Sequencing directly from antigen-detection rapid diagnostic tests in Belgium, 2022: a gamechanger in genomic surveillance?

Background: Lateral flow antigen-detection rapid diagnostic tests (Ag-RDTs) for viral infections consti-tute a fast, cheap and reliable alternative to nucleic acid amplification tests (NAATs). Whereas leftover material from NAATs can be employed for genomic analysis of positive samples, there is a paucity of information on whether viral genetic characterisation can be achieved from archived Ag-RDTs. Aim: To evalu-ate the possibility of retrieving leftover material of several viruses from a range of Ag-RDTs, for molecular genetic analysis. Methods: Archived Ag-RDTs which had been stored for up to 3 months at room tempera-ture were used to extract viral nucleic acids for sub-sequent RT-qPCR, Sanger sequencing and Nanopore whole genome sequencing. The effects of brands of Ag-RDT and of various ways to prepare Ag-RDT mate-rial were evaluated. Results: SARS-CoV-2 nucleic acids were successfully extracted and sequenced from nine different brands of Ag-RDTs for SARS-CoV-2, and for five of these, after storage for 3 months at room tem-perature. The approach also worked for Ag-RDTs for influenza virus (n = 3 brands), as well as for rotavirus and adenovirus 40/41 (n = 1 brand). The buffer of the Ag-RDT had an important influence on viral RNA yield from the test strip and the efficiency of subsequent sequencing. Conclusion: Our finding that the test strip in Ag-RDTs is suited to preserve viral genomic mate-rial, even for several months at room temperature, and therefore can serve as source material for genetic characterisation could help improve global coverage of genomic surveillance for SARS-CoV-2 as well as for other viruses.