In some states like FL, SGTF 5-day avg is 📉 66% on May 9 compared to 71% 10 days before. & SGTF likely still >95% B.1.1.7
So what is the 34% and maybe growing?
3/ You can look at the variants dashboard. It shows sequencing results. public.tableau.com/profile/helix6…
See overall trend. And counts by state (click on specific variant).
Here, we observed 237 counts of P.1. in FL.
4/ Trend in Florida for all vars. And we know B.1.1.7 decreasing ~5% as of May 9. Likely P.1. will be growing to 10-15%, but maybe it is B.1.617.2 appearing or other?
5/ Forgot to mention, that you can see actual counts per day if you scroll over the bar.
ex in screenshot below. P1 represents 10.42% of 144 sequences in FL from samples collected on April 19.
Co-circultation of both variants
20 samples with co-infections
Evidence of a few recombinations in co-infections
& 2 infections with 100% recombinant
Details in 🧵
@shishiluo@my_helix 2/
Recombination is one way a virus can evolve. It allows to 'test' a new combination of mutations, which could provide an advantage or not.
@shishiluo@my_helix@edwardcholmes@SimonLoriereLab 3/
Lots of talk about Delta-Omicron possible recombinations because in worse case scenario, it could be a bad combo. But also simply because
- it was likely to happen de to co-circulation of both
&
- also easier to identify because of high number of unique mutations of each
To try to 'predict' what may happen in the USA in next couple of weeks, we can look what was the BA.1.1 situation in these countries before BA.2 took over.
2/
Screening an entire population is different than doing the exome to identify cause of a rare disorder.
3/
The goal is to select gene <-> disease combinations that look like the one on the right in graph (Disease Z)
A large fraction of carriers (of a genetic variant) will present the disease if nothing is done
& strong enrichment in carriers compared to non-carriers.