Co-infections with Multiple Viruses: A Frequent cause of Community-Acquired Pneumonia in Sarawak Malaysia

Objectives: Equatorial Sarawak, Malaysia, has been the site of important novel respiratory virus detections. During the COVID-19 pandemic, we sought to determine viral causes of pneumonia that were not SARS-CoV-2. Methods: Using an informed consent process, we enrolled patients from four hospitals in Sarawak for this cross-sectional study. Patients permitted a nasopharyngeal (NP) swab collection and completed a risk factor questionnaire. We studied NP swabs with molecular diagnostics for previously recognized respiratory viruses such as influenza A and D viruses, and pan-species assays for adenoviruses, coronaviruses, enteroviruses, pneumoviruses, and paramyxoviruses. Results: Among 441 patients, 78.2% had at least one virus detected, and 24.9% had multiple viruses detected. Among the viruses detected, a commercial multiplexing assay found the most prevalent detections were human rhinoviruses (43.1%), respiratory syncytial virus (18.6%), human metapneumovirus (8.6%), influenza A (7%), adenovirus (6.1%), and influenza B (5.6%). However, the pan-species assays detected evidence of 19 additional respiratory viruses that the commercial multiplexing assay missed. Conclusions: Patients with pneumonia in this hot and humid region often had evidence of multiple viral infections, especially children under 5 years old. Clinicians who rely on singleplex molecular assays for prevalent viruses such as influenza A, SARS-CoV-2, and respiratory syncytial virus may miss other important viral causes of illness in such patients.