Acute
respiratory tract infections are a major cause of respiratory morbidity and mortality in pediatric patients worldwide. However, accurate viral and
immunologic markers to predict clinical outcomes of this patient population are still lacking. Droplet digital PCR assays for
influenza and respiratory syncytial virus (RSV) were designed and performed in 64 respiratory samples from 23 patients with influenza virus
infection and 73 samples from 19 patients with
RSV infection. Samples of patients with
hematologic malignancies, solid
tumors, or
sickle cell disease were included. Clinical information from institutional medical records was reviewed to assess disease severity. Samples from patients with
fever or respiratory symptoms had a significantly higher viral loads than those from asymptomatic patients. Samples from patients with influenza virus and
RSV infection collected at presentation had significantly higher viral loads than those collected from patients after completing a course of
oseltamivir or
ribavirin, respectively. RSV loads correlated positively with clinical symptoms in patients ≤5 years of age, whereas
influenza viral loads were associated with clinical symptoms, irrespective of age. Patients receiving
antivirals for
influenza and RSV had a significant reduction in viral loads after completing
therapy. Digital PCR offers an effective method to monitor the efficacy of
antiviral treatment for
respiratory tract infections in immunocompromised hosts.