Coronavirus (COVID-19): Real-time tracking of the virus

by Fitcoachion | Last Updated: May 15, 2020


Coloured transmission electron micrograph (TEM) of a SARS-CoV-2 coronavirus particle isolated from a UK case of the disease Covid-19.

One of PHE’s core functions is disease surveillance; making sure we have the right information available to us at the right time to inform decisions and actions across the public health system.

Surveillance involves gathering a wide variety of data about a disease from a range of sources, to provide us with situational awareness.

PHE together with researchers at the University of Cambridge are working to regularly nowcast and forecast COVID-19 infections and deaths. This is real-time tracking of the pandemic, as data accumulate over time, and is an essential component of a public health response to a new outbreak.

The R number

In an epidemic, one of the most important numbers is R – the reproduction number. If this is below one, then on average each infected person will infect fewer than one other person; the number of new infections will fall over time.

The lower the number, the faster the number of new infections will fall. When R is above one, the number of new infections is accelerating; the higher the number the faster the virus spreads through the population.

The data analysis by PHE and the University of Cambridge provides valuable information on R and how it varies from region to region across England.  Currently, the data shows that the R value for England stands at 0.75 but ranges from the lowest value in London to the highest in the North East and Yorkshire.

The difference in R number can be explained by the timing of the initial wave of infection which was very different in each region, for example there is a big contrast between the South West and London. Consequently, there will be some regional variation in R even now while we are in lockdown.  This can be seen in the decrease in the number of daily deaths in every region but with a particularly sharp decline in London.

Regions currently estimated to have the highest value for R (North East, South West, East of England) are those which had the lowest level of activity prior to the lockdown, due to a delayed spread into these regions.

How is R calculated?

The R number is calculated using age-stratified regional transmission models. This work uses data on daily COVID-19 confirmed deaths from PHE (by NHS region and age group) and published information on the risk of dying and the time from infection to death, to reconstruct the number of new COVID-19 infections over time; estimate a measure of ongoing transmission (R); and predict the number of new COVID-19 deaths in different regions and age groups.

This data is updated twice weekly and is shared with Government scientific committees including SAGE and the SAGE sub-group, Scientific Pandemic Influenza sub-group on Modelling (SPI-M), to enable them to form the appropriate actions to control the pandemic.

It is important to note however that the R number is only one component that determines the rate of growth of the epidemic, and does not say anything about the rate of occurrence of new infections, the prevalence of infection across communities and the current burden faced by the healthcare system. It should, therefore, not be used as the sole indicator of the current threat posed by an epidemic.