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torsdag 29 februari 2024

ECDC: VOI ja VUM Sars-Cov-2 varianteista taulukot 16.2. 2024

 https://www.ecdc.europa.eu/en/covid-19/variants-concern

SARS-CoV-2 variants of concern as of 16 February 2024

 

Variant classification serves as an important communication tool for alerting EU/EEA countries about the emergence of SARS-CoV-2 variants with concerning properties likely to impact the epidemiological situation in the EU/EEA.

ECDC utilises three categories of variant classification to communicate increasing levels of concern about a new or emerging SARS-CoV-2 variant: variant under monitoring (VUM), variant of interest (VOI) and variant of concern (VOC). Classification criteria and recommended Member state actions are available here:

ECDC variant classification criteria and recommended Member State actions

New evidence is regularly assessed on variants detected through epidemic intelligence, genomic horizon scanning, or other scientific sources. If a decision is made to add, remove, or change the category for any variant, the tables are updated to reflect this change. The tables are regularly sent for consultation to ECDC and WHO Regional Office for Europe’s joint virus characterisation working group.

Variant surveillance data, including the distribution of VOC and VOI variant proportions in the EU/EEA, is presented as part of the European Respiratory Virus Surveillance Summary (ERVISS)(link is external).

Useful links

To review a timeline of variant classification decisions, visit our change log.

Following classification of a VOC or VOI, multiple closely related sub-lineages may emerge. To facilitate reporting of variant detections by countries to TESSy, a table listing sub-lineages assigned to VOCs and VOIs as of 2 February 2024 is available here

An additional table that includes sub-lineages assigned to VUMs as of 2 February 2024 is available here.

Description of the tables

The tables include:

Category: variant of concern (VOC), variant of interest (VOI), or variant under monitoring (VUM).

  1. WHO label: As of 31st May 2021, WHO proposed labels for global SARS-CoV-2 variants of concern and variants of interest(link is external) to be used alongside the scientific nomenclature in communications about variants to the public. This list includes variants on WHO’s global list of VOC and VOI, and is updated as WHO’s list changes.
  2. Lineage and additional mutations: the variant designation specified by one or more Pango lineages and any additional characteristic spike protein changes. An alternate description may be used if the variant is not easy to describe using this nomenclature. For updated information on Pango lineages and definition of lineages and for instructions on how to suggest new lineages, visit the Pango lineages website(link is external). Each lineage in then table is linked to the respective lineage page on the Pango lineages website.
  3. Country first detected: only present if there is moderate confidence in the evidence relating to the first country of detection.
  4. Spike mutations of interest: not all spike protein amino acid changes are included – this is not a full reference for assignment of the variants. It includes changes to spike protein residues 319-541 (receptor binding domain) and 613-705 (the S1 part of the S1/S2 junction and a small stretch on the S2 side), and any additional unusual changes specific to the variant.
  5. Year and month first detected: as reported in the GISAID EpiCoV database. This can be adjusted backwards in time if new retrospective detections are made.
  6. Evidence concerning properties in three different categories:
    • Transmissibility
    • Immunity
    • Infection severity
      Each category is annotated as increased, reduced, similar, unclear, or no evidence depending on the currently available evidence. Increased or reduced means that there is evidence demonstrating that the property is different enough for the variant compared to previously circulating variants that it is likely to have an impact on the epidemiological situation in the EU/EEA. Similar means that there is evidence that demonstrates that the property is not different enough for this variant compared to previously circulating variants that it is unlikely to have an impact. Unclear means that the current evidence is preliminary or contradictory enough to make the assessment uncertain. No evidence means that no evidence has yet been evaluated for this category. The evidence is further annotated with v or m to indicate whether the evidence is available for the variant itself (v) or for mutations associated with the variant (m).
  7. Transmission in the EU/EEA: categorised as dominant, community, outbreak(s), and sporadic/travel. The categories are qualitative, and the assessment is based on surveillance data collected in TESSy, GISAID EpiCoV data, epidemic intelligence data, and direct communications with the affected countries.

