SARS-CoV-2 upscaling of sequencing capacity


The Scottish Government (SG) Testing Strategy Update (external website) published on 17 March 2021 highlights the critical challenges faced in the management of the next stages of the pandemic and the role that an expanded Whole Genome Sequencing (WGS) service for Scotland will play in addressing these challenges.

PHS, in collaboration with the Scottish Specialist Virology Centres and the MRC University of Glasgow Centre for Virus Research (CVR), is working to expand the current capacity for the WGS service in Scotland, in a programme of work running from April 2021 date to 2022.

Comprehensive and timely Whole Genome Sequencing (WGS) as part of an effective end-to-end service integrated with epidemiological data is the only way to comprehensively identify the appearance of SARS-CoV-2 variants and mutations (VAM). In addition, WGS will provide essential surveillance data which will be used to aid understanding of vaccine efficacy, virus transmission chains, virus spread on a geographical scale and determine utility of infection control and public health interventions as control measures. To ensure maximum benefit it is envisaged that comprehensive genetic characterisation of SARS-CoV-2 in Scotland will be necessary on a routine basis.

In addition to the increase in sequencing capacity, the instigation of allele specific PCR tests will be used for rapid screening of known mutations within a variant of concern.  This will facilitate early public health assessment and rapid interventions to minimise community spread.

Supporting information

The supporting information document provides background information of the evolution of viral mutations and the role of sequencing and allele-specific PCR (ASP) for the rapid identification of Variants of Concern (VOC) and Variants Under Investigation (VUI).


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