Pub Med haku dominanteista Sars-Cov-2 varianteista 2023

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1

Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants.

Wang Q, Iketani S et al. . doi: 10.1016/j.cell.2022.12.018. Epub 2022 Dec 14. PMID: 36580913 Free PMC article. Here, we report that neutralization of BQ.1, BQ.1.1, XBB, and XBB.1 by sera from vaccinees and infected persons was markedly impaired, including sera from individuals boosted with a WA1/BA.5 bivalent mRNA vaccine. Titers against BQ and XBB subvariants were lower by 13- to 81-fold and 66- to 155-fold, respectively, far beyond what had been observed to date. Monoclonal antibodies capable of neutralizing the original Omicron variant were largely inactive against these new subvariants, and the responsible individual spike mutations were identified. These subvariants were found to have similar ACE2-binding affinities as their predecessors. Together, our findings indicate that BQ and XBB subvariants present serious threats to current COVID-19 vaccines, render inactive all authorized antibodies, and may have gained dominance in the population because of their advantage in evading antibodies

2

Efficacy of Antiviral Agents against Omicron Subvariants BQ.1.1 and XBB.

Imai M, Ito M et al. 

3

Low neutralization of SARS-CoV-2 Omicron BA.2.75.2, BQ.1.1 and XBB.1 by parental mRNA vaccine or a BA.5 bivalent booster.

Kurhade C, Zou J et al.  Nat Med. 2022 Dec 6. doi: 10.1038/s41591-022-02162-x. Online ahead of print. PMID: 36473500 The newly emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineages, including the BA.2-derived BA.2.75.2 and the BA.5-derived BQ.1.1 and XBB.1, have accumulated additional spike mutations that may affect vaccine effectiveness. Here we report neutralizing activities of three human serum panels collected from individuals 23-94 days after dose 4 of a parental mRNA vaccine; 14-32 days after a BA.5 bivalent booster from individuals with 2-4 previous doses of parental mRNA vaccine; or 14-32 days after a BA.5 bivalent booster from individuals with previous SARS-CoV-2 infection and 2-4 doses of parental mRNA vaccine. The results showed that a BA.5 bivalent booster elicited a high neutralizing titer against BA.4/5 measured at 14-32 days after boost; however, the BA.5 bivalent booster did not produce robust neutralization against the newly emerged BA.2.75.2, BQ.1.1 or XBB.1. Previous infection substantially enhanced the magnitude and breadth of BA.5 bivalent booster-elicited neutralization. Our data support a vaccine update strategy that future boosters should match newly emerged circulating SARS-CoV-2 variants

4

Plasma after both SARS-CoV-2 boosted vaccination and COVID-19 potently neutralizes BQ.1.1 and XBB.1.

Sullivan DJ, Franchini M, Senefeld JW, Joyner MJ, Casadevall A, Focosi D. bioRxiv. 2022 Dec 16:2022.11.25.517977. doi: 10.1101/2022.11.25.517977. Preprint. PMID: 36482971 Free PMC article.

The geometric mean of the geometric mean 50% neutralizing titers (GM (GMT (50) ) were 314, 78 and 204 for BQ.1.1, XBB.1 and BF.7, respectively. Compared to VaxCCP, plasma sampled from COVID-19 naive subjects who also recently within 6 months received at least a third vacci …

5

Coronavirus variant XBB.1.5 rises in the United States - is it a global threat?

Callaway E. Nature. 2023 Jan;613(7943):222-223. doi: 10.1038/d41586-023-00014-3. PMID: 36624320 No abstract available.

6

Imprinted SARS-CoV-2 humoral immunity induces convergent Omicron RBD evolution.

Cao Y, Jian F et al.  Nature. 2022 Dec 19. doi: 10.1038/s41586-022-05644-7. Online ahead of print. PMID: 36535326  Continuous evolution of Omicron has led to a rapid and simultaneous emergence of numerous variants that display growth advantages over BA.5 ¹. Despite their divergent evolutionary courses, mutations on their receptor-binding domain (RBD) converge on several hotspots. The driving force and destination of such sudden convergent evolution and its impact on humoral immunity remain unclear. Here, we demonstrate that these convergent mutations can cause striking evasion of neutralizing antibody (NAb) drugs and convalescent plasma, including those from BA.5 breakthrough infection, while maintaining sufficient ACE2 binding capability. BQ.1.1.10 (BQ.1.1+Y144del), BA.4.6.3, XBB, and CH.1.1 are the most antibody-evasive strains tested. To delineate the origin of the convergent evolution, we determined the escape mutation profiles and neutralization activity of monoclonal antibodies (mAbs) isolated from BA.2 and BA.5 breakthrough-infection convalescents ^2,3. Due to humoral immune imprinting, BA.2 and especially BA.5 breakthrough infection reduced the diversity of the NAb binding sites and increased proportions of non-neutralizing antibody clones, which in turn focused humoral immune pressure and promoted convergent evolution in the RBD. Moreover, we showed that the convergent RBD mutations could be accurately inferred by deep mutational scanning (DMS) profiles ^4,5, and the evolution trends of BA.2.75/BA.5 subvariants could be well-foreseen through constructed convergent pseudovirus mutants. These results suggest current herd immunity and BA.5 vaccine boosters may not efficiently prevent the infection of Omicron convergent variants. ... …

7

Subvariant 'soup' may drive wave.

