Details:

Alternative Title:
Nat Microbiol
Publisher's site:
http://dx.doi.org/10.1038/s41564-021-01019-2
Personal Author:
Lagerborg, Kim A. ; Normandin, Erica ; Bauer, Matthew R. ; Adams, Gordon ; Figueroa, Katherine ; ... More +
Lagerborg, Kim A. ; Normandin, Erica ; Bauer, Matthew R. ; Adams, Gordon ; Figueroa, Katherine ; Loreth, Christine ; Gladden-Young, Adrianne ; Shaw, Bennett M. ; Pearlman, Leah R. ; Berenzy, Daniel ; Dewey, Hannah B. ; Kales, Susan ; Dobbins, Sabrina T. ; Shenoy, Erica S. ; Hooper, David ; Pierce, Virginia M. ; Zachary, Kimon C. ; Park, Daniel J. ; MacInnis, Bronwyn L. ; Tewhey, Ryan ; Lemieux, Jacob E. ; Sabeti, Pardis C. ; Reilly, Steven K ; Siddle, Katherine J. ; Less -
Description:
The global spread and continued evolution of SARS-CoV-2 has driven an unprecedented surge in viral genomic surveillance. Amplicon-based sequencing methods provide a sensitive, low-cost and rapid approach but suffer a high potential for contamination, which can undermine laboratory processes and results. This challenge will increase with the expanding global production of sequences across a variety of laboratories for epidemiological and clinical interpretation, as well as for genomic surveillance of emerging diseases in future outbreaks. We present SDSI + AmpSeq, an approach that uses 96 synthetic DNA spike-ins (SDSIs) to track samples and detect inter-sample contamination throughout the sequencing workflow. We apply SDSIs to the ARTIC Consortium's amplicon design, demonstrate their utility and efficiency in a real-time investigation of a suspected hospital cluster of SARS-CoV-2 cases and validate them across 6,676 diagnostic samples at multiple laboratories. We establish that SDSI + AmpSeq provides increased confidence in genomic data by detecting and correcting for relatively common, yet previously unobserved modes of error, including spillover and sample swaps, without impacting genome recovery.
Subject:
[+]
Article
COVID-19
DNA Primers
Genome, Viral
Humans
Quality Control
Reproducibility Of Results
RNA, Viral
SARS-CoV-2
Sequence Analysis
Whole Genome Sequencing
Workflow

Source:
Nat Microbiol. 7(1):108-119 ;
Pubmed ID:
34907347
Pubmed Central ID:
PMC8923058
Document Type:
Journal Article ;
Funding:
R00 HG008179/HG/NHGRI NIH HHSUnited States/ ; U19AI110818/U.S. Department of Health & Human Services ; NIH ; National Institute of Allergy and Infectious Diseases (NIAID)/ ; K99 HG010669/HG/NHGRI NIH HHSUnited States/ ; ... More +
R00 HG008179/HG/NHGRI NIH HHSUnited States/ ; U19AI110818/U.S. Department of Health & Human Services ; NIH ; National Institute of Allergy and Infectious Diseases (NIAID)/ ; K99 HG010669/HG/NHGRI NIH HHSUnited States/ ; R00HG008179/U.S. Department of Health & Human Services ; National Human Genome Research Institute (NHGRI)/ ; 75D30120C09605/U.S. Department of Health & Human Services ; Centers for Disease Control and Prevention (CDC)/ ; K99HG010669/U.S. Department of Health & Human Services ; R00 HG010669/HG/NHGRI NIH HHSUnited States/ ; U01 AI151812/AI/NIAID NIH HHSUnited States/ ; U19 AI110818/AI/NIAID NIH HHSUnited States/ ; Less -
Collection(s):
CDC Public Access
Main Document Checksum:
[+]
urn:sha256:a47fe1484685573bdc9e0ae3e67ca845b51962570c05d1dd31d91ee414a9326c
File Type:

• Supporting Files:
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