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

Carcereny, A.; Martinez-Velazquez, A.; Bosch, A.; Allende, A.; Truchado, P.; Cascales, J.; Romalde, J. L.; Lois, M.; Polo, D.; Sanchez, G.; Perez-Cataluna, A.; Diaz-Reolid, A.; Anton, A.; Gregori, J.; Garcia-Cehic, D.; QUER, J.; Palau, M.; Gonzalez Ruano, C.; Pinto, R.; Guix, S.

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.