Wong C. New Sci. 2022 Nov 5;256(3411):11. doi: 10.1016/S0262-4079(22)01970-4. Epub 2022 Nov 4. PMID: 36373068 Free PMC article.

The coronavirus subvariants BQ.1.1 and XBB may spread more readily than the original omicron variant and could evade prior immunity to some extent, writes Carissa Wong....

8

Does the COVID-19 XBB Omicron subvariant signal the beginning of the end of the pandemic?

Ngiam JN, Al-Mubaarak A, Maurer-Stroh S, Tambyah PA. Singapore Med J. 2022 Dec 1. doi: 10.4103/singaporemedj.SMJ-2022-180. Online ahead of print. PMID: 36648003 Review.

All pandemic viruses have eventually adapted to human hosts so that they become more transmissible and less virulent. The XBB Omicron subvariant is rapidly becoming the dominant strain of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Singapore from Octobe …

9

Substantial Neutralization Escape by SARS-CoV-2 Omicron Variants BQ.1.1 and XBB.1.

Miller J, Hachmann NP, Collier AY, Lasrado N, Mazurek CR, Patio RC, Powers O, Surve N, Theiler J, Korber B, Barouch DH. N Engl J Med. 2023 Jan 18. doi: 10.1056/NEJMc2214314. Online ahead of print. PMID: 36652339 No abstract available.

10

Antigenic mapping of emerging SARS-CoV-2 omicron variants BM.1.1.1, BQ.1.1, and XBB.1.

Mykytyn AZ, Rosu ME, Kok A, Rissmann M, van Amerongen G, Geurtsvankessel C, de Vries RD, Munnink BBO, Smith DJ, Koopmans MPG, Lamers MM, Fouchier RAM, Haagmans BL. Lancet Microbe. 2023 Jan 16:S2666-5247(22)00384-6. doi: 10.1016/S2666-5247(22)00384-6. Online ahead of print. PMID: 36657480 Free PMC article. No abstract available.

 

Omicron variantin glykosylaatioon vaikuttavat mutaatiot ? Sars-Cov-2 koronaviruksen S-proteiinin tyypilliset glykosylaatiokohdat

 Koetan löytää uusinta tietoa  sars--CoV-2 viruksen piikkiproteiinin glykosylaatioon vaikuttavista mutaatioista ja siitä, miten  virus moduloi  tätä  glykocalixrakennettaan

Löysin  useitekin tuoreita artikkeleita kuten tämän (peer review) katsauksen:

https://pubmed.ncbi.nlm.nih.gov/36415454/

 es Sq . 2022 Nov 16;rs.3.rs-2188138. doi: 10.21203/rs.3.rs-2188138/v1. Preprint

Site Specific N- and O-glycosylation mapping of the Spike Proteins of SARS-CoV-2 Variants of Concern

Asif Shajahan, Lauren Pepi, Bhoj Kumar, Nathan Murray, Parastoo Azadi

• PMID: 36415454
• PMCID: PMC9681045
• DOI: 10.21203/rs.3.rs-2188138/v1

Free PMC article

Abstract

The glycosylation on the spike (S) protein of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, modulates the viral infection by altering conformational dynamics, receptor interaction and host immune responses. Several variants of concern (VOCs) of SARS-CoV-2 have evolved during the pandemic, and crucial mutations on the S protein of the virus led to increased transmissibility and immune escape. In this study, we compare the site-specific glycosylation and overall glycomic profile of the wild type Wuhan-Hu-1 strain (WT) S protein and five VOCs of SARS-CoV-2: Alpha, Beta, Gamma, Delta and Omicron. Interestingly, both N- and O-glycosylation sites on the S protein are highly conserved among the spike mutant variants, particularly at the sites on the receptor-binding domain (RBD). The conservation of glycosylation sites is noteworthy, as over 2 million SARS-CoV-2 S protein sequences have been reported with various amino acid mutations. Our detailed profiling of the glycosylation at each of the individual sites of the S protein across the variants revealed intriguing possible association of glycosylation pattern on the variants and their previously reported infectivity. While the sites are conserved, we observed changes in the N- and O-glycosylation profile across the variants. The newly emerged variants, which showed higher resistance to neutralizing antibodies and vaccines, displayed a decrease in the overall abundance of complex-type glycans with both fucosylation and sialylation and an increase in the oligomannose-type glycans across the sites. Among the variants, the glycosylation sites with significant changes in glycan profile were observed at both the N-terminal domain (NTD) and RBD of S protein, with Omicron showing the highest deviation. The increase in oligomannose-type happens sequentially from Alpha through Delta. Interestingly, Omicron does not contain more oligomannose-type glycans compared to Delta but does contain more compared to the WT and other VOCs. O-glycosylation at the RBD showed lower occupancy in the VOCs in comparison to the WT. Our study on the sites and pattern of glycosylation on the SARS-CoV-2 S proteins across the VOCs may help to understand how the virus evolved to trick the host immune system. Our study also highlights how the SARS-CoV-2 virus has conserved both N- and O- glycosylation sites on the S protein of the most successful variants even after undergoing extensive mutations, suggesting a correlation between infectivity/ transmissibility and glycosylation.

