I am also interested in looking at viral communities with Illumina sequencing, but I am trying to use metagenomics on sediment samples as there are not any suitable viral marker genes. I have been trying to physically separate the viruses from bacteria and eurkaryotes. I first separate the viral particles from the sediment with chemical and physical methods, then lyse the cells with increased ionic concentration, treat with some kind of nuclease, filter, then carry out an SDS or CTAB extraction. I just started using Zymo research "Genomic DNA clean and concentrator" columns to eliminate humics and other contaminants.

You can please refer to the link below to obtain certain valuable informations:-

http://www.illumina.com/products/nextera_xt_dna_library_prep_kit.html

You can also download pdf of the file attached herewith.

Eleanor. Thank you very much for your information. But I wonder if after these treatment the concentration of DNA will be enough

Thanks Fizah,  a very useful answer