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Sci Rep
. 2021 Feb 16;11(1):3934.
doi: 10.1038/s41598-021-83642-x.
Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing
Ki Wook Kim 1 2 , Ira W Deveson 3 4 , Chi Nam I Pang 5 , Malinna Yeang 2 , Zin Naing 2 , Thiruni Adikari 6 7 , Jillian M Hammond 3 , Igor Stevanovski 3 , Alicia G Beukers 8 , Andrey Verich 7 , Simon Yin 9 , David McFarlane 9 , Marc R Wilkins 5 , Sacha Stelzer-Braid 2 6 , Rowena A Bull 6 7 , Maria E Craig 1 2 10 , Sebastiaan J van Hal 8 11 , William D Rawlinson 12 13 14 15
Affiliations
- PMID: 33594223
- DOI: 10.1038/s41598-021-83642-x
Abstract
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.