DOI: 10.5061/dryad.8pk0p2ntr
title: Signatures of adaptive decreased virulence of deformed wing virus in an isolated population of wild honey bees (Apis mellifera)

description: Understanding the ecological and evolutionary processes that drive
 host-pathogen interactions is critical for combating epidemics and
 conserving species. The Varroa destructor mite and deformed wing virus
 (DWV) are two synergistic threats to Western honey bee (Apis mellifera)
 populations across the globe. Distinct honey bee populations have been
 found to self-sustain despite Varroa infestations, including colonies
 within the Arnot Forest outside Ithaca, NY, USA. We hypothesized that in
 these bee populations, DWV has been selected to produce an avirulent
 infection phenotype, allowing for the persistence of both host and
 disease-causing agents. To investigate this, we assessed the titer of
 viruses in bees from the Arnot Forest and managed apiaries, and assessed
 genomic variation and virulence differences between DWV isolates. Across
 groups, we found viral abundance was similar, but DWV genotypes were
 distinct. We also found that infections with isolates from the Arnot
 Forest resulted in higher survival and lower rates of symptomatic deformed
 wings, compared to analogous isolates from managed colonies, providing
 preliminary evidence to support the hypothesis of adaptive decreased viral
 virulence. Overall, this multi-level investigation of virus genotype and
 phenotype across different contexts reveals critical insight into global
 bee health and the ecological and evolutionary processes driving
 host-pathogen interactions.
description: Spreadsheet contains data collected from naturally infected honey
 bee samples (Table 1-14) and experimental infections (Table 15-31).
 Description of each sheet can be found in Metadata sheet. The two R files
 contain code for analyzing the natural infections (Arnot_1.R) and
 experimental infections (Arnot_2.R). Basic pipeline for sequence analysis
 can be found in Arnot_seq_code.txt file. Consensus genomes, as well as raw
 sequence reads, can be found on the NCBI Genome and SRA database
 (PRJNA922567 and PRJNA922218, genome accessions
 OR497372-OR497398). 
description: # Signatures of adaptive decreased virulence of deformed wing virus in an
 isolated population of wild honey bees (Apis mellifera)
 [https://doi.org/10.5061/dryad.8pk0p2ntr](https://doi.org/10.5061/dryad.8pk0p2ntr) Data includes processed qPCR data, results from sequencing analysis of DWV genomes, and infection phenotype data from experimental infections. ## Description of the data and file structure The data from these experiments presented in this study can be split into two parts. Part 1 (Tables 1-14) examines the prevalence and sequence identity of viruses naturally infecting bees sampled from the Arnot Forest, New York, and from managed apiaries in New York and Pennsylvania. After the collection of wild and managed bees, virus was extracted from individual samples. RNA from these viral extracts were subjected to qPCR and Illumina sequencing to characterize the viral sequence identity and load. In Part 2 (Tables 15-31), the virus inocula isolated from the naturally-infected bees from Part 1 are used for experimental infections in developing honey bee pupae to assess potential infection differences across isolates. Data collected from these experimental infections included viral loads at 3 days post-injection, pupation rates, deformed wing rates, and adult survival through time. Results from statistical analyses of this infection data are also included. 1. Table 1 Collections information : Date of collection, Group (Arnot (ie unmanaged), NY and PA (managed), site #, latitude and longitude of site, colony # at site (if applicable), # of bee collected, # of bees assessed (qPCR for presence of bee viruses), and additional information from the collection 2. Table 2 qPCR primers : primer name, primer sequence, and original reference 3. Table 3 eIF3-S8 qPCR results - raw data : Well # (location on qPCR plate), Plate #, Sample Name, raw Ct value, Tm value (melting temperature) 4. Table 4 DWV-A+B (total DWV) qPCR results - raw data : Well # (location on qPCR plate), Plate #, Sample Name, raw Ct value, Tm value (melting temperature) 5. Table 5 DWV-A and DWV-B (NS) qPCR results - raw data : Well # (location on qPCR plate), Plate #, Sample Name, raw Ct value, Tm value (melting temperature) for DWV-A and DWV-B, targeting the putative non-structural (NS) region of the viral genome 6. Table 6 BQCV qPCR results - raw data : Well # (location on qPCR plate), Plate #, Sample Name, raw Ct value, Tm value (melting temperature) 7. Table 7 SBV qPCR results - raw data : Well # (location on qPCR plate), Plate #, Sample Name, raw Ct value, Tm value (melting temperature) 8. Table 8 qPCR cleaned data - ddCT : Sample name, colony\_new (updated ID including site and colony info), site #, colony # (if applicable), group, management status, round of cDNA, [target]\_ddct (mean expression value calculated via the delta delta Ct method), [target]\_Presence (virus 'Present' when normalized qPCR dCt was less than 30) 9. Table 9 Presence/Absence data (long form of viral presence data from qPCR experiments) : Sample name, colony\_new (updated ID including site and colony info), site #, colony # (if applicable), group, management status, round of cDNA, target virus (DWV/BQCV), Presence (Present/Absent) 10. Table 10 Sequence information : file name, num\_seqs pre trim (raw sequence count prior to quality trimming), num\_seqs post trim (raw sequence count after quality trimming), % remaining (percentage of reads surviving quality trimming) 11. Table 11 Read counts for bee viruses : (column 1) sample name, total trimmed reads, number of reads aligning to reference genome for three variants of DWV plus 6 common bee viruses, number of reads aligning to Apis mellifera rRNA, DWV consensus genome Genbank accession numbers across samples (if applicable) 12. Table 12 DWV A variation (raw VCF) : top rows contain variant calling information; #CHROM (DWV accession number), POS (position in genome), ID, REF (reference allele), ALT (variant allele identified in sample), QUAL (quality), FILTER, INFO, FORMAT, then samples (information other than './.:.' indicative of variant allele present in that sample file) 13. Table 13 DWV B variation (raw VCF) : top rows contain variant calling information; #CHROM (DWV accession number), POS (position in genome), ID, REF (reference allele), ALT (variant allele identified in sample), QUAL (quality), FILTER, INFO, FORMAT, then samples (information other than './.:.' indicative of variant allele present in that sample file) 14. Table 14 Cleaned Variant table : DWV (variant A or B), POS (position in genome), Type (type of variant), na\_change (nucleic acid change), protein\_change (amino acid change), then the specificity of variant based on overlaps across groups 15. Table 15 Isolates used in experimental infections : ID in publication (re-named to be more descriptive to reader), ID in supplemental tables, Group, Site/colony/sample description, viral population, assessed in experimental infections 16. Table 16 Eclosion rate data : trial, colony (honey bee colony where pupae were sourced from), High\_Low (dose), round, date (date of experimental infection), DWV, group, eclose (count # successfully eclosed), no\_eclose (count # that did not successfully eclose), total (eclose + no\_eclose), percentage (eclose/total) 17. Table 17 Eclosion timing data : trial, colony (honey bee colony where pupae were sourced from), High\_Low (dose), round, date (date of experimental infection), group, eclosion\_time\_off\_median (time from median eclosion per trial) 18. Table 18 deformed wing rate data : trial, colony (honey bee colony where pupae were sourced from), High\_Low (dose), round, date (date of experimental infection), DWV, group, total (normal + dw), normal (count # of bees with normally developed wings), dw (count # with wing deformities) 19. Table 19 Survival data : trial, colony (honey bee colony where pupae were sourced from), High\_Low (dose), round, date (date of experimental infection), group, time (hours after infection), mort (0=no mortality, 1=mortality observed), day (date of mortality observation) 20. Table 20 eIF3-S8 qPCR results - raw data : Sample Name, raw Ct value, Tm value (melting temperature) 21. Table 21 GAPDH qPCR results - raw data : Sample Name, raw Ct value, Tm value (melting temperature) 22. Table 22 DWV-A+B (total DWV) qPCR results - raw data : Sample Name, raw Ct value, Quantity (determined by standard curve amplification of PCR product of known quantities), Tm value (melting temperature) 23. Table 23 BQCV qPCR results - raw data : Sample Name, raw Ct value, Quantity (determined by standard curve amplification of PCR product of known quantities), Tm value (melting temperature) 24. Table 24 DWV-A and DWV-B (NS) qPCR results - raw data : : Sample Name, raw Ct value, Quantity (determined by standard curve amplification of PCR product of known quantities), Tm value (melting temperature) for DWV-A and DWV-B, targeting the putative non-structural (NS) region of the viral genome 25. Table 25 AKI qPCR results - raw data (AKI = umbrella primer targeting the following paralysis viruses : Acute bee paralysis virus, Kashmir bee virus, Israeli acute paralysis virus) : Sample Name, raw Ct value, Quantity (determined by standard curve amplification of PCR product of known quantities), Tm value (melting temperature) 26. Table 26 qPCR cleaned data (empty values in Variable columns = variable not applicable; empty values in Value columns ([target]\_Mean) = mean could not be calculated) : Sample\_name, Group, DWV, BQCV (presence of BQCV), Colony (honey bee colony where pupae were sourced from), Dose (High or Low), [target]\_Mean Ct or Quantity values 27. Table 27 Viral load (qPCR) p values (output from Tukey post-hoc test) : comparison (Group, or Dose:Group), diff (difference in means), lwr and upr (lower and upper confidence levels), p adj (adjusted p values) 28. Table 28 eclosion rate p values : group1, group2, p (raw), p.adj (adjusted p value), p.adj.signif (ns - no significant p values after adjusting) 29. Table 29 eclosion timing p values : Wilcox rank sum test (p.val &lt;0.05, P value adjustment method: BH) 30. Table 30 Deformed wing rate p values : group1, group2, p (raw), p.adj (adjusted p value), p.adj.signif (ns - no significant p values after adjusting) 31. Table 31 survival p values : Long-Rank test (p.val &lt;0.05, P value adjustment method: BH) Sharing/Access information Consensus genomes, as well as raw sequence reads, can be found on the NCBI Genome and SRA database (PRJNA922567 and PRJNA922218, genome accessions OR497372-OR497398). ## Code/Software The two R files contain code for analyzing the natural infections (Arnot\_1.R) and experimental infections (Arnot\_2.R). Basic pipeline for sequence analysis can be found in Arnot\_seq\_code.txt file.