DNA spike-ins enable confident interpretation of SARS-CoV-2 genomic data from amplicon-based sequencing
DNA spike-ins enable confident interpretation of SARS-CoV-2 genomic data from amplicon-based sequencing
Abstract 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.
Sabeti Pardis C.、Shenoy Erica S.、Zachary Kimon C.、MacInnis Bronwyn L.、Bauer Matthew R.、Figueroa Katherine、Hooper David、Pearlman Leah、Park Daniel J.、Siddle Katherine J.、Reilly Steven K、Adams Gordon、Lemieux Jacob E.、Loreth Christine、Normandin Erica、Gladden-Young Adrianne、Shaw Bennett、Lagerborg Kim A.、Pierce Virginia M.
Broad Institute of Harvard and MIT||Department of Systems Biology, Harvard Medical School||Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Harvard University||Massachusetts Consortium on Pathogen Readiness||Howard Hughes Medical InstituteDivision of Infectious Diseases, Massachusetts General HospitalDivision of Infectious Diseases, Massachusetts General Hospital||Department of Medicine, Harvard Medical School||Infection Control Unit, Massachusetts General HospitalBroad Institute of Harvard and MIT||Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Harvard University||Massachusetts Consortium on Pathogen ReadinessBroad Institute of Harvard and MIT||Harvard Program in Biological and Biomedical Sciences, Harvard Medical SchoolBroad Institute of Harvard and MITDivision of Infectious Diseases, Massachusetts General HospitalBroad Institute of Harvard and MITBroad Institute of Harvard and MITBroad Institute of Harvard and MIT||Department of Systems Biology, Harvard Medical SchoolBroad Institute of Harvard and MIT||Department of Systems Biology, Harvard Medical SchoolBroad Institute of Harvard and MITBroad Institute of Harvard and MIT||Division of Infectious Diseases, Massachusetts General HospitalBroad Institute of Harvard and MITBroad Institute of Harvard and MIT||Department of Systems Biology, Harvard Medical SchoolBroad Institute of Harvard and MITBroad Institute of Harvard and MIT||Division of Infectious Diseases, Massachusetts General HospitalBroad Institute of Harvard and MIT||Harvard Program in Biological and Biomedical Sciences, Harvard Medical SchoolDepartment of Pathology, Massachusetts General Hospital||Pediatric Infectious Disease Unit, MassGeneral Hospital for Children||Department of Pathology, Harvard Medical School
医学研究方法基础医学分子生物学
Sabeti Pardis C.,Shenoy Erica S.,Zachary Kimon C.,MacInnis Bronwyn L.,Bauer Matthew R.,Figueroa Katherine,Hooper David,Pearlman Leah,Park Daniel J.,Siddle Katherine J.,Reilly Steven K,Adams Gordon,Lemieux Jacob E.,Loreth Christine,Normandin Erica,Gladden-Young Adrianne,Shaw Bennett,Lagerborg Kim A.,Pierce Virginia M..DNA spike-ins enable confident interpretation of SARS-CoV-2 genomic data from amplicon-based sequencing[EB/OL].(2025-03-28)[2025-08-15].https://www.biorxiv.org/content/10.1101/2021.03.16.435654.点此复制
评论