 

Variants of Concern (VOC)

As of 3 March 2023, ECDC has de-escalated BA.2, BA.4 and BA.5 from its list of SARS-CoV-2 variants of concern (VOC), as these parental lineages are no longer circulating. ECDC will continue to categorise and report on specific SARS-CoV-2 sub-lineages in circulation that are relevant to the epidemiological situation.

There are currently no SARS-CoV-2 variants meeting the VOC criteria.

Variants of Interest (VOI)

WHO labelLineage + additional mutationsCountry first detected (community)Spike mutations of interestYear and month first detectedImpact on transmissibilityImpact on immunityImpact on severityTransmission in EU/EEA
OmicronXBB.1.5-like (a)United StatesN460K, S486P, F490Sn/aSimilar to Baseline (1, 2)Reduced (v) (1, 3)Similar to Baseline (4)Community
Omicron

XBB.1.5-like + F456L (b)

(e.g. EG.5, FL.1.5.1, XBB.1.16.6, and FE.1)

n/aF456L, N460K, S486P, F490Sn/aBaselineBaseline (5)BaselineCommunity
OmicronBA.2.86n/aI332V, D339H, R403K, V445H, G446S, N450D, L452W, N481K, 483del, E484K, F486Pn/aUnclear (6)Unclear (6-8)No evidenceDominant

a: Monitoring an umbrella of SARS-CoV-2 lineages that have similar Spike protein profiles and characterised by a specific set of mutations (S:Q183E, S:F486P and S:F490S). For the full list of lineages, please look at the table here.

b: Monitoring an umbrella of SARS-CoV-2 lineages that have similar Spike protein profiles and characterised by a specific set of mutations (S:F456L, S:Q183E, S:F486P and S:F490S). For the full list of lineages, please look at the table here.

All sub-lineages of the listed lineages are also included in the variant

 

Variants under monitoring

WHO labelLineage + additional mutationsCountry first detected (community)Spike mutations of interestYear and month first detectedImpact on transmissibilityImpact on immunityImpact on severityTransmission in EU/EEA
OmicronXBB.1.5(link is external)-like + L455F + F456Ln/aL455F, F456L, N460K, S486P, F490Sn/aNo evidenceNo evidenceNo evidenceDetected
OmicronBA.2.87.1South AfricaG75D,S98F,V126A,W152L,R190S,K417T,K444N,V445G,L452M,N481K,V642G,K679R,S691P,T791I,Y796H,D936G (b)2023 SeptemberNo evidenceNo evidenceNo evidenceNot Detected

 

n/a: not applicable

b: Preliminary mutations based on a limited number of genomes

 

De-escalated variants

These additional variants of SARS-CoV-2 have been de-escalated based on at least one the following criteria: (1) the variant is no longer circulating, (2) the variant has been circulating for a long time without any impact on the overall epidemiological situation, (3) scientific evid....

 

 

torsdag 22 februari 2024

sars-Cov-2 ja Ki67 proteiini

 

Observational Study
. 2024 Jan 23:14:1303971.
doi: 10.3389/fimmu.2023.1303971. eCollection 2023.

Persistent CD8+ T cell proliferation and activation in COVID-19 adult survivors with post-acute sequelae: a longitudinal, observational cohort study of persistent symptoms and T cell markers

Affiliations
Free PMC article
Abstract

Introduction: Post-acute sequelae of COVID-19 affects the quality of life of many COVID-19 survivors, yet the etiology of post-acute sequelae of COVID-19 remains unknown. We aimed to determine if persistent inflammation and ongoing T-cell activation during convalescence were a contributing factor to the pathogenesis of post-acute sequelae of COVID-19.

Methods: We evaluated 67 individuals diagnosed with COVID-19 by nasopharyngeal polymerase chain reaction for persistent symptoms during convalescence at separate time points occurring up to 180 days post-diagnosis. Fifty-two of these individuals were evaluated longitudinally. We obtained whole blood samples at each study visit, isolated peripheral blood mononuclear cells, and stained for multiple T cell activation markers for flow cytometry analysis. The activation states of participants' CD4+ and CD8+ T-cells were next analyzed for each of the persistent symptoms.