Syyskuisen rekombinantin XBM alalinjaa ilmennyt uudestaan joulukuussa 2022 lokakuisen katoamisen jälkeen

https://github.com/cov-lineages/pango-designation/issues/1585 

GITHUB-ohjelmassa pohditaan  tämän variantin kasvuetuja linjassaan   vertailevasti   muiden linjojen ohella.  Saapuneiden näyteiden määrästä  ilmotetaan myös viime 10 päivänä saapuneitten näytteiden määrä. XBM rekombinantti muodostuu BA.2 ja BA.5 linjan  eräiden  alalinjojen  kesken.  tarkemmin määriteltynä: "BA.2.75" ja "BF.3"

BA on merkintä  BA.1.1.529  omikronille.

BF on koodimerkintä linjalle BA.5.2.1     omikronipäälinjassa BA.5 ja se sai kohtalaisen monta  alahaara

BA.2.75 on  omikronipäälinjan  BA.2  alalinja  75.

Pandemian alkuvaiheissa  teki eniten rekombinanttejaa  päälinjat BA.1 ja BA.2 , niitten koodaamiseen  käytettiin paljon kirjaimia  Niistä puhuttiin edellisvuosina. . Havaitaan useita rekombinntteja;   paljon niistä on  BA.2 päälinjan  ja sen alalinjojen keskeisiä variantteja, joista  silmiinipistävän dominoiva maailmassa, varsinkin Pohjois-Amerikassa päin,  on nyt XBB.1.5, joka on muodostunut  BA.2:n  alalinjan BA.2.75.3:n alalinjan BM.4   alalinjan BM.1.1.1  ja  toisaalta  BA.2.10.1 1 linjan kanssa Sen  alalinajn koodinimi on BJ.1.  BJ. ja BM.1.1.1 nimillä voi hakea Pangoluetteloista lisätietoja rekombinattienosatekijöistä. 

USA:n koronavarianttitaulukosta . Nebraskan ja CDC:n koronauutisista.

 Nebraskan uutisista  heijastuu panndemian kliiniset vaikutukset nyt tässä kuussa . Päivittäinen kuolleisuus on  vielä tuntuvaa. 

2023.https://www.nebraskamed.com/COVID/what-covid-19-variants-are-going-around

CDC lähteen tiedot vahvistavat USA:n koronatilanteen:

 XBB.1.5 dominoi  se muodostuu BA.2 alalinjojen  kesken muodostuneesta varianttilinjasta.

Toinen dominoiva ryhmä on BQ.1(.1) linjalaiset   , jotka  johtuvat  BA.5:n  alalinjojen puusta. 

Myös BA.5 päälinjallakin ja  BF-alalinjalla on vielä jonkin verran osuutta.  Muut linjat ovat edustettana vähäisin prosentein.

 https://covid.cdc.gov/covid-data-tracker/#variant-proportions

Understanding Variants

• What You Need to Know about Variants
• Understanding Variants

Variants and Genomic Surveillance

• Genomic Surveillance for SARS-CoV-2 Variants
• SARS-CoV-2 Variant Classifications and Definitions
• CDC’s Role in Tracking Variants
• Published SARS-CoV-2 Sequences
• Global Variants Report
• Science Brief: Emerging SARS-CoV-2 Variants

Suomesta signaali, että XBB.1.5 varianttia ilmenee sielläkin(13.1.2023)

 Suomen Terveyden ja Hyvinvoinninlaitos THL antaa  artikkelisaan tietää Suomessakin kiertelevän XBB.1.5 variantin:

SITAATTI: 

• Ajankohtaista
• Tiedotteet ja uutiset
• Tiedote
• Sote-uutiset-mobiilisovellus
• Näistä merkeistä tunnistat väärän tiedon verkossa

Koronaviruksen omikron XBB.1.5 -alalinjaa havaittu myös Suomessa

13.1.2023

Terveyden ja hyvinvoinnin laitoksen (THL) seurannassa on tehty ensimmäinen havainto

 koronaviruksen omikronvariantin XBB.1.5 -alalinjan viruksista Suomessa. 

Omikron XBB.1.5 -alalinjaa havaittiin ensimmäisen kerran lokakuussa 2022 Yhdysvalloissa, jossa se on

 levinnyt voimakkaasti. Sen jälkeen sitä havaittu myös Iso-Britanniassa sekä useissa EU/ETA-alueen 

maissa. 

