Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant.

Paul Elliott ,Ara Darzi ,Graham P Taylor ,Andrew J Page ,Graham Cooke ,Christl A Donnelly ,William Barclay ,Caroline E Walters ,Deborah Ashby ,Oliver Eales ,Claudio Fronterrè ,Christina Atchison ,Kylie E C Ainslie ,Sophie J Prosolek ,Peter J Diggle ,Alexander J Trotter ,David Haw ,Helen Ward ,Haowei Wang ,Steven Riley

doi:10.1126/science.abl9551

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections were rising during early summer 2021 in many countries as a result of the Delta variant. We assessed reverse transcription polymerase chain reaction swab positivity in the Real-time Assessment of Community Transmission–1 (REACT-1) study in England. During June and July 2021, we observed sustained exponential growth with an average doubling time of 25 days, driven by complete replacement of the Alpha variant by Delta and by high prevalence at younger, less-vaccinated ages. Prevalence among unvaccinated people [1.21% (95% credible interval 1.03%, 1.41%)] was three times that among double-vaccinated people [0.40% (95% credible interval 0.34%, 0.48%)]. However, after adjusting for age and other variables, vaccine effectiveness for double-vaccinated people was estimated at between ~50% and ~60% during this period in England. Increased social mixing in the presence of Delta had the potential to generate sustained growth in infections, even at high levels of vaccination.

Highlights

The incidence of reverse transcription-polymerase chain reaction (RT-PCR) confirmed cases of COVID-19 increased substantially in England after the Delta variant became established during April to May 2021 [6]
With first data collection starting in May 2020, we established the REal-time Assessment of Community Transmission-1 (REACT-1) study to track the spread of the COVID-19 pandemic in England and improve situational awareness [9, 10]
Time-series of infections, hospital admissions and deaths We investigated how swab-positivity measured in REACT-1 related to daily hospital admissions and deaths in publicly available data [6], finding a best fitting lag between swab-positivity and hospitalisations of 20 days and between swab-positivity and deaths of 26 days (Fig. 3)

Summary

Introduction

The incidence of reverse transcription-polymerase chain reaction (RT-PCR) confirmed cases of COVID-19 increased substantially in England after the Delta variant became established during April to May 2021 [6]. Prevalence and growth Prevalence of infection with SARS-CoV-2 increased substantially in England between rounds 12 and 13 (Fig. 1) as the third wave took hold, linked to the rapid replacement of Alpha by Delta variant. Growth of Delta against Alpha for round 10 (11 to 30 March 2021) to round 13 corresponded to a daily growth rate advantage of 0.14 (0.10, 0.20) for Delta, which, in turn, implied an additive R advantage of 0.86 (0.63, 1.23) (Fig. 1) This is consistent with estimates based on trends in the proportion of positive PCR assays where S gene was not detected (presumed to be Delta, [12]) and on differences in household attack rate for households where Delta was identified rather than Alpha [13]. Under the assumption that REACT-1 participants provide an unbiased sample of infections, we can exclude, with 95% confidence, a population prevalence of non-Delta lineages greater than 0.004%, corresponding to 2,350 infections in England on average during round 13

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Methods

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Conclusion