Results: Overall, we found that participants with persistent symptoms had significantly higher levels of inflammation at multiple time points during convalescence when compared to those who fully recovered from COVID-19. Participants with persistent dyspnea, forgetfulness, confusion, and chest pain had significantly higher levels of proliferating effector T-cells (CD8+Ki67+), and those with chest pain, joint pain, difficulty concentrating, and forgetfulness had higher levels of regulatory T-cells (CD4+CD25+). Additionally, those with dyspnea had significantly higher levels of CD8+CD38+, CD8+ Granzyme B+, and CD8+IL10+ cells. A retrospective comparison of acute phase inflammatory markers in adults with and without post-acute sequelae of COVID-19 showed that CD8+Ki67+ cells were significantly higher at the time of acute illness (up to 14 days post-diagnosis) in those who developed persistent dyspnea.

Discussion: These findings suggest continued CD8+ T-cell activation following SARS-CoV-2 infection in adults experiencing post-acute sequelae of COVID-19 and that the increase in T regulatory cells for a subset of these patients represents the ongoing attempt by the host to reduce inflammation.

Keywords: CD8+ T cell; COVID-19; SARS-CoV-2; cytotoxic T cells; post-COVID; post-acute sequelae of COVID-19.

PubMed Disclaimer

Conflict of interest statement

BS is employed by Arcturus Therapeutics which is developing a COVID-19 vaccine. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.

Figures

måndag 19 februari 2024

WHO: BA.2.86 variantin piirteitä. BA.2.86 ja sen alalinja JN.1 siirretty VOI-varianteiksi 9.2. 2024.

 https://www.who.int/docs/default-source/coronaviruse/21112023_ba.2.86_ire.pdf?sfvrsn=8876def1_3

1
Executive Summary
BA.2.86 has been reported in multiple countries, and the prevalence has been slowly increasing globally.
However, based on the available limited evidence, the public health risk posed by BA.2.86 is currently
evaluated as low at the global level. Current population immunity globally remains highly cross-reactive tothis variant, especially against severe disease but also against symptomatic disease, and therefore the
emergence of this variant will unlikely add increased burden to national public health systems. BA.2.86  classified as variant under monitoring (VUM) on 17 August 2023 and based on updated information, BA.2.86 and its sublineages (including JN.1) are now being classified as a variant of interest (VOI) (9.2. 2024).


Initial Risk Evaluation of BA.2.86 and its sublineages, 

21 November 2023 BA.2.86 is a descendent lineage of BA.2, with the earliest sample collected on 24 July 2023 (1). This variant and its descendent lineages have a large number of mutations in the spike protein; the initially reported BA.2.86 sequences from Israel and Denmark had 34 amino acid substitutions relative to BA.2 and 36  substitutions relative to XBB.1.5 (the strain recommended for the updated COVID-19 vaccine [2]).
 The number of spike amino acid mutations in the BA.2.86 variant relative to BA.2 and XBB.1.5 is comparable to the number of mutations in the first Omicron strains relative to the SARS-CoV-2 index strain. 
 
BA.2.86 was designated as a VUM on 17 August 2023 (3).
As of 20 November 2023, there were 3 267 BA.2.86 sequences submitted to GISAID (1) from 46 countries, representing 8.9% of the globally available sequences in epidemiological week 44 (30 October to 5 November 2023). The largest proportion of BA.2.86 sequences are from the United Kingdom (19.7%, 643 sequences), France (11.9%, 389 sequences), Sweden (10.7%, 351 sequences), Spain (7.8% 254 sequences), Canada (6.8%, 223 sequences), Denmark (6.6%, 215 sequences) and the United States of America (6.3%, 208 sequences).

