tetano
Editor, Senior Moderator
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[SUP] 1 2 [/SUP], Ira W Deveson[SUP] 3 4 [/SUP], Chi Nam I Pang[SUP] 5 [/SUP], Malinna Yeang[SUP] 2 [/SUP], Zin Naing[SUP] 2 [/SUP], Thiruni Adikari[SUP] 6 7 [/SUP], Jillian M Hammond[SUP] 3 [/SUP], Igor Stevanovski[SUP] 3 [/SUP], Alicia G Beukers[SUP] 8 [/SUP], Andrey Verich[SUP] 7 [/SUP], Simon Yin[SUP] 9 [/SUP], David McFarlane[SUP] 9 [/SUP], Marc R Wilkins[SUP] 5 [/SUP], Sacha Stelzer-Braid[SUP] 2 6 [/SUP], Rowena A Bull[SUP] 6 7 [/SUP], Maria E Craig[SUP] 1 2 10 [/SUP], Sebastiaan J van Hal[SUP] 8 11 [/SUP], William D Rawlinson[SUP] 12 13 14 15 [/SUP]
Affiliations
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.
. 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[SUP] 1 2 [/SUP], Ira W Deveson[SUP] 3 4 [/SUP], Chi Nam I Pang[SUP] 5 [/SUP], Malinna Yeang[SUP] 2 [/SUP], Zin Naing[SUP] 2 [/SUP], Thiruni Adikari[SUP] 6 7 [/SUP], Jillian M Hammond[SUP] 3 [/SUP], Igor Stevanovski[SUP] 3 [/SUP], Alicia G Beukers[SUP] 8 [/SUP], Andrey Verich[SUP] 7 [/SUP], Simon Yin[SUP] 9 [/SUP], David McFarlane[SUP] 9 [/SUP], Marc R Wilkins[SUP] 5 [/SUP], Sacha Stelzer-Braid[SUP] 2 6 [/SUP], Rowena A Bull[SUP] 6 7 [/SUP], Maria E Craig[SUP] 1 2 10 [/SUP], Sebastiaan J van Hal[SUP] 8 11 [/SUP], William D Rawlinson[SUP] 12 13 14 15 [/SUP]
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.