Protocol for the creation and characterization of SARS-CoV-2 variant testing panels using remnant clinical samples for diagnostic assay testing

Leda Bassit; Heather B Bowers; Morgan Greenleaf; Courtney Sabino; Eric Lai; Grace Yu; Anne Piantadosi; Ethan Wang; William O'Sick; Kaleb McLendon; Julie A Sullivan; Raymond F Schinazi; Gregory L Damhorst; Wilbur Lam; Anuradha Rao

doi:10.1016/j.xpro.2024.103146

Protocol for the creation and characterization of SARS-CoV-2 variant testing panels using remnant clinical samples for diagnostic assay testing

STAR Protoc. 2024 Sep 20;5(3):103146. doi: 10.1016/j.xpro.2024.103146. Epub 2024 Jun 20.

Authors

Leda Bassit¹, Heather B Bowers², Morgan Greenleaf³, Courtney Sabino², Eric Lai⁴, Grace Yu⁵, Anne Piantadosi⁶, Ethan Wang⁷, William O'Sick⁸, Kaleb McLendon⁸, Julie A Sullivan⁹, Raymond F Schinazi¹⁰, Gregory L Damhorst¹¹, Wilbur Lam¹², Anuradha Rao¹³

Affiliations

¹ The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA; Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University, Atlanta, GA, USA. Electronic address: [email protected].
² The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA; Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University, Atlanta, GA, USA.
³ The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA; Georgia CTSA, Emory University School of Medicine, Atlanta, GA, USA.
⁴ Personalized Science, San Diego, CA 05403, USA.
⁵ VentureWell, 100 Venture Way, Hadley, MA 01035, USA.
⁶ Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA; Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA.
⁷ Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA.
⁸ The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA; Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA; Emory/Children's Laboratory for Innovative Assay Development, Atlanta, GA, USA.
⁹ The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA; Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
¹⁰ Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University, Atlanta, GA, USA; Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
¹¹ The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA; Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA.
¹² The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA; Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA; Aflac Cancer and Blood Disorders Center at Children's Healthcare of Atlanta, Atlanta, GA, USA; Children's Healthcare of Atlanta, Atlanta, GA, USA; Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA.
¹³ The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA; Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA. Electronic address: [email protected].

Abstract

The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Alpha variant in 2020 demonstrated the need for reanalysis of diagnostic tests to ensure detection of emerging variants. Here, we present a protocol for creating and characterizing SARS-CoV-2 variant testing panels using remnant clinical samples for diagnostic assay testing. We describe steps for characterizing SARS-CoV-2 remnant clinical samples and preparing them into pools and their use in preparing varying quantities of virus. We then detail procedures for verifying variant detection using the resulting sample panel. For complete details on the use and execution of this protocol, please refer to Rao et al.¹^,².

Keywords: Clinical Protocol; Health Sciences; Microbiology; Molecular Biology.

MeSH terms

COVID-19 Nucleic Acid Testing / methods
COVID-19 Testing / methods
COVID-19* / diagnosis
COVID-19* / virology
Humans
SARS-CoV-2* / genetics
SARS-CoV-2* / isolation & purification
Specimen Handling / methods

Supplementary concepts

SARS-CoV-2 variants

Abstract

MeSH terms

Supplementary concepts

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