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Thread about our preprint on the study of emergence and increased prevalence of SARS-CoV-2 B.1.1.7 variant in the US. https://www.medrxiv.org/content/10.1101/2021.02.06.21251159v1
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First, my Conflict of Interest: I am an employee of Helix.
We do a lot of COVID testing (PCR tests) and also receive funding for the viral surveillance program.
See the other COIs from authors of this preprint.
First, my Conflict of Interest: I am an employee of Helix.
We do a lot of COVID testing (PCR tests) and also receive funding for the viral surveillance program.
See the other COIs from authors of this preprint.
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Methods are very similar to the ones used in the regular @my_helix updates with the dashboard.
https://public.tableau.com/profile/helix6052#!/vizhome/SGTFDashboard/SGTFDashboard
The study is based on >500,000 positives PCR tests. We test in all 50 US states, but it is not homogeneous. See map
Methods are very similar to the ones used in the regular @my_helix updates with the dashboard.
https://public.tableau.com/profile/helix6052#!/vizhome/SGTFDashboard/SGTFDashboard
The study is based on >500,000 positives PCR tests. We test in all 50 US states, but it is not homogeneous. See map
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In our initial search, we prioritized sequencing of samples with S gene target failure in PCR tests. As expected, we found B.1.1.7 in many states
The B.1.1.7 sequences were pretty classic. So far, no Eeek (S:E484K) mutation present. Credit to @AineToole for mut name
In our initial search, we prioritized sequencing of samples with S gene target failure in PCR tests. As expected, we found B.1.1.7 in many states
The B.1.1.7 sequences were pretty classic. So far, no Eeek (S:E484K) mutation present. Credit to @AineToole for mut name
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By estimating the fraction of SGTFs that are B117s from the sequences done, & then by looking at fractions of positives that are SGTF, we estimate % of positives that are B117. And can look trend over time.
Trend is
in US.
By estimating the fraction of SGTFs that are B117s from the sequences done, & then by looking at fractions of positives that are SGTF, we estimate % of positives that are B117. And can look trend over time.
Trend is
in US.
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To get the most recent numbers, you can check the @my_helix dashboard with the most recent SGTF and positives info. Last numbers from Feb 3.
https://public.tableau.com/profile/helix6052#!/vizhome/SGTFDashboard/SGTFDashboard
You will see that Florida is going up pretty fast recently. ~10% of positives are SGTF for Feb 1, 2 and 3.
To get the most recent numbers, you can check the @my_helix dashboard with the most recent SGTF and positives info. Last numbers from Feb 3.
https://public.tableau.com/profile/helix6052#!/vizhome/SGTFDashboard/SGTFDashboard
You will see that Florida is going up pretty fast recently. ~10% of positives are SGTF for Feb 1, 2 and 3.
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Based on the 5-day rolling average of % of positives that are B117, we fit logistic growth curves.
So far, curve in the US shows a doubling time of ~10 days. And an increased transmission of 35-45%.
B117 could be dominant at end of March in the US.
Based on the 5-day rolling average of % of positives that are B117, we fit logistic growth curves.
So far, curve in the US shows a doubling time of ~10 days. And an increased transmission of 35-45%.
B117 could be dominant at end of March in the US.
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We then tried to look if the sequences clustered based on geography (note: not all B.1.1.7s are the same. They all have core defining mutations. But they also have some additional ones).
A few clusters (clades) were seen. A very clear Florida cluster, 2 CA, and 1 GA.
We then tried to look if the sequences clustered based on geography (note: not all B.1.1.7s are the same. They all have core defining mutations. But they also have some additional ones).
A few clusters (clades) were seen. A very clear Florida cluster, 2 CA, and 1 GA.
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Therefore the most likely is that there were multiple introductions of B.1.1.7 in the US.
Then we could try to look at The Most Recent Common Ancestor (TMRCA). For FL and CA1 clade, the best estimate is that introduction was end of November.
Therefore the most likely is that there were multiple introductions of B.1.1.7 in the US.
Then we could try to look at The Most Recent Common Ancestor (TMRCA). For FL and CA1 clade, the best estimate is that introduction was end of November.
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Discussion:
We will watch closely the evolution of % of positives that are B.1.1.7. Up to now, our study shows that B.1.1.7 has an increased growth rate compared to non-B.1.1.7 lineages.
Similar or perhaps slightly lower to what other countries have reported .
Discussion:
We will watch closely the evolution of % of positives that are B.1.1.7. Up to now, our study shows that B.1.1.7 has an increased growth rate compared to non-B.1.1.7 lineages.
Similar or perhaps slightly lower to what other countries have reported .
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If it is increasing slower (in CA or other states), it will be important to understand why.
- due to specific measures to prioritize contact tracing for SGTF positives?
- due to competition with other lineages more infectious
- other?
If it is increasing slower (in CA or other states), it will be important to understand why.
- due to specific measures to prioritize contact tracing for SGTF positives?
- due to competition with other lineages more infectious
- other?
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Credit to everybody involved: see list of authors
from @my_helix @scrippsresearch @UAAHGSA @UCSF @illumina @sharphealthcare @SanDiegoCounty @igisci @UCLA
Special mention for @genesareclever @gkay92 @K_G_Andersen
Credit to everybody involved: see list of authors
from @my_helix @scrippsresearch @UAAHGSA @UCSF @illumina @sharphealthcare @SanDiegoCounty @igisci @UCLA
Special mention for @genesareclever @gkay92 @K_G_Andersen
