SARS-CoV-2 sequencing service

The Public Health Microbiology team in PHS coordinates a whole-genome sequencing (WGS) service for COVID-19 viral genotyping in Scotland. The service provides WGS capacity within the NHS.

The service is provided by the:

  • Specialist Virology Centre at the Royal Infirmary of Edinburgh
  • West of Scotland Specialist Virology Centre at the Glasgow Royal Infirmary

The service delivers rapid sequencing of SARS-CoV-2 samples and bioinformatic analysis of genome data. This supports the identification of variants and mutants of concern and the detection and investigation of COVID-19 outbreaks and incidents.

We have produced a video explaining what whole-genome sequencing is.

The service is supported by:

  • Antimicrobial Resistance and Healthcare Associated Infection (ARHAI) Scotland
  • NHS Lothian
  • NHS Greater Glasgow and Clyde

It is funded by:

  • NHS National Services Scotland (NSS)
  • Scottish Government

The service was developed in partnership with the COVID-19 Genomics UK (COG-UK) consortium, and its academic partners at the University of Edinburgh and the Medical Research Council (MRC) University of Glasgow Centre for Virus Research (CVR).


EmailĀ for more information and to submit requests forms.

Expanding the service

On 17 March 2021, the Scottish Government published the Testing Strategy Update (external website).

It highlighted the challenges faced in the management of the next stages of the pandemic and explained how an expanded WGS service for Scotland will help address these challenges.

We will be expanding the current capacity for the WGS service in collaboration with the Scottish Specialist Virology Centres and the Medical Research Council (MRC) University of Glasgow Centre for Virus Research (CVR).

This programme of work started in April 2021 and runs into 2022.

WGS will provide essential surveillance data to help us understand:

  • vaccine efficacy
  • virus transmission chains
  • changes in the virus that alter its properties
  • virus spread on a geographical scale
  • effectiveness of infection control measures
  • effectiveness of public health interventions

To ensure we see the most benefit, we anticipate that we will need to continue routine, comprehensive genetic sequencing of SARS-CoV-2 in Scotland.

As well as increasing our capacity for sequencing, we will start using allele-specific PCR tests when necessary to rapidly screen known mutations within a variant of concern. This will help to minimise community spread through:

  • early public health assessment
  • rapid interventions

Find out more about the evolution of viral mutations.

Request additional sequencing

We routinely sequence all suitable samples which test positive for SARS-CoV-2 in NHS Scotland. This does not require an additional request form. Data generated from this contributes to the routine reporting of the service.

However, in some situations, there may be a clinical or public health need to request additional analysis on an individual's sample or group of samples.

To request this, complete the additional analysis request form.

Find out how to complete and submit the request form in the user manual.

Last updated: 07 February 2023
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