Viral Pharyngitis: This is the most common cause of sore throat and swollen tonsils, often due to viruses such as adenovirus, influenza, or rhinovirus. The prolonged duration of two weeks can still be consistent with a viral etiology, especially if the patient has had repeated exposures or a particularly virulent strain.

Streptococcal Pharyngitis (Strep Throat): Caused by Group A beta-hemolytic streptococcus, this bacterial infection can present with sore throat, swollen tonsils, and fever. It's a common cause of pharyngitis and needs to be considered, especially if symptoms persist.
Mononucleosis (Infectious Mononucleosis): Caused by Epstein-Barr virus (EBV), this condition can lead to prolonged sore throat, swollen tonsils, fever, and fatigue. The two-week duration fits within the timeframe for the development of symptoms.
Tonsillitis: Inflammation of the tonsils, which can be caused by either viral or bacterial pathogens, leading to symptoms of sore throat and swollen tonsils.

Lemierre's Syndrome: A rare but potentially life-threatening condition that starts with pharyngitis and progresses to jugular vein thrombosis and metastatic infections. Early recognition is crucial.
Peritonsillar Abscess: A complication of tonsillitis where an abscess forms beside the tonsils, requiring prompt drainage to prevent airway obstruction and other complications.
HIV Infection: Initial presentation of HIV can include sore throat and swollen lymph nodes, among other symptoms. Given the potential for severe consequences if untreated, it's a diagnosis not to be missed.
Cancer (e.g., Lymphoma or Tonsil Cancer): Although rare, persistent sore throat and swollen tonsils can be symptoms of underlying malignancy, especially in adults with risk factors.

Diphtheria: A bacterial infection caused by Corynebacterium diphtheriae, characterized by a sore throat and a membrane covering the tonsils and throat. It's rare in areas with high vaccination coverage but should be considered in travelers or those with incomplete vaccination.
Tularemia: A rare infectious disease caused by Francisella tularensis, which can present with sore throat and swollen lymph nodes, among other symptoms.
Syphilis: Secondary syphilis can cause a sore throat and swollen lymph nodes. It's an important consideration in individuals with high-risk sexual behavior or exposure history.