Thread by @NathanGrubaugh

🧬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…

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)

Part of the fitness advantage of BA.2.12.1 (and the advantage of BA.2 over BA.1) *may* be due to enhanced intrinsic transmissibility by producing higher viral titers during infection ("brute force").

PCR CT values are not perfect, but they do support this hypothesis. (4/13)

The 📈 in BA.2.12.1 is also corresponding to a 📈 in cases, hospitalizations, and deaths in Connecticut.

Even *if* Omicron is less severe than Delta, ⬇️ immunity, ⬆️ immune escape, & ⬆️ transmissibility means that BA.2.12.1 can still have a significant population impact. (5/13)

While tracking cases is harder with at home tests, wastewater 💩🧬 testing is showing similar trends.

Virus RNA concentrations currently at early December levels when Omicron (BA.1) was just taking off. (6/13)

https://twitter.com/jordan_peccia/status/1526953207653605378?s=20&t=lWokANj5tYoWR1mQPhWoNQ

Last update (May-5) it looked like BA.2.12.1 may be slowing down, which obvi did not happen if you 👀👆.

This may have been a lineage classification issue (i.e. BA.2.12.1 being classified as BA.2.12). (7/13)

https://twitter.com/NathanGrubaugh/status/1522320885859991558?s=20&t=lWokANj5tYoWR1mQPhWoNQ

See this thread for some technical discussion about lineage classification issues (& non-issues) on various databases.

On GISAID I am already seeing some corrections.
E.g., "BA.2.12.1 (marker override: BA.2.12 + Spike_L452Q => BA.2.12.1)"
(8/13)

https://twitter.com/LongDesertTrain/status/1527043933339111427?s=20&t=lWokANj5tYoWR1mQPhWoNQ

Potentially complicating matters is the emergence of Omicron BA.4/5.

As a reminder, the emergence of BA.4/5 was associated with a 5th COVID-19 wave in South Africa, though it is currently trending to be smaller than the previous Omicron wave. (9/13)

https://twitter.com/Tuliodna/status/1526470866762141697?s=20&t=lWokANj5tYoWR1mQPhWoNQ

So far, BA.4 and BA.5 combined represent just 0.3% of the total cases from the last 3 weeks in Connecticut. Here are the totals:

Connecticut
BA.4 = 3
BA.5 = 2

United States
BA.4 = 203
BA.5 = 142
(10/13)

It's not yet clear if BA.4/5 will have a significant impact in the US. In South Africa, they emerged in a primarily BA.2 background.

In the US, the more transmissible sublineage BA.2.12.1 is becoming dominant, and it is not clear to me if BA.4/5 will have an advantage. (11/13)

If you are looking for a PCR assay to differentiate between BA.1, BA.2, and BA.4/5, ours can help! It can produce a simple genotype based on the presence/absence of 2 deletions:

1⃣ORF1a 3675-3677
2⃣spike 69/70
(12/13)
journals.plos.org/plosbiology/ar…

Here are the expected and lab-confirmed results of our VOC PCR assay 👆:

➡️ BA.1 = ORF detected, SGTF
➡️ BA.2 = ORF-GTF, S detected
➡️ BA.4/5 = ORF-GTF, SGTF
(13/13)

P.S. Because the summer is busy with non-work things (🙏), I wont likely be able to post weekly threads, but will try to at least a couple times a month. 🏖️🍹

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