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.
4/10
We have evidence for multiple introductions of B.1.1.7 into CT (left figure), and evidence for community transmission (right figure, identical genomes).
(figures are blurry, so you can look for yourself)

nextstrain.org/community/grub…
5/10
The first case of B.1.351 in CT was announced yesterday (detected in NY, CT resident). Its unrelated to the other B.1.351 sequences from MD and SC.

USA/NY-UL-NP5080/2021
nextstrain.org/community/grub…
6/10
P.1 has not yet been detected in Connecticut, though it is possible that it has been introduced and is circulating.
7/10
B.1.525 is a new variant that we are monitoring. It has several key mutations: E484K, Q677H, F888L and a similar suite of deletions to B.1.1.7. We've detected 5 cases with this variant in CT. We don't yet know its impact on vaccines.

nextstrain.org/community/grub…
8/10
We are also monitoring a lineage of viruses that have a 501T mutation. These are found throughout CT. Significance is unknown.
9/10
Led by @tdalpert, we recently posted a preprint describing the establishment of B.1.1.7 across the US and the urgent need to enhance surveillance.

Read 👇
medrxiv.org/content/10.110…
10/10
Our variant reports will be updated once a week on Tuesdays. Huge thanks to our team that unselfishly keeps this going, every week. @JosephFauver, @tdalpert, @MaryPetrone10, @VogelsChantal, Mallery Breban, @aewatkins6, @AndersonBrito_, @ChaneyKalinich, @RebeccaEarnest1

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More from @NathanGrubaugh

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
18 Aug 20
1/n An overdue thread on #SalivaDirect...

No doubt many of you heard of it, either on this platform, or on the news. It generated a lot of buzz in the media, and not all of it is true. Lets walk through these, and how to get it set up in your lab.

covidtrackerct.com/about-salivadi…
2/n We apologize for the delay in getting information out on this. The FDA issued our EUA on a Saturday, and a media onslaught came before we could get ahead of it. This received much more attention than we ever imagined! We are working through our hundreds of emails...
3/n: Our mission is to remove capitalism from surveillance. We want to make available cheaper tests, and we believe that companies shouldn't overly profit from this. That is why we offer our protocol for free, and we are working with labs to implement cost and time saving steps.
Read 20 tweets
14 Jul 20
Now that our SalivaDirect FDA EUA application for #SARS_CoV_2 diagnostics has been submitted, here is a sneak-peak at our validation results. medRxiv pre-print is forthcoming, but twitter is faster 😉

Overview: saliva w/o special tubes > no RNA extraction > dualplex PCR

1/n
2/n
About SalivaDirect ➡️ covidtrackerct.com/about-salivadi…

Papers & Protocols ➡️ covidtrackerct.com/saliva-related…

SalivaDirect Results ➡️ covidtrackerct.com/salivadirect-r…

NBA validation study "Swish" ➡️ covidtrackerct.com/swish/
3/n
We validated SalivaDirect with multiple reagents & platforms to:
-make it available to more labs
-avoid specific supply chain bottlenecks
-keep costs down.

We'll provide specific information on how to conduct bridging studies to validate additional reagents/equipement
Read 10 tweets

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