2/23
S:N501 link
https://t.co/TfHfPgBEBS
Image link
https://t.co/3aCKv1pAcI
🎉Happy New Year!🎉
To kick off 2021, here's an update on:
- S:N501 variants (501Y.V1/V2) with data from 31 Dec 2020
- 69/70del variants
- 20A.EU1 variant (most prevalent variant in Europe)
(Here are some fireworks that look a bit like phylogenies! 🎆)
1/23
2/23
S:N501 link
https://t.co/TfHfPgBEBS
Image link
https://t.co/3aCKv1pAcI
3/23
In both cases, the sequences are not connected, indicating separate introductions.
4/23
6 new sequences from Netherlands, in orange/yellow (green are older).
1 is clearly separate - zooming in (& in divergence view, coloured by country) it is harder to determine the relationship between the others.
5/23
2 identical sequence at the top are separate introduction(s?) than the larger cluster below.
The other sequences form a tight cluster very indicative of onward transmission.
6/23
From the phylogeny alone, it's hard to say if these are connected or separate, as the sequences are identical. (Vertical order is not meaningful for identical sequences!)
7/23
1 (top) seems to be a separate introduction. The other (zoomed view) may be related to an earlier Italian sequence as they're separated by 1 mutation, but we cannot say for sure.
8/23
Read/see more in the 69del section of my 'SARS-CoVariants' tracking page!
9/23
https://t.co/9eKGmBKKe6
& @MichaelWorobey identify a novel 69/70del lineage in the USA:
https://t.co/6qUN3nlYA9
10/23
Importantly, in this build the cluster appears to be close to 501Y.V2, but this is a focal build so this connection must be interpreted cautiously!
11/23
https://t.co/CgWL7o7W4c
(In the build live at 14.30CET 1 Jan the 'cluster' is only 1 sequence! We'll push the new one later today!)
12/23
18 sequences from the UK, Denmark, Germany & France.
13/23
https://t.co/ZVJDv67PDL
https://t.co/T8xfvuaCto
A small cluster of 6 sequences from England.
https://t.co/fCUAK6mhXA
14/23
We can see ~10 sequences in 20A.EU2 (S:477) from France with 69/70del. Gaps aren't used in the phylogeny building, so they don't cluster here.
16/23
https://t.co/OOkwr8dlyJ
17/23
https://t.co/kIu3woMnbE
I have just counted all genotypes of spike codons 67-71 and all 69/70 deletions have the same nucleotide pattern: pic.twitter.com/BwBIHkYYz3
— Richard Neher (@richardneher) January 1, 2021
This is the variant that expanded in Spain before spreading across Europe over the summer (you can read more in our preprint below). It is the most prevalent variant in Europe, containing ~64,000 sequences.
18/23
https://t.co/tTgE9I2Mdn
But long after summer travel has ended, it persists (in orange below) - & continues to spread...
19/23
https://t.co/zLZ72luHE2
20/23
https://t.co/hXIPuqrCmt
20A.EU1's movement across Europe & the world show how effectively & efficiently #SARSCoV2 #COVID19 can spread.
21/23
https://t.co/AiPX50GRew
More from Dr Emma Hodcroft
Each day brings new challenges, but here's an update to the dedicated S.N501 build, using data from 6 Jan 2021 to keep you going.
There are 42 new non-UK sequences in 501Y.V1 (B.1.1.7) & 7 new non-South-African sequences in 501Y.V2.
1/14
https://t.co/kT1gFsSZn0
There are 42 new non-UK sequences in 501Y.V1 from the Netherlands, Italy, Hong Kong, Finland, Sweden, Germany, USA, Switzerland, Brazil, and the first sequence from 501Y.V1 in Oman.
https://t.co/XA8VR8HiEq
2/14
Oman has their first sequence which falls into 501Y.V1:
3/14
Finland has 12 new sequences (orange), which mostly represent separate introductions. Zooming in (divergence view), we can see 3 of the new sequences are identical (red), which may indicate the cases are connected.
4/14
Sweden has 8 new sequences (orange), which indicate separate introductions.
5/14
There are 42 new non-UK sequences in 501Y.V1 (B.1.1.7) & 7 new non-South-African sequences in 501Y.V2.
1/14
https://t.co/kT1gFsSZn0
There are 42 new non-UK sequences in 501Y.V1 from the Netherlands, Italy, Hong Kong, Finland, Sweden, Germany, USA, Switzerland, Brazil, and the first sequence from 501Y.V1 in Oman.
https://t.co/XA8VR8HiEq
2/14
Oman has their first sequence which falls into 501Y.V1:
3/14
Finland has 12 new sequences (orange), which mostly represent separate introductions. Zooming in (divergence view), we can see 3 of the new sequences are identical (red), which may indicate the cases are connected.
4/14
Sweden has 8 new sequences (orange), which indicate separate introductions.
5/14
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
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://t.co/Cw5u2kuATa
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 https://t.co/wVE7ubYBoy!
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://t.co/Cw5u2kuATa
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
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://t.co/Cw5u2kuATa
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 https://t.co/wVE7ubYBoy!
