New research shows that a shift towards emerging coronavirus variants drove transmission in England during the Spring.

Imperial’s COVID-19 Response Team say that local transmission of non- B.1.1.7 variants of concern (VOC) increased to more than 20 per cent of cases in London between March and April 2021.  

Since its emergence in Autumn 2020, B.1.1.7, known as the variant first detected in Kent, rapidly became the dominant lineage across England and much of Europe. 

Several other VOCs have been identified globally, such as variants first detected in Brazil, India and South Africa. Some of these VOCs possess mutations that may be able to partially evade immunity from vaccination or natural infection. 

The team say that understanding when, whether, and how these additional VOCs pose a threat in settings where B.1.1.7 is currently dominant is vital.

This is particularly true for England, which has high coverage from vaccines that are likely more protective against B.1.1.7 than some other VOCs.

Latest trends 

In this latest report from Imperial's COVID-19 Response Team, the Department of Mathematics and other collaborators, the researchers examined trends in B.1.1.7’s prevalence in London and other regions in England using passive-case detection PCR data, cross-sectional community infection surveys, genomic surveillance, and wastewater monitoring. 

The researchers monitored sewage water in North London and estimate that mutations uniquely linked with B.1.1.7 were detected in over 95% of cases between early January and the middle of March. By mid-April, this had dropped to between 67% and 75%.  

Meanwhile, the frequency of the E484K mutation which is absent in the B.1.1.7 variant but present in many other variants of concern or interest, such as the variant first detected in South Africa, increased to over 30% of cases. 

Sequencing of cases detected through community testing across Greater London show that more than 20% of cases were from non-B.1.1.7 strains by mid-April. However, the fraction is smaller in cases not known to be associated with travel or surge testing. 

Dr Seth Flaxman, from the Department of Mathematics, said: "The recent fast growth of the variant of concern B.1.617.2, which first emerged in India, did not come out of the blue. We observed a consistent signal in London throughout March and April from independent data sources pointing towards growth in a number of diverse variants of interest. This is particularly concerning as it occurred during a period in which cases of B.1.1.7, the variant that arose in Kent, were falling."

Dr Samir Bhatt, from the School of Public Health, said: "The present situation is incredibly complex, and there is no clear answer to fully explain these trends. We recommend caution moving forwards." 

The work is presented in Report 44 from the WHO Collaborating Centre for Infectious Disease Modelling within the MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London. 

Download Report 44 here