Nathan Grubaugh Profile picture
Jun 11, 2021 8 tweets 5 min read Read on X
🧬6/10 Connecticut #SARSCoV2 variant surveillance
@CovidCT | @jacksonlab | @CTDPH | @YaleSPH | @Yalemed | @YNHH

Alpha (B.1.1.7) = 57% (📉11%)
Gamma (P.1) = 10.9% (📈2.7%)
Delta (B.1.617.2) = 6.5% (📈3.2%)

short 🧵 | Report 👉
covidtrackerct.com/variant-survei…
2/7 Gamma (P.1) and Delta (B.1.617.2) continue rising in Connecticut, while Alpha (B.1.1.7) and others decline, following national trends (see next tweet).
3/7 Data from outbreak.info shows that in the US 🇺🇸, Delta (B.1.617.2) is 📈 exponentially, while Alpha (B.1.1.7) is on the 📉. Despite this, COVID-19 cases are still dropping (for now).
4/7 Compare this to the UK 🇬🇧, where Delta (B.1.617.2) is dominant and Alpha (B.1.1.7) is approaching (but probably wont reach) extinction. And this is being following by a recent 📈 in cases.
5/7 What will happen in CT and the 🇺🇸? Delta will likely become dominant. The 🇺🇸 and 🇬🇧 have quite similar 💉 rates, so we may even see an 📈 in cases like the 🇬🇧. But full vaxx can still be effective against Delta, so I'm guessing that it would be a large '🌊'.
(data from NYT)
6/7 How we prevent Delta (and other variants) from causing another 🌊 is pretty simple. Get vaccinated 💉.
7/7 This week I'd like to thank Kaya Bilguvar and our partners at YCGA who stood up COVIDseq and significantly increased our capacity. The entire team has been amazing to work with, and we could not have done this 👇 without them 👏🙌
medicine.yale.edu/keck/ycga/
**would NOT be a large wave. ugh.

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More from @NathanGrubaugh

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
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
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
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
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
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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