501Y.V2 is not downsampled much now, which means it gives a pretty good view of where the variant has spread. Shown in large dots here are the clusters in Mayotte, the French territory off the coast of Africa (yellow circle near Africa).
📅CoVariants.org is updated with data from 2 March📅, as well as a very exciting new change:
Variants & mutations are now separated & clearly labelled - & each Variant of Concern has it's own page & data! 🎉
A new, improved left-menu now clearly indicates whether a page is concerned with a Variant (collection of mutations in one part of the tree) or a Mutation (one change, could be in many places on the tree).
Updated naming helps, too!
And menus collapse to keep things tidy.
And to help you find what you're looking for - a table to help you link up nomenclature!! 🎉
A lot of people have asked for this - it's not yet beautiful but it's already hopefully useful.
And you can go straight to the CoV-Lineages reports on the 3 main VoCs, too!
On conspiracy theories:
"Unfortunately, conspiracy theories have become very dominant in the pandemic. I can understand: [they often] provide much simpler explanations. We scientists should learn from this, to make what we say more accessible and understandable."
"If many people have already been infected, it is an advantage for a virus [to evade] this immunity. A year ago that would not have been of any use to the virus. But now... we just have to be aware that the pandemic is not static. It is constantly changing."
And we've had another few neat feature tweaks thanks to some great contributors!
Enough recent data has come through to push the graphs to the next 2-week mark (they're plotted by sequences per 2-week period to help avoid weekly jitters), so the most recent data point is the 8th Feb now (covering the period two weeks after this).
Linking with our recent preprint on the S:Q677 variants, S:Q677 is now included on CoVariants!
We can particularly see 677 showing up clearly in the USA 'Per Country' graphs.
It's #WomenInSTEM day today! 👩🏻💻👩🏾⚕️👩🏿🎓👩🏽🔬
I'm terrified of making lists of Twitter names as I know I'll leave someone off.
But I want to express how absolutely inspired I have been by the many brilliant women I've had the opportunity to work with this year & throughout my career!🎉
I absolutely remember how important it was (and is!) to be able to see myself in women who were in positions I aimed to achieve. Representation matters *so much.*
It helps to break down the expectations & stereotypes we often unknowingly internalise & realise what's possible!
Just 1 anecdote:
The first time I heard a brilliant women scientist whom I admired matter-of-factly state that she was looking forward both to the conference 🗒️ /and/ to shoe-shopping 👠 in the city it was in was *a revelation* for me. 🤯
Let's take a quick look at some snapshots of what we can see in the latest data.
Important note: the S:N501 build is now being more significantly impacted by downsampling.
I'm working on addressing this, but in the meantime, suggest looking at the S:E484 build for 501Y.V2 & 501Y.V3 & checking out the CoV Lineages report! cov-lineages.org/global_report.…
Israel now has over 200 sequences in 501Y.V1 (B.1.1.7). The latest additions indicate separate introductions (mostly from a month or two ago) and a large and still-growing local cluster.
I'm still getting a *lot* of media enquiries - more than I can even respond to! So here's some of my best tips for how to reach out to me to maximise your chances of success (though I imagine they're true of other scientists too!)
(Just as a disclaimer - even if you use all of these, I can't promise I write back, or that I can say yes. If emails slip off the 'front page' of my inbox they basically fall into a black hole 😬. And sometimes I just cannot take any more interviews, even great ones.)
1. Please tell me what time zone you're in!
If I want to say 'yes' that means a pencilled-in appointment goes into the calendar immediately - so I need to know when you're likely to be awake. If I have to email you to find out... it might not happen.
We're hoping to make this a one-stop location to track not only the 'headline' variants, but many different #SARSCoV2 mutations & variants that scientists are keeping an eye on.
Let's take a tour of the site!
The buttons on the left will take you to pages focused on key variants & mutations, while the menu at the top will help you jump between info pages (FAQ) & pages compiling together information about many variants (ex: Per country).
Let's take a look at the 20A.EU1 page
Here, we can
- Click through to a dedicated @Nextstrain build for the variant (1)
- See a list of the defining mutations (2)
- Learn a bit about the variant & see links to papers (3)
- See a distribution of 20A.EU1 per country (4)
- See a protein model! (pic 2)
In the 501Y.V1 (B.1.1.7) variant, here are a few of the non-UK countries with new sequences in this variant, including Denmark, Italy, Spain, France, Portugal, Norway, Germany, the USA, South Kora, & Switzerland, & the UAE, Austria, & Czech Republic for the 1st time
Denmark has 52 new samples (some yellow), showing both separate introductions and further spread of existing local clusters.
As we head deeper into 2021, a gentle reminder to double-check your #SARSCoV2 sequencing scripts for hardcoded '2020's! 😬
We've seen a real uptick recently in sequences with sampling dates in Jan 2020, with divergence that clearly indicates they meant 2021! 📅🤦🏻♀️
"How can we tell?" you might wonder. Actually, these cases are pretty easy to spot!
Let's take a look at two sequences reported as being from Jan 2020 - 1 in green, 2 in blue. (Spoiler, green is the imposter.)
This view is 'date view' where sequences are plotted on the X-axis by the date they were sampled. Then, we try and infer how they're connected using their genetic information - specifically, what mutations they share & don't share.
3 seqs indicated in red are apparently from the hospital. They're coloured by deletion at position 69, which likely caused them to be flagged (501Y.V1 has it too). However, they're related to other sequences in Germany & Turkey, also w the deletion.
We do see the 69/70 deletion has appeared independently previously. While this is interesting, I don't think it increases concern significantly about this group of sequences, which are part of a larger cluster that's been circulating in Germany since spring 2020.
There are 394 new non-UK sequences in 501Y.V1 from the Netherlands, Denmark, Singapore, Australia, Italy, Spain, France, Ireland, Finland, Sweden, the USA, Switzerland, India, Brazil, Slovakia, & Belgium
A #SARSCoV2 variant with a combination of mutations in Spike (S13I, W152C, L452R) has been making headlines & twitter rounds today, so - a fresh-from-the-oven 🥖 S:L452R focal build is now up - let's take a look:
Importantly, we *don't yet know* if this variant is being pulled along with a general rise in cases, or some other environmental or behavioural change - or whether the mutations change the behaviour of the virus, like transmissibility.
There are two variants circulating predominantly in Brazil:
- 20B/S.484K seems to be older & more widespread. It has (among others) a mutation at position 484
- 20J/501Y.V3 is smaller & detected recently. It has mutations at 501 *and* 484.
There are 244 new sequences in 501Y.V1 (B.1.1.7) from Australia, Belgium, Denmark, Germany, India, Israel, Italy, Netherlands, New Zealand, Norway, Portugal, Singapore, Spain & USA, as well sequences as from Ecuador and Greece for the first time.
Greece has 3 new sequences in 501Y.V1 for the first time. They indicate 2 separate introductions.
Ecuador has 2 sequences for the first time. They also indicate 2 separate introductions.