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

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 t...

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Autores principales:	Ki Wook Kim, Ira W. Deveson, Chi Nam I. Pang, Malinna Yeang, Zin Naing, Thiruni Adikari, Jillian M. Hammond, Igor Stevanovski, Alicia G. Beukers, Andrey Verich, Simon Yin, David McFarlane, Marc R. Wilkins, Sacha Stelzer-Braid, Rowena A. Bull, Maria E. Craig, Sebastiaan J. van Hal, William D. Rawlinson
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/c4c03833f53f460894aa27160ccb23da
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spelling	oai:doaj.org-article:c4c03833f53f460894aa27160ccb23da2021-12-02T12:11:34ZRespiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing10.1038/s41598-021-83642-x2045-2322https://doaj.org/article/c4c03833f53f460894aa27160ccb23da2021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-83642-xhttps://doaj.org/toc/2045-2322Abstract 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.Ki Wook KimIra W. DevesonChi Nam I. PangMalinna YeangZin NaingThiruni AdikariJillian M. HammondIgor StevanovskiAlicia G. BeukersAndrey VerichSimon YinDavid McFarlaneMarc R. WilkinsSacha Stelzer-BraidRowena A. BullMaria E. CraigSebastiaan J. van HalWilliam D. RawlinsonNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-9 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ki Wook Kim Ira W. Deveson Chi Nam I. Pang Malinna Yeang Zin Naing Thiruni Adikari Jillian M. Hammond Igor Stevanovski Alicia G. Beukers Andrey Verich Simon Yin David McFarlane Marc R. Wilkins Sacha Stelzer-Braid Rowena A. Bull Maria E. Craig Sebastiaan J. van Hal William D. Rawlinson Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing
description	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.
format	article
author	Ki Wook Kim Ira W. Deveson Chi Nam I. Pang Malinna Yeang Zin Naing Thiruni Adikari Jillian M. Hammond Igor Stevanovski Alicia G. Beukers Andrey Verich Simon Yin David McFarlane Marc R. Wilkins Sacha Stelzer-Braid Rowena A. Bull Maria E. Craig Sebastiaan J. van Hal William D. Rawlinson
author_facet	Ki Wook Kim Ira W. Deveson Chi Nam I. Pang Malinna Yeang Zin Naing Thiruni Adikari Jillian M. Hammond Igor Stevanovski Alicia G. Beukers Andrey Verich Simon Yin David McFarlane Marc R. Wilkins Sacha Stelzer-Braid Rowena A. Bull Maria E. Craig Sebastiaan J. van Hal William D. Rawlinson
author_sort	Ki Wook Kim
title	Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing
title_short	Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing
title_full	Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing
title_fullStr	Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing
title_full_unstemmed	Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing
title_sort	respiratory viral co-infections among sars-cov-2 cases confirmed by virome capture sequencing
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/c4c03833f53f460894aa27160ccb23da
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Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing

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