Diagnostic Agreement of SARS-CoV-2 Lateral Flow Antigen Assay with the Cycle Threshold Values of RT-PCR

Abstract

COVID-19 detection via lateral flow antigen assays (LFA) are rapid and economically acquiescent to infrastructure facile healthcare settings. Early, prompt identification of cases to facilitate patient isolation and supportive management is the essence of rapid diagnostic tests. Given the backdrop of post COVID-19 pandemic-molecular testing still remains a costly affair. Additionally, molecular assays are incapable of distinguishing remnant RNA from replication competent viruses. In this scenario, we explore the diagnostic consonance of SARS-CoV-2 LFAs with RT-PCR cycle threshold, in a likelihood that it could be used as a surrogate marker for infection transmissibility. Rapid COVID-19 LFA results were compared with Real-time PCR for detection of SARS-CoV-2 in nasopharyngeal swabs. Two hundred rapid antigen positive nasopharyngeal swabs obtained from COVID-19 suspects/contacts/preoperative/screening patients were subjected to RT-PCR to study the correlation with cycle threshold (CT) values obtained for all the antigen positive cases. 200 Rapid COVID-19 LFA positive samples were analyzed in the present study. Amidst the LFA positive samples included in the study 187 (93.5%) were found to have concordant results when subjected to the gold standard Real-time PCR. Discordant results were documented in 13 (6.5%) COVID-19 LFA positive samples which were found to be negative by RT-PCR. The average Cycle threshold values were found to be 23.75 for E gene, 25.36 for N gene and 24.07 for RdRp gene. The average PCR Cycle threshold of LFA positive cases remained significantly undeterred (p<0.5) throughout the time period of the study stipulating the undaunted viral load across the different waves of the pandemic. Maximum association of LFA positivity with symptom-manifestation was seen during the 1st wave of COVID-19 (September-December 2020 in India). The association of symptoms with LFA test positivity reduced to a significant extent during the 3rd wave of the pandemic in January 2022 (p<0.5) indicating the reduced clinical severity but not infectivity of the SARS-CoV-2 infection during the 3rd wave of the pandemic. Lateral flow assay based diagnostic tests are technically & economically convenient modalities with significant interest concordance in comparison with RT-PCR. Definitive advantage in terms of achieving quick patient triage and thereby patient management can be achieved with the use of these tests.

Keywords

• sars-cov-2
• lateral flow antigen assay
• rt-pcr
• cycle threshold
• covid-19