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Metagenomic detection and reconstruction of Lake Sinai Virus from honey bee sequence data


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Cornman, R.S., 2019, Metagenomic detection and reconstruction of Lake Sinai Virus from honey bee sequence data: U.S. Geological Survey data release,


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 [...]


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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.



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



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DOI doi:10.5066/P9F4YR6P

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