APM design and results have been submitted to GEO (design accession GPL11490 and array data accession GSE28235) and are MIAME compliant. All Sanger sequence-confirmed deep sequencing assemblies have been submitted to GenBank (accessions listed in text). Figure S1 Gel electrophoresis of RT-qPCR products from pooled-monthly samples. qPCR products were amplified using the primer sets listed in Table S2 Figure S4 Detection of the LSV genome by denaturing 1.5% agarose gel electrophoresis and Northern blots using three LSV-specific probes. RNA (15 mg) extracted from the supernatants of homogenized honey bees was transferred to a membrane and probed using LSV-specific probes corresponding to different regions of the genome (P1 -1482-1744, P2 -2289-2477, and P3 -4509-4714) as described in Materials and Methods. (TIFF) Figure S5 Detection of the replicative form of LSV1 and LSV2 by negative strand-specific RT-PCR. The pooled July RNA sample was analyzed for the presence of LSV negativestrand RNA, which is indicative of virus replication, using strandspecific RT-PCR as described in Materials and Methods; RT-PCR products from reactions were analyzed by agarose (2%) gel electrophoresis. (TIF) Figure S6 Crithidia mellificae, strain SF movies. Light microscopy of live parasites was performed using a Leica DM6000 microscope (1006 objective) equipped with Hamamatsu C4742-95 camera and Volocity Software (PerkinElmer). (MP4) Figure S7 Crithidia mellificae, strain SF movies. Light microscopy of live parasites was performed using a Leica DM6000 microscope (1006 objective) equipped with Hamamatsu C4742-95 camera and Volocity Software (PerkinElmer). (MP4) Figure 3B , ** denotes qPCR primer sets used to obtain the results in Figure 4 and Figure S3 . (DOCX)  Evaluation of Coseasonality of Influenza and Invasive Pneumococcal Disease: Results from Prospective Surveillance BACKGROUND: The wintertime co-occurrence of peaks in influenza and invasive pneumococcal disease (IPD) is well documented, but how and whether wintertime peaks caused by these two pathogens are causally related is still uncertain. We aimed to investigate the relationship between influenza infection and IPD in Ontario, Canada, using several complementary methodological tools. METHODS AND FINDINGS: We evaluated a total number of 38,501 positive influenza tests in Central Ontario and 6,191 episodes of IPD in the Toronto/Peel area, Ontario, Canada, between 1 January 1995 and 3 October 2009, reported through population-based surveillance. We assessed the relationship between the seasonal wave forms for influenza and IPD using fast Fourier transforms in order to examine the relationship between these two pathogens over yearly timescales. We also used three complementary statistical methods (time-series methods, negative binomial regression, and case-crossover methods) to evaluate the short-term effect of influenza dynamics on pneumococcal risk. Annual periodicity with wintertime peaks could be demonstrated for IPD, whereas periodicity for influenza was less regular. As for long-term effects, phase and amplitude terms of pneumococcal and influenza seasonal sine waves were not correlated and meta-analysis confirmed significant heterogeneity of influenza, but not pneumococcal phase terms. In contrast, influenza was shown to Granger-cause pneumococcal disease. A short-term association between IPD and influenza could be demonstrated for 1-week lags in both case-crossover (odds ratio [95% confidence interval] for one case of IPD per 100 influenza cases = 1.10 [1.02–1.18]) and negative binomial regression analysis (incidence rate ratio [95% confidence interval] for one case of IPD per 100 influenza cases = 1.09 [1.05–1.14]). CONCLUSIONS: Our data support the hypothesis that influenza influences bacterial disease incidence by enhancing short-term risk of invasion in colonized individuals. The absence of correlation between seasonal waveforms, on the other hand, suggests that bacterial disease transmission is affected to a lesser extent. Please see later in the article for the Editors' Summary The seasonal periodicity of pneumonia and influenza deaths in temperate countries is regarded as sufficiently commonplace that the term ''flu season'' is part of the English language vernacular. However, the widespread recognition of wintertime seasonality of severe respiratory disease obscures the fact that remarkably little is understood about the genesis of such seasonality [1, 2] . The wintertime co-occurrence of peaks in viral and bacterial respiratory disease, including severe invasive disease caused by Streptococcus pneumoniae, is well documented, but how and whether wintertime peaks caused by different pathogens are causally related is unknown. Existing work in this field has consisted largely of descriptive analyses that have evaluated week-by-week correlations between respiratory virus activity and invasive bacterial disease, with or without lags [3] [4] [5] .