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Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing


Accumulating evidence supports the high prevalence of co-infections among Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) patients, and their potential to worsen the clinical outcome of COVID-19. However, there are few data on Southern Hemisphere populations, and most studies to date have investigated a narrow spectrum of viruses using targeted qRT-PCR. Here we assessed respiratory viral co-infections among SARS-CoV-2 patients in Australia, through respiratory virome characterization. Nasopharyngeal swabs of 92 SARS-CoV-2-positive cases were sequenced using pan-viral hybrid-capture and the Twist Respiratory Virus Panel. In total, 8% of cases were co-infected, with rhinovirus (6%) or influenzavirus (2%). Twist capture also achieved near-complete sequencing (> 90% coverage, > tenfold depth) of the SARS-CoV-2 genome in 95% of specimens with Ct < 30. Our results highlight the importance of assessing all pathogens in symptomatic patients, and the dual-functionality of Twist hybrid-capture, for SARS-CoV-2 whole-genome sequencing without amplicon generation and the simultaneous identification of viral co-infections with ease.

Type Journal
ISBN 2045-2322 (Electronic) 2045-2322 (Linking)
Authors Kim, K. W.; Deveson, I. W.; Pang, C. N. I.; Yeang, M.; Naing, Z.; Adikari, T.; Hammond, J. M.; Stevanovski, I.; Beukers, A. G.; Verich, A.; Yin, S.; McFarlane, D.; Wilkins, M. R.; Stelzer-Braid, S.; Bull, R. A.; Craig, M. E.; van Hal, S. J.; Rawlinson, W. D.
Publisher Name Scientific Reports
Published Date 2021-02-28
Published Volume 11
Published Issue 1
Published Pages 3934
Status Published in-print
DOI 10.1038/s41598-021-83642-x
URL link to publisher's version