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Monitoring emergence of SARS-CoV-2 B.1.1.7 Variant through the Spanish National SARS-CoV-2 Wastewater Surveillance System (VATar COVID-19) from December 2020 to March 2021

By Albert Carcereny, Adan Martinez-Velazquez, Albert Bosch, Ana Allende, Pilar Truchado, Jenifer Cascales, Jesus L Romalde, Marta Lois, David Polo, Gloria Sanchez, Alba Perez-Cataluna, Azahara Diaz-Reolid, Andrés Antón, Josep Gregori, Damir Garcia-Cehic, JOSEP QUER, Margarita Palau, Cristina Gonzalez Ruano, Rosa Pinto, Susana Guix

Posted 30 May 2021
medRxiv DOI: 10.1101/2021.05.27.21257918

Background: Since its first identification in the United Kingdom in late 2020, the highly transmissible B.1.1.7 variant of SARS-CoV-2, become dominant in several European countries raising great concern. Aim: The aim of this study was to develop a duplex real-time RT-qPCR assay to detect, discriminate and quantitate SARS-CoV-2 variants containing one of its mutation signatures, the HV69/70 deletion, to trace the community circulation of the B.1.1.7 variant in Spain through the Spanish National SARS-CoV-2 Wastewater Surveillance System (VATar COVID-19). Results: B.1.1.7 variant was first detected in sewage from the Southern city of Malaga (Andalucia) in week 20_52, and multiple introductions during Christmas holidays were inferred in different parts of the country, earlier than clinical epidemiological reporting by the local authorities. Wastewater-based B.1.1.7 tracking showed a good correlation with clinical data and provided information at the local level. Data from WWTPs which reached B.1.1.7 prevalences higher than 90% for at least 2 consecutive weeks showed that 8.1+/-1.8 weeks were required for B.1.1.7 to become dominant. Conclusion: The study highlights the applicability of RT-qPCR-based strategies to track specific mutations of variants of concern (VOCs) as soon as they are identified by clinical sequencing, and its integration into existing wastewater surveillance programs, as a cost-effective approach to complement clinical testing during the COVID-19 pandemic.

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