Etelä-Amerikan viimevuotinen Sars-Cov-2viruksen Mu variantti ehti saada kaksi alalinjaa ja yhden sub-alalinjan ( BB.2)

Huomaan vasta tänään Permalink-luettelosta, että MU-variantti (B.1.621)  sai viime vuonna alalinjallensa B.1.621.1 vielä kaksi  sub-alalinjaa.  Mu variantin  alalinja B.1.621.1  merkattiin  "BB" koodilla  ja sitten sen alalinjat saivat virstanpylväät BB.1 ja BB.2 ennen joulua 2021 , jolloin delta-aalto (B.1.617.2, "AY")  alkoi osoittaa saaneensa jo selvää  vastustusta.  Omikronin  (BA.1.1.529, "BA")vaikutus ilmeni vasta hieman myöhemmin- vuodenvaihteessa varsinkin -  ja tässä  lokakuun  marraskuun vaihteessa  ei vielä ollut kovin paljon käsitystä omikronin valtakauden alkamisesta. Otan sitaatin Mu-variantin sub-alaryhmien virstanpylvään asettamisesta 17.12. 2021. Huomaa tammikuinen varianttilinjan tarkistus  tekstin lopussa. Otan sitaatin  päivä päivältä, koska   silloin tätä GITHUB aisaa on helpompi käsittää.

(MU variantti BA.1.621 sai yhden alalinjan ja se merkitään BB, sillä sille tuli alkuhahmottelussa  kaksi sub-alalinjaa: BB.1 ja BB.2. Nämä on merkattu jo varhain ja  GITHUB asiasta #232  on tässä muutamia sitaatteja viime vuodelta). Tarkennuksista  mainittu loppuyhteenvedossa.

 GITHUB  pohdinnan alku: lokakuun alussa 1.10.2021.

Two potential sublineages of B.1.621.1, one with Spike Y449N and E583D, the other with Spike S939F #232

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c1985.... opened this issue on 1 Oct 2021 · 11 comments

Comments

c1985...commented on 1 Oct 2021 

Proposed sublineage 1 Description Sub-lineage of: B.1.621.1 (98 sequences) Earliest sequence: 2021/5/15 (Spain) Most recent sequence: 2021/9/11 (Chile) Countries circulating: Chile (19 sequences); also found in Canada, Colombia, Peru and the US, likely extinct though. Mutations in addition to B.1.621.1: M: R146H N: T391I (defining) S: Y449N, E583D ORF1a: T812I ORF7a: Q94H Genomes: MU Y449N.csv Proposed sublineage 2 Description Sub-lineage of: B.1.621.1 (264 sequences) Earliest sequence: 2021/5/19 (Spain) Most recent sequence: 2021/9/8 (the US-CA) Countries circulating: the US, predominantly California (212 sequences), and other states (41 sequences) Mutations in addition to B.1.621.1: N: T379I (defining) S: S939F (defining) ORF1a: N2147D, K2148R (defining), T2952I ORF3a: V259L Genomes: MU S939F.csv

Andreiil mentioned this issue on 31 Oct 2021

Proposal for a new sublineage of MU with S: 449N + S:583D that seems to resist better than others to Delta Expansion #299

A new GISAID upload just came from Colombia. It continues to look like the issue in #299 is real, and S:E583D+S:Y449N continues to expand even as the rest of Mu is close to extinction

FedeGueli commented on 31 Oct 2021

As cited in #299 there is an interesting thread on twitter on sublineage 1 by Ricardo Rivero

MCB6 commented on 2 Nov 2021

A new GISAID upload just came from Colombia. It continues to look like the issue in #299 is real, and S:E583D+S:Y449N continues to expand even as the rest of Mu is close to extinction

RicardoRH96 commented on 2 Nov 2021

A new GISAID upload just came from Colombia. It continues to look like the issue in #299 is real, and S:E583D+S:Y449N continues to expand even as the rest of Mu is close to extinction

It is necessary to keep an eye on this lineage, hope it gets designated soon.

Corneliusroemer  commented on 2 Nov 2021

It looks interesting, yes, because it seems to be able to almost compete with Delta - but only in Colombia, not Chile. Colombia doesn't sequence much so the uncertainty is huge. But it does seem to have staying powers which is very interesting.

MCB6 commented on 2 Nov 2021

Colombia doesn't sequence much so the uncertainty is huge. That's why I got excited today when they nearly doubled the number of last two month's sequences. I don't think it's visible at covSpectrum yet. But still with the grand total of 5 sequences in October, it's too uncertain, and regional variation may obscure any real trends. In Chile it see to be highly regional too, like Atacama in the North?

