🧬 12/2 Connecticut #SARSCoV2 variant surveillance @CovidCT | @jacksonlab | @CTDPH | @YaleSPH | @Yalemed

👑Delta - 100% (614/614)

📊Top lineages
25% - AY.103
19% = AY.44
14% = AY.25
6% = AY.3
6% = AY.119

0⃣ Omicron or Delta AY.4.2

short 🧵 | Report 👉
covidtrackerct.com/variant-survei…
It's all Delta so far in Connecticut, with no signs (yet) of Omicron via sequencing or PCR signatures (i.e. S-gene target failures). (2/6)
Here is a nice explainer about S-gene target failures, or SGTFs.

As we did for Alpha in early 2021, we'll start to report these trends on our website once we have a confirmed Omicron case. (3/6)

For those looking for an Omicron explainer, look no further than @K_G_Andersen's (and nice to have him back on twitter!) (4/6)

For those looking for a Omicron screening tool, I describe our VOC PCR assay here. A link to the protocol is at the end. (5/6)

This week I'd like to check in on the @OhioStateFB team, hoping that they are doing ok. They had a pretty rough time in The Game last weekend. Lucky for them that they have an open weekend coming up to heal 🙏. (6/6)

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More from @NathanGrubaugh

27 Nov
🧵 Brief update on impact of #Omicron on the CDC #SARSCov2 primers/probes that are commonly used in PCR assays in the US and abroad (1/6)
(2/6) The CDC N1 probe mismatch in Omicron is a C28311T mutation. Of the 91 B.1.1.529 sequences on GISAID:
- 48 have a T (mismatch)
- 19 have a C (exact match)
- 26 have no coverage (NNNs)
(3/6) All of the Omicron sequences with a C at 28,311 (exact match to N1 probe) are from the CERI-KRISP group, so maybe @Tuliodna can provide some info if these are potentially a sequencing artifact (which we've seen with Delta) or if this site is variable within the lineage
Read 6 tweets
26 Nov
B.1.1.529 PCR detection 🧵

Like Alpha (B.1.1.7), B.1.1.529 has the spike 69-70 deletion that causes a S-gene target failure (SGTF) when using the ThermoFisher TaqPath COVID-19 assay. Because most other variants didn't have the deletion, this was helpful for tracking Alpha (1/8)
Likewise, reporting SGTFs will be extremely helpful again for tracking the spread & growth of B.1.1.529, like the amazing folks in South Africa are already demonstrating (2/8)

While the ThermoFisher TaqPath COVID-19 assay is very common, not everyone is using it; and while sequencing is required to confirm B.1.1.529 cases, slow turn-around times can delay its tracking. Here is where other PCR screening assays can be helpful (3/8)
Read 8 tweets
24 Nov
🧬 11/24 Connecticut #SARSCoV2 variant surveillance
@CovidCT | @jacksonlab | @CTDPH | @YaleSPH | @YaleMed

👑Delta - 100% (638/638)

📊Top lineages
24% - AY.103
22% = AY.25
14% = AY.44
9% = B.1.617.2
6% = AY.3

short 🧵 | Report 👉
covidtrackerct.com/variant-survei…
The Delta sublineage leaderboard remained virtually unchanged this week (boring is good), though things could get very interesting through the holidays. (2/4) Image
Unfortunately, we are going into the holidays with transmission and infections estimated to be rising in Connecticut (and across the US). (3/4)

covidestim.org/us/CT Image
Read 4 tweets
28 Oct
🧬10/28 Connecticut #SARSCoV2 variant surveillance
@CovidCT | @jacksonlab | @CTDPH | @YaleSPH | @Yalemed

👑Delta - 100% (408/408)

📊Top lineages
55% = B.1.617.2
19% = AY.25
9% = AY.3
5% = AY.20
3% = AY.39
3% = AY.24
2% = AY.26

short 🧵 | Report 👉
covidtrackerct.com/variant-survei…
Much of the discussion is still about AY.4.2, which is still slowly 📈 in the UK, which they have designated as a 'variant under investigation' (VUI). (2/6)

The early estimates are that AY.4.2 is ~15% more transmissible, which you can learn more about in this great 🧵. (3/6)

Read 7 tweets
21 Oct
🧬10/21 Connecticut #SARSCoV2 variant surveillance
@CovidCT | @jacksonlab | @CTDPH | @YaleSPH | @Yalemed

👑Delta - 99.7% (336/337)

📊Top lineages
39% = B.1.617.2
22% = AY.25
13% = AY.39
7% = AY.3
4% = AY.4 (not UK AY.4.2)
4% = AY.20

short 🧵 | Report 👉
covidtrackerct.com/variant-survei…
Effective reproductive number (Rt) estimates for the top Delta lineages in Connecticut.

➡️All are now <1, suggesting that transmission is 📉.

➡️The relative similar Rt values suggest that they are of similar transmissibility. (2/12)
Last week we reported AY.4 was ~27%, and this week its 4%. The sudden 📉 is not due to more refined classifications. Its hard to distinguish between closely related sequences, and a dropout in some Delta spike sequences makes it even harder. (3/12)

Read 13 tweets
16 Sep
🧬 9/16 Connecticut #SARSCoV2 variant surveillance
@CovidCT | @jacksonlab | @CTDPH | @YaleSPH | @Yalemed

👑Delta - 99.6% (480 sequenced)
Mu - 0.2% (1 sequenced)
Non-VOI/C - 0.2% (1 sequenced, B.1.517)

Delta >99% in last 4 reports

short 🧵 | Report 👉
covidtrackerct.com/variant-survei…
Connecticut Delta sublineage frequencies for the week of 9/6 (weekly % change over previous 3 weeks)

B.1.617.2 - 44% (📉7%, 📉1%, 📉4%)
AY.25 - 23% (📈3%, 0%, 📈2%)
AY.3 - 11% (📈2%, 📈1%, 📉1%)
AY.12 - 10% (📉1%, 📈2%, 📈2%)
All others - 11% combined

(2/6)
B.1.617.2 is decreasing primarily because these sequences are being classified as other sublineages. Otherwise, the Delta AY sublineage frequencies are remaining very stable and there is currently *no evidence that any are more transmissible* in Connecticut. (3/6)
Read 6 tweets

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