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 KR Kalikiri; Faheem Mirza; Sathyavathi Sundararaju; Anju Sharma; Thabisile Xaba; Stephan Lorenz; Hiam Chemaitelly

; Reham A El-Kahlout; Kin Ming Tsui; +8 more... Hadi M Yassine; Peter V Coyle; Abdullatif Al Khal; Roberto Bertollini; Mohamed H Al Thani; Laith J Abu-Raddad; Patrick Tang; National Study Group for COVID-19 Epidemiology in Qatar; National Study Group for COVID-19 Epidemiology in Qatar; (2021) Real-Time SARS-CoV-2 Genotyping by High-Throughput Multiplex PCR Reveals the Epidemiology of the Variants of Concern in Qatar. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases, 112. pp. 52-54. ISSN 1201-9712 DOI: 10.1016/j.ijid.2021.09.006

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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.