SARS-CoV-2 large-scale population testing using LumiraDx SARS-CoV-2 Antigen Test

Introduction/ Background: RT-PCR testing remains the gold standard for the diagnosis of infections. There are limited resources for SARS-CoV-2 RT-PCR, which affects capacity for screening large populations. To meet such demands and reduce transmission, antigen-based methods are being considered. We assess antigen tests performance for large population screening compared to RT-PCR. Methods: The evaluation was conducted on 4146 participants in Senegal and tested at IRESSEF (Institut de Recherche en Sante de Surveillance Epidemiologique et de Formations. Oropharyngeal and nasopharyngeal swaps were collected from each participant into 2 mL of viral transport medium (VTM). We used 400ul of VTM to assess the performance of LumiraDx SARSCoV- 2 antigen assay compared to RT-PCR. Sensibilities and specificities LumiraxDx were computed and compared to those of RT-PCR. Results: Prevalence of SARS-CoV-2 was 4.5% with RT-PCR and 4.1% with LumiraDx. Compared to the RT-PCR, the specificity and specificity of the LumiraDx test in large-scale population were 82.7% [95% CI 74,1-89,7] and 99.9% [95% CI 99,6-99,9] respectively. Based on the threshold cycle range, sensitivity and specificity were 92,1% [95% CI 84,6-96,3] and 99.9 % [95% CI 99,6-99,9], respectively when Ct value was below or equal 33 cycles, and 38.1% [95% CI 18,9-61,3] and 100% [95%CI 99,7-100] respectively when it was above 33. The kappa coefficient was 0.88 when considering all the patients and 0.94 for Ct values below 30 cycles. Impact: The results confirm that antigen-based tests could be used instead of PCR-based test in resource limited settings. Indeed, RT- PCR may not be feasible for large populations screening in resource limited countries and antigen-based testing could be an alternative to quickly diagnose, isolate and treat positive cases. Conclusion: Our data have shown that the LumiraDx SARS-CoV-2 antigen test using oropharyngeal and nasopharyngeal swap samples collected in viral transport elicited comparable prevalence, high sensitivity and good agreement in large scale screening of SARS-CoV-2, when compared to the RTPCR.

Rapidly rising cases with Omicron in Senegal.

•Omicron variant continues to progress in Senegal with the appearance of new contaminations.•IRESSEF detected the first positive case of the Omicron variant on Friday, December 3, 2021.•Since this date, the number of Omicron variant infections has increased over the weeks.•Molecular surveillance of the Omicron variant is carried out in real time to inform the medical authorities.