Tarkennettuja , laajennettuja Aliases XAY ja XBA

"XAU": ["BA.1.1*","BA.2.9*"],

"XAV": ["BA.2*","BA.5*"],

"XAW": ["BA.2*","AY.122"],

"XAY": ["AY.45","BA.4/5*"],

"XAY": ["BA.2*", "AY.45", "BA.2*", "AY.45", "BA.2*"],

"XAZ": ["BA.2.5","BA.5","BA.2.5"],

"XBA": ["AY.45","BA.4/5"],

"XBA": ["BA.2*", "AY.45", "BA.2*", "AY.45", "BA.2*"],

"XBB": ["BJ.1","BM.1.1.1"],

"XBC": ["BA.2*","B.1.617.2*","BA.2*","B.1.617.2*"],

"XBD": ["BA.2.75.2","BF.5"],

@@ -158,9 +158,9 @@

 

XBF rekombinantista ja sen alalinjoista asiaa. Spike: P621S mutaatiosta pohdintaa.

 https://github.com/cov-lineages/pango-designation/issues/1651

ryhisner commented Feb 13, 2023

Description
Sub-lineage of: XBF
Earliest sequence: 2023-1-10, Australia, New South Wales — EPI_ISL_16584770
Most recent sequence: 2023-2-5, Australia, South Australia — EPI_ISL_16902443
Countries circulating: Australia (15), Singapore (2)
Number of Sequences: 17
GISAID Query: Spike_F486P, Spike_P621S, NSP1_K120N
CovSpectrum Query: Nextcladepangolineage:XBF* & [5-of: T3442C, T9931C, C12970T, C13255T, C22000T, C23423T, T25039C]
Substitutions on top of XBF:
Spike: P621S
Nucleotide: T3442C, T9931C, C12970T, C13255T, C22000T, C23423T, T25039C

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/subtreeAuspice1_genome_37cb4_a1b030.json

 Evidence
For reasons unknown, S:P621S has become a mutational hotspot of ate, particularly in lineages and individual sequences with other notable mutations. It seems meaningful, though I have no idea what is behind it. This lineage only recently appeared but seems to be growing quickly. Whether that is due to chance or an isolated outbreak or because it possesses some advantage isn't yet clear, but I think it bears watching. There are an unusual number of synonymous mutations in this lineage, all C->T or T->C.

Genomes

Genomes

 

FedeGueli

i think two new ones have been added from England! it seems really fast, unluckily

maybe unrelated @ryhisner could u check them: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3be10_a668b0.json?c=userOrOld&label=id:node_8273022

ryhisner commented Feb 13, 2023

 Oh, wow, nice spot, Fede! It looks like there are actually six sequences from England altogether, though four of them are not yet on GISAID. Usher puts the English sequences on a separate branch from the Australian ones, but I'm almost certain they really belong together. The giveaway is that both branches have the synonymous mutation C23423T. Hard to believe that's a coincidence. The four artifactual "reversions" (T3796C, T3927C, T4586C, T5183C) that appear on every uploaded XBF sequence (but not on the other sequences on the tree) might be mucking things up somehow.'

AngieHinrichs commented Feb 14, 2023

Those two branches have C23423T (S:P621S, non-synonymous) in common, but they each have several other mutations after XBF with no overlap aside from C23423T. The branch with most of the uploaded sequences is

XBF > C12970T > T9931C > T3442C,C22000T > C13255T,C23423T,T25039C

and the branch with the two sequences from England with C23423T (S:P621S) is

XBF > C24378T > G3728T > C23423T,A23989G

(The four artifactual "reversions" (T3796C, T3927C, T4586C, T5183C) that appear on every uploaded XBF sequence (but not on the other sequences on the tree) might be mucking things up somehow).

Sorry about the reversions. Those are true for XBF (because that part of it comes from BA.5.2 not BA.2.75), but are masked out of the entire BA.2.75 branch of the UShER tree (where XBF is placed) because false reversions were an awful problem with BA.2.75 sequences. The masking on the BA.2.75 branch (but not in uploaded sequences) mucks up the details of how sequences are placed in the web interface relative to existing sequences in the tree, but should not affect which existing branches the sequences are placed on within XBF (because all of the BA.2.75 branch has those sites masked).

 

BTW there is a new, hopefully more readable, source of info about branch-specific masking in the UShER tree -- instead of a bash script that just performed the masking, there is now a YAML specification of the masking (and a separate script that performs the masking according to the spec):

https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml

2 days ago Label: recombinant sublineage 

-----

oobb45729 commented Feb 15, 2023

S:P621S may be about immune escape.

