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Abstract
Objectives Importations of novel variants of concern (VOC), particularly B.1.617.2, have become the impetus behind recent outbreaks of SARS-CoV-2. Concerns around the impact on vaccine effectiveness, transmissibility and severity are now driving the public health response to these variants. This paper analyses the patterns of growth in hospitalisations and confirmed cases for novel VOCs by age groups, geography and ethnicity in the context of changing behaviour, non-pharmaceutical interventions (NPIs) and the UK vaccination programme. We seek to highlight where strategies have been effective and periods that have facilitated the establishment of new variants.
Design We have algorithmically linked the most complete testing and hospitalisation data in England to create a data set of confirmed infections and hospitalisations by SARS-CoV-2 genomic variant. We have used these linked data sets to analyse temporal, geographic and demographic distinctions.
Setting and participants The setting is England from October 2020 to July 2021. Participants included all COVID-19 tests that included RT-PCR CT gene target data or underwent sequencing and hospitalisations that could be linked to these tests.
Methods To calculate the instantaneous growth rate for VOCs we have developed a generalised additive model fit to multiple splines and varying day of the week effects. We have further modelled the instantaneous reproduction number Rt for the B.1.1.7 and B.1.617.2 variants and included a doubly interval censored model to temporally adjust the confirmed variant cases.
Results We observed a clear replacement of the predominant B.1.1.7 by the B.1.617.2 variant without observing sustained exponential growth in other novel variants. Modelled exponential growth of RT PCR gene target triple-positive cases was initially detected in the youngest age groups, although we now observe across all ages a very small doubling time of 10.7 (95% CI 9.1 to 13.2) days and 8 (95% CI 6.9 to 9.1) days for cases and hospitalisations, respectively. We observe that growth in RT PCR gene target triple-positive cases was first detected in the Indian ethnicity group in late February, with a peak of 0.06 (95% CI 0.07 to 0.05) in the instantaneous growth rate, but is now maintained by the white ethnicity groups, observing a doubling time of 6.8 (95% CI 4.9 to 11) days. Rt analysis indicates a reproduction number advantage of 0.45 for B.1.617.2 relative to B.1.1.7, with the Rt value peaking at 1.85 for B.1.617.2.
Conclusions Our results illustrate a clear transmission advantage for the B.1.617.2 variant and the growth in hospitalisations illustrates that this variant is able to maintain exponential growth within age groups that are largely doubly vaccinated. There are concerning signs of intermittent growth in the B.1.351 variant, reaching a 28-day doubling time peak in March 2021, although this variant is presently not showing any evidence of a transmission advantage over B.1.617.2. Step 1b of the UK national lockdown easing was sufficient to precipitate exponential growth in B.1.617.2 cases for most regions and younger adult age groups. The final stages of NPI easing appeared to have a negligible impact on the growth of B.1.617.2 with every region experiencing sustained exponential growth from step 2. Nonetheless, early targeted local NPIs appeared to markedly reduced growth of B.1.617.2. Later localised interventions, at a time of higher prevalence and greater geographic dispersion of this variant, appeared to have a negligible impact on growth.
- epidemiology
- COVID-19
Data availability statement
Data are available upon reasonable request. To access the data used for this study, an application can be made to Public Health England, Department of Health and Social Care. Data requests can be made to the Office for Data Release (https://www.gov.uk/government/publications/accessing-public-health-england-data/about-the-phe-odr-and-accessing-data) and contacting odr@phe.gov.uk. All requests to access data are reviewed by the ODR and are subject to strict confidentiality provisions in line with the requirements of the common law duty of confidentiality, data protection legislation (including the General Data Protection Regulation), 8 Caldicott principles, the Information Commissioner’s statutory data-sharing code of practice and the national data opt-out programme.
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Data availability statement
Data are available upon reasonable request. To access the data used for this study, an application can be made to Public Health England, Department of Health and Social Care. Data requests can be made to the Office for Data Release (https://www.gov.uk/government/publications/accessing-public-health-england-data/about-the-phe-odr-and-accessing-data) and contacting odr@phe.gov.uk. All requests to access data are reviewed by the ODR and are subject to strict confidentiality provisions in line with the requirements of the common law duty of confidentiality, data protection legislation (including the General Data Protection Regulation), 8 Caldicott principles, the Information Commissioner’s statutory data-sharing code of practice and the national data opt-out programme.
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Footnotes
Contributors TW conceived the idea of the article. TW wrote the article. TW, LP, IH, FX and AG developed the model methodology. AG and TW created the graphical representations. LP, AJ, TW and IH reviewed the final draft. TW is the guarantor of the paper.
Funding The authors have not declared a specific grant for this research from any funding agency in the public, commercial or not-for-profit sectors.
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Competing interests None declared.
Patient and public involvement Patients and/or the public were not involved in the design, or conduct, or reporting, or dissemination plans of this research.
Provenance and peer review Not commissioned; externally peer reviewed.