Rapid and Flexible RT-qPCR Surveillance Platforms To Detect SARS-CoV-2 Mutations
Katja Spieß, Vithiagaran Gunalan, Ellinor Marving, Sofie Holdflod Nielsen, Michelle Grace Pinto Jørgensen, Anna S. Fomsgaard, Line Nielsen, Alonzo Alfaro‐Núñez, Søren Michael Karst, Shila Mortensen, Morten Rasmussen, Ria Lassaunière, Maiken Worsøe Rosenstierne, Charlotta Polacek, Jannik Fonager, Arieh S. Cohen, Claus Henrik Nielsen, Anders Fomsgaard
Abstract
Denmark weathered the SARS-CoV-2 crisis with relatively low rates of infection and death. Intensive testing strategies with the aim of detecting SARS-CoV-2 in symptomatic and nonsymptomatic individuals were available by establishing a national test system called TestCenter Denmark. This testing regime included the detection of SARS-CoV-2 signature mutations, with referral to the national health system, thereby delaying outbreaks of variants of concern. Our study describes the design of the large-scale RT-qPCR platform established at TestCenter Denmark in conjunction with whole-genome sequencing to report mutations of concern to the national health system. Validation of the large-scale RT-qPCR platform using paired WGS consensus genomes showed high sensitivity and specificity. For smaller laboratories with limited infrastructure, we developed a flexible small-scale RT-qPCR platform to detect three signature mutations in a single run. The RT-qPCR platforms are important tools to support the control of the SARS-CoV-2 endemic in Denmark.