Real-Time SARS-CoV-2 Genotyping by High-Throughput Multiplex PCR Reveals the Epidemiology of the Variants of Concern in Qatar.

Hasan, Mohammad R; Kalikiri, Mahesh KR; Mirza, Faheem; Sundararaju, Sathyavathi; Sharma, Anju; Xaba, Thabisile; Lorenz, Stephan; Chemaitelly, Hiam

; El-Kahlout, Reham A; Tsui, Kin Ming; +8 more...Yassine, Hadi M; Coyle, Peter V; Al Khal, Abdullatif; Bertollini, Roberto; Al Thani, Mohamed H; Abu-Raddad, Laith J; Tang, Patrick; and 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.