Real-Time SARS-CoV-2 Genotyping by High-Throughput Multiplex PCR Reveals the Epidemiology of the Variants of Concern in Qatar
Mohammad R. Hasan, Mahesh Kumar Reddy Kalikiri, Faheem Mirza, Sathyavathi Sundararaju, Anju Sharma, Thabisile Xaba, Stephan Lorenz, Hiam Chemaitelly, Reham A. El-Kahlout, Kin Ming Tsui, Hadi M. Yassine, Peter Coyle, Abdullatif Al Khal, Roberto Bertollini, Mohamed H. Al Thani, Laith J. Abu‐Raddad, Patrick Tang
Abstract
Complementing whole genome sequencing strategies with high-throughput multiplex RT-qPCR genotyping allows for more comprehensive and real-time tracking of SARS-CoV-2 variants of concern. During the second and third waves of COVID-19 in Qatar, PCR genotyping, combined with Sanger sequencing of un-typeable samples, was employed to describe the epidemiology of the Alpha, Beta and Delta variants. A total of 9792 nasopharyngeal PCR-positive samples collected between April-June 2021 were successfully genotyped, revealing the importation and transmission dynamics of these three variants in Qatar.