2/8 In Connecticut, the % of sequenced cases that are the Delta variant (B.1.617.2) decreased in recent weeks. This is probably more of a reflection of noisy data when trying estimate frequencies from a small number of cases vs an actual decline in delta.
3/8 Looking at our neighbors in Massachusetts and New York, delta is 10-20%, so we in Connecticut are probably pretty close to that. My guess is that we'll see a 📈 in delta in the coming weeks to reflect the trends of our neighbors.
4/8 The continuing good news is that COVID-19 cases in CT continue to remain very low, meaning that we are not yet seeing any real impacts of delta locally. Given this, a common question that I am being asked is: "why should we even care about delta?"
5/8 The answer: If delta continues to become more prevalent, it has the ability to make outbreaks among unvaccinated populations a lot worse, furthering the health disparities in our communities. As a result, we may also see an increase in total cases, as seen in the UK.
6/8 For the vaccinated populations, delta is not an immediate threat. However, our vaccines work best when they have less work to do. So if delta increases transmission in our communities, it will provide more opportunities for some vaccines to fail.
7/8 As for any variant, the best way to prevent your vaccination from failing is to increase the vaccination rates in your networks. Please talk to your family and friends about the benefits of vaccines. cdc.gov/coronavirus/20…
8/8 This week I'd like to thank our @YaleSPH summer interns, @BilligKendall & @rtobiaskoch, who are learning how to complete our entire process - from sequencing to analysis - and will help lead our partnerships in the Caribbean 🌎👏🙌
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)
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)
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)
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)
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)
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)
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)