I believe that that answer to your question depends on virus type, host organism, infected (affected) cell type and response mechanism and definition used to recognised the normal versus disease cells. That would be a great job if you could discover one common regulatory mechanism across all those conditions! :)  I would prose to start with the most common host response mechanism, eg. innate immunological response or apoptosis or ... and develop the methodology to measure that response. Them virus type, host , ... : ) Good Luck !

I believe that that answer to your question depends on virus type, host organism, infected (affected) cell type and response mechanism and definition used to recognised the normal versus disease cells. That would be a great job if you could discover one common regulatory mechanism across all those conditions! :)  I would prose to start with the most common host response mechanism, eg. innate immunological response or apoptosis or ... and develop the methodology to measure that response. Them virus type, host , ... : ) Good Luck !

If the other tissue is diseased one then I think that the tissue for sure show differential expression (certain pathway affected). But what kind of pathway?- depends on the virus and the host you have. And if is an open question then RNA seq might give you an answer to this. And if you wanna see what  upstream and downstream members of the pathway is affected, then may be you can do different time point experiment to see that. (rna seq at different time point).

Hope that helps. Good luck.

Thank you all for answering! Now I know that maybe there is no definite answer currently. If I find any information related to this issue, I will share with you. Thank you again!