“In the five years since COVID-19 was declared a pandemic, we’ve learnt a lot – not just about the virus that causes COVID-19 (SARS-CoV-2) but also how to track the spread and evolution of microbes that cause disease on a large scale.

Genomic surveillance emerged as a powerful tool in pandemic response, which looks at the genetic material of the virus to track how it changes over time. During the COVID-19 pandemic, genetic material from SARS-CoV-2 came from PCR tests. These tests detect and amplify the genetic material of the virus in a lab setting. These differed from lateral flow tests, which just detected the virus, giving a positive or negative result.

In the UK, this was led by the COVID-19 Genomics UK Consortium (COG-UK) which included scientists at the Quadram Institute. Read more about our involvement with COG-UK here.

While SARS-CoV-2 no longer has pandemic status, it hasn’t disappeared, and the knowledge we’ve gained since the start of the pandemic is valuable in helping us respond to the next one. The huge amounts of genomic data collected during the pandemic tracks the virus from its emergence in the UK and throughout the pandemic. This allows us to look back and understand the virus, alongside helping us prepare for the next one.

Identifying variants of concern in Norfolk

We analysed nearly 30,000 SARS-CoV-2 genomes which represented roughly 10% of regionally recorded COVID-19 cases in Norfolk. SARS-CoV-2 was highly diverse in Norfolk, with 401 different lineages, which are closely related versions of the virus, detected throughout the pandemic. However, only few of these lineages significantly impacted public health in Norfolk with only 34 lineages present in over 100 cases each.

We observed three main variants of concern (VOC) in Norfolk – Alpha, Delta & Omicron. VOCs are made up of a single, or group of lineages which had advantages over earlier versions of the virus, for example by spreading or getting around our immune systems more easily, caused by different mutations. These variants of concern were named by the World Health Organisation throughout the pandemic.

Four epidemic waves in Norfolk

There were four epidemic waves in Norfolk, three of which were caused by VOCs. When a new VOC appeared and became widespread, it took over from the previous variant which then disappeared from circulation.

The four waves were as follows:

1. The first wave (March to December 2020) was caused by early viral lineages, before major VOCs emerged
2. The second wave was driven by the Alpha variant (December 2020 to May 2021)
3. The third wave as caused by the Delta variant (May to December 2021)
4. The fourth wave was driven by the Omicron variant (December 2021 to December 2022)

How Norfolk compared to the rest of the UK

The patterns in VOCs and epidemic waves observed in Norfolk mostly matched the national picture but there were some timing differences in epidemic waves. The Alpha and Delta waves started roughly two weeks later in Norfolk compared to the UK overall, with the Omicron wave starting in the same week as national estimates.

We also compared our findings to Hertfordshire, a centrally located county with different demographics to Norfolk – including a higher population density, a lower average age and closer links to Greater London. These demographics may indicate different behaviour within the population – for example, a larger proportion of working age individuals commuting into Greater London, increasing the chances of transmission of the virus between these areas. We observed epidemic waves in Hertfordshire beginning up to three weeks before those in Norfolk, likely due to this different populational behaviour impacting how the virus moved throughout the county.

Using the past to prepare for the future

A large amount of the research that took place during the pandemic focused on national trends or analyses of outbreaks. Our local level study gives a more detailed view of a pandemic virus in a specific area, ensuring we don’t lose important local detail.

Our research shows the power of using genomics in real time surveillance in pandemic response and preparedness. Particularly it shows the need for flexible, locally tailored approaches to outbreak management as the national picture doesn’t always reflect what is happening in your own area.”

• Read more about the research in Eleanor’s paper published in Microbial Genomics

This work was undertaken as part of Eleanor Hayles’ PhD supported by the Microbes, Microbiomes and Bioinformatics Doctoral Training Partnership (MMB DTP) and the Medical Research Council [grant number MR/W002604/1].