WHO: lakoninen raportti

 

Weekly epidemiological update on COVID-19 - 1 June 2022

Edition 94

1 June 2022

 | Emergency Situational Updates

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Overview

Globally, the number of new weekly cases has continued to decline since a peak in January 2022. During the week of 23 until 29 May 2022, over 3.3 million cases were reported, an 11% decrease as compared to the previous week.

The number of new weekly deaths also continues to decline, with over 9 600 fatalities reported, representing a 3% decrease as compared to the previous week.

As of 29 May 2022, over 526 million confirmed cases and over six million deaths have been reported globally.

In this edition, we provide updates on circulating SARS-CoV-2 variants of concern (VOCs).

https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports

Omicron 5.2.1 alalinja määritelty

 InfrPopGen added a commit that referenced this issue 2 days ago

Merge pull request #700 from InfrPopGen/master

46e564d

InfrPopGen commented 2 days ago

Thanks for submitting. We've added lineage BA.5.2.1 with 201 newly designated sequences, and 125 updated designations. Defining mutation(s) C1627T and A27038G.

Omicron BA.5.3.1

 Proposal for a sublineage of BA.5
Earliest sequence: 3/17/2022 (South Africa)
Countries detected: mainly South Africa, with recent spread to various other European countries (e.g. UK, Denmark, Austria)
Defining mutations:
G16935A = ORF1b:M1156I

This sublineage represents c. 10% of all current BA.5 genomes but is apparently expanding since it is already present in multiple European countries (UK, Denmark). The sublineage was recently detected in Austria where it represents c. 40% of all BA.5 genomes (6/14).
It is apparently a sublclade of the clades containing N:E136D and ORF1a:Q556K (#550) so these issues may have to be resolved first before this one is designated. However, this is a not a sublineage of the big branch proposed in #551 since it is not defined by ORF9b:D16G.

BA.5 uusimmista alalinjoista pohdintoja :

Asia #680

RajLABN mentioned this issue 6 days ago

Potential BA.5 sub-lineage circulating mainly in USA with ORF1a:A76V mutation [52 sequences] #680

 

agamedilab commented 6 days ago

Hi, thank you for proposing! At the moment the growth advantage of BA.5 + S:T76I is strong against BA.5 (#656). As you mentioned, this is a sublineage BA.5 + S:T76I (#656) therefore the growth advantage as measured now could be derived from S:T76I instead of orf1a:A76V. In fact when you compare BA.5 + S:T76I versus BA.5 + orf1a:A76V than the advantage of the latter is not so clear tight now.

 

BA.5 näyttää saavan alalinjoilleenkin jonkin alalinjan. (Uusimpia asiankäsittelynumeroita on #656).

 Eräs näitä uusia alalinjkandidaatteja on sellainen BA.5 rakenne, jossa ilmenee  muuan lambda tunnusmutaatio piikkiproteiinin alueella: S: T61I. Tämän variantin  kasvuetuja on punnittu muiden BA.5 varianttien suhteen.  Tämä tuli keskustelupintaan 15 päivää sitten ja  sitä seurataan. Se ei näy vielä PANGO-listassa, koska se ei ole vielä saanut varmaa leimaansa eikä  riittävää sekvenssimäärää Otan tästä väliaikatiedotuksesta  sitaatin:  Asian aukaisia on   tunnusmerkiltään  "Agamedilab".