Initially I have some doubts about it since P621 is not in the main epitope. However, a closer look reveals that the growth of P621S or P621H does follow a similar pattern like E554K or E554V.
E554K

-----

ryhisner commented Feb 15, 2023

@AngieHinrichs, thanks for the insight on the tree! My assumption was that the South Australian sequences in particular are so shabby as to make branches that belong together appear as if they don't belong together. Possibly the tree is different now, but when I last checked, it showed four independent acquisitions of ORF1ab:N4899I on this lineage's branch as well as at least two independent acquisitions of ORF1a:L3715N and N:L139F, which seems unlikely. But since South Australia apparently doesn't show where there is missing coverage in their sequences, putting those branches together would probably require positing multiple reversions, which is even more unlikely.

Are there any efforts to standardize certain ways of reporting sequences? I imagine it would make things a lot clearer—and make your job a lot easier—if all labs indicated where their sequences lack coverage instead of reverting to the reference genome in those places, producing multitudes of artifactual reversions. The public health lab in the state of Utah in the USA is probably the worst offender in this regard. Sometimes I wish there was a way to screen out sequences from certain countries (Pakistan, Turkey, Chile, etc) or regions (Utah, Louisiana, Kerala) from GISAID/Covspectrum searches and Usher trees.

 

 

 

Uusimpien designaatioitten lista v18 tullut 9.2.2023 nettiin Github tietueessa

Päivitys tags v1.18 

https://github.com/cov-lineages/pango-designation/releases/tag/v1.18.1

Sen jälkeen tullut seuraavat lyhennyskoodit  käyttöön:

"EH": "B.1.1.529.5.3.1.1.1.1.1.1.28",

"EJ": "B.1.1.529.2.75.5.1.3.8",

"EK": "XBB.1.5.13",

"EL": "XBB.1.5.14",

Pandemian ajalta tietoa LAOSin valtion alueelta:

 GITHUB mainitsee tänään että Laosin sars-2-sekvensseissä näyttää olevan BN.1.3 variantin alalinjaa  runsaahkosti. Toisaaltt taas näiden pandemiavuosien aikan Laos on sekvensoinut vain runsaat 1000 varianttia. TAi siis tiedottanut ulkopuollel GISAIDiin asti. Katsoin tittoa  Laosin kansasta. Kansaa on  vajat 9 miljoonaa ja maa on toisten valtioiden ympäröimä ilman merirajaa.  WHO jäsenlistassa ei näy Laosin nimeä.  Suomalaisia on siellä käynyt ja  on kontakteja seurakuntaelämään. www.irrtv.fi Laosia käsitteleviä katsauksia takavuosilta. 

PubMed tietoja, joissa LAOS mainitaan

(1)

• Author Correction: Bat coronaviruses related to SARS-CoV-2 and infectious for human cells.

  Temmam S, Vongphayloth K, Baquero E, Munier S, Bonomi M, Regnault B, Douangboubpha B, Karami Y, Chrétien D, Sanamxay D, Xayaphet V, Paphaphanh P, Lacoste V, Somlor S, Lakeomany K, Phommavanh N, Pérot P, Dehan O, Amara F, Donati F, Bigot T, Nilges M, Rey FA, van der Werf S, Brey PT, Eloit M. Nature. 2022 Jul;607(7920):E19. doi: 10.1038/s41586-022-05048-7. PMID: 35798954 Free PMC article. No abstract available.

Abstract

The animal reservoir of SARS-CoV-2 is unknown despite reports of SARS-CoV-2-related viruses in Asian Rhinolophus bats^1-4, including the closest virus from R. affinis, RaTG13 (refs. ^5,6), and pangolins^7-9. SARS-CoV-2 has a mosaic genome, to which different progenitors contribute. The spike sequence determines the binding affinity and accessibility of its receptor-binding domain to the cellular angiotensin-converting enzyme 2 (ACE2) receptor and is responsible for host range^10-12. SARS-CoV-2 progenitor bat viruses genetically close to SARS-CoV-2 and able to enter human cells through a human ACE2 (hACE2) pathway have not yet been identified, although they would be key in understanding the origin of the epidemic. Here we show that such viruses circulate in cave bats living in the limestone karstic terrain in northern Laos, in the Indochinese peninsula. We found that the receptor-binding domains of these viruses differ from that of SARS-CoV-2 by only one or two residues at the interface with ACE2, bind more efficiently to the hACE2 protein than that of the SARS-CoV-2 strain isolated in Wuhan from early human cases, and mediate hACE2-dependent entry and replication in human cells, which is inhibited by antibodies that neutralize SARS-CoV-2. None of these bat viruses contains a furin cleavage site in the spike protein. Our findings therefore indicate that bat-borne SARS-CoV-2-like viruses that are potentially infectious for humans circulate in Rhinolophus spp. in the Indochinese peninsula. © 2022. The Author(s), under exclusive licence to Springer Nature Limited. 

