Study population and setting
This study reports on the frequency and transmissibility of SARS-CoV-2 variant of concern (VOC) 202012/01 in England between September 28 and December 1, 2020. The frequency and proportion of the VOC in England was estimated from routine diagnostic PCR data. Diagnostic assays fail to detect the spike glycoprotein (S-gene) in the VOC, and so samples exhibiting S-gene target failure (i.e. S gene drop-out) that are positive for other SARS-CoV-2 genes, can be used as a proxy for VOC in the absence of whole-genome sequencing, and was shown to be 97% specific for the VOC in the UK during the analysis period. After estimating the proportion of all positive samples with S gene drop-out, the authors used a two-strain age and regionally structured transmission model fit to COVID-19 hospitalization and death data from seven regions to explain observed increases in COVID-19 diagnoses and frequency of the VOC during the observation period. Four hypotheses to explain the coincident rise in overall cases and the VOC were evaluated: 1) increased infectiousness of the VOC; 2) immune escape (i.e., reinfection of individuals who had been previously infected with a different variant by the VOC); 3) increased susceptibility to the VOC among children as compared to other variants, and 4) a shorter generation time. The model was also used to assess whether there were differences in odds of hospitalization or relative risk of death due to the VOC. The authors also assessed whether changes in contact patterns over time might explain observed changes in transmission using Google mobility data and age-specific contact data from the CoMix social contact survey. Lastly, the authors projected the course of the epidemic under various control strategies, including lockdowns, school closures, and mass vaccination, through the summer.
Summary of Main Findings
The authors found that the proportion of COVID-19 cases in England due to the VOC has rapidly increased since November. The increasing proportion of VOC cases was also associated with a significant increase in the effective reproductive number, Rt. Of the four hypotheses tested to explain the coincident rise in the VOC and Rt, the observed data were most consistent with the model including increased transmissibility of the VOC relative to pre-existing variants. The authors estimated that the VOC was 56% more transmissible (95% credible interval: 50-74%) than previously observed SARS-CoV-2 variants combined. However, there was no evidence that the VOC led to higher rates of hospitalizations or deaths. Changing contact patterns did not appear to explain the rise in the VOC. Lastly, the authors found that unless schools are closed and vaccinations increased to 2 million per week, the effective reproductive number is unlikely to fall below 1 as a consequence of increased frequency and transmissibility of the VOC.
This study assessed multiple alternative mechanisms for the rapid rise in COVID-19 cases along with increasing frequency of the VOC in England, including increased transmissibility of the VOC, increased, susceptibility to the VOC among children (which has major implications for school re-openings/closures), and changes in social contact patterns. Implications of the VOC on vaccination strategies were also explored.
Limited information was reported on testing rates or genomic sampling across NHS regions or age-groups over the observation period which may impact interpretation of results. While unlikely, this study does not rule out the possibility that founder and super spreading events with subsequent spread of the VOC to other regions explain the observed data. Of note, there were apparent increases in social contacts among persons <18 years of age immediately prior to the rise in the VOC, which was not addressed in the limitations, despite reported outbreaks among schools over the same time frame. Further, estimates of Rt from contact data appear to fit the data relatively well, except for a brief time period between/during October and November.
This is the first study to estimate the relative transmissibility of the novel SARS-CoV-2 variant, VOC 202102/01, compared to pre-existing variants and its implications for future transmission dynamics and control.