Answer. The influenza (flu) virus, as well as other common viral infections like the common cold, often cause irritation of the throat as part of the entire constellation of the illness they cause, which also includes nasal congestion, cough, aches and pains, and, sometimes, fever. Flu Shot (Definition) Also known as influenza vaccines, flu shots are given out once a year to protect against the flu. The flu shot stimulates the immune system to build antibodies to three or four strains of flu viruses in the hopes that it will offer protection from the current strains present in the community. Misconceptions about Seasonal Flu and Flu Vaccines. fever, cough, runny nose or sore throat. The most common reaction to the flu shot in adults has been.