To remove contaminating human gDNA present in clinical samples, we designed a pre-treatment protocol including centrifugation, filtration and DNase treatment. It has been demonstrated that filtration, DNase and RNase treatment can increase the efficiency of downstream amplifications [26, 27] . During DNase treatment the viral NA should be protected inside the viral particle [28] . After pre-treatment, the viral particles were lysed, viral NA purified and later Phi29-amplified using GenomiPhi V2 Amplification kit (GE Healthcare). During purification, the addition of carrier RNA did not improve the yield and interfered with the downstream Phi29-amplification, and was therefore left out (data not shown). Quantitative analysis of viral DNA or human gDNA before and after pre-treatment or Phi29-amplification was done by real-time PCR (Figure 1 and Table S1 ). Only centrifugation and filtration left large amounts of human gDNA still present in a HSV1 + sample (Ct = 22), while DNase treatment reduced the ßactin signal 1000-fold (Ct = 32) ( Figure 1A) . The DNase treatment also had an effect on the HSV1, resulting in a 3-to 20-fold decrease in virus signal after DNase treatment (Table S1 ). However, this was accompanied by a much larger fold increase after Phi29-amplification compared to without DNase treatment (e.g. 88,292 compared to 1176), resulting in lower Ct-values and more viral DNA available for downstream analysis (Table S1 ). This was also seen for the RNA virus HCV (Table S1 ) as well as for other DNA and RNA viruses (data not shown). To investigate to what extent Phi29-amplification of remaining human gDNA would occur we performed a time-course experiment with the amplification-time extended up to 16 hours ( Figure 1B) . The ßactin signal was still at acceptable background level (3000-fold increase in signal), while the HSV1 signal showed an 80,000-100,000-fold increase in signal. In conclusion, our pre-treatment removed a significant amount of human gDNA, which allowed for good virus amplification.