I was posed a question over a week ago: can we count actual virus particles in the soil? The premise for this question is simple enough. The relative number of virus DNA reads (yes, I realise I’m excluding RNA viruses) varies with soil environmental variables. But we can’t actually comment on the absolute abundances of virus-like particles.
Challenges encountered with counting virus particles include their size range overlapping regular living cells (from teeny tiny to ‘giant’), their ‘quasi-species’ property meaning viruses that are effectively the same having non-identical genetic information, their enormous capsid/envelope diversities, and a large amount of ‘junk’ virus particles – particles that are defective in some way.
On the surface, the answer is yes – one can use special high powered cell flow cytometers to do ‘flow virometry’. But this technique seems best used for investigating specific viruses in specific systems rather than the chaotic and dirty disaster that is environmental samples. Regardless, it looks like flow virometry is something we’re going to give a shot at the lab. Should be interesting at least.