GITHUB mainintoja Japanissa esiintyvistä Sars-2 varianttien alalinjoista viime aikoina

 Otan sitaatteja GITHUB tekstissä,  ja muutaman eritysimaininnan siitä  vyyhdimäisestä tilanteesta, jota  tiedemiehet ovat tottuneet tässä selvittelemään  etsiessään  johtolankoja joihinkin  erityisiin mutaatioihin Minusta jotkut mutaatiot eivät varsinaisesti ole evoluutiota, vaan vain energiatilan loppumista  viruksen rakenteen  koostamisyrityksissä ja  sitten stoikkastisesta  muutoksesta, joka ihan  sattumoisin on tapahtunut  ja kuitenkin on saattanut koostumusta vielä  muutaman kerran  toistua, mutta linjaa ei  sen koommin  ole  esiintynyt eikä merkattu.  Jokin kohta  rakeknteessa saattaa olla erityisen altis muuttumaan eri varianteissa olosuhteista ja energiatilasta ( tai lähinnä energian puutteesta)  riippuen, eikä siksi että  ne olisivat jotain samaa linjaa.  Japanissa on kuitenkin päivittäiset tartuntatapaukset vielä suuri luku! Tämä virus on tosi loinen, sillä se kehrää ihmisen proteiinit ja mineraalit niin että moni laihtuu tämän infektion aikana haitallisesti- lisäksi hajun ja makuaistin poissaolo vähentää  ravinnonottoa ja ihmisen yleiskunnon heiketessä virus menestyy  edelleen. Vaikka pandemia muuttuisi endemiaksi se ei tarkoita että  ei pitäisi asiaan kiinnittää huomiota. Endemiaksi muuttuminen voi olla yleiskuntojen alenemistilaa.  

Closed GITHUBs

#687, BA.2.3.18 Japan 138 sekvenssiä. Milestone 14.7.2022

https://github.com/cov-lineages/pango-designation/issues/687

Spike:I692F, Membrane:I76V.

#745, BA.2.56.1 Milestone 13.6. 2022

https://github.com/cov-lineages/pango-designation/issues/745,

Description Potential sublineage of: BA.2.56 (the European sublineage with spike L452M from the BA.2 root) Earliest sequence: 2022/03/27 (Japan-Hyogo prefecture) Most recent sequence: 2022/05/21 (Japan-Kochi prefecture)Mutations on top of BA.2:

Gene	Amino changes
ORF1a	R226K  (67/75)
Spike	H69Y, L452M, W886L
ORF3a	A31S (48/75)

#605, BA.2.3.11 Milestone 13.6. 2022.

https://github.com/cov-lineages/pango-designation/issues/605

Proposal for new sub-lineage of BA.2.3 with C13326T (ORF1ab: T4354I) and A20214G (synonymous) in Japan (858 sequences as of 2022-06-07, 13.4% of BA.2.3 in Japan) #605

".. this proposed sublineage is only 4.5% (=130/2864) of the BA.2.3 isolated in Japan, which is a small number.However, our proposed sublineage is characterized by its high locality within Japan.
Therefore, I believe that it would be useful for genome surveillance in Japan if this proposed sublineage can be easily confirmed together with the conventional BA.2.3 and BA.2.3.1, the main lineage of the BA.2 lineage in Japan. Thank you in advance for your consideration.

7.6. 2022: For the updated data, the proposed lineage has increased to 13.4 % (= 858 / 6399) of BA.2.3 in Japan.

13.6.2022 Chrisruis: Thanks @takaabe8050 The geographical focus of this clade in Japan means that it has an associated epidemiological event so warrants a designation. We spotted this independently and added it as BA.2.3.11. Thanks again

#600 , BA.2.24, Milestone 2.5. 2022.

https://github.com/cov-lineages/pango-designation/issues/600

A BA.2 lineage with Spike:339N seems to be growing in Tokyo.

#590, XAC Milestone 10.6. 2022

Potential BA.2*/BA.1*/BA.2* Recombinant with Double Breakpoints (244 Seqs in Israel, Germany, Canada, Ireland, Netherland, Sweden, Japan, India, UK and US as of 2022-06-10) #590

https://github.com/cov-lineages/pango-designation/issues/590

c19850727 commented on 2 Jun

171 sequences as of 2022-06-01, and now newly found in India-KA and Japan ex-US.

• (Tärkeä välihuomautus! TÄSTÄ SAA YLEISKÄSITYSTÄ NÄITTEN VARIANtTIEN ANALYSOIMISESTA!)

AngieHinrichs commented on 2 Jun

"Tangential, but I still want to make the distinction: BA.2 and its descendants (BA.3, BA.4, BA.5) BA.3, BA.4 and BA.5 are not believed to be descendants of BA.2 (or they would be BA.2.X), but rather separate emergences from the Omicron reservoir along with BA.1 and BA.2. (There is some discussion for BA.3 in #367; the Pango lineage designation committee had some internal discussions about BA.4/BA.5 that unfortunately didn't make it into #517.) BA.4 and BA.5 are similar to BA.2, but lacking enough BA.2 mutations that it seems more likely that they arose separately within the Omicron reservoir. BA.4 and BA.5 split off from the BA.2 branch of the UCSC/UShER tree, but that is only because that's where they fit in with the fewest substitutions (including reversions to reference for BA.2 mutations that are not found in BA.4 & BA.5). The tree's basal Omicron branches are a mess because there are many different combinations of false reversions found in sequences, and (as far as I know) no actual pre-BA.* ancestral Omicron sequences. ktmeaton commented on 2 Jun: "Thank you for catching and correcting that @AngieHinrichs! Just to clarify, the topology of 22A (BA.4) and 22B (BA.5) falling within the diversity of 21L (BA.2) is not true to their evolutionary origin because there is underlying mutation conflicts? Or am I misinterpreting the tree or your explanation? Thanks!" https://user-images.githubusercontent.com/14981272/171708141-6364bdf6-4e70-4b62-9b4f-9dafe617bdb6.png