 

(2) https://pubmed.ncbi.nlm.nih.gov/34278365/

. 2021 Aug;13:100197.

doi: 10.1016/j.lanwpc.2021.100197. Epub 2021 Jul 14.

Low seroprevalence of COVID-19 in Lao PDR, late 2020

Siriphone Virachith  ¹ , Virginie Pommelet  ¹ , Elodie Calvez  ¹ , Vilaysone Khounvisith  ¹ , Somphou Sayasone  ² , Sengchanh Kounnavong  ² , Mayfong Maxay  ^{3   4   5} , Phonepadith Xangsayarath  ⁶ , Sarah Temmam  ⁷ , Marc Eloit  ^{7   8} , Nicolas Escriou  ⁹ , Thierry Rose  ¹⁰ , Khamsing Vongphayloth  ¹ , Judith M Hübschen  ¹¹ , Vincent Lacoste  ¹ , Somphavanh Somlor  ¹ , Darouny Phonekeo  ¹ , Paul T Brey  ¹ , Antony P Black  ¹

Affiliations

• PMID: 34278365
• PMCID: PMC8277598
• DOI: 10.1016/j.lanwpc.2021.100197

Free PMC article

Abstract

Background: In 2020 Lao PDR had low reported COVID-19 cases but it was unclear whether this masked silent transmission. A seroprevalence study was done August - September 2020 to determine SARS-CoV-2 exposure.

Methods: Participants were from the general community (n=2433) or healthcare workers (n=666) in five provinces and bat/wildlife contacts (n=74) were from Vientiane province. ELISAs detected anti- SARS-CoV-2 Nucleoprotein (N; n=3173 tested) and Spike (S; n=1417 tested) antibodies. Double-positive samples were checked by IgM/IgG rapid tests. Controls were confirmed COVID-19 cases (n=15) and pre-COVID-19 samples (n=265). Seroprevalence for the general community was weighted to account for complex survey sample design, age and sex.

Findings: In pre-COVID-19 samples, 5·3%, [95% CI=3·1-8·7%] were anti-N antibody single-positive and 1·1% [0·3-3·5%] were anti-S antibody single positive. None were double positive. Anti-N and anti-S antibodies were detected in 5·2% [4·2-6·5%] and 2·1% [1·1-3·9%] of the general community, 2·0% [1·1-3·3%] and 1·4% [0·5-3·7%] of healthcare workers and 20·3% [12·6-31·0%] and 6·8% [2·8-15·3%] of bat/wildlife contacts. 0·1% [0·02-0·3%] were double positive for anti-N and anti-S antibodies (rapid test negative).

Interpretation: We find no evidence for significant SARS-CoV-2 circulation in Lao PDR before September 2020. This likely results from early decisive measures taken by the government, social behavior, and low population density. High anti-N /low anti-S seroprevalence in bat/wildlife contacts may indicate exposure to cross-reactive animal coronaviruses with threat of emerging novel viruses.

Funding: Agence Française de Développement. Additional; Institut Pasteur du Laos, Institute Pasteur, Paris and Luxembourg Ministry of Foreign and European Affairs ("PaReCIDS II"). 

(3)  WILDLIFE study, LAO PDR  wildlife tutkimus:

. 2020 Aug;165(8):1869-1875.

doi: 10.1007/s00705-020-04683-7. Epub 2020 Jun 1. Coronavirus surveillance of wildlife in the Lao People's Democratic Republic detects viral RNA in rodents

David J McIver  ¹ , Soubanh Silithammavong  ^{2   3} , Watthana Theppangna  ⁴ , Amethyst Gillis  ^{3   5} , Bounlom Douangngeun  ⁴ , Kongsy Khammavong  ² , Sinpakone Singhalath  ² , Veasna Duong  ⁶ , Philippe Buchy  ^{6   7} , Sarah H Olson  ⁸ , Lucy Keatts  ⁸ , Amanda E Fine  ⁸ , Zoe Greatorex  ⁸ , Martin Gilbert  ⁸ , Matthew LeBreton  ⁹ , Karen Saylors  ^{3   10} , Damien O Joly  ^{1   2   11} , Edward M Rubin  ³ , Christian E Lange  ¹²

