Purpose: Community-acquired (CA) infection is a major public-health problem worldwide. Yet despite extensive laboratory diagnosis, the etiology remains unknown in >50% of the patients. Improving our knowledge of the causative agents is essential for improving disease burden.
Methods & Materials: A deep-sequencing based viral metagenomics approach was employed to analyze 493 clinical samples (384 plasma, 92 pooled nasal- and throat swabs, 10 stools and 7 CSF) from 386 CA infected patients with unknown origin (children and adults) recruited from 6 hospitals cross Vietnam in 2014-2015. Sensitive specific PCRs were used to confirm deep sequencing results.
Results: 22 viruses were detected in 54/493 samples (including 11 viruses in 32 plasma samples), corresponding to a detection rate of 14% (54/386). The detected viruses included enteroviruses (n = 14), hepatitis B virus (10), rhinovirus (5), rotavirus A (3), measles virus, respiratory syncytial virus, parainfluenza virus, adenovirus, hepatitis C virus, dengue virus, influenza A/B virus, parechovirus 1/6 (2 each), metapneumovirus, human immunodeficiency virus, coronavirus, WU-polyomavirus, saffold virus, salivirus (1 each) and recently described viruses including human pegivirus 2 and gemycircularvirus (1 each).
Conclusion: Multiple viral pathogens were detected by deep sequencing in 54/386 (14%) CA infected patients with unknown origin. Metagenomics can be a sensitive pan-pathogen assay for unbiased/sequence-independent detection of known/unknown pathogens in clinical samples. The results warrant further active surveillance for novel pathogens in Asia where there is a high risk of emerging infections.