Globally, there has been a slow but steady increase in the proportion of BA.2.86 reported, with its global prevalence at 8.9% in epidemiological week 44, Table 1. This is a substantial rise from the data reported four weeks prior (week 40, 2 to 8 October 2023), when the global prevalence of BA.2.86 was 1.8% 

( Table 1: Global proportions of SARS-CoV-2 Variants, week 40 to week 44 of 2023)

*Table 2 below shows the BA.2.86 descendent lineages and the additional mutations relative to BA.2.86 in the spike and other proteins. A notable descendent lineage of BA.2.86 is JN.1 (BA.2.86 + S:L455S) with a global proportion of 3.2% in epidemiological week 44
 


As population immunity remains heterogenous globally due to differences in SARS-CoV-2 variants circulating around the world and in vaccination coverage, the immune escape potential of BA.2.86 will greatly depend on the immune background of the population tested. With this important caveat in mind, the immune escape of BA.2.86 relative to concurrently circulating variants appears to be limited, and certainly not as extensive as when Omicron emerged in the background of Delta (4-6). Sera from patients who had Omicron breakthrough infections (including XBB), exhibited robust neutralizing activity against BA.2.86, suggesting that upcoming XBB.1.5 monovalent vaccines could confer added protection, by triggering the expansion of existing B cells that will enhance cross-protection against BA.2.86 and its descendant lineages (7-8).
Importantly, T-cell memory has been reported to be highly durable and cross-reactive to BA.2.86 (9). This would suggest that there is sustained protection against severe disease caused by BA.2.86 infection as such protection is associated with T-cell memory (10). Initial observations of the reported BA.2.86 cases do not suggest a change in the clinical presentation or an increase in severity of this variant compared to other Omicron sublineages (11). 
Preliminary data from France also does not suggest differences with BA.2.86 in
terms of age, sex, symptoms or other risk factors (12).
WHO and its Technical Advisory Group on SARS-CoV-2 Evolution (TAG-VE) continue to recommend that Member States prioritize specific actions to better address uncertainties relating to antibody escape and severity of BA.2.86. The suggested timelines are estimates and will vary from one country to another based on national capacities:
• Share information on the growth advantage of BA.2.86 in your country and/or provide sequence
information (one to four weeks).
• Conduct neutralization assays using human sera, representative of the affected community(ies), and
BA.2.86 live virus isolates (two to four weeks).
• Perform a comparative evaluation to detect changes in rolling or ad hoc indicators of severity (four to
12 weeks).
The WHO and its Technical Advisory Group on COVID-19 Vaccine Composition (TAG-CO-VAC) continue to regularly assess the impact of variants on the performance of COVID-19 vaccines to inform decisions on updates to vaccine composition (2).

The risk evaluation below follows the WHO framework (13) and is based on currently available evidence. It will be revised regularly as more evidence and data from additional countries become available.
 
* Table1: BA.2.86 descendent lineages and mutations
Lineage
Variant Parent Lineage
Additional Spike Mutations relative to BA.2.86
Additional Mutations in other proteins relative to BA.2.86
BA.2.86        BA.2             NA           NA
BA.2.86.1     BA.2.86        None        ORF1a:K1973R
JN.1             BA.2.86.1     S:L455S  ORF1a:F499L, ORF1a:K1973R, ORF1a:R3821K, ORF7b:F19L
JN.2             BA.2.86.1    None         ORF1a:Y621C, ORF1a:K1973R
JN.3            BA.2.86.1     None         ORF1a:K1973R, ORF1a:T2087I
BA.2.86.2    BA.2.86       None         ORF7a:E22D
BA.2.86.3    BA.2.86      None           None
JQ.1            BA.2.86.3     S:T95I       ORF1a:D1742N

Sars-CoV-2 virusvarianttiseurannasta

 https://www.who.int/activities/tracking-SARS-CoV-2-variants


Currently circulating variants of interest (VOIs) (as of 9 February 2024)

 

 

Pango lineageNextstrain cladeGenetic featuresEarliest documented samplesDate of designation and risk assessments
XBB.1.523A

Recombinant of BA.2.10.1 and BA.2.75 sublineages, i.e. BJ.1 and BM.1.1.1, with a breakpoint in S1. 