Affiliations

• PMID: 32488616
• PMCID: PMC7265875
• DOI: 10.1007/s00705-020-04683-7

Free PMC article

Nicknames, lempinimiä dominoiville varianteille

 Tästä linkistä saa lisätietoja joka koodista: koodi alkaa  Wuhan variantin A-linjasta, joten täytyy  selata siihen asti, kun alkaa omicron, B.1.1.529  ja siten kaikki  BA-linnjt ja niiden alakoodit. Aivan listan alapäässä siten löytyy X koodeja,XA-XZ, XAA-XAZ, XBA- jne . tärkeä monitoroitu alue on XBB . tämä allaoleva linkki on päivitetty muutamia viikkoja siten.  Niihin tehtävät muutokset ovat GITHUB Commits-listoissa kertymässä.  Käsiteltävänä olevat ovat  GITHUB Issues# asioissa.   Varianttien rakenteesta:  monomeerisestä peptidistä (ORF1a, ib, Spike, Orf3a, E, M, Orf6, Of7a, Orf7b, Orf8, Orf9, Orf10)  saa käsitystä PANGO luettelosta lisätietolinkeistä. Myös esiintymiskäyrät ovat  siinä CovLineages-linkissä. 

Näihin  pääsee WHO Omicron ikonista, siinä  oikealla listassa olevasta " sars-Cov-2 variants" linkistä ja  siitä avautuvasta VOC-taulukosta. VOC- taulukon alla on linkki PANGO-luetteloon.  Cov Lineages. Kun menee sille sivulle, mistä voi hakea eri linjoja, huomaa otsikkosivun yläreunassa linkin GITHUB-tietueeseen ( aktuelleihin  asiankäsitteyihin ja pohdintoihin).  ( Toinen tietue GISAID ottaa maailmalta vastaan sekvenssejä ja tiedottaa niistä).

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

B.1.1.529 = Omicron. Saa lyhennyksen BA

BA.1 (BA.1.1)

BA.1 linjan alakoodeja:BC,BD.

BA.1.1.1= BC

BA.1.17.2 =BD.

BA.2

BA.2:n alakoodeja: BG, BW, BJ, BL, BM, BN, BP, BR, BS, BY, CA, CB, CH, CJ, CV, DD,DS.

BA.2.3.20, lempinimi “Basilisk”

BA.2.10 , lempinimi “Pisces”

BA.2.10, lempinimi “Argus”

BA.2.38.3.1, (BH.1). Lempinimi “Almops”

BA.2.75, lempinimi “Centaur”

BA.2.75.1 (BL)

BA.2.75.2 . (CA), lempinimi “Alcyon”

BA.2.75.3 (BM)

BA.2.75.3.1.1.1

BM.1.1.1 (CJ), lempinimi “Mimas”

BA.2.75.3.4.1.1, (CH)

CH.1.1.1 = DV

BA.2.75.4 (BR)

BA.2.75.5 (BN)

BN.1, lempinimi “Hydra”

(acbasiliqued S494P in BN.1.1)

BA.2.75.6 (BY)

BA.2.75.9 (CB)

XBB on rekombinaatio BA.2 alalinjojen kesken.

“Argus” x “Mimas” = Gryphon tai “Griffon”

(BA.3 on hyvin vähän haaroittunut päälinja)

BA.4 pääryhmä.

Tällä ryhmällä on suhteellisen vähän alaryhmiä ja lisäkoodeja on tarvittu vain muutama.

BA.4.1.10 (CS)

BA.4.6 , “Aeterna

BA.4.6.5 (DC)

(BA.5.4 on poistettu nimi, koska kyse ei ollut omasta erillisestä linjasta , vaan BA.2 linjasta, josta kehkeytyi linja BA.4/5. Kun asia havaittiin , poistgettiintettiin turha merkintä BA.5.4)

BA.5.= omicron 5 eli B.1.1.529.5 = BA.5.

BA.5 pääryhmä

Sillä on alaryhmät .1, .2, .3, .5. jne. Jouduttiin jälkeenpäin poistamaan BA.5 .4, koska huomattiin, että kyse oli BA.2 linjasta, joka alkoi aiheuttaa näitä jatkohaaroja eli se tyvi olikin se BA.2)

BA.5.1 -ryhmästä alakoodeja: BK, CL, CU, DE, DH, DJ, DL.

BA.5.2 -ryhmästä alakoodeja: , BT, BU, BZ, CD, CE, CF, CG, CK, CN, CP, CR,CT, CY, DA, DB.

BA.5.2.1=BF

BF.7 (BA.5.2.1.7) , “Minotaur”

BA.5.3-ryhmästä alakoodeja: BE, BQ, CC, CQ, CW, CZ, DK, DM, DN, DP, DQ, DR, DT, DU.

BA.5.3.1=BE.

BE.1.1.1 = BQ.

BE.1.2.1=DW.

BA.5.3.1.1.1.1=BQ= B.1.1.529.5.3.1.1.1.1

BQ.1, “Typhon”

BQ.1.1, “Cerberus”

BA.5.6-linjasta alakoodi: BW.

BA.5.10-linjasta alakoodi:DF.

 

Pub Med haku dominanteista Sars-Cov-2 varianteista 2023

20 results

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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.