Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England

Status: Paper under peer review | First online: 23-12-2020 | Last update: 06-02-2021

This study has not yet been peer reviewed.

A novel SARS-CoV-2 variant, VOC 202012/01, emerged in southeast England in November 2020 and is rapidly spreading towards fixation. Using a variety of statistical and dynamic modelling approaches, we assessed the relative transmissibility of this novel variant. Depending on the analysis, we estimate that VOC 202012/01 is 43–82% (range of 95% credible intervals 38–106%) more transmissible than preexisting variants of SARS-CoV-2. We did not find clear evidence that VOC 202012/01 results in greater or lesser severity of disease than preexisting variants. Nevertheless, the increase in transmissibility is likely to lead to a large increase in incidence. To assess the potential impact of VOC 202012/01, we fitted a two-strain mathematical model of SARS-CoV-2 transmission to observed COVID-19 hospital admissions, hospital and ICU bed occupancy, and deaths; SARS-CoV-2 PCR prevalence and seroprevalence; and the relative frequency of VOC 202012/01. We find that without stringent control measures, COVID-19 hospitalisations and deaths are projected to reach higher levels in 2021 than were observed in 2020. Control measures of a similar stringency to the national lockdown implemented in England in November 2020 are unlikely to reduce the effective reproduction number Rt to less than 1, unless primary schools, secondary schools, and universities are also closed. We project that large resurgences of the virus are likely to occur following easing of control measures. It may be necessary to greatly accelerate vaccine roll-out to have an appreciable impact in suppressing the resulting disease burden.

Read version 2 of the preprint here.

Measuring the growth rate of VOC 202012/01. (A) Average relativized fitness in the 31 days following initial phylogenetic observation (IPO) for all lineages in the COG-UKdataset, highlighting many lineages that have risen to prominence including B.1.177, the lineage with the highest relative abundance during the IPO of VOC 202012/01. The shaded regions show conservative 95% rejection intervals and VOC is the first strain to exceed this threshold of faster relativized growth. While many lineages exhibit above-average rates of growth post-IPO, VOC 202012/01 has had the highest average relativized growth of any lineage in the history of COG-UK surveillance of SARS-COV-2. (B) Plotting all lineages’ relativized growth rates as a function of days since IPO with conservative 95% rejection intervals highlights the significantly faster growth of VOC 202012/01 relative to other lineages at comparable times since their IPO. Later declines in VOC and B.1.177 correspond to highly uncertain estimates of growth rates for data that are yet to be backfilled, and so these declines in $\rho (t)$ are sensitive to the processing of future sequences from recent dates (Fig. S1). (C) Muller plots of the relative abundances of the major SARS-CoV-2 variants in the UK, based on a multinomial spline fit to COG-UK sequence data (separate-slopes multinomial spline model, Table 1). A model extrapolation until the end of January is shown (shaded area). Minority variants are 440 circulating SARS-CoV-2 strains that never reached >15% in any week overall. (D) Mean reproduction number over 7-day periods in 149 upper-tier local authorities of England (coloured by the NHS region they are within) plotted against the weekly proportion of Pillar 2 community SARS-CoV-2 tests with SGTF shows the spread of VOC 202012/01, a corresponding increase in the reproduction number by local authority, and the eventual impact of government restrictions. Testing data are shown for the week following the reproduction number estimates to account for delays from infection to test.

Other links

medRxiv preprint

31 December 2020 - Update 1

23 December 2020 - Original preprint