I think this (source: http://www-ccd.usc.edu/assets/sites/27/docs/sybr_protocol.pdf) summarizes the situation quite well:

"DAPI has been used for counting viruses; however, this dye does not produce bright staining of virus particles, making counting difficult and prone to inaccuracy."

Regards, Christian

Hello Dr Christian,

My Colleagues were telling me that Virus in its native form might not be stained because the capsid would protect the DNA inside. Is that a valid argument?

The classical method of  the staining of virus particles for fluorescence microscopy is a dyeing of proteins (FITC, etc). It is possible to stain the virus nucleic acid by specific dyes, but this way is used very seldom and it does not have any advantages.     

The capsid poses a barrier that can interfere with the staining of the enclosed DNA. I would say that it also depends on the kind of virus under investigation. I found a paper that goes into more detail how to improve virus DNA staining. Maybe it is of help to you.

Cheers, Christian

Article Optimization of Procedures for Counting Viruses by Flow Cytometry

Recently, I've been looking at cells by immunofluorescence following infection with inactivated human cytomegalovirus and can see clear DAPI staining at 0.1 pfu/cell (~400 particles). If you want to know whether the same works for HSV-1, why don't you try it? I wouldn't use DAPI staining to count particles, but you should easily know whether the cells have been infected or not.

Hello David

The point here was that my colleagues were doing a study where they infected a cornea with a GFP-Virus. Then were observing the spread of infection in the cornea over 5 days. On the 5th day, one of my colleagues asked the student to stain the sample with DAPI. The intention was that cells would flouresce with DAPI and virus would fluoresce with GFP. So there would be a colorful picture for better representation. My doubt was whether the DAPI would stain the virus too, inturn implying a wrong interpretation of where the cells were and where the virus was. Hence my search for answers.

I think that using DAPI to stain virus is impractical as as the virus particle is too small to visualize directly and that is why electron microscope is generally used for virus study and antibody conjuated with fluorescent tag is used to detect virus. Besides, the virus particle itself might prevent the staining of virus also. 

You can see some HSV-1 particles in infected cells with DAPI but they are very dim due to capsid barrier preventing easy access to DNA. In case of assay you described even if some viral particles are visible with DAPI in the cells it won't change interpretation of the experiment. DAPI will mainly stain the nucleus and GFP viruses will be visible in the cytoplasm (depending on the protein which was fused to GFP).