Clinical Evaluation of Direct Reverse Transcription PCR for Detection of SARS-CoV-2 Compared to Conventional RT-PCR in Patients with Positive Rapid Antigen Test Results during Circulation of Emerging Viral Variants

Abstract

The emergence of the Omicron (B.1.1.529) variant of SARS-CoV-2 has precipitated a new global wave of the COVID-19 pandemic. The rapid identification of SARS-CoV-2 infection is imperative for the effective mitigation of transmission. Diagnostic modalities such as rapid antigen testing and real-time reverse transcription polymerase chain reaction (RT-PCR) offer expedient turnaround times of 10–15 min and straightforward implementation. This preliminary study assessed the correlation between outcomes of commercially available rapid antigen tests for home use and conventional reverse transcription polymerase chain reaction (RT-PCR) assays using a limited set of clinical specimens. Patients aged 5–99 years presenting to the emergency department for SARS-CoV-2 testing were eligible for enrollment (n = 5652). Direct PCR and conventional RT-PCR were utilized for the detection of SARS-CoV-2. The entire cohort of 5652 clinical specimens was assessed by both modalities to determine the clinical utility of the direct RT-PCR assay. Timely confirmation of SARS-CoV-2 infection may attenuate viral propagation and guide therapeutic interventions. Additionally, direct RT-PCR as a secondary confirmatory test for at-home rapid antigen test results demonstrated sensitivity comparable to conventional RT-PCR, indicating utility for implementation in laboratories globally, especially in resource-limited settings with constraints on reagents, equipment, and skilled personnel. In summary, direct RT-PCR enables the detection of SARS-CoV-2 with a sensitivity approaching that of conventional RT-PCR while offering expedient throughput and shorter turnaround times. Moreover, direct RT-PCR provides an open-source option for diagnostic laboratories worldwide, particularly in low- and middle-income countries.