clades
Lake Sinai Viruses (Sinaivirus) are commonly detected in honey bees (Apis mellifera) but no disease phenotypes or fitness consequences have yet been demonstrated. This viral group is genetically diverse, lacks obvious geographic structure, and multiple lineages can co-infect individual bees. While phylogenetic analyses have been performed, the molecular evolution of LSV has not been studied extensAuthorsRobert S. Cornman - Connect