XBB.1 + S:F486P (similar Spike genetic profile as XBB.1.9.1)

Includes

XBB.1.5.70 (23G): XBB.1.5 + S:L455F and S:F456L


21-10-2022
11-01-2023





XBB.1.1623B

 

Recombinant of BA.2.10.1 and BA.2.75 sublineages, i.e. BJ.1 and BM.1.1.1

XBB.1 + S:E180V, S:K478R and S:F486P 
09-01-2023

17-04-2023

XBB.1.16 Initial Risk Assessment, 17 April 2023

XBB.1.16 Updated Risk Assessment, 05 June 2023

EG.5Not assigned

 

 

XBB.1.9.2 + S:F456L

Includes

EG.5.1 (23F): EG.5 + S:Q52H

HK.3 (23H): EG.5 + S:Q52H, S:L455F

HV.1: EG.5 + S:Q52H, S:F157L, S:L452R

 

17-02-2023

09-08-2023

EG.5 Initial Risk Evaluation, 09 August 2023

EG.5 Updated Risk Evaluation, 21 September 2023

EG.5 Updated Risk Evaluation, 21 November 2023

BA.2.86$23I

 

Mutations relative to BA.2

 

 

24-07-2023

21-11-2023

BA.2.86 Initial Risk Evaluation, 21 November 2023

 

JN.1

 

Not assigned

BA.2.86 + S:L455S

25-08-2023

09-02-2024

JN.1 Initial Risk Evaluation 18 December 2023

JN.1 Updated Risk Evaluation 9 February 2024

 

 

 

Currently circulating variants under monitoring (VUMs) (as of 29 January 2024)

 

Pango lineage§

Nextstrain clade

Genetic features

Earliest documented samples

Date of designation and risk assessments

XBB*

22F

BA.2+ S:V83A, S:Y144-, S:H146Q, S:Q183E, S:V213E, S:G252V, S:G339H, S:R346T, S:L368I, S:V445P, S:G446S, S:N460K, S:F486S, S:F490S

19-08-2022

12-10-2022

XBB.1.9.1

23D

Recombinant of BA.2.10.1 and BA.2.75 sublineages, i.e. BJ.1 and BM.1.1.1

XBB.1 + S:F486P (similar Spike genetic profile as XBB.1.5)

05-12-2022

30-03-2023

XBB.2.3

23E

Recombinant of BA.2.10.1 and BA.2.75 sublineages, i.e. BJ.1 and BM.1.1.1

XBB + S:D253G, S:F486P, S:P521S

09-12-2022

17-05-2023

 

$ Excludes BA.2.86 sublineages listed here as VOIs.

* Excludes XBB sublineages listed here as VOIs and VUMs.

§ A VUM is de-escalated if its prevalence is <1% at the global level and in all WHO regions for 8 consecutive weeks.

 

 

 

Technical Advisory Groups

 

tisdag 13 februari 2024

Sars-Cov-2 mutaatioitten seurannasta hahmottavat taulukot netissä

 https://outbreak.info/situation-reports#voc

 

SARS-CoV-2 (hCoV-19) Mutation Reports

Lineage | Mutation Tracker 

Tästä lähteestä pääsee näkeään varianttien  mutaatiokoostumukset ja prevalenssikäyrät. 
Esim. JN linjoja on
JN.1, JN.1.1, JN.1.1.1
JN.1.2, JN.1.3 
JN.2, JN.2.1
JN.3, JN.3.1
JN.4
JN.5
JN.5.1
JN.6
JN.7
JN.8
JN.9
JN.10
BA.2.86
BA.2.86.1 =JN
BA.2.86.2
BA.2.86.3=JQ
JQ.1
BA.2.86.4

Löytyy suomalainen rekombinanttivirus! GITHUB areenalla pohdinnassa.

 https://github.com/cov-lineages/pango-designation/issues/2489

JN.1.1/HW.1.1 (XBC.1.6.3.1.1) recombinant, Finland, 4 samples #2489

Created an issue in cov-lineages/pango-designation that received 4 comments

Credit to @NkRMnZr, who found this one before I did. Description: JN.1.1/HW.1.1 (XBC.1.6.3.1.1), HW.1.1 Spike, JN.1 beginning and end. Private muta…

 From HW.1.1: G17144A
Breakpoints: between nucleotide 3565 and 4184 and between 26270 and 26529
Earliest sequence: 2024-01-07 from Finland
Most recent sequence: 2024-01-17 from Finland
Countries circulating: Finland 4
GISAID query: T24529C, C25854T, G26529C

 (tiedemiesten keskustelua asiasta)...

