High-precision and cost-efficient sequencing for real-time COVID-19 surveillance

Abstract COVID-19 global cases have climbed to more than 33 million, with over a million total deaths, as of September, 2020. Real-time massive SARS-CoV-2 whole genome sequencing is key to tracking chains of transmission and estimating the origin of disease outbreaks. Yet no methods have simultaneou...

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Autores principales:	Sung Yong Park, Gina Faraci, Pamela M. Ward, Jane F. Emerson, Ha Youn Lee
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/37e624297e014915ab42e372f7b8c1b9
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spelling	oai:doaj.org-article:37e624297e014915ab42e372f7b8c1b92021-12-02T14:33:57ZHigh-precision and cost-efficient sequencing for real-time COVID-19 surveillance10.1038/s41598-021-93145-42045-2322https://doaj.org/article/37e624297e014915ab42e372f7b8c1b92021-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-93145-4https://doaj.org/toc/2045-2322Abstract COVID-19 global cases have climbed to more than 33 million, with over a million total deaths, as of September, 2020. Real-time massive SARS-CoV-2 whole genome sequencing is key to tracking chains of transmission and estimating the origin of disease outbreaks. Yet no methods have simultaneously achieved high precision, simple workflow, and low cost. We developed a high-precision, cost-efficient SARS-CoV-2 whole genome sequencing platform for COVID-19 genomic surveillance, CorvGenSurv (Coronavirus Genomic Surveillance). CorvGenSurv directly amplified viral RNA from COVID-19 patients’ Nasopharyngeal/Oropharyngeal (NP/OP) swab specimens and sequenced the SARS-CoV-2 whole genome in three segments by long-read, high-throughput sequencing. Sequencing of the whole genome in three segments significantly reduced sequencing data waste, thereby preventing dropouts in genome coverage. We validated the precision of our pipeline by both control genomic RNA sequencing and Sanger sequencing. We produced near full-length whole genome sequences from individuals who were COVID-19 test positive during April to June 2020 in Los Angeles County, California, USA. These sequences were highly diverse in the G clade with nine novel amino acid mutations including NSP12-M755I and ORF8-V117F. With its readily adaptable design, CorvGenSurv grants wide access to genomic surveillance, permitting immediate public health response to sudden threats.Sung Yong ParkGina FaraciPamela M. WardJane F. EmersonHa Youn LeeNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Sung Yong Park Gina Faraci Pamela M. Ward Jane F. Emerson Ha Youn Lee High-precision and cost-efficient sequencing for real-time COVID-19 surveillance
description	Abstract COVID-19 global cases have climbed to more than 33 million, with over a million total deaths, as of September, 2020. Real-time massive SARS-CoV-2 whole genome sequencing is key to tracking chains of transmission and estimating the origin of disease outbreaks. Yet no methods have simultaneously achieved high precision, simple workflow, and low cost. We developed a high-precision, cost-efficient SARS-CoV-2 whole genome sequencing platform for COVID-19 genomic surveillance, CorvGenSurv (Coronavirus Genomic Surveillance). CorvGenSurv directly amplified viral RNA from COVID-19 patients’ Nasopharyngeal/Oropharyngeal (NP/OP) swab specimens and sequenced the SARS-CoV-2 whole genome in three segments by long-read, high-throughput sequencing. Sequencing of the whole genome in three segments significantly reduced sequencing data waste, thereby preventing dropouts in genome coverage. We validated the precision of our pipeline by both control genomic RNA sequencing and Sanger sequencing. We produced near full-length whole genome sequences from individuals who were COVID-19 test positive during April to June 2020 in Los Angeles County, California, USA. These sequences were highly diverse in the G clade with nine novel amino acid mutations including NSP12-M755I and ORF8-V117F. With its readily adaptable design, CorvGenSurv grants wide access to genomic surveillance, permitting immediate public health response to sudden threats.
format	article
author	Sung Yong Park Gina Faraci Pamela M. Ward Jane F. Emerson Ha Youn Lee
author_facet	Sung Yong Park Gina Faraci Pamela M. Ward Jane F. Emerson Ha Youn Lee
author_sort	Sung Yong Park
title	High-precision and cost-efficient sequencing for real-time COVID-19 surveillance
title_short	High-precision and cost-efficient sequencing for real-time COVID-19 surveillance
title_full	High-precision and cost-efficient sequencing for real-time COVID-19 surveillance
title_fullStr	High-precision and cost-efficient sequencing for real-time COVID-19 surveillance
title_full_unstemmed	High-precision and cost-efficient sequencing for real-time COVID-19 surveillance
title_sort	high-precision and cost-efficient sequencing for real-time covid-19 surveillance
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/37e624297e014915ab42e372f7b8c1b9
work_keys_str_mv	AT sungyongpark highprecisionandcostefficientsequencingforrealtimecovid19surveillance AT ginafaraci highprecisionandcostefficientsequencingforrealtimecovid19surveillance AT pamelamward highprecisionandcostefficientsequencingforrealtimecovid19surveillance AT janefemerson highprecisionandcostefficientsequencingforrealtimecovid19surveillance AT hayounlee highprecisionandcostefficientsequencingforrealtimecovid19surveillance
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High-precision and cost-efficient sequencing for real-time COVID-19 surveillance

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