Reactive Lymphoid Hyperplasia or Acute Pharyngitis: Given the patient's symptoms of sore throat worsening at night and a history of smoking and GORD (Gastroesophageal Reflux Disease), a reactive lymphoid hyperplasia or an acute pharyngitis, possibly exacerbated by acid reflux and irritants from smoking, seems the most plausible initial diagnosis. The negative flu and Covid tests help to rule out common infectious causes.

Chronic Pharyngitis: This could be related to the patient's smoking habit and GORD, causing persistent irritation to the throat.
Tonsillitis: Although the patient has had a sore throat for two weeks, tonsillitis (either bacterial or viral) could still be a consideration, especially if there are signs of tonsillar inflammation.
Laryngopharyngeal Reflux (LPR): Given the patient's history of GORD, LPR is a possible diagnosis, where stomach acid flows back into the throat, causing irritation and soreness.

HIV Infection: Although less likely, a persistent sore throat can be an early symptom of HIV infection. Given the potential severity of missing this diagnosis, it's crucial to consider, especially if the patient has risk factors.
Tuberculosis (TB): TB can cause a chronic sore throat among other symptoms. It's essential to consider this, especially if the patient has been exposed to TB or has risk factors.
Malignancy (e.g., Oropharyngeal or Hypopharyngeal Cancer): Though rare in a young individual, any persistent sore throat, especially one worsening at night, necessitates consideration of malignancy, particularly in smokers.

Granulomatosis with Polyangiitis (formerly known as Wegener's Granulomatosis): A rare autoimmune disorder that can cause a sore throat among other systemic symptoms.
Sarcoidosis: Another rare condition that can affect various parts of the body, including the throat, causing soreness and other symptoms.
Lemierre's Syndrome: A rare condition characterized by a sore throat followed by neck pain and other symptoms due to a bacterial infection.