commented 15 days ago •

Proposal for a sublineage of BA.5 Earliest sequence: 2022-03-22 South Africa) Countries detected: South Africa (2), USA (99), United Kingdom (1), France (1), Mexico (1) Defining mutations: C21789T = S:T76I This variant defined by S:T76I was first detected in South Africa but has managed to spread to multiple other countries (USA, Mexico, UK and France). Within the USA it is currently the dominant BA.5 variant (c. 66%, 104/158 GISAID) and was detected in 23 states (Michigan, Oklahoma, Missouri, North Carolina, Mississippi, Illinois, Tennessee, Florida, Maryland, Kansas, Virginia, Minnesota, New York, Texas, Indiana, Nevada, Arizona, Wisconsin, New Jersey, California, Massachusetts, Nebraska, Utah). The variant is apparently distinct from variants defined by  N:E136D (#550),  ORF1ab:Q556K (#550),  Orf9b:D16G (#551),  ORF10:L37F (#621),  ORF1b:M1156I (#625)  and S:V1230A, ORF1a:P2685S, C2338T (#652)."  (Kommenttia:  Variantin havaitseva laboratorio toteaa, että  tämä uusi ( vielä ilman määritelmää oleva) löytö BA.5-linjaa eroaa selvästi aiemmin määritellyistä BA.5-linjoista, joita mainitaan niiden asiankäsittelynumeron avulla ja tunnusmutaatioilla yllä).  Linja BA.5.1  sai määritelmänsä  allaolevan  alkukeskustelun ´päätteeksi:( Sitaatti asiasta  #621): "silcn commented 25 days ago Proposal for a sublineage of BA.5 Earliest sequence: 2022-03-08 (South Africa) Countries detected: mainly Portugal (136 seq), with spread to various other European countries Defining mutations: C29666T = ORF10:L37F, T27438C I'm assuming here that ORF10 is counted as a coding protein and thus this lineage can be designated. Please correct me if I'm mistaken and this is why the lineage hasn't already been proposed! FedeGueli commented 24 days ago Great catch @silcn i suggest to follow the evolution of this one on the fantastic INSAFLU weekly update report page: https://insaflu.insa.pt/covid19/ corneliusroemer commented 22 days ago Good catch, I agree. This one stands out very well as a Portugese introduction. Let's hope ORF10 counts ;) FedeGueli commented 18 days ago I saw a BA.5.1 designated from Portugal  is this one? Yeah, it is, well spotted. It was actually added less than a day after I started this issue so was likely already going to be designated. I'll close and let someone with the necessary powers add the tags. FedeGueli commented 16 days ago • Thx @silcn .I have checked the growth advantage of BA.5.1 since you proposed and it seems higher than other BA.4/BA.5 in other European countries. lets see if it changes with time and settles down a bit. ( .... Tiedemiehet tässä keskustelevat siitä Portugalin  BA.5-alalinjasta, josta nyt on lehdessä uutisia. tämä alalinja BA.1 on sikäli muista  näistä alalinjoista poikkeava, että siinä esiintyy tuo  harvinainen Orf10 mutaatio Sen kasvuetuja muihin BA.4 / BA.5 linjoihin  verrataan).  Muita linjojakin  mainitaan vertailtaessa tähän uuteen löytöön, joka on  todella poikkeava niistä, mutta sen esiintymä on vielä  vähäinen, joten  tiedemiehet   sanoivat, että on odotettava pari viikkoa sen määrittelyn suhteen.    Toinen esimerkki: BA.5.2 linja on saanut jo määrittelynsä aiemmin:   Määrittävä mutaatio on Orf9b:D16G. Sitaatti:  InfrPopGen commented 10 days ago Thanks for submitting. We've added lineage BA.5.2 with 3 newly designated sequences, and 62 updated designations from BA.5. Defining mutation(s) A28330G (ORF9b:D16G). Kolmas esimerkki on BA.5.3 linjasta  Sitaatti:  N:E136D (#550), ORF1ab:Q556K (#550), Neljäs esimerkki edellisen alalinjasta BA.5.3.1 Tämä alalinja on saanut alalinjan BA.5.3.1 viime päivinä: sillä on löytynyt vielä yksi  ala-alalinjan tunnusmerkki  Orf1b: M1156I. Sitaatti:  InfrPopGen.Added new lineage BA.5.3.1 from cov-lineages#625 with 63 new sequence designations, and 19 updated designations from BA.5.3

Omikronlinja BA.5.1 omaa harvinaisen ORF10 mutaation ( Orf10: L38F)

 Aiemmin on tutkittu ORF10:n  proteiinin merkitystä. Sillä on 38 aminohappoa. Maailmasta ei ole löytynyt kovin montaa  Sars-2 sekvenssiä, joissa ilmenisi  ORF10 mutaatio. 

 Niistä harvoista löydöistä on tehty tieteellinen artikkeli.

  https://www.sciencedirect.com/science/article/pii/S0141813021025563#t0010

Tämä BA.5.1 linjassa esiintyvå ORF10 mutaatio on L37F. Sekin muaatio kuuluu artikkelissa esitettyyn listaan ORF10 omaa  N-terminaalisessa osassa metioniini-glysiini-tyrosiini-motiivin (MGY) ja sen avulla  se rekrytoituu  CLR2 kompleksiin On mahdollista, että ORF10 omaa merkitystä taudin   paranemisen hitaudessa ja tarttuttavuusajan pidentymisessä.  CLR2-kompleksi kuuluu kehon ubikitiini-proteosomitien jäseniin ja  sars-2 saattaa olla kaapannut  tämän järjestelmän tavalla tai toisella. 

Sitaatteja artikkelista :

Continent-wise unique variations of ORF10 proteins and their mutations with predicted effects are presented in the following subsections.

 ORF10 variants and transmembrane topology of SARS-CoV-2 ORF10

Continent-wise distribution of the total 140 unique ORF10 variants is presented in Table 1. The highest frequency of unique ORF10 variants was found in North America among the total of 140 SARS-CoV-2 ORF10 variants.

BA.2 omikronvarianttijoukko on saanut lisää linjamäärityksiä BA.2.42:n jälkeenkin.

 

BA.2.42			75 designated	0 assignated	Alias of B.1.1.529.2.42, mainly found in Australia, from pango-designation issue #610
BA.2.43			25	0	Alias of B.1.1.529.2.43, mainly found in India, from pango-designation issue #612
BA.2.44			149	0	Alias of B.1.1.529.2.44, mainly found in Belgium and Luxembourg, from pango-designation issue #613
BA.2.45			438	0	Alias of B.1.1.529.2.45, mainly found in Sweden and Denmark, from pango-designation issue #616
BA.2.46			117	0	Alias of B.1.1.529.2.46, mainly found in Scotland, from pango-designation issue #626