Dutch participatory surveillance framework for evaluating evolutionary changes on SARS-CoV-2 affecting rapid diagnostic test sensitivity in 2022 − 2023

BACKGROUND: Rapid Diagnostic Tests (RDTs) for SARS-CoV-2 have been pivotal for diagnostics, and shaping policies regarding self-isolation. In case of decreased sensitivity of RDTs to novel virus variants, viral spread can increase. In order to monitor for reduced sensitivity of RDTs we used a collection of SARS-CoV-2 positive samples from RDT negative patients. Infectieradar, a national participatory surveillance that registers respiratory symptoms and investigates the causative pathogen(s), is used here as a framework to study false-negative RDT results and possible relation of the emergence of new virus variants. METHODS: Participants reported weekly on RDT use and symptoms linked to Acute Respiratory Illness (ARI). Each week, all RDT-positive samples and a subset of 200 symptomatic, participants with RDT negative samples were invited to send in nose throat swabs (NTS). SARS-CoV-2 Ct-values were determined using RT-PCR on RDT-positive and RDT-negative NTS samples and compared using unpaired T-tests. Sequencing was performed on all eligible samples to compare the proportion of mutations in the N encoding gene and investigate the clustering patterns of genome sequences through analyses. NTS samples of participants with discordant RT-PCR and RDT results were also analyzed using RDTs by professionals in the laboratory. Between October 2022 and October 2023, our study had 16,893 participants and we collected 1,757 self-test-positive/NTS PCR-positive samples (RDT+/PCR+) and 359 self-test-negative/NTS PCR positive samples (RDT-/PCR+), which is 4.3% of RDT-negative samples. RESULTS: We observed overall higher Ct-values in the RDT-negative group, but saw no changes in viral loads throughout our sampling period. Few and relatively small differences in prevalence of amino acid substitutions were observed when we compared the RDT-negative group and to RDT-positive group. No specific clusters within the phylogenetic tree were observed from the RDT-negative sequences, which suggested there were no distinctive genetic properties of RDT-negative specimens. This was further confirmed by laboratory analyses. CONCLUSIONS: Evaluating RDT performance in the Dutch population and in-depth analysis of false-negative RDT specimens, led to no evidence for SARS-CoV-2 evolution affecting RDT sensitivity of the tests used. The participatory surveillance program Infectieradar is a powerful tool for our national surveillance of acute respiratory illnesses, as well as for research purposes. Since this framework offered both self-testing and the gold standard of PCR testing results.