https://www.who.int/activities/tracking-SARS-CoV-2-variants 2023
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2024 Currently circulating variants of interest (VOIs) (as of 9 February 2024)
Emergency: Diseases outbreak News
https://www.who.int/emergencies/disease-outbreak-news
Huom: Covid-19 uutiset eivät ole enää mitenkään tässä WHO:n kriitisten seurantojen listassa päällimmäistä asiaa.
Katselin ensin Suomen THL raporttia koronavirustapahtumien runsaudesta. Tällä viikolla on ilmoitettu 23 sairastumistapausta ja joulukuun jälkeen sairastumismäärät ovat laskeneet nelinumeroisesta luvusta kaksinumeroisiin lukuihin per viikko.
Siten katsoin mitä Github tietuissa on uutta. Silmää pisti uusi mutaatio, jota ei ole missään sars-Cov-2 variantissa vielä ennen n-itä viime aikoja esiintyyt. Mutaatio on kahdeksan nukleotidin ituinen (ONM) ja sijaitsee translatoimattomassa 3prim päädyssä ( 3`-UTR). Sekvenssejäkin on ilmaantunut yli tuhat jo.
https://www.ecdc.europa.eu/en/covid-19/variants-concern
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).
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.
The tables include:
Category: variant of concern (VOC), variant of interest (VOI), or variant under monitoring (VUM).
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.
| WHO label | Lineage + additional mutations | Country first detected (community) | Spike mutations of interest | Year and month first detected | Impact on transmissibility | Impact on immunity | Impact on severity | Transmission in EU/EEA |
|---|---|---|---|---|---|---|---|---|
| Omicron | XBB.1.5-like (a) | United States | N460K, S486P, F490S | n/a | Similar 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/a | F456L, N460K, S486P, F490S | n/a | Baseline | Baseline (5) | Baseline | Community |
| Omicron | BA.2.86 | n/a | I332V, D339H, R403K, V445H, G446S, N450D, L452W, N481K, 483del, E484K, F486P | n/a | Unclear (6) | Unclear (6-8) | No evidence | Dominant |
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
| WHO label | Lineage + additional mutations | Country first detected (community) | Spike mutations of interest | Year and month first detected | Impact on transmissibility | Impact on immunity | Impact on severity | Transmission in EU/EEA |
|---|---|---|---|---|---|---|---|---|
| Omicron | XBB.1.5(link is external)-like + L455F + F456L | n/a | L455F, F456L, N460K, S486P, F490S | n/a | No evidence | No evidence | No evidence | Detected |
| Omicron | BA.2.87.1 | South Africa | G75D,S98F,V126A,W152L,R190S,K417T,K444N,V445G,L452M,N481K,V642G,K679R,S691P,T791I,Y796H,D936G (b) | 2023 September | No evidence | No evidence | No evidence | Not Detected |
n/a: not applicable
b: Preliminary mutations based on a limited number of genomes
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.
Copyright © 2024 LaVergne, Dutt, McFann, Baxter, Webb, Berry, Tipton, Stromberg, Sullivan, Dunn, Henao-Tamayo and Ryan.
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.
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,
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)
https://www.who.int/activities/tracking-SARS-CoV-2-variants
| Pango lineage | Nextstrain clade | Genetic features | Earliest documented samples | Date of designation and risk assessments |
| XBB.1.5 | 23A | 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.1.16 | 23B |
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 |
| EG.5 | Not 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 |
| BA.2.86$ | 23I |
| 24-07-2023 | 21-11-2023 |
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
|
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.