..."Thanks! I also remember seeing this one, would be good to wait for a different lab to see this but then worth designating.

 

Tuoreita GITHUB  pohdintoja on runsaasti : https://github.com/cov-lineages/pango-designation/issues

"KN" alias XBB.1.5.70.1.10.1 alias GK.10.1 saa alalinjat KN.1 ja KN.1.1 eilen

 https://github.com/cov-lineages/pango-designation/commit/2fcf851e2e140b6f2aacb5e14cb9a758dbee589a

" KN" linjaan  tullut uusia alavariantteja.

KN.1

KN.1.1 saaneet määritelmänsä eilen 12.2. 2024.

Designate KN.1 (GK.1.10.1.1, S:Y200C, Brazil) and KN.1.1 (S:N450D)
Resolves #2479

Muistiin Lintuinfluenssa A(H10N5) viruksen ja kausiluontoisen A(H3N2) viruksen samanaikaisesiintymä ihmisessä

 https://www.who.int/emergencies/disease-outbreak-news/item/2024-DON504

 

Avian Influenza A(H10N5) and Influenza A(H3N2) coinfection - China

13 February 2024

Situation at a Glance

On 27 January 2024, the National Health Commission of the People’s Republic of China notified the World Health Organization (WHO) of one confirmed case of human coinfection with avian influenza A(H10N5) virus and seasonal influenza A(H3N2) virus. This is the first case of human infection with avian influenza A(H10N5) virus reported globally. The case occurred in a female farmer over 60 years of age, with a history of chronic comorbidities, from Xuancheng Prefecture, Anhui Province. She had onset of symptoms on 30 November 2023 and passed away on 16 December 2023. The authorities isolated seasonal influenza A(H3N2) subtype and avian influenza A(H10N5) subtype viruses from the patient’s samples on 22 January 2024, which were affirmed in confirmatory testing on 26 January 2024. The patient had exposure to live poultry, and poultry samples also tested positive for H10N5. No new suspected human cases have been detected through the investigation and testing done by authorities. Currently available epidemiologic information suggests that avian influenza A(H10Nx) viruses have not acquired the capacity for sustained transmission among humans. Thus, the likelihood of human-to-human spread is considered low.

måndag 12 februari 2024

JN.1 varianttilinjalle tyypillistä

 https://outbreak.info/situation-reports/ba.2.86*%20(ba.2.86x)?xmin=2023-08-29&xmax=2024-02-29&loc&selected

BA.2.86*X   19  linjaa  kuvaajassa .

 https://outbreak.info/situation-reports?xmin=2023-08-12&xmax=2024-02-12&pango=JN.1

https://outbreak.info/situation-reports?xmin=2023-08-12&xmax=2024-02-12&pango

https://outbreak.info/situation-reports?pango=BA.2.86&loc&selected

Mutation prevalence across lineages

Mutations with > 75% prevalence in at least one lineage.

Mutation prevalence in lineage
0100%
not detected
Variant / Mutation of Concern Variant / Mutation of Interest


Most Omicron sequences also contain a 3 amino acid insertion (EPE) at position 214 in the Spike protein.

outbreak.info currently only reports substitution and deletion changes, due to the computational challenges with identifying insertions in 5+ million sequences every day. We’re working towards incorporating insertions into our data processing pipeline, and we encourage you to refer back to the sequence data available on GISAID for more information about these insertions.

