The immune system develops various defence mechanisms against pathogenic microorganisms and the main goal of these mechanisms is to eliminate the virus and the virus-infected host cells by humoral and cellular immune system components. The fact that viruses can only reproduce inside the cell (endogenous) and antibodies are only effective against extracellular (exogenous) viral antigens leads to insufficient humoral immune response alone in viral infections. Therefore, CD8+ T (Cytotoxic) and CD4+ T (T helper) cells play crucial roles in the combat against viral infections, such as the destruction of infected cells and the prevention of virus reactivation.

The detection of T cells whether stimulated previously or not (antigen-experienced T cell) is one of the trend topics in both pre-clinical and clinical studies. There are different flow cytometric analysis methods that have been developed to observe T cell responses. Owing to these techniques, the structure and functioning of the immune system, the reaction of organisms to the virus and virus-borne infections have been comprehensively evaluated. Moreover, the determination of the immune-epitopes on the protein-peptide foreign to the host has enabled effective vaccine studies to be conducted.

This review dedicated to summarising main flow cytometry-based analysis methods used to evaluate the immune-phenotype, function, and the measurement of antigen-specific CD8+ and CD4+ T cell response levels that play an important role in viral infections.