Viral DNA was amplified by Phi29 polymerase amplification using GenomiPhi V2 Amplification kit (GE Healthcare) or Repli-g Midi kit (typical yield ,40 mg from a 50 ml reaction, Qiagen), following manufacturer's protocols. Briefly, using GenomiPhi V2 Amplification kit, 1 ml of purified DNA was added to 9 ml of sample buffer, incubated at 95uC for 3 minutes and cooled on ice. Ten microliters of GenomiPhi reaction was added, containing Phi29 polymerase and random primers, and the reaction incubated at 30uC for 1 K hours. The reaction was terminated by incubation at 65uC for 10 minutes. The amplified viral DNA was stored at 280uC or immediately used. Briefly, using Repli-g Midi kit, 5 ml of purified DNA was mixed with 5 ml denaturation buffer, incubated at room temperature for 3 minutes and the reaction terminated by the addition of 10 ml stop solution. Thirty microliters of Repli-g reaction mix, containing Phi29 and random primers, was added and the reaction incubated at 30uC for 16 hours. The reaction was terminated by incubation at 65uC for 3 minutes. Amplified material was purified using QIAamp DNA mini kit (Qiagen) using a modified protocol (www.qiagen.com), and checked for purity and concentration using a NanoDrop spectrophotometer (Thermo Scientific) and agarose gel electrophoresis. The DNA was stored at 280uC or immediately used for microarray analysis.