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

Details

• Alternative Title:
  Nat Microbiol
• Personal Author:
  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.
  More +
• 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.
• Subjects:
  • COVID-19
  • DNA Primers
  • Genome, Viral
  • Humans
  • Quality Control
  • RNA, Viral
  • Reproducibility of Results
  • SARS-CoV-2
  • Sequence Analysis
  • Whole Genome Sequencing
  More +
• 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/ ; R00HG008179/U.S. Department of Health & Human Services ; NIH ; National Human Genome Research Institute (NHGRI)/ ; R43 CK000523/CK/NCEZID CDC HHSUnited States/ ; 75D30120C09605/U.S. Department of Health & Human Services ; Centers for Disease Control and Prevention (CDC)/ ; K99HG010669/U.S. Department of Health & Human Services ; NIH ; National Human Genome Research Institute (NHGRI)/ ; R00 HG010669/HG/NHGRI NIH HHSUnited States/ ; U01 AI151812/AI/NIAID NIH HHSUnited States/ ; U19 AI110818/AI/NIAID NIH HHSUnited States/
  More +
• Volume:
  7
• Issue:
  1
• Download URL:
  https://stacks.cdc.gov/view/cdc/115460/cdc_115460_DS1.pdf
• File Type:
  [PDF - 4.73 MB]
• Collection(s):
  CDC Public Access
• Main Document Checksum:
  urn:sha256:a47fe1484685573bdc9e0ae3e67ca845b51962570c05d1dd31d91ee414a9326c