All the focal builds linked from CoVariants.org are now updated with data from 2 Mar.

This includes the new focal builds for 501Y.V1, 501Y.V2 & 501Y.V3 (B.1.1.7, B.1.351, P.1) - links in the thread....

1/7

501Y.V1 (B.1.1.7) is still significantly downsampled due to the extremely high number of sequences in this cluster - but the focal build helps a bit!

2/7

nextstrain.org/groups/neherla…

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).

3/7

nextstrain.org/groups/neherla…

📅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! 🎉

1/8

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.

2/8

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!

3/8

While not downplaying our current careful situation, I think we've got a lot to be optimistic about in 2021, if we can think globally 🌍 & act appropriately 💉😷

I thoroughly enjoyed reading this interview with @fabiennekatrin: '1 year of #SARSCoV2'

1/5

blick.ch/schweiz/epidem…

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."

2/5

On mutations:
"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."

3/5

📅CoVariants.org is now updated with data up to the 18th Feb! 📅

Plus! A new mutation has been added 😉

And we've had another few neat feature tweaks thanks to some great contributors!

1/6

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).

2/6

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.

3/6

https://twitter.com/firefoxx66/status/1361305250750169091

Tweets haven't been happening as times get busy, but CoVariants.org is now updated to data from 15 Feb! Focal builds are in the oven 🥖

This update also includes some neat new improvements - let's take a quick look!

1/4

Thanks to @jamesscottbrown, pages are now a little tidier, with the link icons placed after the links!

Thanks to a suggestion by @theosanderson the proportion of 'other' variants on the 'Per Country' page are now grey - easier to see and label!

2/4

@ivan_aksamentov has helped greatly improve the 'Per Variants' page! Tool-tip legends now show the lines so you can see the difference between solid & dashed!

And you can now select what kind or order you'd like the legend to show - frequency or country!

3/4

We found the same #SARSCoV2 mutation at position 677 in Spike has appeared at least 7 times in US-focused clusters in the past few months. What have we seen, & what does it mean?

New preprint out now! With @DDomman @macroliter @macroliter & more!

medrxiv.org/content/10.110…

1/17

Sparked by @macroliter & @DDomman independently spotting a rise in Q677P mutants in New Mexico & Louisiana, we teamed up & started investigating!

We noticed an increase in both Q677H and Q677P mutants around the world and within the USA, in particular since autumn 2020.

2/17

On a S:Q677-focused Nextstrain build, it quickly became apparent that there were multiple separate branches where Q677 mutants had arisen independently. We focused in on those in the USA.

Nextstrain build, filtered to 677H & P in the USA: nextstrain.org/groups/neherla…

3/17

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. 🤯

The focal builds for S:N501 & S:E484 are now updated to data from the 8th Feb!

nextstrain.org/groups/neherla…

nextstrain.org/groups/neherla…

Let's take a quick look at some snapshots of what we can see in the latest data.

1/15

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.…

2/15

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.

3/15

New focal builds for S:N501 & S:E484 are now live!

nextstrain.org/groups/neherla…

nextstrain.org/groups/neherla…

1/5

As well as the major variants of concern, we can spot a couple of other clusters stemming from an 'old' #SARSCoV2 clade, 19B (originating in late 2019).

19A & 19B haven't been around much since early 2020, as they were overtaken by 20A, B & C (which carry D614G).

2/5

However, a few branches of 19B seem to be popping back up again recently.

In the UK, we can see a recent cluster that's acquired S:E484K (along with other mutations in S).

@theosanderson illustrated this one a few days ago!

https://twitter.com/theosanderson/status/1356978433386049541

3/5

nextstrain.org/groups/neherla…

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!)

1/7

(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.)

2/7

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.

3/7

The new focal builds are now up, with data up to 2nd Feb.

Updated S:N501 build:
nextstrain.org/groups/neherla…

Updated S:E484 build:
nextstrain.org/groups/neherla…

1/15

Unfortunately it takes too long for me to do the detailed tweet threads I did originally. However, I'll try to hit a few highlights...

In 20I/501Y.V1 (B.1.1.7):

2/15

The Netherlands now has over 300 sequences in 501Y.V1, with clear signs of community transmission.

