➡️We have now a detailed map of the likely spread of the VUI-202012/01 #SARSCoV2 variant among *63,000 positive #COVID19 cases throughout England*!
📌All thanks to a brilliant stroke of luck—allowing a *shortcut PCR test* instead of full 🧬test.🧵
2) Long story short, there is a special PCR test used by Lighthouse labs that tests for 3 genes of #SARSCoV2. But new UK variant has a key Deletion at 69/70–this PCR only positive for 2 genes, but no longer records positive signal for mutated spike gene!
This gives a SHORTCUT 👀
3) While some other variants also have the 69-70 deletion mutation, the VUI-202012/01 is the main variant that has it—97% of all viruses with the special spike deletion belong to the troublesome new strain. Hence we can use the “S Gene failure” as a proxy shortcut PCR test! HUGE!
4) And so we can now FULLY MAP the location of all the likely problem UK variant throughout England that used this special 3-gene LIghthouse Lab PCR shortcut instead of needing to slowly sequence the RNA on slower expensive 🧬 tests.
Here: % variant (*S Gene Failure PCR)
5) The map represents the overall average in England between Sept and December. But what about over time! Let’s break it further by time and region here in this figure. ORANGE is the special S Gene failure — proxy for the VUI-202012/01 variant. #COVID19
6) Some seem to call it the 3 gene PCR test by Lighthouse Labs, while others call the special test the TaqPath PCR test. I’m not in the U.K., so I don’t know how to order this test per se. but hope this is useful to people!
7) and what is the implied R(t) increase? Well, there’s some different calculations- either +0.39 unweighted or +0.93 if weighted analysis, or 48% increase in transmission rate.
8) here is also further details on the new mutation and children.
2) “When patients get really sick with Covid, they’re in the hospital for weeks,” said Dr. Arghavan Salles, a physician who has worked in I.C.U.s in New York and Arizona over the course of the pandemic.
3) “When patients get really sick with Covid, they’re in the hospital for weeks,” said Dr. @arghavan_salles, a physician who has worked in I.C.U.s in New York and Arizona over the course of the pandemic.
2) Outside Greater London, the variant has higher viral loads. Within Greater London, the new variant does not have significantly higher viral loads. But this could be due to demographics, such as a faster variant growth rate in particular age-groups.
3) So is it higher or not? Or is it some London / non-London effect? ➡️ it’s really higher.
➡️In a multivariable model (adjusting mutually), what won was the B.1.1.7 variant’s 501Y mutation as key—**higher viral load**
❌London/other region interaction effect not significant.
📍Huge blow—UK had halted plans to open rapid-turnaround #COVID19 tests across England amid concerns about the accuracy. Huge blow to UK’s £100bn “Operation Moonshot” mass-testing plan, to increase daily tests from 430k to 10mil. Poor 🇬🇧 case surging too. theguardian.com/world/2020/dec…
2) Experts in testing and understand immunology like @michaelmina_lab think the test is good in capturing **INFECTIOUS** virus, which is key.
2) Pastor Todd Dunn had been preaching “Faith over fear!” since the COVID-19 pandemic started. Before Thanksgiving, he posted a message on Facebook dismissing precautionary measures by CDC to keep wearing masks and avoid gatherings w/ family members who don’t live in same house.
2) “Dunn, who is the pastor of 2nd Mile Church in north Fort Worth where his parents were members, admitted that he was surprised by the sudden surge in COVID cases in recent weeks in Tarrant County.”
.. SURPRISED THAT EPIDEMIOLOGISTS ARE RIGHT??? 🤦🏻♂️