”Oli odotettavissa, että kyseistä virusmuunnosta löytyy ennen pitkää myös Suomesta. XBB.1.5-alalinjan 

virusten arvioidaan tarttuvan herkästi, ja kuten tällä hetkellä Suomessa kiertävät omikron variantit,

 XBB.1.5 väistää tehokkaasti immuunisuojaa. Tällä hetkellä sen ei kuitenkaan tiedetä aiheuttavan

 muita omikronvirusmuunnoksia vakavampaa tautia, ja rokotesuoja vakavaa tautia vastaan on säilynyt 

erinomaisena varianteista riippumatta”, sanoo THL:n johtava asiantuntija Carita Savolainen-Kopra.    

THL seuraa eri koronavirusvarianttien esiintymistä Suomessa niin sanotulla kokogenomisekvensoinnilla.

 Sen avulla määritetään otoksena väestössä kiertävien virusten linjat sekä niissä esiintyvät mutaatiot. 

 Tulokset raportoidaan tartuntatautirekisteriin sekä koosteena THL:n verkkosivuilla 2–3 viikon

 viiveellä näytteenotosta.

Lisätiedot 

Muuntuneet koronavirukset (THL)

SARS-CoV-2-koronaviruksen genomiseuranta (THL)

Koronavirus SARS-CoV-2 (THL)

Carita Savolainen-Kopra
johtava asiantuntija 
THL

Hanna Nohynek
ylilääkäri
THL 

Hahmotusta: GITHUB asioita, oivalluksia , valmiita listaluetteloita viruslinjoista 18.1. 2023 ja taapäin ajassa

 Koetan vähän hahmottaa itselleni näitä linjoja ja koodinimiä 18.1.2023:

Uusimmat vasta-avatut GITHUB aiheet tästä linkistä: #issue, (opened 104) (closed 1163).

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

Aivan tuorein asia 41  minuutteja sitten tällä hetkellä.

Viimeinen INSIGHT-palsta 7.1.2023 : https://github.com/cov-lineages/pango-designation/pulse

4 päivää sitten: Esim: #issue , closed

Uusin BA.5.1*- ryhmän haara: BA.5.1.32

Rekombinantti: XBN

Viimeisin lisäys kasvaneeseen CH-alalinjaan.CH.1.1 .

Uusin lisätty alalinjakoodi DU ja sen edustajalinja DU.1

VIIMEISIMMÄT tag-luettelot: https://github.com/cov-lineages/pango-designation

TAGS

v1.18

https://github.com/cov-lineages/pango-designation/releases/tag/v1.18

BQ.1.1.1 merkataan CZ-koodilla ja se taas saa usean sisarlinjan, jotka ovat BQ.1.(1) alalinjoja.

Näkyy lisäkoodeja: DL, DM, DN, DQ, DP, DR.

BN.1.2.1 merkataan DS. BQ.1.1.32- linja merkataan DT.

XBM

 

( Omia yhteenvetojani tässä myös: Uusia päälinjoja kuten BA.1,- .2,-.3,.4,.5) ei ehkä enää ilmesty). BA.2* ja BA.5* alalinjajoukkoineen dominoi. Tietyt ala-alalinjat niistä saavat diversiteettiä runsaasti edelleen. Uusia mutaatioita kertyy hyvin paljon kaiken kaikkiaan ihan kuin “random” yli kaikkien haara-alueiden ilman  näennäistä logiikkaa mielestäni, niin että määrittelemättömien , ratkaisemattomien sekvenssien joukkokin kasvaa koko ajan ja kliinistä merkitystä koetetaan kliinisellä puolella WHO:n toivomuksesta hahmottaa. Ajattelin että syy voi  esim.olla UTR-mutaatioissa, mutta eivät ne selitä asiaa. Ehkä virus vain virttyy vanhenee omassa plasmaatisessa olomuodossaan  tai erilaiset , tosiaalta eri paikoissa samanlaiset ulkoiset tekijät tekevät samanlaisen muutoksen. Toistaiseksi vaikuttavat kaikki omikroneilta sanotaan WHO:ssa ja käsittääkseni ja kliinisesti vakavuudeltaan samantapaisiks, mutta  kuolleisuutta esiintyy edelleen. KAikissa  respiratorisissa oinfektíoissa on tosin aina kuolleisuutensa. Tämä vain on myös muuta kudostakin laajasti rusikoiva.  Kiinan asia - jos siellä on erityistä vaarallisuutta, se johtuu osin  myöhemmästä pandemisesta suuraallosta siellä. Tosin siinä piilee vaaransa, koska virus on error prone tyyppinen osaksi, vaikka UTR on hyvin konservatiivinen, ehkä ei varmaan tule sellaista denguen tapaista 4 sairastamista tai 4 eri rokotetta vaativaa tautia, sen sijaan kuten uumoillaan, influenssarokotuksen tapaan jonkin valenssin vuosittainen sesonkikoronarokote vuodestta toiseen. Muutama varianttiryhmä omaa suurta diversiteettiä ja niitä näkyy viimeisissä designaatiolistoissa  selvitetyn  paljon: BQ.1.(1) ja XBB- ryhmää edelleen selvitellään ja havainnoidaan. Toisaalta esim BG ja BF kasvoivat aluksi, mutta alkoivat osoittaa rajoittumista kuten moni muu koodin saanut. Koodin saaminen helpottaa hahmttamista. Moni  haara loppuu siihen, kun ne on hahmotettu tarkasti ja aikansa seurattu.  Rekombinanttien muodostus on siirtynyt alkuvaiheen BA.1/BA.2 rekombinanteista BA.2- alalinjojen tai BA.2/BA.5 linjojen tai alalinjojen  tai rekombinanttien rekombinanteiksi. Jotkut ovat multirekombinantteja, ristitsevät 2 kertaa tai useamman kerran. .Tietokoneelta valmiista luetteloista nuo listat ovat nopeasti selvillä, mutta jos itselleen tekee muistiinpanot ja koettaa saadan loogisen käsityksen haaroittumiskaavasta ja uusista mutaatioista, niin se kyllä on aikaa vievää, toisaalta antaa valaisevan kuvan, jos saa jonkin linjan puun kuvan itselleen).

