UKHSA Sequencing Prioritisation Update

We have received a UK Health Security Agency sequencing prioritisation update and would like to share the information broadly with our members. The letter is reproduced in full below:

To: Pathology Incident Directors | Laboratory Leads | Regional Testing Leads

Dear Colleagues,

Re: UKHSA Sequencing Prioritisation Update

Thank you for continuing to refer samples for the genomic surveillance of new variants in Pillar 1.

In times of low prevalence, Pillar 1 NHS laboratories have been asked to refer all samples as there is the capacity to sequence. However, we are in a time of high prevalence, which means the volume of samples referred by Pillar 1 NHS laboratories may exceed the volume required and those received above this threshold will be not be sequenced.

In this peak period to enable effective surveillance, UKHSA no longer requires Pillar 1 NHS laboratories to refer all samples .

UKHSA is requesting that all Pillar 1 NHS laboratories should refer a minimum of 50% of their eligible positive PCR SARS-CoV-2 samples (i.e Ct<30) to UKHSA for sequencing.

Please continue, as usual, to refer samples daily and avoid batching of samples. This will help to prevent delays, facilitate efficient workflow management in sequencing laboratories and enable real-time reporting of variants in the UK.

Guidance on safe packaging requirements for clinical samples can be found via this gov.uk link.

Our laboratories play an essential role in supporting the surveillance programme for COVID19. We would like to thank you for your ongoing support.

Kind regards

Prof Saheer Gharbia
Co-Director of COVID Genomics, UKHSA

Prof Dame Sue Hill
Co-Director of COVID Genomics, UKHSA