Additional data file 1:

All files are available for download in PDF, JPG, GIF, TIFF, HTML or ZIP formats as indicated on the webpage [25]. Supplementary methods: sample amplification and microarray protocols (PDF); RT-PCR modeling and amplification efficiency score (AES); pathogen detection algorithm (PDA). Supplementary figures. Figure S1: Probe design schema. Probes (40-mers) were tiled at an average 8-base resolution across each of the 35 viral genomes in the manner depicted above. Numbers represent the start and end positions of each probe. Figure S2: Choice of primer tag in random RT-PCR has significant effect on PCR efficiency. Heatmap of probe signal intensities for a clinical hMPV sample following random RT-PCR using original primer (a) A1 or (b) AES-optimized primer A2. Figure S3: Comparison of amplification efficiency of original primer A1 and AES-optimized primer A2. RNA from patients infected with RSV B (n = 5) or hMPV (n = 3) were reverse-transcribed and amplified using primer A1 or A2 and the percentage of r-signature probes with signal above detection threshold was determined. Figure S4: Diagnostic PCR results for RSV patient 412 show that the patient does not have a coronavirus infection. (a) PCR using pancoronavirus primers. Lane 1, 1 kb ladder; lane 2, blank; lane 3, OC43 coronavirus positive control; lane 4, 229E coronavirus positive control; lane 5, RSV patient 412; lane 6, PCR primers and reagents only, as a negative control. (b) PCR using OC43 specific primers. Lane 1, 50 bp ladder; lane 2, blank; lane 3, OC43 coronavirus positive control; lane 4, RSV patient 412; lane 5, purified RSV from ATCC; lane 6, PCR negative control. (c) PCR using 229E specific primers. Lane 1, 229E coronavirus positive control; lane 2, RSV patient 412; lane 3, PCR negative control; lane 4, 1 kb ladder. Supplementary tables. Table S1: List of genomes represented on the pathogen detection microarray. Table S2: Comparison of E-Predict and PDA algorithms. Pathogen microarray data: data have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO accession number GSE3779 [45]. Software downloads. Amplification efficiency score software: Primerselect Readme.txt; Primerselect.java. Pathogen detection algorithm (PDA): WKL Readme.txt; WKL.cpp.

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