Imperial COVID-19 Response Team share new tool to assess threat of new variants

Imperial’s COVID-19 Response Team have developed a new tool to assess the threat of new variants in real-time.

The MV-EpiEstim tool (MV: multivariant) can be used to estimate the transmission advantage of new coronavirus variants.

"We have designed a freely available, generic, and fast tool to estimate the transmission advantage of new variants in real-time. I hope it will be widely adopted by public health bodies around the world." Dr Anne Cori Imperial College Covid-19 Response Team

The team say that the method can be a useful tool for surveillance programmes around the world that are monitoring the spread of B.1.1.529, now classified by WHO as  Omicron, and other variants that may emerge.

The tool, that was developed with the University of Sussex, is designed to estimate in real-time the effective transmission advantage of a new variant compared to a reference variant. This can be used as an important first step towards quantifying the threat of new variants.

The method, published in Report 47, can combine information across multiple locations and over time, and was validated using extensive simulations, designed to mimic a variety of real-time epidemic contexts.

The team also used the tool to retrospectively analyse the Alpha variant and found that it is 1.46 and 1.29 times more transmissible than the wild type, using data from England and France respectively. The team explain that their tool could have estimated the effective transmission advantage of the Alpha variant a few weeks before the earliest published estimate.

They also found that the Beta and Gamma variants combined are 1.25 times more transmissible than the wildtype, using data from France.

All the results were in line with previous scientific estimates but could have been obtained earlier and more easily with the open-source tool.

The tool only requires routinely collected disease surveillance data, making it easy for national surveillance programmes to use in real-time. The method could also be used to monitor other pathogens with multiple co-circulating strains such as influenza or streptococcus pneumoniae.

Detected numbers of Omicron cases outside of South Africa are currently too low to assess the transmissibility of the new variant of concern using the tool. However, data emerging from South Africa could likely be used with MV-EpiEstim to rapidly characterise the transmissibility of Omicron compared to Delta.

Rapid estimates of new variants

Dr Anne Cori said: ”Being able to rapidly estimate the transmissibility of new SARS-CoV-2 variants, including B.1.1.529 now known as Omicron, is critical for a timely response. We have designed a freely available, generic, and fast tool to estimate the transmission advantage of new variants in real-time.

"It requires simple inputs, has been extensively tested and is implemented in the popular EpiEstim R package. I hope it will be widely adopted by public health bodies around the world and will contribute to the rapid characterisation of novel variants.”

Dr Sangeeta Bhatia said: “We have developed a fast and generic tool that can easily be used to estimate the effective transmission advantage of new SARS-CoV-2 variants. Our tool only requires variant-specific incidence data. In the continuously changing landscape, our tool provides a fast and easy way to monitor the risk posed by new variants.”