Hunting variants and how Delta dealt a blow to Alpha

2nd November 2021

The publication today of a new paper in the journal Science demonstrates how genomic sequencing undertaken at the Quadram Institute has helped the country keep track of how SARS-CoV-2 was evolving in the face of the vaccine rollout.

The findings from the Imperial College London-led REACT-1 study, supported by researchers at the Quadram Institute, are based on home swab tests taken by more than 200,000 people between May and July 2021 and show how the Delta variant quickly replaced the Alpha variant.

Behind those numbers are a team of scientists and bioinformaticians at the Quadram Institute who have sequenced all the samples for the REACT-1 study and back in 2020 found themselves working flat out over Christmas and New Year to sequence 2,000 REACT-1 samples.

Today’s paper in Science “Exponential growth, high prevalence of SARS-CoV-2 and vaccine effectiveness associated with Delta variant” shows how in the third wave of infections in England the Delta lineage came to dominate and was driven by infection in younger, unvaccinated people.

The highest prevalence of infection was during June to July 2021 amongst 13 to 24 year olds. The rapid roll-out of the vaccination programme in England has so far limited the number of cases and severity of illness but with more social mixing and more time spent indoors through autumn and winter continued surveillance is still needed and adjustments to vaccines may be needed in future.

Dr Andrew Page said: “We’re proud co-authors in this important, ongoing study which demonstrates just how important it is for children aged 12 and above to get vaccinated to help curb the spread of infection.

“Vaccination makes a big difference but we do still all need to take precautions in our daily lives and we need to keep up our surveillance to track changes in the virus and to ensure vaccines are a match for new variants.”

These findings from the ongoing REal-time Assessment of Community Transmission (REACT-1) programme, carried out in partnership with Ipsos MORI and commissioned by the UK Health Security Agency. Data are continually reported to the government to inform decision-making.

Monitoring COVID-19

REACT (REal-time Assessment of Community Transmission) is a series of studies that are using home testing to improve our understanding of how the COVID-19 pandemic is progressing across England. This major research programme was commissioned by the Department of Health and Social Care (DHSC) and is being carried out by Imperial College London in partnership with Ipsos MORI and Imperial College Healthcare NHS Trust. Here’s the announcement from when the study first launched in April 2020.

The REACT-1 study is tracking current coronavirus infections in the community by testing more than 100,000 randomly selected people each month over roughly a two-week period. The study recruits new people each month to help ensure the sample represents the wider population and offers a high-resolution snapshot of the situation across a particular time period.
This is different from the ONS COVID-19 Infection Survey which runs continuously and samples the same people over time to understand household transmission. Because the studies use different methods, this means that sometimes they report different figures.