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Dr Emma Hodcroft Profile picture
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22 Jan, 4 tweets, 3 min read
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…
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
I hope this reassures those who were worried by the original announcement & is a reminder to all of us scientists that we should be careful when making announcements. It's often better to err on the side of caution, particularly before you have a sequence.

4/4

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More from @firefoxx66

Dr Emma Hodcroft Profile picture
21 Jan
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
Read 19 tweets
Dr Emma Hodcroft Profile picture
18 Jan
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

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
Read 10 tweets
Dr Emma Hodcroft Profile picture
17 Jan
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
Read 16 tweets
Dr Emma Hodcroft Profile picture
15 Jan
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
Read 11 tweets
Dr Emma Hodcroft Profile picture
14 Jan
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

Read 14 tweets
Dr Emma Hodcroft Profile picture
14 Jan
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
Read 19 tweets

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