Throughout the coronavirus pandemic considerable effort has been spent on monitoring, surveying, and responding to the spread of SARS-CoV-2, the virus that causes COVID-19 disease, within Scotland. In November 2020, Public Health Scotland (PHS), in association with the COVID-19 Genomics UK (COG-UK) Consortium, launched a SARS-CoV-2 Sequencing Service to inform the pandemic response in Scotland. This laboratory service has been integral in monitoring and tracking the virus, especially with the emergence of different variants, such as Delta.  The Delta variant was first seen in India in late 2020 and was named a variant of concern in the UK in July 2021.

Whole genome sequencing technology is used to characterize the genetic material of a virus. As part of our role in supporting the pandemic response, we then analyse any changes detected to inform policy around infection prevention and control measures. For example, these data can help to assess how effective vaccines are and supporting the detection and investigation of outbreaks.

What are variants and mutations?

Like all other viruses, SARS-CoV-2 mutates and evolves over time. A virus can mutate in different directions, leading to different variants or lineages of the same virus. Like branches on a tree, these variants all look slightly different while sharing the same trunk. To take the analogy further, any twigs that grow from the branches are like sub-lineages, and will have all the same characteristics of the original lineage, but might have one or two distinct mutations.

As the genetic materials of a virus changes it can give certain strains of the virus advantages over other strains such as making it more infectious or may cause higher rates of severe illness. With the Delta variant we saw that the changes lead to people becoming more infectious more quickly after being exposed to the virus, spreading the virus further, and leading to larger and more frequent outbreaks.

Variants of concern are prioritised for research and monitoring, to understand how they spread and change within the population. They can, and have, developed both within and outside the UK. Using whole genome sequencing, current and potential variants of concern can be monitored as they spread, to allow for a quicker response.

Delta and other common variants of concern in Scotland

In Scotland, there have been several concerning variants– you have probably heard of Alpha and Delta, and possibly Beta and Gamma variants. These images show how the different variants of concern (external website) have changed over time in Scotland. Currently, almost all cases of COVID-19 in Scotland are caused by Delta.

Image caption Number of sequences over time by lineage within Scotland, February – September 2021. Credit: David Robertson, MRC University of Glasgow Centre for Virus Research (adapted from original figure).
Number of sequences over time by lineage within Scotland, February – September 2021.
Image caption Number of cases by lineage in Scotland over time. Credit: Real Time Epidemiology Cell, Public Health Scotland. NB: VUI stands for variant under investigation, which is the step before variant of concern.
Number of cases by lineage in Scotland over time.

The Delta variant has several mutations, some of which make it more infectious, but others can cause more severe illness. While the majority of cases of COVID-19 in Scotland are caused by the Delta variant, there will be different minor mutations or some sub-lineages. For this reason, it’s important to monitor these mutations closely so that any growth or changes can be identified quickly. One of the Delta variant sub-lineages is called AY and for example, AY.4.2 has recently been associated with an increase in cases.

Why do we keep sequencing if most cases are Delta?

As we’ve seen, understanding how the SARS-CoV-2 virus is evolving and spreading has important implications for decision-makers who can use whole genome sequencing data to inform policy around public health mitigations and the roll out of vaccinations.

The plans to grow Scotland’s SARS-CoV-2 Sequencing Service, coordinated by PHS, will increase our capacity to identify, monitor, and respond to, developments within the COVID-19 pandemic. Improving capacity to provide and analyse whole genome sequencing data is also important in the long-term, as it can be applied to other bacteria or viruses, such as flu.  This service strengthens the public health capacity to manage outbreaks at both national and local levels and is a key component to the world-class health system we’re all working to deliver for people in Scotland.

Find out more about whole genome sequencing

Last updated: 06 October 2022