Breaking—UK 🇬🇧 VARIANT MAPPED:

➡️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

khub.net/documents/1359…
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.

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More from @DrEricDing

24 Dec
On the brink—

📌Over 2 in 5 U.S. hospitals with intensive care units have reached occupancy levels of >=85%.

📌Contrast with early Oct, just 1 in 4 that full. #COVID19

📌The 85% occupancy’ is the threshold to trigger regional stay-at-home orders.
nytimes.com/interactive/20… Image
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. Image
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. Image
Read 5 tweets
23 Dec
BIOLOGICAL SIGNIFICANCE B.1.1.7 🇬🇧 variant #SARSCoV2:

Read these 4 key circled sentences from @CovidGenomicsUK on why the mutations are worrisome.

Experts don’t think it will strongly affect vaccines, but some say maybe slightly.

See 🧵 for details. cogconsortium.uk/wp-content/upl… Image
2) This table also explains how much the variant B.1.1.7 has been seen recently. Notice how much of the total within last 28 days. Image
3) brand new details on the viral load.
Read 6 tweets
23 Dec
💡New—VIRAL LOAD OF UK🇬🇧 b.1.1.7 VARIANT:

➡️New study by @OxfordViromics group indeed finds **higher viral load** for new variant w/ 501 mutation & 69-70 deletion.

📌How much higher? “Inferred viral loads were *3-fold higher* in people w/ new variant”.🧵
coronavirus-fraser-group.org/files/files/up… Image
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. Image
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. Image
Read 4 tweets
23 Dec
📍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… Image
2) Experts in testing and understand immunology like @michaelmina_lab think the test is good in capturing **INFECTIOUS** virus, which is key.
3) it indeed caught the critical high viral cases
Read 10 tweets
23 Dec
Welp—Pastor who told parishioners not to fear pandemic—parents then die of COVID after Thanksgiving.

🔥“I’m not wearing a mask—There will be no social distancing CDC. Faith over fear!”

➡️A few weeks later, both parents died of #COVID19 in Fort Worth 🏥.
dallasnews.com/news/public-he… Image
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. Image
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??? 🤦🏻‍♂️
Read 6 tweets
23 Dec
NOT EVEN REMOTELY TRUE:

Donald Trump Jr. claims “red states” had fewer #COVID19 transmissions than “blue states” due to “common sense.”

2) Which of these are red states and blue states again @DonaldJTrumpJr? Are my eyes kinda bloodshot or is it the figure just red? Image
3) I swear my eyes must be bleeding red or some reason @DonaldJTrumpJr. Image
Read 5 tweets

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