Dr Lisa Levett, Director of Genetics and Molecular Pathology, explains how HSL is preparing for the next phase of the COVID-19 virus.

With the national vaccination programme progressing well, we’re able to draw a collective breath and look beyond the reactive programme of testing.

The reality is that we must be prepared for the inevitable mutation of the virus, and the various impacts that will have.
Any virus has the potential to mutate in a way that can adversely affect assay performance. Mutation may also affect vaccine efficiency and pathogenicity and virulence which may then require changes in clinical and public health decisions.

The current protocol is that SARS-CoV-2 variants, if considered to have concerning epidemiological, immunological or pathogenic properties, are raised for formal investigation.

At this point they are designated Variant Under Investigation (VUI) with a year, month, and number. Following risk assessment with the relevant expert committee, they may be designated Variant of Concern (VOC).

Whilst Whole Genome Sequencing (WGS) affords accurate data on identification and characterisation of new variants, the process is currently time and resource limited.

Rapid genotyping assays are available. These can be deployed at diagnostic laboratories, and facilitate rapid identification of key mutations which can indicate variant identity in the short term, until full WGS characterisation can be used for confirmation.

HSL has been chosen to represent the NHS England laboratories in the London 2 Region to test all postive Covid samples within 24 hours to determine the presence of key variants of concern.

This enables Test and Trace to home in quickly on people who may be positive for such variants to help stop the spread before the full viral genome is sequenced. The variant PCR testing is important to identify known variants and the sequencing is important to find new ones. This testing is also being performed in the surge laboratory on level 9.

Once again, HSL is at the forefront of the national effort to understand and contain this virus.