2/6 We now have 8 cases of B.1.617.2 (5 shown in the π²) and 2 of B.1.617.1. To my knowledge, none of these are associated with βοΈ. Our phylo π² shows that there are at least 4 independent transmission chains of these viruses, spanning at least 3 counties. Definately one to π
3/6 The π in B.1.1.7 shown in tweet 1 is probably a combination of noisy data with few cases and the emergence of other lineages. The figure π 1 is from TaqPath SGTF data, which is a week ahead of the sequencing shown π, where we don't yet see the sudden π.
4/6 Interesting that the "Non-VOC/VOI" cases (shown as grey π) passed B.1.526 this week (11% vs 10%). Looking at the Non-VOC/VOIs closer, its mostly due to an increase in R.1, a lineage that has E484K and that we have detected at low levels for a long time.
5/6 P.1 continues to fluctuate and remain at relatively low frequencies. We haven't sequenced a B.1.351 in a couple of weeks.
6/6 This week I'd like to thank our funders ππ. We received a contract from the @CDC_AMD in Sep to get things started, then a boost from fastgrants.org in Dec to respond to the variants. Now we have a contract with the @CTDPH to keep the program going πͺ.
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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 π). Neither cases are known to be linked to international travel.
3/5 B.1.1.7 is still π 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 π by 87% since late March.
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.
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.
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 π this week in both the sequencing and TaqPath SGTF data (shown π). 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.
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.
3/9 For the first time we saw B.1.1.7 π 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 π
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.
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.