Cytomegalovirus (CMV) is a significant clinical pathogen posing risks, especially for immunocompromised individuals. This study investigates the transport dynamics of CMV within viscoelastic saliva, focusing on factors influencing viral mobility. We employed mathematical models, including the Basset-Boussinesq-Oseen (BBO) equation, to analyze how viral density, particle diameter, saliva viscosity, and external electric and magnetic fields affect CMV movement in the oesophagus. Novel insights include the discovery that smaller CMV particles move significantly faster compared to larger ones, highlighting a critical aspect of viral infectivity. Additionally, we found that increased peristaltic wave amplitudes in the oesophagus greatly enhance viral velocity. More notably, our investigation reveals that the application of external magnetic fields can manipulate CMV transport by exerting forces that reduce viral mobility, thus potentially lowering infection rates through electromagnetic interactions. These findings underscore the complex interplay between fluid rheology, particle shape, and external fields in viral dynamics, suggesting novel therapeutic interventions aimed at controlling CMV spread based on saliva viscosity and electromagnetic manipulation. Our research paves the way for innovative strategies in viral infection management and therapeutic development.