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

Abstract

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.