 

(Eilinen merkintä C.R 12.2.2024: 

JN.1.4.3, I haven't designated the 346T yet, just the 572I

Let's wait a bit more with 346T until it's something like 25

 

 

 

 

JN.1 tietoutta. BA.2.86 alalinjoja

BA.2.86* (BA.2.86X)

BA.2.86

Sublineages:BA.2.86.1BA.2.86.2BA.2.86.3BA.2.86.4JN.1JN.2JN.2.1JN.3JN.3.1JN.4JN.5JN.5.1JN.6JN.7JN.8JN.9JN.10JQ.1
WHO: BA.2.86* (BA.2.86X
 
 
 

JN.1 Publications & Resources

8 results

BA.2. 86 omikronlinja ja sen alalinjat JN ovat kiinnittämässä yhä enemmän huomoota

 JN.1 variant lineage?  Haku:


Distinct evolution of SARS-CoV-2 Omicron XBB and BA.2.86 lineages combining increased fitness and antibody evasion.
Planas D, Staropoli I, Michel V, Lemoine F, Donati F, Prot M, Porrot F, Guivel-Benhassine F, Jeyarajah B, Brisebarre A, Dehan O, Avon L, Boland WH, Hubert M, Buchrieser J, Vanhoucke T, Rosenbaum P, Veyer D, Péré H, Lina B, Trouillet-Assant S, Hocqueloux L, Prazuck T, Simon-Loriere E, Schwartz O. bioRxiv. 2023 Dec 6:2023.11.20.567873. doi: 10.1101/2023.11.20.567873. Preprint. PMID: 38045308 Free PMC article.
The unceasing circulation of SARS-CoV-2 leads to the continuous emergence of novel viral sublineages. Here, we isolated and characterized XBB.1, XBB.1.5, XBB.1.9.1, XBB.1.16.1, EG.5.1.1, EG.5.1.3, XBF, BA.2.86.1
Early detection of the emerging SARS-CoV-2 BA.2.86 lineage through integrated genomic surveillance of wastewater and COVID-19 cases in Sweden, weeks 31 to 38 2023.
Espinosa-Gongora C, Berg C, Rehn M, Varg JE, Dillner L, Latorre-Margalef N, Székely AJ, Andersson E, Movert E. Euro Surveill. 2023 Nov;28(46):2300595. doi: 10.2807/1560-7917.ES.2023.28.46.2300595. PMID: 37971659 Free PMC article.
The SARS-CoV-2 BA.2.86 Omicron subvariant was first detected in wastewater in Sweden in week 31 2023, using 21 highly specific markers from the 50 investigated. We report BA.2.86's introduction and subsequent spread to all 14 regions performing wastewater sampling, and on …
Early Estimates of Updated 2023-2024 (Monovalent XBB.1.5) COVID-19 Vaccine Effectiveness Against Symptomatic SARS-CoV-2 Infection Attributable to Co-Circulating Omicron Variants Among Immunocompetent Adults - Increasing Community Access to Testing Program, United States, September 2023-January 2024.
Link-Gelles R, Ciesla AA, Mak J, Miller JD, Silk BJ, Lambrou AS, Paden CR, Shirk P, Britton A, Smith ZR, Fleming-Dutra KE. MMWR Morb Mortal Wkly Rep. 2024 Feb 1;73(4):77-83. doi: 10.15585/mmwr.mm7304a2. PMID: 38300853 Free PMC article.
During fall 2023, XBB lineages co-circulated with JN.1, an Omicron BA.2.86 lineage that emerged in September 2023. ...XBB lineages predominated through December 2023, when JN.1 became predominant in the United States. ...

PANGO määritelmiäm alias nimiä, kertauslinkki

 "BA": "B.1.1.529",
    "BB": "B.1.621.1",
    "BC": "B.1.1.529.1.1.1",
    "BD": "B.1.1.529.1.17.2",
    "BE": "B.1.1.529.5.3.1",
    "BF": "B.1.1.529.5.2.1",
    "BG": "B.1.1.529.2.12.1",
    "BH": "B.1.1.529.2.38.3",
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     "XDT": ["BA.2.86.4","GK.1"]

https://github.com/cov-lineages/pango-designation/blob/master/pango_designation/alias_key.json

 

https://github.com/cov-lineages/pango-designation/releases/tag/v1.25