Single vs replicate Real-Time PCR SARS-CoV-2 testing: Lessons learned for effective pandemic management

Coronavirus Disease 19 (COVID-19) caused by the SARS-CoV-2 virus remains a global pandemic having a serious impact on national economies and healthcare infrastructure. Accurate infection detection protocols are key to policy guidance and decision making. In this pilot study, we compared single versus replicate PCR testing for effective and accurate SARS-CoV-2 infection detection. One-Step Real-Time RT-PCR was employed for the detection of SARS-CoV-2 RNA isolated from individual nasopharyngeal swabs. A total of 10,014 swabs, sampled from the general public (hospital admissions, A&E, elective surgeries, cancer patients, care home residents and healthcare staff), were tested using standard replicate testing. Our analysis demonstrates that approximately 19% of SARS-CoV-2 infected individuals would have been reported as false negative if single sample Real-Time PCR testing was used. Therefore, two replicate tests can substantially decrease the risk of false negative reporting and reduce hospital and community infection rates. As the number of variants of concern increases, we believe that replicate testing is an essential consideration for effective SARS-CoV-2 infection detection and prevention of further outbreaks. A strategic approach limiting the number of missed infections is crucial in controlling the rise of new SARS-CoV-2 variants as well as the management of future pandemics.