3/15

🎉The new and improved CoVariants.org is here! 🎉

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!

1/12

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

2/12

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)

3/12

The S:N501 build is now updated with data from 25th Jan.

Remember, you can always check on any country by just typing that country name in the 'Filter' box on the left menu!

1/18

nextstrain.org/groups/neherla…

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

2/18

Denmark has 52 new samples (some yellow), showing both separate introductions and further spread of existing local clusters.

3/18

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.

I got a lot of messages last week about a 'new variant' in Bavaria, Germany.

Notably, scientists at @ChariteBerlin have announced this is *not* a new variant. Link may stop working so screenshot attached.

Read on to see the sequences...

1/4

spiegel.de/wissenschaft/c…

https://twitter.com/vmcorman/status/1352531294584975360

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.

2/4

nextstrain.org/groups/neherla…

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.

3/4

The S:N501 and S:E484 builds are now updated with data from 20 Jan! 🎉

There are almost 400 new non-UK and non-South Africa sequences in 501Y.V1 (B.1.1.7 #b117) & 501Y.V2.

And 8 new sequences in 501Y.V3 & 20B/S.484K (primarily circulating in Brazil)

#SARSCoV2

1/19

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

2/19

nextstrain.org/groups/neherla…

Denmark has 125 new sequences (orange) - many linking to older sequences & clusters, indicating ongoing local transmission (pic 1).

Netherlands has 14 new sequences (yellow) - many linking to older sequences and clusters, likely indicating local transmission (pic 2).

3/19

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:

1/10

https://twitter.com/cychiu98/status/1350985418628587520

This combination of mutations falls in 20C, and is found predominantly in the US, especially in California. Here's a zoomed view and link.

2/10

nextstrain.org/groups/neherla…

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.

Be wary of headlines claiming this!

3/10

The focal S:N501 build has been updated with data from 15 Jan, & includes 164 non-UK, non-South African sequences in 501Y.V1 (B.1.1.7 #b117) & 501Y.V2.

The S:E484 build has also been updated. Includes 501Y.V3 & 20B/S.484K (predominantly in Brazil).

1/16

nextstrain.org/groups/neherla…

There are 161 new, non-UK sequences in 501Y.V1 (B.1.1.7) from the Netherlands, Denmark, Australia, Spain, Norway, Germany, the USA, & Switzerland, and from Turkey and Ecuador for the first time.

2/16

Turkey has 19 sequences in 501Y.V1 for the first time. These indicate many independent introductions, though a few clusters may indicate local transmission, and pairs with common exposure.

3/16

Lots of tweets about this today!
Let's see what we can see in the focal S:E484 build!

Phylogenetics (what I do - making 'family trees' from virus genetics) can be very informative to see how different variants are spreading, and how cases link🙂

1/10

independent.co.uk/news/health/br…

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.

2/10

nextstrain.org/groups/neherla…

The variant predominantly in the UK (501Y.V1 / B.1.1.7) and the variant predominantly in South Africa (501Y.V2) also both have 501. 501Y.V2 *also* has the 484K mutation.

Why are there concerns about these mutations? You can read more at CoVariants.org!

3/10

There's been a lot of news today about 'new variants in Brazil' & 'S:E484' and 'Ohio variants'. A short thread discussing what we know about each.

1/11

#SARSCoV2 #Ohio #BrazilVariant #Brazil #COVID19

There are two variants circulating in Brazil: 20J/501Y.V3, recently detected in Japan & prevalent in Manaus. And temporarily-labelled '20B/S.484K', a larger clade circulating more widely in Brazil.

They both carry the spike mutation 484K, though this arise separately.

2/11

S:E484K is also found in 501Y.V2 (primarily circulating in South Africa).

Why are we particularly concerned about S:E484K? You can read more at CoVariants.org, as discussed in a tweet from earlier this week:

3/11

https://twitter.com/firefoxx66/status/1348939611578503168

The focal S:N501 build is now updated with data from 13 Jan!

There are a total of 247 non-UK & non-South African sequences in 501Y.V1 (B.1.1.7 #b117) & 501Y.V2.

I'll do an additional thread later on, covering S:E484 & the 'Ohio variants'.

1/18

nextstrain.org/groups/neherla…

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.

2/18

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.

3/18