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25 Mar, 5 tweets, 4 min read
3/25 Connecticut #SARSCoV2 variant surveillance report
@CovidCT | @jacksonlab | @CTDPH | @YaleSPH

- B.1.1.7 continues to 📈
- B.1.526 continues to 📈
- First detection of B.1.1.7 + E484K ⚡️ in CT.

Short 🧵 | Report 👇
covidtrackerct.com/variant-survei…
2/5 TaqPath SGTF data from YNHH (mostly New Haven County) and JAX (New Haven, Hartford, and some other counties) shows that the frequency of B.1.1.7 keeps 📈. Thankfully, the B.1.1.7 cases and total cases are still way down. Lets work to keep it that way.
3/5 We detected a B.1.1.7 sequence with the E484K mutation from a sample collected from New Haven County (CT). The genome is very closely related to others sequenced in CT so its likely acquired this mutation independently. This is potentially concerning for vaccines.
4/5 ~20% of all SARS-CoV-2 genomes sequenced from CT last week (n=176) had the E484K mutation on 7 different lineages. Hence it is imperative that we keep improving our sequencing capacity. The graph below shows our progress, and we expect to cross the 5% threshold very soon.
5/5 I always give credit to our team in these threads - this time I want to specifically thank @ChaneyKalinich for putting a huge amount of work this week to improve our website reports. We'll have some new features to explore the data next week💪

grubaughlab.com/team/chaney-ka…

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More from @NathanGrubaugh

Nathan Grubaugh Profile picture
18 Mar
New (3/18) Connecticut #SARSCoV2 variant surveillance report @CovidCT | @jacksonlab | @CTDPH | @YaleSPH

- First case of P.1 (first detected in Brazil) in CT
- B.1.1.7 continues to 📈
- B.1.526 📈
- B.1.427/9 added to the VOC list

Short 🧵 | Report 👇
covidtrackerct.com/variant-survei…
2/3 TaqPath SGTF data from YNHH (mostly New Haven County) and JAX (New Haven, Hartford, and some other counties) shows that probable B.1.1.7 cases keep 📈 as non-B.1.1.7 cases slowly 📉.

B.1.1.7 is now ~35% of the total cases (~40% from YNHH and ~26% from JAX).
3/3 (YNHH TaqPath data only)

Our earlier projections of B.1.1.7 frequency growth are still pretty close. We expect the YNHH B.1.1.7 numbers to cross 50% this week, and the combined (YNHH and JAX) to cross 50% next week.
Read 4 tweets
Nathan Grubaugh Profile picture
4 Mar
1/3 New Connecticut #SARSCoV2 variant surveillance report - @CovidCT

B.1.1.7 is rising rapidly, now close to 25% of positives in the New Haven area (based on SGTF results, purple). I'm worried that a rebound in cases will follow.

report here 👇
covidtrackerct.com/connecticut-sa…
2/3 Most of the *confirmed* B.1.1.7 cases have been found in New Haven County because that is were we do most of our sequencing (primary catchment area of Yale diagnostic labs). We are working to increase sequencing from across the state.
3/3 In addition to the variants of concern - B.1.1.7 and B.1.351 - we've detected several *variants of interest*.

B.1.429, first reported in CA, may be increasing in frequency.

B.1.525 and B.1.526 (first reported from NY) are of interest because they have the E484K mutation.
Read 4 tweets
Nathan Grubaugh Profile picture
25 Feb
1/n Weekly #SARSCoV2 variant report from Connecticut - data from @YaleSPH, @jacksonlab, and @CTDPH.

- B.1.1.7 = 63 cases
- B.1.351 = 1 case
- P.1 = 0 cases

B.1.1.7 cases by county 👇. Most in New Haven due to surveillance biases.

Report:
covidtrackerct.com/variant-survei…
2/n
 Temporal distribution of B.1.1.7 cases doesn't accurately reflect the growth of B.1.1.7 in CT as the sequence reporting is still lagging. Next week we'll have temporal est of frequency based on SGTF. B.1.1.7 is currently associated with 5-10% of the COVID-19 cases in CT.
3/n Phylogenetics of B.1.1.7 cases show many different clusters, some associated with NY.
Read 7 tweets
Nathan Grubaugh Profile picture
17 Feb
New SARS-CoV-2 variant update for Connecticut.
- 42 cases of B.1.1.7
- 1 case of B.1.351
- 5 cases of B.1.525 (not of concern yet, but we are monitoring)

Partnership with @jacksonlab, @CTDPH, and diagnostic labs

Follow the 🧵(1/10)

Or read the report 👇
covidtrackerct.com/variant-survei…
2/10
B.1.1.7 cases in Connecticut by county.
- New Haven County: 33
- Fairfield County: 3
- Litchfield County: 3
- Hartford County: 2
- Windham County: 1

We do most of our surveillance from New Haven County, hence the higher numbers. We'll have a map next week.
3/10
B.1.1.7 cases in Connecticut are on the rise, but we don't yet know its frequency in the community. Its likely still <3% based on the PCR data.
Read 11 tweets
Nathan Grubaugh Profile picture
27 Jan
🧬Latest #SARSCoV2 B.1.1.7 update from Connecticut.
- 9 B.1.1.7 cases detected in CT
- Most travel related
- We sequenced 28 SGTF samples from CT, 5 (18%) are B.1.1.7.

1/4, short 🧵

covidtrackerct.com/variant-survei…
2/4
 We sequenced 5 B117 cases in CT all (all in New Haven County, where we do most of our surveillance). The other four have been reported by The Jackson Labs (3, sequences not yet available) and Quest Diagnostics (1). They represent at least 4 seperate introductions.
3/4
 We also sequenced 39 SGTF samples from out of state: FL, TX, TN, AZ, NJ, MA, NY, and IL. Combined with 28 form CT:
- 20 (30%) are B.1.1.7
- 40 (60%) are B.1.375
- 7 (10%) are other lineages

We'll break these down by date/location as we collect more data.
Read 4 tweets
Nathan Grubaugh Profile picture
25 Jan
⚡️Our multiplex PCR assay has been updated to detect #SARSCOV2 variants B.1.1.7, B.1.351, and P.1 by targeting 2 deletions:
-ORF1a 3575-3677
-spike 69-70.

Preprint submission later today, short 🧵 for now 1/n

Detailed protocol: protocols.io/view/multiplex…
2/n This protocol is an update from our developmental versions that we previously posted on twitter and virological.

3/n Adding the ORF1a 3675-3677 deletion was key, and s/o to @richardneher for the tip.

Read 14 tweets

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