S2 Table -

Primers used in (a) real time-qPCR quantification and (b) high-throughput sequencing, and Illumina adapters. For the preparation of high-throughput sequencing libraries, new forward and reverse oligos were created for each virus using the following construction: 5’-Illumina adapter + 1 to 4 random nucleotide (N) + virus primer -3’. BQCV- Black queen cell virus; LSV- Lake Sinai virus; CBPV- Chronic bee paralysis virus; SBV- Sacbrood virus; BeeMLV-Bee macula-like virus; AKI–Acute bee paralysis virus, Kashmir bee virus and Israeli acute paralysis virus. The LSV primer pairs (#) are consensual for LSV-1, LSV-2, LSV-3 and LSV-4. The references for the assays are as follows: 1 = Locke et al. (2012) Acaricide treatment affects viral dynamics in Varroa destructor-infested honey bee colonies via both host physiology and mite control. Applied and Environmental Microbiology 78: 227–235. 2 = Daughenbaugh et al. (2015) Honey bee infecting Lake Sinai viruses. Viruses 7: 3285–3309. 3 = de Miranda et al. (2015) Genome characterization, prevalence and distribution of a Macula-Like virus from Apis mellifera and Varroa destructor. Viruses 7: 3586–3602. 4 = Evans (2006) Beepath: An ordered quantitative-PCR array for exploring honey bee immunity and disease. Journal of Invertebrate Pathology 93: 135–139. 5 = Mondet et al. (2014) On the front line: Quantitative virus dynamics in honeybee (Apis mellifera L.) colonies along a new expansion front of the parasite Varroa destructor. PLoS Pathogens 10: e15.
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