European countries have likely bought time by stopping/restricting UK flights to reduce 501Y.V1 (B.1.1.7) import. Vaccine rollouts are progressing, & spring is around the corner.
But what do the next few months have in store? What should we be preparing for? 🗓️🤔 #SARSCoV2
1/24
First, some good news: The fact we have a vaccine 💉 is fantastic🎉, & it will make a difference - but we likely won't have enough people vaccinated to really impact transmission levels in the next few months. We must hold fast to other methods until more are vaccinated.😷
2/24
More good news: Last spring & summer brought reductions in cases: the virus does seem seasonal.
This means spring🌸& summer🌞2021 should help reduce transmission📉, giving us a great window to scale-up vaccination before autumn🍂 & hopefully a break in strict restrictions.
3/24
But we currently sit at the cusp of January: we have cold, hard months ahead before spring arrives. 🥶❄️
On top of that, we have failed to keep cases low over the winter 📈, & we face a new, seemingly more transmissible variant (501Y.V1/B.1.1.7) 🦠.
What lies ahead?
4/24
In the UK where the new variant is prevalent, many hospitals are now more full than in the 1st wave (spring 2020). The UK has had over 50,000 cases/day for >5 days in a row last week.
In England, the case rates are growing almost vertically:
Hospitalization rates in England are also growing at worrying rates, as reflected in the photos and stories of ambulances waiting outside of full ICUs.
Healthcare staff, exhausted from a year of overwork, are at risk of being overwhelmed again.
Ireland, whose proximity to the UK means it likely has the new variant in circulation, has gone from one of the lowest-case-rate countries in Europe at the start pf Dec (87/100,000) to fast deterioration by the end: 321/100,000.
This is also reflected in the proportion of sequences that are 501Y.V1: 11% of cases are sequenced - of those, the percent that are the new variant is increasing: 0.2%, 0.5%, 0.9%, 2.3%... 📈
While UK travel restrictions have likely bought time by reducing imports, we need to prepare for some possibilities:
a) Cases already spreading within countries, just undetected 🔍
b) Imports may start coming from non-UK countries (where travel is less restricted) 🌍
13/24
What can we do to prepare for these? A few options:
- Increase sequencing/testing within countries 🧪🧬
- Get cases down within countries 📉
- Reevaluate our travel policies 🛬
- Consider schools 🏫
14/24
🧪🧬 Increasing testing & sequencing gives a better chance of detecting 501Y.V1 (& others) & shutting down transmission, as well as tracking it, if it starts to spread more widely (Are we containing it? Where is it? Is it increasing?)
These are our 'eyes' on the variant!
15/24
📉Reducing cases helps overall (worst case: we get them so low we can relax some restrictions: not such a worse case!) - but in the context of the variant, it also allows #TestandTrace & sequencing systems to work better & frees up resources in case of a surge in cases 🌊
16/24
🛬While the variant is low-prevalence in a country, reducing further imports can make a difference. We should prepare that those may not come only from the UK in the future.
That means re-examining our travel policies more broadly while we are trying to reduce imports.
17/24
🛬Over the summer, 20A.EU1 showed that quarantine may not have worked as well as hoped to stop #SARSCoV2 spread.
Some countries require tests🧪 before travelling, others can do them on arrival.
Improving test & trace catches those who slip through.
🏫Closing or reducing schools is not to be taken lightly -I've spoken before about the impact this has on children & parents.
But it must be part of the response we consider.
Schools are safest when cases are low: if they aren't, what do we do?
🏫Keeping schools open & finding safe ways to do so should be prioritized.
But that means doing away with the narrative that children don't get #SARSCoV2 & that schools might not be spreading the virus. We can't take appropriate action until we fully recognize the issue.
21/24
Unfortunately again, I am brought back to remembering times in the past, when we've watched #SARSCoV2 cases climb in other countries while imagining we are safe - it could never happen here.
