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.


#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.

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, as discussed in a tweet from earlier this week:


The focal build for S:E484 is updated with data from 13 Jan & includes the sequences from Manaus, Brazil which cluster with the recent Japanese travel sequences in new Nextstrain clade 20J/501Y.V3:…

Read about the Manaus seqs:…

20J/501Y.V3 sequences have both 484K & 501Y (like 501Y.V2, mostly in South Africa) - they are shown in orange below.

They are clearly separate from the other, larger S:E484K cluster circulating in Brazil (in green, with temporary label 20B/S.484K)

In divergence (mutation) view, the 501Y.V3 variant has a 'long branch' - it sticks out to the right. This means it has a high number of mutations relative to surrounding sequences.

Zooming in, we can see that the Japanese samples are nested within the Brazilian diversity.

There have also been some news reports circulating about 2 'Ohio variants'.

From press release data, one is a 20G clade sequence with S:N501Y. As shown below (blue) 501Y mutations have popped up in the past. While worth keeping an eye on, I think this isn't so remarkable.

The other variant identified seems to have 3 mutations, 1 each in the Spike, Membrane, & Nucleocapsid proteins in a 20G background. There are 17 USA seqs with the same mutations (Only 1 of these is currently visible in N America Nextstrain build).

The Ohio samples are not yet online, but the 17 existing samples that seem to have the same mutations are from Massachusetts, Maryland, Minnesota, New York, Texas, & Wisconsin.

Another USA-state focused build captures 5 of them, all dating between 9 Dec & 12 Jan.

The preprint states that in Columbus, OH, at end of Dec, the variant went from 10% prevalence to 60% prevalence (10-20 samples per week) in 3 weeks.

I'd be curious to hear if other states have seen this variant & if so, also if they've seen similar rises.

I have been careful here not to mention the mutations as, so far as I can tell, the preprint is not yet out. I'll update with a link to the preprint & the exact mutations when I hear it's up.

You can read more below:……

The preprint is still not out, but the mutations seem to be common knowledge on Twitter - so they are S:Q677H, M:A85S, N:D377Y, or nucleotides 23593, 26775, 29402.

These are present in around 17 sequences in the US, though not all show up in the same Nextstrain builds.

You can see the cluster I picture up-thread in the SPHERES New York build - mouse-over 'T/T/T' in legend to see them.

The 'Ohio preprint' is now up! Check it out here:…

Thanks to @craiccomputing for the heads-up!


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More from @firefoxx66

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🙂

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… Image
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!

3/10 ImageImage
Read 11 tweets
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'.

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.

Read 19 tweets
12 Jan
Happy Tuesday! The latest focal S:N501 build is now updated with sequences from 11 Jan.
There are 101 new sequences in the 501Y.V1 (B.1.1.7 #b117) & 501Y.V2 variants.

Additionally, I'll include some updates on S:E484K in this thread.

There are 97 new non-UK sequences in 501Y.V1, including the first sequences in the cluster from Slovakia, Mexico, & Belgium, plus additional sequences from the Netherlands, Denmark, Australia, Spain, Ireland, & Sweden.

Slovakia has 10 sequences that fall in 501Y.V1 for the first time. These are closely linked, & likely indicate a single introduction and ongoing transmission (remember: vertical distance is not meaningful on the same branch - position of the 2 English samples is arbitrary).

Read 23 tweets
9 Jan
To add to the excitement of your Saturday evening, the focal S:N501 build is now updated with data from 8th Jan, including 48 new seqs in 501Y.V1 (B.1.1.7 #b117) & 501Y.V2.

There are 46 new non-UK sequences in 501Y.V1, from the Netherlands, Italy, Israel, Ireland, Norway, Sweden, the USA, and Luxembourg.
And 2 new non-South African sequences in 501Y.V2, from Australia for the first time.

In 501Y.V1:

Ireland has 4 new sequences (orange). 2 sit separately but are identical, indicating an additional introduction. 2 link to a previous sequence (green), 1 mutation away each. This could indicate location transmission, unsampled diversity, or a common exposure.

Read 12 tweets
9 Jan
I'm getting some questions about this, so here you go: We do not have sequence evidence of a new, more transmissible "US variant" - it seems to be a misinterpretation.

Still, more sequencing in the US (& globally) will help us better track existing & emerging #SARSCoV2 variants!
Importantly: you can have spikes & rises in #SARSCoV2 infections without needing a new variant. We can see this clearly in Europe in autumn: we have a good idea of the variants circulating & no new (or old) variant is responsible. It was likely weather-related.
Similarly, season & holiday related changes in travel & behaviour, changing restrictions/mandates, school & university terms, & 'restriction fatigue' - just to name a few - can play a role in #SARSCoV2 case numbers. We can't & shouldn't blame every rise on a new variant.
Read 4 tweets
8 Jan
A brief update to the focal S:N501 builds to start your Friday off right! This one includes data from 7 Jan 21.

We have about 20 new sequences each in 501Y.V1 (B.1.1.7 #b117) & 501Y.V2.

Let's take a look at the new sequences, starting with 501Y.V1

There are 22 new non-UK sequences in 501Y.V1, including for the first time from Luxembourg (3), & additional seqs from Singapore (1), Australia (4), France (12), & Switzerland (2).

First, Luxembourg has 3 sequences in 501Y.V1 for the first time. Each represents a separate introduction.

Read 14 tweets

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