Thread by @TTBikeFit

How are they flagging tests + for Omicron? S-gene deletion. Meaning a PCR test that tests for 3 genes (S=spike protein, N=nucleocapsid protein, ORF1ab=accessory proteins) shows a positive result for only ORF and N.

But I found some ONS data, and I have questions 🤔
🧵

My initial question was, how common were S-gene deletion positive tests BEFORE Omicron?

If they were common, are they subtracting this base rate from the new rate of supposed Omicron positives?

And if they were common, how are we certain that Omicron "started" in mid Nov?

Here is the answer to question number 1: S gene deletion PCR tests were running 0-33% of all tests pre-Omicron. 🤔

Note that in the discussion of the data they state that those S-gene deletion positive tests are NOT Omicron pre Nov 15 - that they suddenly became a reliable indicator of Omicron starting w Nov 18 data. Ummm, unless all samples are sequenced (they aren't) how can they say this?

If we just look at England where the numbers are larger and smoother, they were tracking at a solid 10% of tests w S-gene deletion before Omicron. Now they are up to 35%.

Seems to me they either need to subtract prior baseline rates of S-gene deletion positive tests (dropping current percentages of Omicron significantly), or admit that Omicron has been here for a while.

I have questions.

Data: ons.gov.uk/peoplepopulati…