https://github.com/cov-lineages/pango-designation/releases/tag/v1.18

V1.17 tag ( edellinen lista)

Uusia sub-alalinjakoodeja: DA, DB, DC, DD, DE, DF, DG, DH, DJ, DK

Rekombinantit: XBF, XBG, XBH, XBJ. XBK, XBL, XBM.

https://github.com/cov-lineages/pango-designation/releases/tag/v1.17

v.1.16 tag ( edellisen edellinen lista jne)

Marraskuun 2. pv. Linjakoodi BN.

Lisätään koodeja: CH, CJ, CK, CL,CM, CQ, CP, CR, CT, CU, CV (BM.1.1.3), CY. ‘

Varsinkin BE (BA.5.3.1) on alkanut saada lisää alalinjoja kuten BQ ,ja se saa alalinjojen alalinjoja CW (BQ,1,1,14).  Rekombinaatiot määritetty: XBD, XBE.

aineniamh released this 02 Nov 11:17 233 commits to master since this release v1.16

v1.15 tag

Useat linjat haaroittuvat. Tarvitaan useita uusia alakoodeja. Lokakuun 3. luetellaan uudet alalinjat koodeineen BL,BM, BN, BP, BQ, BP, BR, BS, BT, BU, BV, BW, BY, BZ, CA, CB, CC, CD, CE, CF, CG, Uudet rekombinantit: XAS, XAT, XAU, XAV, XAW, XAY, XAZ, XBA, XBB, XBC.

Cornelius Roemer 3.Oct.https://github.com/cov-lineages/pango-designation/releases/tag/v1.15

v.1.14

Tarvitaan jo koodit BH ( linja BA.2.38.3), BJ ( linja BA.2.10.1 ), BK ( BA.5.1.10). Lisää rekombinantteja määritetty:XAQ, XAR . chrisruis released this 19 Aug 16:06 634 commits to master since this release v1.14

v1.13 tag.

BA.5* ja BA.4* saavat alalinjoja lisää, ei niin paljon kuin BA.2*. Rekombinanttilinjoja lisää: XAJ, XAK, XAL, XAM, XAN, XAP. Ei lisämainintoja BA.1 ja BA.3 linjoista. chrisruis released this 01 Aug 10:32 694 commits to master since this release v1.13

v.1.12 tag.

BE ( BA.5.3.1) vaikuttaa tekevän poikkeavan runsaasti alalinjoja

Myös BA.5.2.1 saa koodinsa BF, joka on runsas alahaaralinja.

BA.2* tekee paljon alalinjoja, varsinkin havaittu kroonisesti infektoituneissa paljon uusia mutaatioita. BA.2.75 alkaa erottua joukosta (ja saa useita alalinjakoodeja ajan mittaan)

(kuten myös BA.2.12.1 alalinjakoodi BG).

chrisruis released this 09 Jul 13:39· 787 commits to master since this release v1.12

v1.11 tag

BG ( BA.2.12.1) havaitaan erityisen runsaasti haaroittuneena.

XAH mainitaan päivitettynä.

Chrisruis ,June 22, released this 22 Jun 09:18 · 861 commits to master since this release v1.11

v.1.10 tag

( Tässä jaksossa BA.1* linjat ja BA.2* linjat saavat runsaasti määriteltyjä haaroja Havaitaan BA.4* ja BA.5*. joilla on spikehahmo kuten BA.2:lla. BA.1 spike rakenteen omaavat vähenevät esiintymiseltään. Deltan (AY) runsaitten haarojen nimeäminen jatkuu vielä.

Otetaan käyttöön koodit : BC, BD, BE, BF, BG.

