Synthetic DNA spike-ins (SDSIs) enable sample tracking and detection of inter-sample contamination in SARS-CoV-2 sequencing workflows.

Document Type

Article

Publication Date

1-2022

Publication Title

Nat Microbiol

Keywords

JMG, COVID-19, DNA Primers, Genome, Viral, Humans, Quality Control, RNA, Viral, Reproducibility of Results, SARS-CoV-2, Sequence Analysis, Whole Genome Sequencing, Workflow

JAX Source

Nat Microbiol 2022 Jan; 7(1):108-119

Volume

7

Issue

1

First Page

108

Last Page

119

ISSN

2058-5276

PMID

34907347

DOI

https://doi.org/10.1038/s41564-021-01019-2

Abstract

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.

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