Journal
SCIENTIFIC REPORTS
Volume 11, Issue 1, Pages -Publisher
NATURE PORTFOLIO
DOI: 10.1038/s41598-021-83642-x
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Funding
- UNSW COVID-19 Rapid Response Research Initiative
- NCI Australasian Leadership Computing COVID-19 Grant
- MRFF Investigator Grant [APP1173594]
- Cancer Institute NSW Early Career Fellowship [2018/ECF013]
- NSW State Government RAAP Scheme
- UNSW ResTech Support Scheme
- JDRF International Postdoctoral Fellowship [3-PDF-2020-940-A-N]
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There is a high prevalence of viral co-infections among SARS-CoV-2 patients, which may worsen the clinical outcome of COVID-19. Studies in Australia show the importance of assessing all pathogens in symptomatic patients, and the dual-functionality of Twist hybrid-capture for SARS-CoV-2 whole-genome sequencing and simultaneous identification of viral co-infections.
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.
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