Rekombinantteja nimetään lisää XY, XZ, XAA, XAB, XAC, XAD, XAE, XAF, XAG, XAH.

chrisruis released this 17 Jun 07:13 867 commits to master since this release v1.10

( Näitä listoja on sitten  aiemmiin ihan  alkuluetteloon asti linkissä)

Sars-CoV-2 linjamäärittelyjä. PANGO tietueen päivitettyjä INSIGHTS listoja : v1.18

 https://github.com/cov-lineages/pango-designation/releases/tag/v1.18

SARS-CoV-2 rekombinanttien viimeisin PANGO-linjapäivitys valmiiksi saaduista GITHUB määritelmistä

 

https://github.com/cov-lineages/pango-designation/blob/master/lineage_notes.txt

Valmiiksi saadut rekombinanttimääritelmät viime GITHUB-master päivityksissä n. 14.1.2023 aikoihin sitaattina. Varsinkin XBB.1.5 rekombinanttiklusteri on työn alla.

XA Recombinant lineage with parental lineages B.1.1.7 and B.1.177, UK lineage

XB Recombinant lineage with parental lineages B.1.634 and B.1.631, Central and North America lineage, discussed in pango-designation issue #189. Formally B.1.628

XC Recombinant lineage with parental lineages AY.29 and B.1.1.7, Japan lineage, from pango-designation issue #263

XD Recombinant lineage of Delta and BA.1, France and Denmark lineage, from pango-designation issue #444

XE Recombinant lineage of BA.1 and BA.2, UK lineage, from pango-designation issue #454

XF Recombinant lineage of Delta and BA.1, UK lineage, from pango-designation issue #445

XG Recombinant lineage of BA.1 and BA.2, Denmark lineage, from pango-designation issue #447

XH Recombinant lineage of BA.1 and BA.2, Denmark lineage, from pango-designation issue #448

XJ Recombinant lineage of BA.1 and BA.2, Finland lineage, from pango-designation issue #449

XK Recombinant lineage of BA.1 and BA.2, Belgium lineage, from pango-designation issue #460

XL Recombinant lineage of BA.1 and BA.2, UK lineage, from pango-designation issue #464

XM Recombinant lineage of BA.1.1 and BA.2, European lineage, from pango-designation issue #472

XN Recombinant lineage of BA.1 and BA.2, UK lineage, from pango-designation issue #480

XP Recombinant lineage of BA.1.1 and BA.2, UK lineage, from pango-designation issue #481

XQ Recombinant lineage of BA.1.1 and BA.2, UK lineage, from pango-designation issue #468

XR Recombinant lineage of BA.1.1 and BA.2, UK lineage, from pango-designation issue #469

XS Recombinant lineage of Delta and BA.1.1, USA lineage, from pango-designation issue #471

XT Recombinant lineage of BA.1 and BA.2, South Africa lineage, from pango-designation issue #478

XU Recombinant lineage of BA.1 and BA.2, lineage in India and other countries, from pango-designation issue #522

XV Recombinant lineage of BA.1 and BA.2, lineage in Denmark and Italy, from pango-designation issue #463

XW Recombinant lineage of BA.1 and BA.2, USA, Germany, England lineage, from pango-designation issue #591

XY Recombinant lineage of BA.1 and BA.2, predominantly in USA, from pango-designation issue #606

XZ Recombinant lineage of BA.2 and BA.1, USA lineage, from pango-designation issue #636

XAA Recombinant lineage of BA.1 and BA.2, USA lineage, from pango-designation issue #664

XAB Recombinant lineage of BA.1 and BA.2, Germany lineage, from pango-designation issue #665

XAC Recombinant lineage of BA.1 and BA.2, Canada and USA lineage, from pango-designation issue #590

XAD Recombinant lineage of BA.2 and BA.1, Germany lineage, from pango-designation issue #607

XAE Recombinant lineage of BA.2 and BA.1, USA and Chile lineage, from pango-designation issue #637

XAF Recombinant lineage of BA.1 and BA.2, Costa Rica lineage, from pango-designation issue #676

XAG Recombinant lineage of BA.1 and BA.2, lineage in Brazil and other countries, from pango-designation issue #709

XAH Recombinant lineage of BA.2 and BA.1, lineage in Slovenia and other countries, from pango-designation issue #755

XAJ Recombinant lineage of BA.2.12.1 and BA.4, predominantly in England, from pango-designation issue #826

XAK Recombinant lineage of BA.1 and BA.2, Germany lineage, from pango-designation issue #823

XAL Recombinant lineage of BA.1 and BA.2, Germany lineage, from pango-designation issue #757

XAM Recombinant lineage of BA.1.1 and BA.2.9, lineage mainly found in Panama and USA, from pango-designation issue #759

XAN Recombinant lineage of BA.2 and BA.5.1, lineage found most often in Spain and Denmark, from pango-designation issue #771

XAP Recombinant lineage of BA.2* and BA.1*, USA lineage, from pango-designation issue #789

XAQ Recombinant lineage of BA.1* and BA.2*, lineage mainly found in Canada, from pango-designation issue #798

XAR Recombinant lineage of BA.1* and BA.2*, Reunion lineage, from pango-designation issue #860

XAS Recombinant lineage of BA.5* and BA.2*, USA lineage, from pango-designation issue #882

XAT Recombinant lineage of BA.2.3.13 and BA.1*, Japan lineage, from pango-designation issue #885