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://t.co/Cw5u2kuATa
More from Society
The UN just voted to condemn Israel 9 times, and the rest of the world 0.
View the resolutions and voting results here:
The resolution titled "The occupied Syrian Golan," which condemns Israel for "repressive measures" against Syrian citizens in the Golan Heights, was adopted by a vote of 151 - 2 - 14.
Israel and the U.S. voted 'No' https://t.co/HoO7oz0dwr
The resolution titled "Israeli practices affecting the human rights of the Palestinian people..." was adopted by a vote of 153 - 6 - 9.
Australia, Canada, Israel, Marshall Islands, Micronesia, and the U.S. voted 'No' https://t.co/1Ntpi7Vqab
The resolution titled "Israeli settlements in the Occupied Palestinian Territory, including East Jerusalem, and the occupied Syrian Golan" was adopted by a vote of 153 – 5 – 10.
Canada, Israel, Marshall Islands, Micronesia, and the U.S. voted 'No'
https://t.co/REumYgyRuF
The resolution titled "Applicability of the Geneva Convention... to the
Occupied Palestinian Territory..." was adopted by a vote of 154 - 5 - 8.
Canada, Israel, Marshall Islands, Micronesia, and the U.S. voted 'No'
https://t.co/xDAeS9K1kW
View the resolutions and voting results here:
The resolution titled "The occupied Syrian Golan," which condemns Israel for "repressive measures" against Syrian citizens in the Golan Heights, was adopted by a vote of 151 - 2 - 14.
Israel and the U.S. voted 'No' https://t.co/HoO7oz0dwr
The resolution titled "Israeli practices affecting the human rights of the Palestinian people..." was adopted by a vote of 153 - 6 - 9.
Australia, Canada, Israel, Marshall Islands, Micronesia, and the U.S. voted 'No' https://t.co/1Ntpi7Vqab
The resolution titled "Israeli settlements in the Occupied Palestinian Territory, including East Jerusalem, and the occupied Syrian Golan" was adopted by a vote of 153 – 5 – 10.
Canada, Israel, Marshall Islands, Micronesia, and the U.S. voted 'No'
https://t.co/REumYgyRuF
The resolution titled "Applicability of the Geneva Convention... to the
Occupied Palestinian Territory..." was adopted by a vote of 154 - 5 - 8.
Canada, Israel, Marshall Islands, Micronesia, and the U.S. voted 'No'
https://t.co/xDAeS9K1kW
I’ll address every nonsense argument and lie used to defend the suicidal gender ideology Thats in vogue today:
3:45 - “So what if you don’t have gametes?”
It’s called a birth defect. You’re still male or female.
~5:00 *nonsense trying to say the sexes of seahorses could be swapped coz male carry the eggs*
male doesn’t produce eggs, he produces the sperm. He’s still the male. If I impregnated a chick then carried the amniotic sac in a backpack ‘til the baby was done I’ll still be male🤦♂️
5:10 - we could say there’s 4 sexes of fruit fly cause there’s 3 producers of different sized sperm
No. They’re still producing sperm. They’re males. This is idiotic. Is this whole video like this? (Probably. 99% likely. Abandon hope.)
~6:10 - hermaphroditism and sequential hermaphroditism exists therefore....
No. Some animals being hermaphrodites, which is meaningless w/o the existence of binary sex to contrast it to, still doesn’t make gender ideology or transgenderism valid.
Intersex ≠ transgenderism 🙄
6:20 - bilateral gynandromorphism is a disorder in some species (not in humans). Has nothing to do w/ “gender” or transgenderism.
Ova-testes in humans are also a disorder, usually found in those w/ the karyotype disorders that you ppl also try to appropriate (extra X’s/Y’s).
3:45 - “So what if you don’t have gametes?”
It’s called a birth defect. You’re still male or female.
*one horrible doctor does a horrible thing* "oh I guess gender is horrible" miss me with that transphobic nonsense
— Goob \u26a1 (@Goob999) February 17, 2021
Here's a video to even disprove your take on sex (not gender) and the binary:https://t.co/bpmqqJWoJX
~5:00 *nonsense trying to say the sexes of seahorses could be swapped coz male carry the eggs*
male doesn’t produce eggs, he produces the sperm. He’s still the male. If I impregnated a chick then carried the amniotic sac in a backpack ‘til the baby was done I’ll still be male🤦♂️
5:10 - we could say there’s 4 sexes of fruit fly cause there’s 3 producers of different sized sperm
No. They’re still producing sperm. They’re males. This is idiotic. Is this whole video like this? (Probably. 99% likely. Abandon hope.)
~6:10 - hermaphroditism and sequential hermaphroditism exists therefore....
No. Some animals being hermaphrodites, which is meaningless w/o the existence of binary sex to contrast it to, still doesn’t make gender ideology or transgenderism valid.
Intersex ≠ transgenderism 🙄
6:20 - bilateral gynandromorphism is a disorder in some species (not in humans). Has nothing to do w/ “gender” or transgenderism.
Ova-testes in humans are also a disorder, usually found in those w/ the karyotype disorders that you ppl also try to appropriate (extra X’s/Y’s).
