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 https://www.independent.co.uk/news/health/brazil-coronavirus-variant-uk-b1787815.html

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

https://nextstrain.org/groups/neherlab/ncov/S.E484?c=region&f_clade_membership=20B/S.484K,20J/501Y.V3&label=clade:20B/S.484K&p=grid&r=country

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 http://CoVariants.org !

3/10

The view below is from an analysis focusing on sequences with a mutation at 484. It shows all the samples in the 2 variants (20B/S.484K & 20J/501Y.V3) & how they're related. More closely related = closer together (very, very roughly).

4/10

We can colour these samples by region to see where they're from. As we expect - most are in Brazil! A few are in Argentina (also red).

5/10

https://nextstrain.org/groups/neherlab/ncov/S.E484?c=region&f_clade_membership=20B/S.484K,20J/501Y.V3&label=clade:20B/S.484K&p=grid&r=country

If we look just at 20B/S.484K (top cluster), we can see there are clusters of sequences in the UK, Canada & the USA, and exports to Norway, Malaysia, & Australia.

6/10

https://nextstrain.org/groups/neherlab/ncov/S.E484?c=region&f_clade_membership=20B/S.484K&label=clade:20B/S.484K&p=grid&r=country

Importantly, the clusters in the USA & Canada are identical (though each country also has an additional imports), so they may be from a group of travellers returning, rather than local transmission (left pic). They also date from Nov - so not recent (right pic).

7/10

We can see 8 UK sequences in the 20B/S.484K cluster. There are 2 clusters, but neither are identical. They could be from a common exposure (same part of Brazil, same travel group), or possibly be local transmission. These samples are from Nov & Dec.

8/10

https://nextstrain.org/groups/neherlab/ncov/S.E484?c=region&f_clade_membership=20B/S.484K&f_country=United%20Kingdom&p=grid&r=region

If we look at 20J/501Y.V3, we can see that sequences only are found in Brazil and Japan (known travel to Brazil), but no other countries.

9/10

https://nextstrain.org/groups/neherlab/ncov/S.E484?c=region&f_clade_membership=20B/S.484K,20J/501Y.V3&label=mlabel:20B/A6613G&p=grid&r=region

Hopefully, this thread helps distinguish what the '2 variants' are that are circulating in Brazil, and from which there have been samples detected in the UK.

And, I hope it shows how phylogenetics can help us 'tell viruses apart' & follow them as they move & change!

10/10

To add: why are scientists concerned about these variants circulating primarily in Brazil?

@BillHanage write a fantastic thread here:

11/10 https://twitter.com/BillHanage/status/1349943613514526723