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.

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More from @NathanGrubaugh

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
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
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
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
18 Jan
Brief update on TaqPath N gene target failure (NGTF). We believe that it is caused by a 6nt deletion (positions 28914-28919; N:214/215del) that has emerged independently at least 3 times in the US.

short 🧵

nextstrain.org/community/grub…
The @yalepathology clinical diagnostic lab recently detected 8 NGTFs from a related cluster of cases. We have so far sequenced 2 of these (Yale-S047 & Yale-S048) & they do not cluster with other N:214/215del seqs. Rather looks like it emerged within a local lineage (B.1.1.107).
33 N:214/215del seqs are located in the Pango lineage B.1.3, and have been detected in New York and Maryland.
Read 6 tweets
31 Dec 20
DRAFT protocol for B.1.1.7 screening by PCR. It includes primers/probes for:
- 69/70del
- 144del
- CDC_N1 (+control)

If N1 positive, 69/70del + 144del drop out, likely B.1.1.7

We have not tested this yet, but making it available for others to try.

docs.google.com/document/d/1zo…
Designed by @JosephFauver, @VogelsChantal, and myself in response to some great feedback and DMs from this thread:
Please let us know if you try it, and if you wouldn't mind, share your results. We just ordered the primers and will test next week, but we don't have any B.1.1.7 viruses to test. Will make protocol adjustments as we go, and will post a final version on protocols.io
Read 8 tweets

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