So Brent, if the virus hypothesis is validated by the morphology (clusterization and both dimensions as well shape of the particles), I still don't understand what are those membranes around the viral particles. Do you have any explanation?
Sorry Denis to disagree, but I have worked a lot on herpesvirus morphogenesis, and I do not think these are herpesviruses. Herpesvirus capsids bud through the nuclear membranes and then into round Golgi derived vesicles. Additionally you would expect to see capsids in the nuclei of infected cells, I assume you did not find this, Francesco?
Looks to me like budding at ER membranes? At first glance I thought of Flavivirus, but I don't think that's it. Francesco, you could determine the diameter of the viral particles and then take a look at morphogenesis of potential candidates in the literature. Then possibly PCR.
I wouldn't argue that it's 100% herpesvirus, and you are right about nuclei (indeed, should be some capsids there, but not necessary on all slices). But the virion structure and size (85-120 nm) look pretty similar to herpesviruses. Depending on the virus and cell line, the membrane structures can be pretty different and it's not so obvious how they were formed.
sorry to disagree again :) For one, Herpesvirus secondary envelopment just looks different. Furthermore, from your measurement we can derive that the fully enveloped virus particles are around 100 nm in diameter. This would contain the capsid (which here I estimate to be around 50 nm), the tegument, and the surrounding membrane. Herpesvirus virions are bigger than that, the capsid alone is already around 100 nm wide.
Francesco, if the diagnosis of the virus is of interest to you, it will be helpful to provide information about the cell type, as well as pictures of the entire viral factory.
In terms of virion size, it's tricky to say having just a couple of slices, because they could be sliced not precisely on diameter. But in general you are right, they should be bigger. PCR or even sequencing would provide the final answer. I hope you agree that based on the EM data we can confidentially say only that it looks like "morphogenesis of some virus", just speculating what viral family could it be, e.g. Herpesviridae contains 100+ herpesviruses, which could have some minor morphological and replicative differences. But there are lots of other viruses in the world...