High-throughput sequencing of patients with symptoms of unknown etiology

Routine clinical diagnosis of patients with a suspected viral infection involves screening with multiple assays, often limited to only a single genus or species. This approach, however, may fail to detect novel species, atypically presenting viruses (i.e a ‘respiratory’ virus causing neurological symptoms) and viruses that are imported from other countries; often due to clinicians focusing on the ‘likeliest’ candidates. High-throughput sequencing (HTS) allows for the identification viruses present within a sample, by sequencing all viral genomes present. Without the inherent bias of limiting screening targeted assays, these unusual viruses are more likely to be detected. Samples taken from patients with an illness of unknown etiology, were grouped into 5 pools; 2 Respiratory, 2 CSF and an EDTA blood pool. The CSF Pools each contained 200 samples, the Respiratory pools 100 and the EDTA blood pool 80. HTS libraries were created from each of these pools and an additional CSF sample from a single patient with encephalitis and were then sequenced using an Illumina HiSeq platform. Human Pegivirus was detected in both CSF Pools, the EDTA pool and a single respiratory pool. Picobirnavirus was detected in a respiratory pool. RT-PCR was used to screen individual samples compromising these pools. BK Polyomavirus and Mastadenovirus C were detected in the CSF of a patient who had presented with encephalitis. Coinfection of these viruses typically cause neurological symptoms only in immune-compromised patients, so this exemplifies the advantage of using HTS for the detection of atypically presenting viruses.