SARS-CoV-2 surveillance data from @my_helix is here: github.com/myhelix/helix-…
Stats on
>300,000 positives from last 4 months
2,503 sequences (1/3 SGTF, 2/3 random non-SGTF)
🧵on vars of concerns & interest in 7 states
>2% of positives are B.1.1.7 in: CA, FL, GA, PA & TX
Stats on
>300,000 positives from last 4 months
2,503 sequences (1/3 SGTF, 2/3 random non-SGTF)
🧵on vars of concerns & interest in 7 states
>2% of positives are B.1.1.7 in: CA, FL, GA, PA & TX
@my_helix tests (PCR tests) in all states & all available on Github.
Analysis here limited to states with >100 positives PER DAY (and with N gene Cq<27) in December & January.
7 states: CA, FL, GA, IN, NC, PA, TX.
AZ, MA, MI were just under cutoff.
Analysis here limited to states with >100 positives PER DAY (and with N gene Cq<27) in December & January.
7 states: CA, FL, GA, IN, NC, PA, TX.
AZ, MA, MI were just under cutoff.
And analysis is focused on variants of concerns
B.1.1.7
B.1.351 (not present)
P.1 (not present)
variants of interest
B.1.427
B.1.429
See outbreak.info/situation-repo… from @K_G_Andersen or covariants.org from @firefoxx66 for info on these variants.
B.1.1.7
B.1.351 (not present)
P.1 (not present)
variants of interest
B.1.427
B.1.429
See outbreak.info/situation-repo… from @K_G_Andersen or covariants.org from @firefoxx66 for info on these variants.
California
Close to 50% of sequences are B.1.427 or B.1.429. Work is still ongoing to establish whether these variants are of concern or not.
cc @EricTopol
Close to 50% of sequences are B.1.427 or B.1.429. Work is still ongoing to establish whether these variants are of concern or not.
cc @EricTopol
Florida
B.1.1.7 numbers still going up. Went from ~9.5% to ~11.8% of positives in 3 days.
B.1.429 present.
B.1.1.7 numbers still going up. Went from ~9.5% to ~11.8% of positives in 3 days.
B.1.429 present.
Georgia
SGTF numbers going up, and majority of these seem to be B.1.1.7.
Definitely worth monitoring closely (same as TX).
@DrEricDing
SGTF numbers going up, and majority of these seem to be B.1.1.7.
Definitely worth monitoring closely (same as TX).
@DrEricDing
Indiana
B.1.1.7 is there. Last 7 days have shown at least 1 or 2 SGTF per day (of 80-100 positives).
Still noisy, but lower case count overall may favor a quicker expansion of B.1.1.7 in coming weeks.
B.1.1.7 is there. Last 7 days have shown at least 1 or 2 SGTF per day (of 80-100 positives).
Still noisy, but lower case count overall may favor a quicker expansion of B.1.1.7 in coming weeks.
North Carolina
Among the states where Helix tests the most, this is the state with the fewer SGTF and therefore fewer B.1.1.7 cases.
Among the states where Helix tests the most, this is the state with the fewer SGTF and therefore fewer B.1.1.7 cases.
Pennsylvania
SGTF is present. Recently the fraction of SGTF that were B.1.1.7 has been increasing. Our best estimate is that B.1.1.7 represents just above 2% of positive cases in PA.
SGTF is present. Recently the fraction of SGTF that were B.1.1.7 has been increasing. Our best estimate is that B.1.1.7 represents just above 2% of positive cases in PA.
Texas
SGTF numbers have been increasing rapidly in the last 2 weeks. And the large majority of SGTF we sequenced from Texas are B.1.1.7.
Texas and Georgia are now at levels similar to California for B.1.17.
Few B.1.429 (nothing like California for this variant)
SGTF numbers have been increasing rapidly in the last 2 weeks. And the large majority of SGTF we sequenced from Texas are B.1.1.7.
Texas and Georgia are now at levels similar to California for B.1.17.
Few B.1.429 (nothing like California for this variant)
That is a wrap. You can make your own graphs on the @my_helix dashboard: public.tableau.com/profile/helix6…
This is a huge team effort. In addition to lab, bioinformatics, research teams ... this is only possible thanks to a great engineering team. @EmreColak_Sr @Maglaar
This is a huge team effort. In addition to lab, bioinformatics, research teams ... this is only possible thanks to a great engineering team. @EmreColak_Sr @Maglaar
Additional context for Texas from @dallasnews and quotes from @firefoxx66 . dallasnews.com/news/2021/02/1…
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