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Nathan Grubaugh Profile picture
@NathanGrubaugh
May 20, 2021 • 7 tweets • 5 min read • Read on X
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🧬 5/20 Connecticut #SARSCoV2 variant surveillance
@CovidCT | @jacksonlab | @CTDPH | @YaleSPH | @YaleWestCampus | @YNHH

- 2nd case of B.1.617.2 in CT
- B.1.1.7 >75% of all cases, but..
- COVID-19 cases lowest since early October 🥳

short 🧵 | Report 👉
covidtrackerct.com/variant-survei…
2/5 The second case of B.1.617.2 was from the same county as the first case (Fairfield), but they are unrelated (see tree 👇). Neither cases are known to be linked to international travel.
3/5 B.1.1.7 is still 📈 frequency not because the lineage is rapidly expanding, but because it is dying out slower than the non-B.1.1.7 lineages. So the total number of B.1.1.7 cases 📉 by 87% since late March.
4/5 The total COVID-19 cases in Connecticut are the lowest since early October. I just wanted to say that again 😀🍻
5/5 This would have been possible without the expertise of @JosephFauver who established our sequencing and processing pipelines while we were all trying to put out various fires. I am so grateful for his efforts.

Here he is sequencing one of our first samples in March 2020.
Bonus: Here is an article discussing some of the work that @JosephFauver led using genomic epidemiology to investigate SARS-CoV-2 transmission and evaluate COVID-19 protocols for sports leagues.

wsj.com/articles/decod…
Double bonus: @JosephFauver recently received the 2021 Distinguished Service Award from his alma matter @PeruState for providing COVID-19 guidance to the College prepared for fall classes on campus. Well deserved 👏

peru.edu/news/2021/fauv…

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More from @NathanGrubaugh

Nathan Grubaugh Profile picture
Jul 15, 2022
⚡️We developed & performed initial validation on an amplicon-based sequencing protocol (PrimalSeq) for Monkeypox virus (MPXV).

It improves genome coverage compared to metagenomic sequencing, especially at CTs >20.

🧵 1/8 | Protocol 👉
protocols.io/view/monkeypox…
It's based on a design led by @Scalene & @pathogenomenick originally for Zika virus that was adapted for SARS-CoV-2 ("ARTIC protocol") and used by labs around the world.

Our goal was for this to be plug n' play with current SARS-CoV-2 protocols. (2/8)
nature.com/articles/nprot…
The primers were designed using PrimalScheme using a pre-outbreak A.1 clade reference genome (GenBank accession: MT903345).

The scheme comprises a total of 163 primer pairs with an amplicon length ranging between 1597 and 2497 bp (average length of 1977 bp). (3/8)
Read 8 tweets
Nathan Grubaugh Profile picture
Jul 14, 2022
🧬July-14 Connecticut #SARSCoV2 variant surveillance
@CovidCT|@CTDPH|@CDC_AMD|@YaleSPH|@Yalemed

📈BA.5 is now the dominant variant in CT (53% from 6/27-7/4), followed by BA.2 (34% & 📉) and BA.4 (11% & 📈)

🚫No detection of BA.2.75

🧵 (1/8) | Report 👉
kphamyale.shinyapps.io/variant_report/
Using a logistic regression of the daily frequencies, we predict that as of today (July-14), BA.5 is probably 80-90% in Connecticut.

BA.4 is still 📈 as it outcompetes BA.2, but will probably start to 📉 in frequency soon after BA.2 is gone. (2/8)
We created a new dashboard to report variant sequencing data in Connecticut. You can still access it through our main website by clicking on the "Read the latest Connecticut report" link. (3/8)

👉 covidtrackerct.com
Read 8 tweets
Nathan Grubaugh Profile picture
May 19, 2022
🧬May-19 Connecticut #SARSCoV2 variant surveillance
@CovidCT|@CTDPH|@CDC_AMD|@YaleSPH|@YaleMed

📊Sequencing last 3 weeks
➡️ BA.2.12.1 = 44% (📈 8%)
➡️ BA.2 (other lineages) = 56% (📉 7%)
➡️ BA.4/5 = 0.3% (5 total)

🧵 (1/13) | Report 👉
covidtrackerct.com/variant-survei… Image
Omicron BA.2.12.1 is still 📈 in Connecticut as it is across most of the US. Fitting the % of sequenced cases to a logistic growth curve, we estimate that BA.2.12.1:

1⃣ is ~80% frequency today (May019)
2⃣ surpassed 50% in early May
3⃣ may reach 95% in early/mid June
(2/13) Image
From the same logistic growth curve, we also estimate that BA.2.12.1 is:

➡️ ~24% more transmissible than background (mostly other BA.2 lineages)
➡️ doubling in proportion every ~12 days
(3/13) Image
Read 15 tweets
Nathan Grubaugh Profile picture
May 5, 2022
🧬May-5 Connecticut #SARSCoV2 variant surveillance
@CovidCT|@CTDPH|@CDC_AMD|@YaleSPH|@Yalemed

Last 3 weeks
➡️BA.1.1 = 4%
➡️BA.2.12.1 = 23% (may be slowing down)
➡️BA.2 (other lineages) = 73%
➡️BA.4/BA.5 = 0% (might still be coming)

🧵 (1/9) | Report 👉
covidtrackerct.com/variant-survei…
We no longer have TaqPath data from YNHH to track SGTF, but we will use our "VOC" PCR assay that detect SGTF and ORF1a target failures (ORFTF).

BA.1 = SGTF
BA.2 = ORFTF

BA.1 is barely hanging on. (2/9)
👆 here is the "VOC" PCR assay referenced above. (3/9)

journals.plos.org/plosbiology/ar…
Read 9 tweets
Nathan Grubaugh Profile picture
Mar 17, 2022
🧬 March-17 Connecticut #SARSCoV2 variant surveillance
@CovidCT | @CTDPH | @CDC_AMD | @YaleSPH | @Yalemed

📊Sequencing data last 3 weeks
BA.1/.1 = 84%📉
BA.2 = 16%📈
Delta = 0%

📊PCR data this week
BA.1/.1 = 41%📉
BA.2 = 59%📈

🧵 (1/7) | Report 👉
covidtrackerct.com/variant-survei…
Based on our TaqPath PCR data (S-gene detected), we estimate that:

➡️ BA.2 is >50% in Southern Connecticut
➡️ At this rate - BA.2 will be 95% by early April
➡️ BA.2 doubling rate = 7.8 days (BA.1 in December = 3-4 days)
➡️ BA.2 ~43% more transmissible than BA.1/.1

(2/7)
Over the past 4 weeks, all of the sequenced S-gene positive samples have been Omicron BA.2 and not Delta. So we trust the 👆 PCR results reflecting the rise in BA.2. (3/7)
Read 8 tweets
Nathan Grubaugh Profile picture
Feb 3, 2022
Here are comparative results between 10 TaqPath S-gene detected samples tested by YNHH and with our validated VOC PCR assay. Most with our assay were actually SGTF, and looking at the YNHH results, the S-gene CTs for those were 5-7 higher than N/ORF. (5/16) Image
We are looking into these low level spike amplification samples that should be SGTF to see if this is a lab/TaqPath assay artifact or if there is something about these BA.1 sequences. So far doesn't seem to be sequence-related. Will report (6/16)
Our initial SGTF case definition – ORF/N <30 CT, S “not detected” - was conservative to not over-call BA.1.

We updated it yesterday to include S-gene 5 CTs higher than ORF/N, and compared the results. (7/16) Image
Read 13 tweets

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