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6 May, 7 tweets, 5 min read
🧬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 πŸ“ˆ in frequency, following US trends

short 🧡 | Report πŸ‘‡
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.

πŸ‘‡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…
4/7 P.1 (first detected in Brazil) is one of the fastest growing variants in the *United State* - it now represents ~10% of the sequenced cases.

πŸ‘‡from outbreak.info
5/7 We are starting to see similar trends of P.1 πŸ“ˆ in *Connecticut*, and it's now up to about ~6% of the sequenced cases.

From our very preliminary data, P.1 doesn't seem to be driving a large proportion of vaccine breakthrough cases, but its obviously something to watch.
6/7 Will end with some πŸ‘ news - both B.1.1.7 and non-B.1.1.7 cases continue to drop to the lowest point in 2021 πŸ₯³πŸŽ‰πŸ™Œ

Continued vaccinations πŸ’‰ will ensure that this πŸ“‰ trend continues.
7/7 This week I'd like to highlight the work of @jessroth95 - our awesome statistician and spatial modeler. She is leading our analysis of variant introductions using travel data and helps with just about every project. Oh, and she also does all of our GISAID submissions 🍻

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More from @NathanGrubaugh

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 πŸ‘‡
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 πŸ“ˆ this week in both the sequencing and TaqPath SGTF data (shown πŸ‘‡). 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 πŸ“ˆ
- B.1.526 πŸ“‰
- Still not much P.1 & B.1.351

short 🧡 | Report πŸ‘‡
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 πŸ“‰ 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 πŸ“ˆ 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 πŸ“ˆ, and we now predict it to be the dominant lineage in CT based on TaqPath SGTF data from Yale + JAX

Short 🧡 | Report πŸ‘‡
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 πŸ“ˆ
- More B.1.351, P.1, & E484K cases

Short 🧡 | Report πŸ‘‡
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 πŸ‘‡ 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 πŸ“ˆ
- B.1.526 continues to πŸ“ˆ
- First detection of B.1.1.7 + E484K ⚑️ in CT.

Short 🧡 | Report πŸ‘‡
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 πŸ“ˆ. 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
Nathan Grubaugh Profile picture
18 Mar
New (3/18) Connecticut #SARSCoV2 variant surveillance report @CovidCT | @jacksonlab | @CTDPH | @YaleSPH

- First case of P.1 (first detected in Brazil) in CT
- B.1.1.7 continues to πŸ“ˆ
- B.1.526 πŸ“ˆ
- B.1.427/9 added to the VOC list

Short 🧡 | Report πŸ‘‡
covidtrackerct.com/variant-survei…
2/3 TaqPath SGTF data from YNHH (mostly New Haven County) and JAX (New Haven, Hartford, and some other counties) shows that probable B.1.1.7 cases keep πŸ“ˆ as non-B.1.1.7 cases slowly πŸ“‰.

B.1.1.7 is now ~35% of the total cases (~40% from YNHH and ~26% from JAX).
3/3 (YNHH TaqPath data only)

Our earlier projections of B.1.1.7 frequency growth are still pretty close. We expect the YNHH B.1.1.7 numbers to cross 50% this week, and the combined (YNHH and JAX) to cross 50% next week.
Read 4 tweets

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