To target viral RNA / DNA you would have to do some kind of selection for the viral fraction first. Be it filtration to only target viral fraction, iron chloride flocculation to target viral fraction prior to extraction. Then check that there is no host dna within the viral fraction by PCR for host 16S or  18S genes. Running on a standard gel will not confirm that it is viral dna. You would need to use PFGe to determine the size rang e of DNA yiu have 

Thank you.

I've treated the sample previously with a PEG protocol to separate virus fraction of another kind of microorganisms and with the objective to reconcentrate. This is the reason because I suppose that the isolation will only be viral RNA/DNA. Before to proceed with other assays, I would like to validate by electrophoresis although I will try other tecniques for quantification (nanodrop or QUBIT). But I also would like to know what are the best conditions to run agarose gel to visualize viral RNA and DNA. I've read some papers that made electorphoresis to check the results but I don't  know under what conditions.

Thanks.

It depends from what viruses are you looking for.

Virosphere counts 100 million of species 

http://www.worldwidewords.org/turnsofphrase/tp-vir2.htm

I think you can see only a smear in 1% agarose gel in TBE buffer  because in enviromental samples there are many different organisms with different genome in lenght. For this reason you should load in the gel at least 10 ug of Nucleic acid as estimeted by nanodrop. As your enviromental samples are precious  go on with a diagnostic PCR for your virus 

Thanks Paola, In this case, I would have to select several pairs of primers to cover a high spectre of viruses (like bacteriophages, animal viruses... etc)?