Viral Upper Respiratory Tract Infection (URTI): This is the most common cause of the symptoms described, such as fatigue, cough, sore throat, and low-grade fever, especially when they persist for several weeks. Many viruses can cause URTIs, and they often resolve on their own with supportive care.

Influenza: Although the duration of symptoms might be longer than typical for influenza, some cases can have a prolonged course, especially if complications or secondary infections occur.
Allergic Rhinitis: Could present with similar symptoms, especially if the allergic reaction leads to chronic fatigue and low-grade fever, though fever is less common.
Sinusitis: Either acute or chronic, can cause prolonged cough, sore throat, and fatigue, especially if there's a secondary bacterial infection.
Bronchitis: Either acute or chronic, could explain the cough and fatigue, especially if the bronchitis is chronic and related to smoking or environmental exposures.

Tuberculosis (TB): Although less common, TB can present with chronic cough, low-grade fever, and fatigue. It's crucial to consider TB, especially in individuals with risk factors such as immunocompromised states or exposure history.
Lymphoma: Certain types of lymphoma can present with prolonged fever, fatigue, and sore throat due to lymphadenopathy.
HIV Infection: Acute HIV infection can cause symptoms similar to mononucleosis, including sore throat, fever, and fatigue. Chronic HIV infection can lead to a range of symptoms due to immunosuppression.
Endocarditis: Though typically presents with more severe symptoms, subacute endocarditis can cause prolonged low-grade fever, fatigue, and sometimes a persistent cough if there's an embolic phenomenon affecting the lungs.

Sarcoidosis: A systemic granulomatous disease that can affect the lungs and cause symptoms like cough and fatigue, along with systemic symptoms such as fever and weight loss.
Histoplasmosis: A fungal infection that can cause chronic symptoms similar to TB, including cough, fever, and fatigue, especially in endemic areas.
Cystic Fibrosis: Though typically diagnosed in childhood, late diagnoses can occur, and it might present with chronic respiratory symptoms like cough and fatigue due to recurrent infections.
Primary Immunodeficiency Diseases: A group of disorders that affect the immune system, leading to recurrent or chronic infections that could present with the described symptoms.