We seem to prefer to wait & see 🕰️, rather than prepare.
We've been in this pandemic long enough to know that waiting has never yet been the answer. Those who have acted fast & decisively, & ensured they had a plan, have faired best.
"The greatest error is not to move ... You need to be prepared"
We have yet another chance now to try & avoid further & stricter future restrictions. To reduce loss of lives & livelihoods. And these steps will help us, with or without the new variant.
Getting a lot of responses to this so let me clarify: The seasonality comes from human changes in behaviour, not changes in the virus. It was aided in 2020 by the spring lockdowns. Warmer weather can *help* us control transmission more easily - but it won't save us by itself.
It's been brought to my attention that the Guardian article above is not a reflection of the latest work, & is a bad source to cite. This is true, & I'm sorry for including it. Science is still working on the exact impact of schools and transmission. (cont)
However, there are great scientists out there working on this in detail!
I really recommend following @mugecevik for up-to-date information on research with children & schools. Some of her work is linked below. (cont)
It's also unlikely that primary, secondary & universities play an equal role here either. And is likely also dependent on community rate: even if schools are relatively safer, if overall cases go high enough, you'll start to see cases in schools.
• • •
Missing some Tweet in this thread? You can try to
force a refresh
Mutations at nucleotide 23012 causes changes in the amino-acid (AA) at position 484 in Spike. We can see here it changes from E (green) to Q (yellow), K (blue), & R (red).
2/8
Changes at position 484 are found most prominently in the 501Y.V2 variant (originating in South Africa), ID by @Tuliodna@rjlessells & team
as well as in a cluster of sequences primarily in Brazil, ID by @atrvlncc & team
The latest focal S:N501 build is now up! It includes data from 4 Jan 2021.
We have new sequences in 501Y.V1/B.1.1.7 from Denmark, Singapore, Australia, Italy, Spain, France, Portugal, Germany, Brazil, Jamaica, Luxembourg, Pakistan & the USA.
Denmark has 43 new sequences (in orange). These indicate additional introductions, as well as further expansion of the existing large local transmission cluster we saw previously (shown in zoomed divergence view).
2/12
10 new sequences from Portugal (orange) indicate additional, separate introductions.
To kick off 2021, here's an update on:
- S:N501 variants (501Y.V1/V2) with data from 31 Dec 2020
- 69/70del variants
- 20A.EU1 variant (most prevalent variant in Europe)
(Here are some fireworks that look a bit like phylogenies! 🎆)
1/23
The latest sequences from 31 Dec show new sequences in the S:N501Y.V1 variant (originating from SE England) from Netherlands, Denmark, Australia, Italy, Canada, the USA, Germany, Switzerland, & India.
There is 1 sequence now from Sweden, 2 from Norway, & 2 from Finland. The 2 Finnish sequences & 2 Norwegian sequences are separated on the tree, indicating 2 separate introductions in each country.
2/8
There are 3 sequences from South Korea clustering together. Zooming in (& in divergence view) we can see they are closely related, and likely indicate 1 introduction.
The latest S:N501 focal build is now up, with data from 28th Dec:
We can see new sequences from Italy, Israel, Spain, France, & Ireland in the SE England variant (501Y.V1) & Switzerland in the South African variant (501Y.V2).
Many are interested in using the 69/70 deletion to scan for cases of the new #SARSCoV2 variants.
As it can impact some primers (seen as an 'S drop-out' in PCR), it can be a high-throughput way to check for the 'SE England' variant - but some important things to remember!
1/5
First, the 69/70 deletion has arisen multiple times independently: not everything with 69/70 is the SE England variant!
You can see that 69/70del appears many times here: notably it's associated with 501Y.V1 (English variant) AND 453 & 439.
In particular, S:N439K is widespread across Europe, and about 3/4 of the sequences in this cluster have the 69/70del.
So there's a fair chance a 69/70del in continental Europe is part of this cluster, not the 'new variant' from England.