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

https://nextstrain.org/groups/neherlab/ncov/S.N501?p=grid

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

The USA has 61 new sequences (orange), from Florida, Minnesota, California, Pennsylvania, & New York.

A few of these represent separate introductions. Others form distinct clusters that may indicate ongoing local transmission.

4/18

Israel has 35 new sequences (orange). Some of these show separate introductions, but many link with older sequences, indicating ongoing local transmission.

5/18

The Netherlands has 34 new sequences (orange). A few of these represent separate introductions, but most form a large cluster with older sequences from the Netherlands, indicating ongoing local transmission.

6/18

Portugal has 31 new sequences (orange). Though hard to see in the zoomed-out view, most of these represent separate introductions. There is one case where 2 new seqs are identical to an older one, but this could be a common exposure source.

7/18

Denmark has 20 new sequences (orange). A few of these indicate separate introductions, but must cluster with older sequences in smaller groups or in the very large Danish group previously identified, indicating local transmission.

8/18

Norway has 14 new sequences (orange). Most indicate separate introductions, but a few are identical to or related to an older sequence, which may indicate local transmission.

9/18

Spain has 11 new sequences (orange). All of these indicate separate introductions, though some new sequences link together to form tight clusters. This could indicate local transmission or a common source.

10/18

New Zealand has 10 new sequences (orange). All represent separate introductions, though some new sequences are linked together.

11/18

Singapore has 6 new sequences (orange). Though hard to see in zoomed-out view, most of these indicate separate introductions.

12/18

Italy has 6 new sequences (orange). It's a bit hard to see in the zoomed-out view, but none of these link directly with older samples, indicating separate introductions - though 2 new seqs link together.

13/18

Germany has 4 new sequences (orange). Though hard to see in the zoomed-out view, these all represent separate introductions.

14/18

Australia also has 4 new sequences (orange), including the first from Western Australia. These indicate separate introductions, though 2 of the new sequences are identical (marked in red).

15/18

India has 2 new sequences (orange, one hidden behind the green - pic 1). One is a separate introduction, the other links with a previous sequence (pic 2).

Belgium has 1 new sequence, which links 1 mutation away from a previous sequence (pic 3).

16/18

There are 3 new non-South African sequences in 501Y.V2, from Germany for the first time. They are identical, which may indicate a common exposure.

17/18

The updated country plots will go up soon, and I'll add another thread later on S:E484 & the 'Ohio variants'.

18/18

The updated country plots are now up. As always, be careful interpreting plots as many countries are selectively sequencing S:N501 & S-drop outs (which often increases S:N439), so frequencies are often not representative!

19/18

https://github.com/hodcroftlab/covariants/blob/master/country_overview.md