Viral Upper Respiratory Tract Infection (URTI): This is the most common cause of nighttime cough and fever, often presenting with other symptoms such as sore throat, runny nose, and fatigue. The justification for this being the most likely diagnosis is the high prevalence of viral URTIs in the general population and the typical presentation of symptoms.

Acute Bronchitis: Often caused by a viral infection, acute bronchitis can lead to a persistent cough, which worsens at night, accompanied by fever. This diagnosis is likely due to the similarity in symptoms and the commonality of bronchitis as a complication of URTIs.
Pneumonia: Bacterial or viral pneumonia can cause cough and fever, with the cough often being worse at night. This is a likely diagnosis due to the severity of symptoms and the potential for pneumonia to develop from an initial URTI.
Asthma: In patients with asthma, nighttime cough can be a prominent symptom, especially if exacerbated by a respiratory infection. Fever might not be a direct symptom of asthma but can occur if there's a concurrent infection.

Pertussis (Whooping Cough): Although less common due to vaccination, pertussis can cause a severe cough that worsens at night, often accompanied by a whooping sound during inhalation. It's crucial not to miss this diagnosis due to its contagiousness and potential severity, especially in infants and young children.
Tuberculosis (TB): TB can cause chronic cough and fever, among other symptoms. While less common in some regions, TB is a critical diagnosis not to miss due to its public health implications and the need for specific treatment.
Pneumocystis jirovecii Pneumonia (PCP): In immunocompromised patients, PCP can cause severe pneumonia with cough and fever. This diagnosis is critical not to miss due to the high mortality rate if left untreated.

Cystic Fibrosis: This genetic disorder can lead to recurrent respiratory infections, causing chronic cough and fever. While rare, it's an important diagnosis to consider in patients with recurrent or severe respiratory symptoms.
Foreign Body Aspiration: In children, aspiration of a foreign body can cause sudden onset of cough and potentially fever if infection develops. This is a rare but critical diagnosis due to the potential for airway obstruction.
Lymphoma: Certain types of lymphoma can cause symptoms similar to pneumonia, including cough and fever. This diagnosis is rare but important to consider in patients with persistent or unexplained symptoms.