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18 Jan, 6 tweets, 3 min read
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.
23 N:214/215del seqs are located in a yet-to-be assigned B.1 Pango lineage (bat-signaling @AineToole) sequenced from Florida.
N:214/215del doesn't effect the CDC N1 (left) and N2 (right) primers/probes.
We don't know of any phenotypic effects of N:214/215del, but given its impact on the TaqPath - @thermofisher (@ThermoFisherPR) and users of this assay should be aware.

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More from @NathanGrubaugh

Nathan Grubaugh Profile picture
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
Nathan Grubaugh Profile picture
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
Nathan Grubaugh Profile picture
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
Nathan Grubaugh Profile picture
24 Jun 20
In collaboration with @jordan_peccia + @DougBrackney, we are posting regular SARS-CoV-2 surveillance updates on our website. We were a little concerned by a spike late last week, but new data show that was an anomaly. 1/n

covidtrackerct.com/wastewater-cur…
2/n As opposed to testing wastewater, @jordan_peccia's team collects sewage sludge, which is concentrated. This allows us to detect SARS-CoV-2 above the PCR detection limits and track daily trends.

For more info 👇
covidtrackerct.com/why-wastewater/
3/n Importantly, we found that surveillance from sewage sludge is an early indicator for SARS-CoV-2 transmission, so we watch these trends closely. This is highlighted in our preprint led by @jordan_peccia + @SaadOmer3

medrxiv.org/content/10.110…
Read 5 tweets
Nathan Grubaugh Profile picture
22 Jun 20
Excited to announce our new study to develop and validate an inexpensive and sensitive saliva-based method for #SARS_CoV_2 testing in partnership with the @NBA.

Will be led by @awyllie13, @hmkyale, & myself from the @YaleSPH side.

usatoday.com/story/sports/n…
We'll be using our new #SalivaDirect protocol developed by @VogelsChantal + @DougBrackney. We'll have sensitivity data and a study design overview available on our website soon.

protocols.io/view/salivadir…
Our study has 2 aims:

On the lab side, we are preparing #SalivaDirect for FDA EUA, and are validating with many different vendor reagents to drive down costs and not add supply chain bottlenecks. We are not seeking to commercialize any aspect. Our goal is to get this to $1/test
Read 9 tweets
Nathan Grubaugh Profile picture
8 May 20
I was misquoted in the NYT for having said that "infections spreading from New York account for 60 to 65 percent of the cases across the country."

I DID NOT SAY THAT

It's now causing these spinoff stories with this in the headlines.

businessinsider.com/travel-from-ne…
The interview was initially about my teams work finding that our sequenced #SARSCoV2 genomes from Connecticut fit into mostly 2 clades - one related to genomes from WA and one related to NY. To better visualize this data, I took them to Nextstrain.
From there I showed the reporters that most of the sequenced viruses from the US were related to those sequenced from NY, suggesting that a lot of domestic spread has happened from there. Which is true, and probably not surprising given the travel in and out of NY.
Read 8 tweets

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