DNA spike-ins enable confident interpretation of SARS-CoV-2 genomic data from amplicon-based sequencing.
Kim A LagerborgErica NormandinMatthew R BauerGordon AdamsKatherine FigueroaChristine LorethAdrianne Gladden-YoungBennett M ShawLeah PearlmanErica S ShenoyDavid HooperVirginia M PierceKimon C ZacharyDaniel J ParkBronwyn L MacInnisJacob E LemieuxPardis C SabetiSteven K ReillyKatherine J SiddlePublished in: bioRxiv : the preprint server for biology (2021)
The rapid global spread and continued evolution of SARS-CoV-2 has highlighted an unprecedented need for viral genomic surveillance and clinical viral sequencing. Amplicon-based sequencing methods provide a sensitive, low-cost and rapid approach but suffer a high potential for contamination, which can undermine lab processes and results. This challenge will only increase with expanding global production of sequences by diverse research groups for epidemiological and clinical interpretation. We present an approach which uses synthetic DNA spike-ins (SDSIs) to track samples and detect inter-sample contamination through a sequencing workflow. Applying this approach to the ARTIC Consortium's amplicon design, we define a series of best practices for Illumina-based sequencing and provide a detailed characterization of approaches to increase sensitivity for low-viral load samples incorporating the SDSIs. We demonstrate the utility and efficiency of the SDSI method amidst a real-time investigation of a suspected hospital cluster of SARS-CoV-2 cases.
Keyphrases
- sars cov
- single cell
- respiratory syndrome coronavirus
- low cost
- healthcare
- risk assessment
- circulating tumor
- copy number
- human health
- primary care
- public health
- drinking water
- electronic health record
- health risk
- single molecule
- pulmonary embolism
- emergency department
- machine learning
- gene expression
- big data
- deep learning
- adverse drug