Magnetic hydrogel particles improve nanopore sequencing of SARS-CoV-2 and other respiratory viruses

被引：7

作者：

Andersen, P. ^{[1
]}

Barksdale, S. ^{[1
]}

Barclay, R. A. ^{[1
]}

Smith, N. ^{[1
]}

Fernandes, J. ^{[1
]}

Besse, K. ^{[1
]}

Goldfarb, D. ^{[1
]}

Barbero, R. ^{[1
]}

Dunlap, R. ^{[1
]}

Jones-Roe, T. ^{[1
]}

Kelly, R. ^{[1
]}

Miao, S. ^{[1
]}

Ruhunusiri, C. ^{[1
]}

Munns, A. ^{[1
]}

Mosavi, S. ^{[1
]}

Sanson, L. ^{[1
]}

Munns, D. ^{[1
]}

Sahoo, S. ^{[1
]}

Swahn, O. ^{[1
]}

Hull, K. ^{[1
]}

White, D. ^{[1
]}

Kolb, K. ^{[1
]}

Noroozi, F. ^{[1
]}

Seelam, J. ^{[1
]}

Patnaik, A. ^{[1
]}

Lepene, B. ^{[1
]}

机构：

[1] Ceres Nanosci Inc, Manassas, VA 20110 USA

来源：

SCIENTIFIC REPORTS | 2023年 / 13卷 / 01期

基金：

美国国家卫生研究院;

关键词：

COVID-19;

D O I：

10.1038/s41598-023-29206-7

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Presented here is a magnetic hydrogel particle enabled workflow for capturing and concentrating SARS-CoV-2 from diagnostic remnant swab samples that significantly improves sequencing results using the Oxford Nanopore Technologies MinION sequencing platform. Our approach utilizes a novel affinity-based magnetic hydrogel particle, circumventing low input sample volumes and allowing for both rapid manual and automated high throughput workflows that are compatible with Nanopore sequencing. This approach enhances standard RNA extraction protocols, providing up to 40 x improvements in viral mapped reads, and improves sequencing coverage by 20-80% from lower titer diagnostic remnant samples. Furthermore, we demonstrate that this approach works for contrived influenza virus and respiratory syncytial virus samples, suggesting that it can be used to identify and improve sequencing results of multiple viruses in VTM samples. These methods can be performed manually or on a KingFisher automation platform.

引用

页数：13

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