MCB6 , you could search on CovSpectrum just the mutations.

https://cov-spectrum.ethz.ch/explore/South%20America/AllSamples/Past3M/variants?aaMutations=S%3A449N%2CS%3A583D

And one can click on Chile's regions to realize that at one point, this Mu variety accounted for almost all of Atacama's sequences. But apparently not anymore. The strain dynamics in this region has several weirdly quick sweeps. Before mid-August it was Chile's usual Gamma / Lambda mix. Then Mu arrived and in just one months achieved total dominance (mostly, but not only, this substrain). Then Delta arrived and in another month the sweep was complete, with the classic Mu going away first, and the Mu+S:449N+S583D holding for only a little bit longer.
The number of cases in Atacama has been quite low during all this era of sweeps, mostly in single digits daily, so we may be dealing with founder outbreaks rather than with true strain competition? Which might explain the unrealistically fast changes?

MCB6 commented on 14 Nov 2021

Mu+S:449N+S583D was also in Lima, Peru in early August, seems to have disappeared by mid-September. 10 samples from Peru (they only started extensive sequencing in recent weeks, added over 3,000 genomes so far). Colombia added more October samples today. Mu+S:449N+S583D still accounts for ~10% of the recently collected samples (8 / 85 samples)

InfrPopGen  self-assigned this on 21 Nov 2021

MCB6 commented on 21 Nov 2021

Another batch from Colombia uploaded, including some late-October samples. The slight expansion trend of Mu+Spike_E583D,Spike_Y449N is holding well. In contrast, other varieties of Mu are nearly extinct.

InfrPopGen pushed a commit to InfrPopGen/pango-designation that referenced this issue on 17 Dec 2021

Added new lineages BB.1 and BB.2 from cov-lineages#232 with 91 and 23…

2c7ae24

  InfrPopGen added the designated label on 17 Dec 2021

InfrPopGen commented on 17 Dec 2021

Thanks for submitting. We've added proposal 1 as lineage BB.1 with 91 designated sequences in v1.2.113 and proposal 2 as lineage BB.2 with 238 designated sequences in v1.2.113

chrisruis added a commit that referenced this issue on 17 Dec 2021

Merge pull request #372 from InfrPopGen/master

fb87467

  chrisruis added this to the BB.1 BB.2 milestone on 17 Dec 2021 

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Kommentti: Mitä CovLineages mainitsevat sen jälkeen näistä   varianteista? Tarkistan:

B.1.621	United States of America 39.0%, Colombia 26.0%, Chile 9.0%, Ecuador 5.0%, Spain 4.0%	2020-12-15	13;	11266	Lineage predominantly in Colombia with several spike mutations, pango-designation issue #57	Mu
B.1.621.1	United States of America 64.0%, Spain 9.0%, Dominican_Republic 6.0%, Colombia 3.0%, Austria 2.0%	2021-04-09	97;	1938	Lineage in multiple countries, pango-designation issue #115
B.1.621.2	Colombia 64.0%, Chile 18.0%, United States of America 10.0%, Peru 4.0%, Canada 2.0%	2021-04-11	91;	691	Lineage in multiple countries, from pango-designation issue #232

BB.2

United States of America 97.0%, Dominican_Republic 1.0%, Canada 1.0%, France 1.0%, Spain 0.0%

2021-05-19

238,

358

Alias of B.1.621.1.2, from pango-designation issue #232

 (Kommenttini:  Huomaan tammikuulta 2022 merkinnän):

chrisruis commented on 7 Jan

It looks like BB.1 clusters outside of B.1.621.1 in recent UShER trees. It still clusters within B.1.621 so we've updated BB.1 to B.1.621.2 and withdrawn BB.1 in v1.2.122  YHTEENVETONA:  Tässä  tammikuisessa (2022)  päivityksessä on  joulukuussa  (2021)  ryhmitelty BB.1 siirretty suoraan  Mu variantin toiseksi  alalinjaksi BA.1.621.2  , joten  ensimmäisen  alalinjan  BA.1.621.1  sub-alalinjaksi 2  jää vain  BB.2.   Tarkemmin ilmaistuna B.1.621.1.2 Nimitys BB.1 poistettiin luettelosta kokonaan pois , koska  siihen  aluksi ryhmitetyt  virusnäytteet  osoittautuivat olevan  suoraa Mu-alalinjaa ( joka ei tarvitse koodia BB eli   alalinjan sub-linjamerkintää), kun oli usheroitu  varianttien  klusteroitumista  edelleen.  Ne klusteroituivat  päälinjalle (mu) , eikä  sen ensimmäiselle alalinjalle.  Siksi niistä tuli toinen Mu  alalinja. Ihmettelinkin ensin, että mistä se tuli, mutta GITHUB-teksti selvensi  asian.