Javid’s contact tracing optimism looks misplaced in the fight against Omicron

Sajid Javid told Andrew Marr this morning that it would be possible to quarantine the contacts of those with Omicron, because the new Covid variant comes up negative for the ‘S’ gene in PCR tests (what he called ‘S gene drop out’), unlike Delta.

I had already been told about this helpful characteristic of some PCR tests, which would allow rapid detection of Omicron relative to Delta. But I was also told that just a portion of tests carried out by NHS Test and Trace had the ability to check for the S gene. I made inquiries and the UK Health Security Agency (UKHSA) gave me this statement:

’50 per cent of the Lighthouse laboratory network carrying out Pillar 2 community testing can assess samples for S gene target failure. We routinely monitor these outputs to look for spikes and variance patterns of testing’

So although this characteristic of some PCR tests would help the UKHSA chart Omicron’s growth, it would not achieve just-in-time quarantining of their contacts, because for half of Covid positives, gene sequencing would be required.

There is reason to fear that the UK lacks the infrastructure to detect contacts of those infected with Omicron fast enough to meaningfully slow the spread of a variant thought to be extremely transmissible.