Federico Gueli 🇺🇳 Profile picture
Aug 24 10 tweets 2 min read Twitter logo Read on Twitter
Late night in Europe but variant community is not asleep! A lot of designation made by the awesome @CorneliusRoemer , he does alone half of the global work on variants! @redbull you should sponsor him for life!
A lot of new things around got designated tonight:
3d >>>
and kudos to @wolfeagle1989: he is updating in real time #Collection42 so you can check all of them if fast or not.
Remember: any variant itself is not a reason to panic and our work is useful to design vaccine treatments and to inform timely the public health agencies
New Lineages:
we got designated the first triplete lineages (FLip + 478R) a step further in convergent evolution and one more bubble in the mega table updated by @dfocosi !
They are JF.1 (XBB.1.16.6 descendant ) and GK.1.4 (XBB.1.5.70 ) descendant
Then FL.1.5.2 sibling of Fornax but with different mutations: it adds 481K and 681R (convergent with BA.2.86 btw)
then JB.2.1 from South Africa with 245- 403-478-554 mutated ( all but 478 are mutated also in BA.2.86 )
HK.6 is Eris (EG.5.1.1) that got in addition also the XBB.2 defining mutation S:D253G
HG.2,GS.2 GS.3 GS.4 GS.4.1 and GE.1.3 are all Acrux XBB.2.3 different descendants, all with S:478R, which gained a few more commoly convergent mutations in the spike or outside the spike. Interestingly GS.4/4.1 has M:A104V as BA.2.86
Last ( If Cornelius got asleep) JE.1 it is a GJ.1 (XBB.2.3.3) Acrux descendant with 478R 450D (and 521S) so a new different combo on a fast backbone something to keep watched.
and @CorneliusRoemer, lucky us , is not sleeping so it got designated maybe the fastest lineage we are tracking HK.3.1 it is Eris with FLip and S:F157L (Convergent with Centaurus BA.2.75)
Hope i have made things as easy as possible.
take a look at collection42 to weigh them by yourself looking at the lower Confidential interval the one that more is close to the reality (if the number of sequences is more than 100 it starts to be reliable )
cov-spectrum.org/collections/42
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More from @siamosolocani

May 31
12/ a big kudos to women/men in the labs and behind genomic tools as Pango Usher Nextclade Covspectrum,Collections (@and to workers in Gisaid and all variant spotters community and variant naming group.dre
2/ without bothering you with stats the main fact is China is uploading a lot and very quickly after sampling while the UK/Den bulk of sequences was largely reduced
3/ So i think a more descriptive than quantitative approach is useful right now.
So lets start with main regional/global trends
Read 14 tweets
Jan 15
While BA.5.2 lost the world but took China and while XBB.1.5 is fastly arising there are many countries with unique variants dominating/leading there:
1 Philippines BA.2.3.20
2 New Zealand CH.1.1
3 Russia CL.1
4 Australia XBF BR.2.1
5 India XBB
6 South Korea BN.1.3
7 Japan BF.5
8 Singapore XBB.1*
9 Hong Kong CH.1.1

this to say that nothing is certain, be dubious always never stop searching.
While BQ.1* is technically still the global dominating lineage
Read 5 tweets
Jan 3
Update on China: nothing new, just confirmation that
BA.5.2* made it to be the main driver of the ongoing wave.
There are two main lineages 1)BF.7+Orf7a:H47Y+S:C1243F
2) BA.5.2+t17208C with 4 sublineages:
a) N:Q241K
b) Orf1a:T1788M
c) Orf1b:T2432I
d) S:A570S

1/cont
..then much smaller
3) BA.5.2+S:T883I + Orf1b:S997P
and really small
4) BA.5.1 + N:S79I + N:A273S

2/cont
the BA.2.3.20 +Orf8:T12I
the BA.5.2.1 + N:P6T
the BA.5.2 + Orf6:N28H
turned to be more Hong Kong lineages with sporadic exportations to China than circualting in ML China, buw we will see.
(thx to scientists from HK for uploading more sequences to clarify this )
Read 5 tweets
Dec 27, 2022
Little update on variants circulating in China.
First a big thanks to all scientists in ML China and in other countries doing the sequencing lab.
Second thx to other variant hunters as Silcn, who working alone without any support found the main two variants circulating there 1/
2/ (and he already done it with BA.4,BA.5/BA.2.75 )

All the contents of this 3d are from the @PangoNetwork
github page: github.com/cov-lineages/p… and another big thx to people still running this as @CorneliusRoemer @PeacockFlu @AngieSHinrichs and InfrPopgen
3/ and another thx to @GenSpectrum ,@GISAID @nextstrain for keeping things easy to track.

So here what has been found there

maybe @EricTopol is interested in.

The lineages circulating in China seem to have been seeded quite a bit ago, they are not super recent,
Read 12 tweets
Dec 27, 2022
Wild Type:
Wuhan - Gennaio 2020
Lodi- Febbraio 2020
Bergamo- Marzo 2020
Madrid - Marzo 2020
New York Aprile 2020
Brasile estate 2020
Florida estate 2020
Europa autunno 2020
Beta
Sudafrica Dicembre 2020
Alpha
Uk Gennaio 2021
Gamma
Amazzonia Gennaio 2021
Delta
India febbraio-aprile 2021
Russia-Est Europa estate 2021
Usa estate 2021
Germania autunno 2021
Omicron BA.1
World Gennaio 2022
Omicron BA.2
Denmark, India Gennaio 2022
Hong Kong Marzo 2022
BA.2.3
South Korea Marzo 2022
BA.5.1
Portogallo Maggio 22
BA.5.2
Japan Luglio 22
BF.7
Europa settembre 22
BQ.1
Francia Novembre 22
BF.5
Japan Dicembre 22
BF.7
China Dicembre 22
Read 4 tweets
Sep 15, 2022
A short 3d on BQ.1.1

Real name: B.1.1.529.5.3.1.1.1.1.1.1.

It sums history of SC2 variant hunting .

I would like to walk back this history with you if interested:
B.1 and B.1.1 are the first wave dominant strains ,
they got the lead in Italy then in Europe (Except Spain that had a A driven first wave) and then worlwide.
I think they have been first identified and designated by @PangoNetwork Team Core @arambaut, @AineToole @EvolveDotZoo
At the time most of the wonderful tools we use now ,
as USHER or CovSpectrum,
didnt exist and designations were mostly based on @nextstrain manually uploaded trees.
Read 11 tweets

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