Honey bees (Apis mellifera), a critical agricultural pollinator in many areas, have a high rate of infection with a large DNA virus, Apis mellifera filamentous virus (AmFV), yet little is known about its ecology or impact on honey bee colonies, other than its ubiquity and apparent low virulence. This study scanned over 5,000 public data sets to detect AmFV sequences in honey bees as well as a parasitic mite of honey bees, Varroa destructor, that is a potential vector of AmFV. The data release consists of these files: 1. AmFV.genome.assemblies.aligned.fas, which contains new AmFV draft genome sequences generated by this study aligned with existing reference genome accessions downloaded from the National Center for Biotechnology Information (NCBI). 2. kmer.list.txt, a list of kmers that were extracted from reference sequences and searched for in Sequence Read Archive (SRA) accessions. 3. sample.metadata.txt, which lists all accessions of the SRA, and NCBI database of high-throughput sequence data, that were used in this study. The file also includes the raw occurrence counts of kmers listed in kmer.lists.txt, summed by category.

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 recombinant backgrounds. High abundance of VDV kmers was largely restricted to recombinant forms. Non-metric multidimensional scaling identified genotypic clusters among DWV isolates, which was corroborated by read mapping and consensus generation. The recently described DWV-C lineage was not detected in the searched accessions. The data further highlight the utility of high-throughput sequencing to monitor viral polymorphisms and statistically test biological predictors of titer, and point to the need for consistent methodologies and sampling schemes.

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 recombinant backgrounds. High abundance of VDV kmers was largely restricted to recombinant forms. Non-metric multidimensional scaling identified genotypic clusters among DWV isolates, which was corroborated by read mapping and consensus generation. The recently described DWV-C lineage was not detected in the searched accessions. The data further highlight the utility of high-throughput sequencing to monitor viral polymorphisms and statistically test biological predictors of titer, and point to the need for consistent methodologies and sampling schemes.

Lake Sinai Viruses (LSV) are common ribonucleic acid (RNA) viruses of honey bees (Apis mellifera) that frequently reach high abundance but are not linked to overt disease. LSVs are genetically heterogeneous and collectively widespread, but despite frequent detection in surveys, the ecological and geographic factors structuring their distribution in A. mellifera are not understood. Even less is known about their distribution in other species. Better understanding of LSV prevalence and ecology have been hampered by high sequence diversity within the LSV clade. We developed a new genetic assay that detects all currently known lineages. We also performed pilot metagenetic sequencing to quantify the diversity of LSV sequences. The resulting data are summarized herein.

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.

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.

,Vector-borne disease prevalence is increasing at a time when surveillance capacity in the United States is decreasing. One way to address this surveillance deficiency is to utilize established infrastructure, such as zoological parks, to investigate animal disease outbreaks and improve our epidemiological understanding of vector-borne pathogens. During fall 2020, an outbreak of epizootic hemorrhagic disease (EHD) at the Minnesota Zoo resulted in morbidity and seroconversion of several collection animals. In response to this outbreak, insect surveillance was conducted, and the collected insects were tested for the presence of epizootic hemorrhagic disease virus (EHDV) by RT-qPCR to better understand the local transmitting vector populations responsible for the outbreak. Six pools of Culicoides biting midges were positive for EHDV, including three pools of Culicoides sonorensis, two pools of Culicoides variipennis, and a pool of degraded C. variipennis complex midges. All three endemic serotypes of EHDV (1, 2, and 6) were detected in both animals and midge pools from the premises. Despite this outbreak, no EHDV cases had been reported in wild animals near the zoo. This highlights the importance and utility of using animal holding facilities, such as zoos, as sentinels to better understand the spatio-temporal dynamics of pathogen transmission.,

To investigate the role of migratory birds in the dissemination of West Nile virus (WNV), we measured the prevalence of infectious WNV and specific WNV neutralizing antibodies in birds, principally Passeriformes, during spring and fall migrations in the Atlantic and Mississippi flyways from 2001-2003. Blood samples were obtained from 13,403 birds, representing 133 species. Specific WNV neutralizing antibody was detected in 254 resident and migratory birds, representing 39 species, and was most commonly detected in northern cardinals ( Cardinalis cardinalis ) (9.8%, N = 762) and gray catbirds ( Dumetella carolinensis ) (3.2%, N = 3188). West Nile virus viremias were detected in 19 birds, including 8 gray catbirds, and only during the fall migratory period. These results provide additional evidence that migratory birds may have been a principal agent for the spread of WNV in North America and provide data on the occurrence of WNV in a variety of bird species.

,These data represent V. destructor genomic annotations to be used for evolutionary comparison with other arthropods.,The ectoparasitic mite Varroa destructor has emerged as the primary pest of domestic honey bees (Apis mellifera). Here we present an initial survey of the V. destructor genome carried out to advance our understanding of Varroa biology and to identify new avenues for mite control. This sequence survey provides immediate resources for molecular and population-genetic analyses of Varroa-Apis interactions and defines the challenges ahead for a comprehensive Varroa genome project.,