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20 May, 7 tweets, 5 min read
🧬 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
6 May
🧬5/6 Connecticut #SARSCoV2 variant surveillance
@CovidCT | @jacksonlab | @CTDPH | @YaleSPH | @YaleWestCampus | @YNHH

- 1st detection of B.1.617.2 (reported in India) in CT
- P.1 📈 in frequency, following US trends

short 🧵 | Report 👇
covidtrackerct.com/variant-survei…
2/7 B.1.617 first reported in India comes in 4 different flavors primarily defined by their spike gene mutations. While the CDC currently recognizes all 4 as VOIs, the B.1.617.2 lineage that we detected importantly does not have the E484Q mutation.

👇from outbreak.info
3/7 The B.1.617.2 case was not associated with travel, suggesting that there is some level of local transmission. Though the presence of other highly transmissible variants in CT - like B.1.1.7 - may limit its ability to become established.

nextstrain.org/community/grub…
Read 7 tweets
Nathan Grubaugh Profile picture
22 Apr
🧬4/22 Connecticut #SARSCoV2 variant surveillance
@CovidCT | @jacksonlab | @CTDPH | @YaleSPH | @YaleWestCampus | @YNHH

- B.1.1.7 >60%
- Detected 2 B.1.1.7 + E484K (3 total)
- New CDC VOI list: B.1.526 + B.1.526.1, but not B.1.526.2

short 🧵 | Report 👇
covidtrackerct.com/variant-survei…
2/8 Last week we saw a dip in the probably B.1.1.7 cases determined by TaqPath SGTF results. I showed how the sequencing tracked with the SGTF data, and that the dip was probably a blip...

3/8 That "blip" was confirmed: B.1.1.7 📈 this week in both the sequencing and TaqPath SGTF data (shown 👇). While we expect B.1.1.7 to continue this trend until it dominates (like in the UK), the good news is that we are seeing a reduction in both B.1.1.7 and non-B.1.1.7 cases.
Read 8 tweets
Nathan Grubaugh Profile picture
15 Apr
⚡️4/15 Connecticut #SARSCoV2 variant surveillance report 🧬
@CovidCT | @jacksonlab | @CTDPH | @YaleSPH

- B.1.1.7 📈
- B.1.526 📉
- Still not much P.1 & B.1.351

short 🧵 | Report 👇
covidtrackerct.com/variant-survei… Image
2/9 While we continue to see the rapid decline of non-VOCs/VOIs, the competition between B.1.1.7 & B.1.526 is quite interesting, and could have significant public health importance. Currently B.1.1.7 is "winning", though things could rapidly change as more people get vaccinated. Image
3/9 For the first time we saw B.1.1.7 📉 from TaqPath data, which could mean that it is slowing down (it has to at some point). Below I also plotted the B.1.1.7 frequency estimates from our sequencing data, which has tracked with TaqPath and importantly still shows B.1.1.7 📈 Image
Read 9 tweets
Nathan Grubaugh Profile picture
8 Apr
⚡️4/8 Connecticut #SARSCoV2 variant surveillance report
@CovidCT | @jacksonlab | @CTDPH | @YaleSPH

Primary news is that B.1.1.7 📈, and we now predict it to be the dominant lineage in CT based on TaqPath SGTF data from Yale + JAX

Short 🧵 | Report 👇
covidtrackerct.com/variant-survei…
2/6 This news follows @CDCDirector Rochelle Walensky saying that B.1.1.7 is "now the most common lineage circulating in the United States".

npr.org/sections/coron…
3/6 We predicted that B.1.1.7 would become dominant in CT in our recent paper led by @tdalpert, @AndersonBrito_, & co. However, we thought that this would have happened earlier in March. The slowdown of B.1.1.7 was likely due to the rapid rise of B.1.526.

cell.com/cell/fulltext/…
Read 6 tweets
Nathan Grubaugh Profile picture
1 Apr
🧬4/1 Connecticut #SARSCoV2 variant surveillance report @CovidCT | @jacksonlab | @CTDPH | @YaleSPH

- B.1.1.7 *may* be leveling off
- B.1.526 continues to 📈
- More B.1.351, P.1, & E484K cases

Short 🧵 | Report 👇
covidtrackerct.com/variant-survei…
2/8 We didn't see an increase in the % of B.1.1.7 from the sequencing data last week, and the TaqPAth SGTF data also suggests that the expansion of B.1.1.7 *might* be slowing down in CT.

While this is good news, I think that it points to something else...
3/8 That something else is B.1.526.

It made up 32% of the sequenced cases analyzed this week, a 9% increase from the week before.

Its proportion is higher in Fairfield county, which is close to NY - where B.1.526 is currently dominating.

Data 👇 since 2/1
Read 8 tweets
Nathan Grubaugh Profile picture
25 Mar
3/25 Connecticut #SARSCoV2 variant surveillance report
@CovidCT | @jacksonlab | @CTDPH | @YaleSPH

- B.1.1.7 continues to 📈
- B.1.526 continues to 📈
- First detection of B.1.1.7 + E484K ⚡️ in CT.

Short 🧵 | Report 👇
covidtrackerct.com/variant-survei…
2/5 TaqPath SGTF data from YNHH (mostly New Haven County) and JAX (New Haven, Hartford, and some other counties) shows that the frequency of B.1.1.7 keeps 📈. Thankfully, the B.1.1.7 cases and total cases are still way down. Lets work to keep it that way.
3/5 We detected a B.1.1.7 sequence with the E484K mutation from a sample collected from New Haven County (CT). The genome is very closely related to others sequenced in CT so its likely acquired this mutation independently. This is potentially concerning for vaccines.
Read 5 tweets

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