AngieHinrichs commented on 2 Jun :

"21L on that tree is much broader than BA.2. It includes recombinants (the sequences that appear below the 22A label; England/PHEC-YYFJF3T/2022 says BA.2 in the pop-up but it's XW), BA.4, BA.5, and BA.2 (the yellow-orange and red sequences above 22B). 21L is more like "Omicron minus BA.1 and BA.3". "I think it actually does show the separation of BA.2, BA.4 and BA.5, if you define BA.2 as the sequences above 22B. Some reversions are still required to get that structure -- the branch leading to 22A and 22B has a reversion on 23040 (shared by BA.1, BA.2 and BA.3), and the branch to 22B has 5 more reversions (again, tree structures can't be perfect when recombination might have been involved). 22A and 22B are also missing C9866T which is in nearly all BA.2 sequences, although as @corneliusroemer has pointed out, lack of C9866T might actually be ancestral for BA.2.

Hi @InfrPopGen, I think we've resolved the major outstanding issue in this proposal with the consensus that this is a BA.1/BA.2 recombinant with double breakpoints. Are there any other problems to resolve before an official designation?  Title: Potential BA.2*/BA.1*/BA.2* Recombinant with Double Breakpoints (244 Seqs in Israel, Germany, Canada, Ireland, Netherland, Sweden, Japan, India, UK and US as of 2022-06-10) on 10 Jun

InfrPopGen commented on 10 Jun

"Thanks for submitting (and apologies for the delay). We've added recombinant lineage XAC with 126 newly designated sequences, and 3 updated designations".

#591 , XW, Milestone 10.6. 2022.

Potential BA.1*/BA.2* Recombinant with Likely Breakpoint at NSP3 (53 Seqs as of 2022-05-11 in Japan, Germany, Slovenia, Canada, UK and US) designated recombinant

c19850727 commented on 28 Apr

Although this potential recombinant sublineage doesn't meet the minimum criteria of 50 sequences, I thought it's still worth proposing considering it has been found in multiple regions in a relatively short period of time. Recombinant between: BA.1* & BA.2* Earliest sequence: 2022/3/13 (Japan ex-Finland) Most recent sequence: 2022/4/17 (UK-England) Countries circulating: UK (England), US (MD, CO, NY), Canada (ON), Germany (BW, NW, BB, BE, NI, SN), Japan (ex-Finland) Likely breakpoint: between 2834 and 4183 (NSP3). Private mutations: C10507T, C12756T (ORF1a:T4164I), G16020T Conserved Nuc mutations (those in red frames are likely from the donor from the BA.1 side):

 

#587   Possible BA.2.3 sublineage with ORF1a:K798N starting in Northern Mariana Islands and Guam (779 sequences in Cov-Spectrum) #587

 https://github.com/cov-lineages/pango-designation/issues/587

InfrPopGen commented on 11 May

Thank you for proposing this lineage for designation. Unfortunately, it does not quite meet the criteria for designation at present. There is no clear estimated growth advantage for BA.2.3* + ORF1a:K798N, ORF1b:A88V above BA.2* or BA.2.3*, according to CoV-spectrum (indeed it is estimated as negative in comparison with BA.2.3*). Although, this lineage appears to have played a major role in the N Marianas, it is not associated with any other epidemiological trait (e.g. increased hospitalisation, transmissibility). Should the situation change, please feel free to re-propose, as a new issue, for designation with the additional evidence.

#569   BA.2.10.2   Milestone 10.5. 2022.

https://github.com/cov-lineages/pango-designation/issues/569

fedeGueli: " While checking for japanese airport surveillance sequences from India @c19850727 (Sakaguchi Hitoshi) highlighted me that a significant share of the last samples was carrying the E:R61L mutation.
Looking at Japanese sequences we found that a BA.2.10 sublineage with E:R61L circulates there .
Here we want to propose it, but it is worth mentioning and monitoring that multiple BA.2 sublineages carry this sublineage and one of them is actually growing quite fast in Switzerland.

InfrPopGen commented on 10 May

Thanks for submitting. We've added lineage BA.2.10.2 with 50 newly designated sequences, and 1 updated designations from BA.2.10. Defining mutation(s) G26426T (E:61L).   #522, XU , BA.1/BA.2 https://github.com/cov-lineages/pango-designation/issues/522   Description Recombinant between: BA.1* & BA.2 Earliest sequence: 2022/1/20 (Japan ex-India) Most recent sequence: 2022/3/4 (India-Maharashtra) Countries circulating: India (3 seqs in Gurajat and 2 seqs in Maharashtra), Japan (1 seq from imported case with travel history to India) Likely breakpoint: between 6518 and 9343 (NSP3 or NSP4). Conserved Nuc mutations (those in red frames are likely from the donor from the BA.1 side): chrisruis commented on 19 Apr Thanks @c19850727 We've added this as XU.