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

• Published in: STAR protocols 2024-09, Vol.5 (3), p.103146, Article 103146
• Main Authors: Bassit, Leda, Bowers, Heather B., Greenleaf, Morgan, Sabino, Courtney, Lai, Eric, Yu, Grace, Piantadosi, Anne, Wang, Ethan, O’Sick, William, McLendon, Kaleb, Sullivan, Julie A., Schinazi, Raymond F., Damhorst, Gregory L., Lam, Wilbur, Rao, Anuradha
• Format: Article
• Language: English
• Subjects: Clinical Protocol; Health Sciences; Microbiology; Molecular Biology
• ISSN: 2666-1667; 2666-1667
• DOI: 10.1016/j.xpro.2024.103146

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 [Display omitted] •Selection and quality control of remnant clinical SARS-CoV-2 variant samples for pooling•Pooling of samples, aliquoting of pool, freezing, and preparation of mini test panel•Preparation, aliquoting, and freezing of multiple test panels using pooled samples•Final panel quality control, testing with two EUA “bookend” LFAs and GE/mL determination Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. 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.