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

Kim, Ki Wook; Deveson, Ira W.; Pang, Chi Nam I.; Yeang, Malinna; Naing, Zin; Adikari, Thiruni; Hammond, Jillian M.; Stevanovski, Igor; Beukers, Alicia G.; Verich, Andrey; Yin, Simon; McFarlane, David; Wilkins, Marc R.; Stelzer-Braid, Sacha; Bull, Rowena A.; Craig, Maria E.; van Hal, Sebastiaan J.; Rawlinson, William D.

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.