> To gain insight into the spread of the Omicron variant in our community, we are working with a large number of partners to track S-gene target failures (SGTFs). SGTFs are a feature of the TaqPath PCR assay that fails to detect the spike gene of certain variants of interest due to a deletion in these viruses' spike gene. Most Omicron sequences have this deletion while most Delta sequences do not. As a result, the proportion of SGTF in positive tests can be used to estimate the prevalence of Omicron.
Worse, the key part of the reasoning is problematic: (emphasis mine)
> Assuming, as data has indicated, that Delta cases stayed approximately constant during this time, these numbers correspond to Omicron case numbers growing approximately twenty fold in one week, a doubling time of approximately thirty six hours, sustained over a two week period.
> This is out of touch with what we know about Omicron. Responsible estimates of the growth rates of Omicron in populations with better data (like the UK and Denmark) and prior data on the USA, have suggested doubling times in the range of TWO TO FOUR DAYS. This has caused us (and the real experts) to characterize its rate of growth as “explosive,” and to say in late November and early December that it might attain dominance in the USA in a matter of weeks. And that’s all true. But a doubling time of 36 hours, sustained for over two weeks, is out of step with all the other data. It’s not credible.
Even if 36 hours is a bit lower than most (but not all) measurement, it's not that far of the reality, while the “2 to 4 days” discussed in the article is too optimistic. A few example of doubling times:
San Diego: 1.4 days [1], in the different regions of the UK, the doubling time varies from 1.5 to 2.2 days (median: 1.6 days) [2]. In France, the estimated doubling time varies from 1.6 to 2.2 days.
Excerpt from [2]:
> We are observing doubling time central estimates of less than 2 days for every region except the South West. This may be related to poor PCR gene target reporting coverage in this region.
Oh, and in this sentence, just click on his link (which now includes data from yesterday and completely defeats his argument)
> And this points to another big problem. These numbers don’t comport with the national case numbers and what we know about how variants interact[link to 3]. While huge case surges have been seen in the states in Region 2, which was already 2.4% Omicron in the latest measurements (the week ending December 4), as well as other Omicron-dominant areas like the UK, they haven’t been seen in most states elsewhere in the country. This pattern was also seen as Delta took over from Alpha in the USA this summer, but we’re not seeing it in most of the USA now.
[1]: https://searchcovid.info/dashboards/omicron-estimates/ [2]: https://assets.publishing.service.gov.uk/government/uploads/... page 6. [3]: https://www.google.com/search?q=us+covid+cases