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24 Nov, 4 tweets, 3 min read
🧬 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
I wish everyone a wonderful start to the holiday season, and I hope that you are able to enjoy time with your family and friends. Please remember to celebrate safely. (4/4)

yalemedicine.org/news/covid-19-…

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More from @NathanGrubaugh

Nathan Grubaugh Profile picture
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) Image
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
Nathan Grubaugh Profile picture
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
Nathan Grubaugh Profile picture
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
Nathan Grubaugh Profile picture
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
Nathan Grubaugh Profile picture
2 Sep
🧬 9/2 Connecticut #SARSCoV2 variant surveillance
@CovidCT | @jacksonlab | @CTDPH | @YaleSPH | @Yalemed

Delta - 99.6% (530 sequenced)
Gamma - 0.4% (2 sequenced)
Mu - 0%
All others - 0%

short 🧵 | Report 👉
covidtrackerct.com/variant-survei…
Delta is split up into 25 sub-lineages - mostly for tracking purposes. These are the top in CT, along with their defining mutations.

B.1.617.2 - 57%
AY.25 - 18% - synonymous mutation
AY.12 - 10% - Spike T791I
AY.3 - 8% - Orf1ab I3731V

Please read on...
(2/8)
Delta sub-lineage AY.12, with the Spike T791I mutation, has received some attention because its 60-80% in Israel, but its not currently increasing globally. Its been mostly hovering between 4-6% since mid-June.

Fig from @DiseaseOutbreak
tinyurl.com/3xvnhvyh
(3/8)
Read 8 tweets
Nathan Grubaugh Profile picture
19 Aug
🧬8/19 Connecticut #SARSCoV2 variant surveillance
@CovidCT | @jacksonlab | @CTDPH | @YaleSPH | @YaleMed

Delta - 96% (📈1%)
B.1.621 - 2.5% (📉1%)
Alpha - 0.8% (📈0.8%)
All others - 0.6%

*0⃣ sequenced other VOC cases this week*

short 🧵 | Report 👉
covidtrackerct.com/variant-survei…
Delta was recently split into several sublineages to help investigate clusters and spread. Here are their frequencies in CT:

B.1.617.2 - 46-56%
AY.4 - 14-28%
AY.12 - 11-14%
AY.3 - 5-8%
AY.6 - 4-6%
AY.3.1 - 1%
AY.10 - <1%

These are all Delta (not 'Delta-plus', just Delta) (2/7) Image
There are lots of people seeing these sublineage data👆 and speculatively wildly about some being more transmissible/dangerous.

**The lineages were assigned based on epidemiology**

Please read this thread before falling victim to speculation. (3/7)

Read 7 tweets

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