Hospitalization and mortality associated with SARS-CoV-2 viral clades in COVID-19

Abstract The COVID-19 epidemic of 2019–20 is due to the novel coronavirus SARS-CoV-2. Following first case description in December, 2019 this virus has infected over 10 million individuals and resulted in at least 500,000 deaths world-wide. The virus is undergoing rapid mutation, with two major clad...

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Autores principales:	Kenji Nakamichi, Jolie Z. Shen, Cecilia S. Lee, Aaron Lee, Emma A. Roberts, Paul D. Simonson, Pavitra Roychoudhury, Jessica Andriesen, April K. Randhawa, Patrick C. Mathias, Alex L. Greninger, Keith R. Jerome, Russell N. Van Gelder
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/84198a9862a940ed87aebea5c6b31bfe
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spelling	oai:doaj.org-article:84198a9862a940ed87aebea5c6b31bfe2021-12-02T13:20:21ZHospitalization and mortality associated with SARS-CoV-2 viral clades in COVID-1910.1038/s41598-021-82850-92045-2322https://doaj.org/article/84198a9862a940ed87aebea5c6b31bfe2021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-82850-9https://doaj.org/toc/2045-2322Abstract The COVID-19 epidemic of 2019–20 is due to the novel coronavirus SARS-CoV-2. Following first case description in December, 2019 this virus has infected over 10 million individuals and resulted in at least 500,000 deaths world-wide. The virus is undergoing rapid mutation, with two major clades of sequence variants emerging. This study sought to determine whether SARS-CoV-2 sequence variants are associated with differing outcomes among COVID-19 patients in a single medical system. Whole genome SARS-CoV-2 RNA sequence was obtained from isolates collected from patients registered in the University of Washington Medicine health system between March 1 and April 15, 2020. Demographic and baseline clinical characteristics of patients and their outcome data including their hospitalization and death were collected. Statistical and machine learning models were applied to determine if viral genetic variants were associated with specific outcomes of hospitalization or death. Full length SARS-CoV-2 sequence was obtained 190 subjects with clinical outcome data. 35 (18.4%) were hospitalized and 14 (7.4%) died from complications of infection. A total of 289 single nucleotide variants were identified. Clustering methods demonstrated two major viral clades, which could be readily distinguished by 12 polymorphisms in 5 genes. A trend toward higher rates of hospitalization of patients with Clade 2 infections was observed (p = 0.06, Fisher’s exact). Machine learning models utilizing patient demographics and co-morbidities achieved area-under-the-curve (AUC) values of 0.93 for predicting hospitalization. Addition of viral clade or sequence information did not significantly improve models for outcome prediction. In summary, SARS-CoV-2 shows substantial sequence diversity in a community-based sample. Two dominant clades of virus are in circulation. Among patients sufficiently ill to warrant testing for virus, no significant difference in outcomes of hospitalization or death could be discerned between clades in this sample. Major risk factors for hospitalization and death for either major clade of virus include patient age and comorbid conditions.Kenji NakamichiJolie Z. ShenCecilia S. LeeAaron LeeEmma A. RobertsPaul D. SimonsonPavitra RoychoudhuryJessica AndriesenApril K. RandhawaPatrick C. MathiasAlex L. GreningerKeith R. JeromeRussell N. Van GelderNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Kenji Nakamichi Jolie Z. Shen Cecilia S. Lee Aaron Lee Emma A. Roberts Paul D. Simonson Pavitra Roychoudhury Jessica Andriesen April K. Randhawa Patrick C. Mathias Alex L. Greninger Keith R. Jerome Russell N. Van Gelder Hospitalization and mortality associated with SARS-CoV-2 viral clades in COVID-19
description	Abstract The COVID-19 epidemic of 2019–20 is due to the novel coronavirus SARS-CoV-2. Following first case description in December, 2019 this virus has infected over 10 million individuals and resulted in at least 500,000 deaths world-wide. The virus is undergoing rapid mutation, with two major clades of sequence variants emerging. This study sought to determine whether SARS-CoV-2 sequence variants are associated with differing outcomes among COVID-19 patients in a single medical system. Whole genome SARS-CoV-2 RNA sequence was obtained from isolates collected from patients registered in the University of Washington Medicine health system between March 1 and April 15, 2020. Demographic and baseline clinical characteristics of patients and their outcome data including their hospitalization and death were collected. Statistical and machine learning models were applied to determine if viral genetic variants were associated with specific outcomes of hospitalization or death. Full length SARS-CoV-2 sequence was obtained 190 subjects with clinical outcome data. 35 (18.4%) were hospitalized and 14 (7.4%) died from complications of infection. A total of 289 single nucleotide variants were identified. Clustering methods demonstrated two major viral clades, which could be readily distinguished by 12 polymorphisms in 5 genes. A trend toward higher rates of hospitalization of patients with Clade 2 infections was observed (p = 0.06, Fisher’s exact). Machine learning models utilizing patient demographics and co-morbidities achieved area-under-the-curve (AUC) values of 0.93 for predicting hospitalization. Addition of viral clade or sequence information did not significantly improve models for outcome prediction. In summary, SARS-CoV-2 shows substantial sequence diversity in a community-based sample. Two dominant clades of virus are in circulation. Among patients sufficiently ill to warrant testing for virus, no significant difference in outcomes of hospitalization or death could be discerned between clades in this sample. Major risk factors for hospitalization and death for either major clade of virus include patient age and comorbid conditions.
format	article
author	Kenji Nakamichi Jolie Z. Shen Cecilia S. Lee Aaron Lee Emma A. Roberts Paul D. Simonson Pavitra Roychoudhury Jessica Andriesen April K. Randhawa Patrick C. Mathias Alex L. Greninger Keith R. Jerome Russell N. Van Gelder
author_facet	Kenji Nakamichi Jolie Z. Shen Cecilia S. Lee Aaron Lee Emma A. Roberts Paul D. Simonson Pavitra Roychoudhury Jessica Andriesen April K. Randhawa Patrick C. Mathias Alex L. Greninger Keith R. Jerome Russell N. Van Gelder
author_sort	Kenji Nakamichi
title	Hospitalization and mortality associated with SARS-CoV-2 viral clades in COVID-19
title_short	Hospitalization and mortality associated with SARS-CoV-2 viral clades in COVID-19
title_full	Hospitalization and mortality associated with SARS-CoV-2 viral clades in COVID-19
title_fullStr	Hospitalization and mortality associated with SARS-CoV-2 viral clades in COVID-19
title_full_unstemmed	Hospitalization and mortality associated with SARS-CoV-2 viral clades in COVID-19
title_sort	hospitalization and mortality associated with sars-cov-2 viral clades in covid-19
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/84198a9862a940ed87aebea5c6b31bfe
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Hospitalization and mortality associated with SARS-CoV-2 viral clades in COVID-19

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