Early epidemiological signatures of novel SARS-CoV-2 variants: establishment of B.1.617.2 in England

Challen, R.; Dyson, L.; Overton, C.; Guzman-Rincon, L.; Hill, E.; Stage, H.; Brooks-Pollock, E.; Pellis, L.; Scarabel, F.; Pascall, D. J.; Blomquist, P.; Tildesley, M. J.; Williamson, D.; Siegert, S.; Xiong, X.; Youngman, B.; Consortium, J.; Read, J. M.; Gog, J. R.; Keeling, M. J.; Danon, L.

The rapid emergence of SARS-CoV-2 mutants with new phenotypic properties is a critical challenge to the control of the ongoing pandemic. B.1.1.7 was monitored in the UK through routine testing and S-gene target failures (SGTF), comprising over 90% of cases by March 2021. Now, the reverse is occurring: SGTF cases are being replaced by an S-gene positive variant, which we associate with B.1.617.2. Evidence from the characteristics of S-gene positive cases demonstrates that, following importation, B.1.617.2 is transmitted locally, growing at a rate higher than B.1.1.7 and a doubling time between 5-14 days. S-gene positive cases should be prioritised for sequencing and aggressive control in any countries in which this variant is newly detected.