The protocol established here enabled us to get proof of concept that microarray analysis can be used to correctly identify viruses present in a diverse set of clinical samples. However, the protocol is at the moment to time and labour intensive to be used in a Figure 3 . Microarray analysis performed on WTA-amplified clinical samples. Results from the microarray data analysis of WTA-amplified clinical samples, using the maximum likelihood method developed at LLNL [19] , with additional stringency criteria applied. The lighter and darkercoloured portions of the bars represent the unconditional and conditional log-odds scores, respectively. The conditional log-odds scores shows the contribution from a target that cannot be explained by another, more likely target above it, while the unconditional score illustrates that some very similar targets share a number of probes. routine set up. We are currently focusing on reducing the overall assay time and the costs to develop a more suitable protocol for routine usage. Incubation times throughout the protocol might be shortened and some assays substituted or combined to make it both cheaper and faster to perform. Furthermore, the microarray design can be changed to multiplex, e.g. 12-plex as offered by the Roche NimbleGen system, instead of 1-plex as used now to increase the number of samples that can be run per slide. Future data analysis software needs to be customized for routine diagnostic analysis both regarding data handling and easy-to-use. The cost for the assay at the moment is in the hundreds of dollars per sample, but once established and refined as a technique, the cost is estimated to drop significantly but probably never to levels comparable to PCR. However, the benefit with this assay is that it replaces hundreds of PCR reactions with just one reaction, and often hospitals requests more than one PCR assay per patient in the search for a correct diagnose. Furthermore, since the microarray also contains probes for bacteria, it can combine both viral and bacterial diagnostics. Another benefit is that both DNA and RNA viruses can be analysed using the same protocol. In recent years WGA by MDA has been applied extensively, enabling researchers to get enough material from as little as a single cell for down-stream analysis [13, 32, 33] . Phi29 polymerase amplifies all accessible DNA present in a sample, including any exogenous DNA contamination. For viral or bacterial diagnostic purposes, where presence rather than abundance is important, the main concern is contaminating human gDNA that can compete with pathogen DNA. We show that our pre-treatment can reduce this impact from gDNA and thereby allowing for a greater amplification of the viral DNA. However, in some cases this is not enough due to large amounts of gDNA being present that can not be completely removed and this, combined with low viral copy number, might make certain types of clinical samples less suitable for efficient amplification and microarray analysis. This is currently under investigation. Our microarray analysis of BKV + urine samples indicated that as little as 5 genomic copies of a circular DNA genome could be enough to generate enough material by Phi29-amplification to enable successful identification by the LLMDA. Such a high sensitivity might not be achievable for other types of viral genomes, and is therefore under further investigation. Furthermore, to increase the chance of producing enough material from low copy number samples, we found that the WTA reaction should be allowed to run to completion (8 hours). The sample volume used for purification could also be increased.