The microarray used was the LLMDA version 2, developed at Lawrence Livermore National Laboratory (LLNL), USA and already described elsewhere [19, 20] . Briefly, the LLMDA contains 388,000 probes designed from all sequenced virus and bacteria, resulting in a large number of probes covering each genome. The microarray was designed for both detection and discovery, to both identify known organisms and to detect unsequenced or emerging organisms, while strain or subtype identification was not a goal. The array have both conserved and unique probes within each family, where oligos that were conserved, to the extent possible, within a family, and unique relative to other families and kingdoms, were prioritized [19] . Labelling and microarray hybridization was performed at NimbleGen Systems-Iceland, Iceland, or in-house at SSI, Denmark according to manufacturer's protocol (Gene expression analysis, Roche NimbleGen). Briefly, 1 mg of heat-denatured WTA-amplified sample was labelled using nick translation with Cy3-labeled random nonamer primers (TriLink Biotechnologies) and Klenow fragment (exo-) (NEB) at 37uC for 2 hours. Labelled DNA was iso-propanol precipitated and the pellet washed, dried, reconstituted and quantitated. For hybridization, the in-house assay used 12 mg of labelled DNA whereas NimbleGen Systems-Iceland used 6 mg. Hybridization was performed in a NimbleGen Hybridization system using the NimbleGen Hybridization kit (Roche NimbleGen).