XAU Recombinant lineage of BA.1.1* and BA.2.9*, predominantly in Spain, England and France, from pango-designation issue #894

XAV Recombinant lineage of BA.2* and BA.5*, mainly France, USA, and Scotland lineage, from pango-designation issue #911

XAW Recombinant lineage of BA.2* and AY.122, Russia lineage, from pango-designation issue #895

XAY Recombinant lineage of BA.2 and AY.45, South Africa lineage, from pango-designation issue #844

XAY.1 South Africa/US lineage with 4 AA substitutions including S:D253G

XAY.1.1 South Africa with S:R346T and ORF1a:K2108N, from issue #1255

XAY.1.2 Europe, ORF1a:T3646I

XAY.2 South Africa/Denmark/Israel lineage with ORF1a:Y3765C

XAY.3 South Africa/Mauritius/Switzerland/France, ORF1b:D1869Y

XAZ Recombinant lineage of BA.2.5, BA.5. and BA.2.5, predominantly found in France, Germany, Croatia, Denmark and USA, from pango-designation issue #797

XBA Recombinant lineage of perhaps AY.45 and perhaps BA.2 (with perhaps 5 breakpoints), South_Africa lineage, constellation 2 from pango-designation issue #844

XBB Recombinant lineage of BJ.1 and BA.2.75 with breakpoint in S1, found in USA and Singapore, from issue #1058

XBB.1 Mostly Bangladesh and Singapore, defined by S:G252V, from issue #1088

XBB.1.1 Singapore/Denmark, defined by ORF1a:P309L

XBB.1.2 Singapore, defined by S:S640F

XBB.1.3 Singapore, India/Italy, defined by S:A484T

XBB.1.4 Europe, S:T883I

XBB.1.4.1 Mainly Denmark, Norway and Sweden, defined by S:S673G, from pango-designation issue #1352

XBB.1.5 USA, S:F486P

XBB.1.6 USA, S:L216F, S:H146K, from issue #1428

XBB.1.7 USA-NY, S:V608I

XBB.1.8 Denmark, S:186insSGG, C3241T

XBB.1.9 ORF1a:G1819S, ORF1a:T4175I

XBB.1.9.1 S:F486P, England/South Korea/Singapore/Denmark

XBB.2 Defined by S:D253G, from issue #1173

XBB.2.1 Defined by S:N764S

XBB.2.2 Defined by S:Q613H

XBB.3 Defined by ORF1b:I1988V on ORF1a:D82G branch

XBB.3.1 Defined by S:Q677R, India-TN/Singapore, from issue #1241

XBB.3.2 Defined by S:M177T

XBB.3.3 Defined by S:V1122L, USA

XBB.4 Defined by S:K444R on ORF1a:D82G branch, from issue #1239

XBB.4.1 England/Austria, S:L5F, S:T470N

XBB.5 Defined by S:A653V on ORF1a:D82G branch, India-TN, Singapore, Australia

XBB.6 Defined by C14178T, USA/India/England

XBB.6.1 Defined by S:F486P, USA, from #1459

XBC Recombinant lineage of BA.2 and B.1.617.2*, predominantly in Philippines, from pango-designation issue #1100

XBC.1 Mostly Philippines, South Korea, US, Singapore, defined by S:L452M, from issue #1130

XBC.1.1 Mostly Australia, ORF1a:I3619T, ORF8:V114L

XBC.1.1.1 Australia, S:G476S

XBC.1.2 Philippines/Netherlands/Denmark, T11269C

XBC.1.2.1 Denmark, ORF1b:T132I

XBC.2 Mostly Philippines, defined by S:K97R

XBD Recombinant lineage of BA.2.75.2 and BF.5, India and world, from pango-designation issue #1137

XBE Recombinant lineage of BA.5.2 and BE.4.1, predominantly in USA and England, from pango-designation issue #1246

XBF Recombinant lineage of BA.5.2.3 and CJ.1, Australia, from pango-designation issue #1259

XBG Recombinant lineage of BA.2.76 and BA.5.2, predominantly in UK, from pango-designation issue #896

XBH Recombinant lineage of BA.2.3.17 and BA.2.75.2, predominantly in Brunei, from pango-designation issue #1229

XBJ Recombinant lineage of BA.2.3.20 and BA.5.2, possibly Philippines, from pango-designation issue #1268

XBK Recombinant lineage of BA.5.2 and CJ.1, Denmark/Europe, from pango-designation issue #1418

XBL Recombinant lineage of XBB.1 with S:F486P and BA.2.75, Malaysia, from issue #1532

XBM Recombinant lineage of BA.2.76 and BF.3, India/USA/Canada, from issue #1441

SARS-CoV-2, BA.1 variantin PANGO-linjoista

(Viimeisimpiä Sars-CoV-2 omicronvarianttien PANGO-listapäivityksiä GITHUB-master lähteestä 14.1.2023)

BA.1

https://github.com/cov-lineages/pango-designation/blob/master/lineage_notes.txt

BA.1.1.529 South Africa and Botswana lineage, from pango-designation issue #343 Tämä on Omicron parent

