Thread by @NathanGrubaugh

12/14 Yale SGTF update

We can now track daily TaqPath tests from Yale New Haven Hospital, and of the pos tests with ORF target < 30 CT, report the fraction likely Omicron (SGTF) and Delta (non-SGTF).

From tests on Dec 13, *23/214 (9.7%)* had a SGTF
Explanation & caveats in 🧵

Our data represent a fraction of the samples tested by YNHH, and the catchment is primarily New Haven and Fairfield Counties. So they don’t represent all of Connecticut. I’ve heard from others tracking SGTFs elsewhere in the state that they are not seeing a high % yet. (2/11)

Not all non-SGTFs are Delta and not all SGTFs are Omicron (see BA.2). But of the 184 sequences on GISAID from the US collected after 11/25 with the spike 69/70 del that causes SGTF:

163 (89%) = Omicron (BA.1)
15 (8%) = Delta (most AY.44 & AY.103)
6 (3%) = B.1.637

(3/11)

We haven’t sequenced all of our SGTFs, but so far they’ve all turned out to be Omicron. Some probably wont be though.

Also, our daily denominators (100-200 +samples w/ CTs <30) are fairly small and individual data points can be noisy.
(4/11)

I expect that Omicron frequencies are very different by location, and what we are seeing in parts of Connecticut is probably behind the growth in NYC and other big cities, but probably ahead of many other parts of the country not as connected to major travel/urban hubs. (5/11)

Interestingly, our trends are similar to what @pavitrarc reported from @UWVirology - <1% through early December then a rapid increase starting around Dec 6th. (6/11)

https://twitter.com/pavitrarc/status/1470447735585214464

The rapid rise in Omicron that we are seeing here should not be surprising considering what we saw in South Africa. (7/11)

outbreak.info/location-repor…

And the trends that we are seeing with the YNHH Connecticut data are similar to the SGTF % from Denmark. It looks like we are about 1 week behind their rates, which seems about right. (8/11)

https://twitter.com/MadsAlbertsen85/status/1470766064539783191?s=20

Keeping the caveats above in mind, I expect SGTFs (mostly Omicron) from the YNHH testing catchment area (mostly New Haven & Fairfield Counties, CT) to surpass 50% within 1-2 weeks.

That’s *if* the current growth rate at 0.26/day (0.1-0.3) remains the same. (9/11)

The rapid doubling time of ~3.8 days estimated from the YNHH SGTF data above is consistent with early estimates from Europe, but this may decrease as explained by @richardneher. (10/11)

https://twitter.com/richardneher/status/1470484564942462997

I am hoping that by presenting these early findings that individuals and public health agencies will start to take more precautions. Lets not put more stress on our already over-stressed healthcare system when this should be a time to enjoy our friends and family. (11/11)