Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7

Analysis code and data for

Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7

Nicholas G. Davies^1†, Christopher I. Jarvis¹, CMMID COVID-19 Working Group, W. John Edmunds¹, Nicholas P. Jewell^2,3, Karla Diaz-Ordaz^2,3*, Ruth H. Keogh^2,3*

Article published in Nature (2021)

1. Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK.

2. Department of Medical Statistics, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK.

3. Centre for Statistical Methodology, London School of Hygiene and Tropical Medicine, London, UK.

^†Corresponding author. E-mail: nicholas.davies@lshtm.ac.uk

*Equal contribution

This repository is maintained at https://github.com/nicholasdavies/cfrvoc.

SARS-CoV-2 lineage B.1.1.7, a variant first detected in the UK in September 2020, has spread to multiple countries worldwide. Several studies have established that B.1.1.7 is more transmissible than preexisting variants, but have not identified whether it leads to any change in disease severity. Here we analyse a dataset linking 2,245,263 positive SARS-CoV-2 community tests and 17,452 COVID-19 deaths in England from 1 September 2020 to 14 February 2021. For 1,146,534 (51%) of these tests, the presence or absence of B.1.1.7 can be identified because of mutations in this lineage preventing PCR amplification of the spike gene target (S gene target failure, SGTF). Based on 4,945 deaths with known SGTF status, we estimate that the hazard of death associated with SGTF is 55% (95% CI 39–72%) higher after adjustment for age, sex, ethnicity, deprivation, care home residence, local authority of residence and test date. This corresponds to the absolute risk of death for a 55–69-year-old male increasing from 0.6% to 0.9% (95% CI 0.8–1.0%) within 28 days after a positive test in the community. Correcting for misclassification of SGTF and missingness in SGTF status, we estimate a 61% (42–82%) higher hazard of death associated with B.1.1.7. Our analysis suggests that B.1.1.7 is not only more transmissible than preexisting SARS-CoV-2 variants, but may also cause more severe illness.