BA.1 Alias of B.1.1.529.1, from pango-designation issue #361

BA.1.1 Alias of B.1.1.529.1.1, from pango-designation issue #360

BA.1.1.1 Alias of B.1.1.529.1.1.1, European lineage

BC.1 Alias of B.1.1.529.1.1.1.1, Japan lineage

BC.2 Alias of B.1.1.529.1.1.1.2, Peru lineage, from pango-designation issue #570

BA.1.1.2 Alias of B.1.1.529.1.1.2, Japan lineage

BA.1.1.3 Alias of B.1.1.529.1.1.3, Switzerland lineage

BA.1.1.4 Alias of B.1.1.529.1.1.4, UK lineage

BA.1.1.5 Alias of B.1.1.529.1.1.5, South Korea lineage

BA.1.1.6 Alias of B.1.1.529.1.1.6, Canada lineage

BA.1.1.7 Alias of B.1.1.529.1.1.7, lineage in India and other countries

BA.1.1.8 Alias of B.1.1.529.1.1.8, USA lineage

BA.1.1.9 Alias of B.1.1.529.1.1.9, New Zealand lineage

BA.1.1.10 Alias of B.1.1.529.1.1.10, Canada lineage

BA.1.1.11 Alias of B.1.1.529.1.1.11, European lineage

BA.1.1.12 Alias of B.1.1.529.1.1.12, UK lineage

BA.1.1.13 Alias of B.1.1.529.1.1.13, UK lineage

BA.1.1.14 Alias of B.1.1.529.1.1.14, European lineage

BA.1.1.15 Alias of B.1.1.529.1.1.15, Europe and Australia lineage

BA.1.1.16 Alias of B.1.1.529.1.1.16, Canada and USA lineage

BA.1.1.17 Alias of B.1.1.529.1.1.17, USA lineage, from pango-designation issue #452

BA.1.1.18 Alias of B.1.1.529.1.1.18, USA lineage

BA.1.2 Alias of B.1.1.529.1.2, Mayotte and Reunion lineage

BA.1.3 Alias of B.1.1.529.1.3, Canada lineage

BA.1.4 Alias of B.1.1.529.1.4, France lineage

BA.1.5 Alias of B.1.1.529.1.5, UK lineage

BA.1.6 Alias of B.1.1.529.1.6, Canada and Sint Maarten lineage

BA.1.7 Alias of B.1.1.529.1.7, UK lineage

BA.1.8 Alias of B.1.1.529.1.8, European lineage

BA.1.9 Alias of B.1.1.529.1.9, Brazil lineage

BA.1.10 Alias of B.1.1.529.1.10, UK lineage

BA.1.12 Alias of B.1.1.529.1.12, UK lineage

BA.1.13 Alias of B.1.1.529.1.13, European lineage

BA.1.13.1 Alias of B.1.1.529.1.13.1, Indonesia lineage

BA.1.14 Alias of B.1.1.529.1.14, lineage in Brazil and other countries

BA.1.14.1 Alias of B.1.1.529.1.14.1, Brazil lineage, from pango-designation issue #506

BA.1.14.2 Alias of B.1.1.529.1.14.2, Brazil lineage

BA.1.15 Alias of B.1.1.529.1.15, lineage in USA and other countries

BA.1.15.1 Alias of B.1.1.529.1.15.1, UK lineage

BA.1.15.2 Alias of B.1.1.529.1.15.2, USA lineage, from pango-designation issue #508

BA.1.15.3 Alias of B.1.1.529.1.15.3, Peru lineage, from pango-designation issue #573

BA.1.16 Alias of B.1.1.529.1.16, UK lineage

BA.1.16.1 Alias of B.1.1.529.1.16.1, Thailand, Cambodia and Indonesia lineage

BA.1.16.2 Alias of B.1.1.529.1.16.2, Greece lineage

BA.1.17 Alias of B.1.1.529.1.17, European lineage

BA.1.17.1 Alias of B.1.1.529.1.17.1, Australia lineage

BA.1.17.2 Alias of B.1.1.529.1.17.2, lineage from pango-designation issue #462

BD.1 Alias of B.1.1.529.1.17.2.1, UK lineage, from pango-designation issue #461

BA.1.18 Alias of B.1.1.529.1.18, Europe and North America lineage, from pango-designation issue #474

BA.1.19 Alias of B.1.1.529.1.19, Europe lineage

BA.1.20 Alias of B.1.1.529.1.20, USA lineage, from pango-designation issue #375

BA.1.21 Alias of B.1.1.529.1.21, lineage from pango-designation issue #505

BA.1.21.1 Alias of B.1.1.529.1.21.1, Italy lineage, from pango-designation issue #409

BA.1.22 Alias of B.1.1.529.1.22, Peru lineage from pango-designation issue #529

BA.1.23 Alias of B.1.1.529.1.23, mainly found in USA, from pango-designation issue #663

BA.1.24 Alias of B.1.1.529.1.24, found in Spain, from pango-designation issue #666