A program for real-time surveillance of SARS-CoV-2 genetics

被引：0

作者：

Brochu, Hayden N. ^{[1
]}

Song, Kuncheng ^{[1
]}

Zhang, Qimin ^{[1
]}

Zeng, Qiandong ^{[1
]}

Shafi, Adib ^{[1
]}

Robinson, Matthew ^{[1
]}

Humphrey, Jake ^{[1
]}

Croy, Bobbi ^{[2
]}

Peavy, Lydia ^{[3
]}

Perera, Minoli ^{[3
]}

Parker, Scott ^{[3
]}

Pruitt, John ^{[3
]}

Munroe, Jason ^{[4
]}

Ghatti, Rama ^{[5
]}

Urban, Thomas J. ^{[3
]}

Harris, Ayla B. ^{[3
]}

Alfego, David ^{[1
]}

Norvell, Brian ^{[3
]}

Levandoski, Michael ^{[3
,9
]}

Krueger, Brian ^{[3
,10
]}

Williams, Jonathan D. ^{[3
]}

Boles, Deborah ^{[3
]}

Nye, Melinda B. ^{[6
]}

Dale, Suzanne E. ^{[6
]}

Sapeta, Michael ^{[6
]}

Petropoulos, Christos J. ^{[7
]}

Meltzer, Jonathan ^{[6
]}

Eisenberg, Marcia ^{[3
]}

Cohen, Oren ^{[8
,11
]}

Letovsky, Stanley ^{[1
]}

Iyer, Lakshmanan K. ^{[1
]}

机构：

[1] Labcorp Ctr Excellence Data Sci AI & Bioinformat, Burlington, NC 27215 USA

[2] Labcorp, Burlington, NC 27215 USA

[3] Labcorp Res & Dev, Burlington, NC 27215 USA

[4] Labcorp, Burlington, NC 27215 USA

[5] FVSAI, San Diego, CA 92121 USA

[6] Labcorp Ctr Esoter Testing, Burlington, NC 27215 USA

[7] HIBio, South San Francisco, CA 94080 USA

[8] Labcorp Drug Dev, Burlington, NC 27215 USA

[9] Q2 Solut, IQVIA Business, Durham, NC 27703 USA

[10] BaseX Sci LLC, Chapel Hill, NC 27516 USA

[11] Alura Inc, Durham, NC 27703 USA

来源：

SCIENTIFIC REPORTS | 2024年 / 14卷 / 01期

关键词：

D O I：

10.1038/s41598-024-70697-9

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：

The COVID-19 pandemic brought forth an urgent need for widespread genomic surveillance for rapid detection and monitoring of emerging SARS-CoV-2 variants. It necessitated design, development, and deployment of a nationwide infrastructure designed for sequestration, consolidation, and characterization of patient samples that disseminates de-identified information to public authorities in tight turnaround times. Here, we describe our development of such an infrastructure, which sequenced 594,832 high coverage SARS-CoV-2 genomes from isolates we collected in the United States (U.S.) from March 13th 2020 to July 3rd 2023. Our sequencing protocol ('Virseq') utilizes wet and dry lab procedures to generate mutation-resistant sequencing of the entire SARS-CoV-2 genome, capturing all major lineages. We also characterize 379 clinically relevant SARS-CoV-2 multi-strain co-infections and ensure robust detection of emerging lineages via simulation. The modular infrastructure, sequencing, and analysis capabilities we describe support the U.S. Centers for Disease Control and Prevention national surveillance program and serve as a model for rapid response to emerging pandemics at a national scale.

引用

页数：15

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