Now, a more technical tweet thread to give updates on the science - which is moving fast. Again, I recommend following @arambaut, @firefoxx66, @EBIgoldman, @The_Soup_Dragon, @pathogenomenick and @jcbarret along with others to stay on the cutting edge of this

Most important has been the paper by the @CovidGenomicsUK consortium on the new variant, here: https://t.co/b7yFFPXmsE
(This is super-rapid pre-print on https://t.co/PHmxAcVUoB - other people will pick over this no doubt - but the openness of the data and quality of analysis from this group means this is super solid, and any updates on discussion likely to happen fast)
Two key take aways from this paper for me:
1. There is a big jump in number of changes - too big to be explainable with the natural progression over time. @arambaut and colleagues point out that similar big jumps have happened in immunocompromised patients treated via convalescent plasma + drugs
2. This means there are both a number of potential things that could have changed and that it might be that there is synergistic effects - one now needs to test out what things are different in the lab and then work through each one in turn if there is a difference.
The other complication to this is that the 69/70 deletion is present on this branch. This deletion is complex for a variety of reasons
1. Firstly it is recurrent. We have seen this globally in Lyon (but to stress - *just* this event not the whole strain) and in the Danish outbreak that ended up in Mink farms (again, *just* this change not the whole set).
It is unusual to have sequenced so many individuals where one has a slow(ish) moving mutation rate and recurrent mutation. This is what gives @EBIgoldman and colleagues some new headaches (should one collapse multiple observations of the same sequence in likelihood calcs?)
2. This site overlaps with primer sites for some widely used RT-PCR tests. To stress, nearly all RT-PCR tests use 3 (sometimes more!) sites to assess, so having one "drop out" as it is called is ok.
This sounds concerning at first glance but shouldn't be (this is why they do 3 sites!) and for sure the test site will be moved. However, it does mean we can see this in the RT-PCR testing itself.
Here is Tony Cox, @The_Soup_Dragon showing how this variant rose over time. Please note that early on the red line here is likely to be a mixture of viral versions which have this change, but then you can see it take off. https://t.co/BWCHYFR1qy
This means we've got the numbers for lineage displacement (not just growth), meaning scientists can be pretty confident that this version of the virus is growing.
The recurrent mutation of this virus is interesting, and this variant also shares a mutation with a South African strain that also came into the news for potential faster transmission - to stress, these are certainly different lineages.

More from Science

JUST ONE PERSON—UK 🇬🇧 scientists think one immunocompromised person who cleared virus slowly & only partially wiped out an infection, leaving behind genetically-hardier viruses that rebound & learn how to survive better. That’s likely how #B117 started. 🧵 https://t.co/bMMjM8Hiuz


2) The leading hypothesis is that the new variant evolved within just one person, chronically infected with the virus for so long it was able to evolve into a new, more infectious form.

same thing happened in Boston in another immunocompromised person that was sick for 155 days.

3) What happened in Boston with one 45 year old man who was highly infectious for 155 days straight before he died... is exactly what scientists think happened in Kent, England that gave rise to #B117.


4) Doctors were shocked to find virus has evolved many different forms inside of this one immunocompromised man. 20 new mutations in one virus, akin to the #B117. This is possibly how #B1351 in South Africa 🇿🇦 and #P1 in Brazil 🇧🇷 also evolved.


5) “On its own, the appearance of a new variant in genomic databases doesn’t tell us much. “That’s just one genome amongst thousands every week. It wouldn’t necessarily stick out,” says Oliver Pybus, a professor of evolution and infectious disease at Oxford.
All modern research questions frame your mindset and self-frame research paradigm. Broad thinking: how little of everything can a citizen survive on; how cheap can your upkeep be? /1


When an American patient lands in an Austrian hospital for a back problem, a doctor tells him to perform a set of exercises.

- How many?
- Do you have anything else to do? /2

This interchange illustrates two mindsets colliding at bedside. How little can I get away with vs there is no limit to effort when it comes to your wellness. /3

When you were robbed of movement, somebody started selling you exercise. To understand that digging a ditch, to build a house, or to carry a child around, or waking to your grandparents for an hour is not the same as jogging on a treadmill... will reveal what research hides.
/4

When I talk about doing a purposeful activity outdoors, I look at complexity of movement, purpose, meaning, sun, and air, even an opportunity to meet a neighbor... that is now reduced to a calcium pill, vitamin D, an antidepressant, an osteoporosis shot, and an oxygen tank. /5

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