WHO tilannekatsaus COVID-19 vaiheesta tullut 29.6. 2023 sekä 6.7. 2023 ( viikoilta 23- 24)

Lisäys 9.7. 2023  Päivitystä WHO edit. 150,  6.7 2023

 https://www.who.int/publications/m/item/weekly-epidemiological-update-on-covid-19---6-july-2023

 

 https://www.who.int/emergencies/situation-reports

Overview

Globally, over one million new cases and over 5700 deaths were reported in the last 28 days (29 May to 25 June 2023). While five WHO regions have reported decreases in both cases and deaths, the African Region has reported a decrease in cases but an increase in deaths. As of 25 June 2023, over 767 million confirmed cases and over 6.9 million deaths have been reported globally. Reported cases are not an accurate representation of infection rates due to the reductions in testing and reporting globally. During this 28-day period, only 62% (146 of 234) of countries and territories reported at least one case – a proportion that has been declining since mid-2022.

In this edition, we include:

• The COVID-19 epidemiological update at the global and the regional levels
• An update on hospitalizations and ICU admissions
• An update on the SARS-CoV-2 variants of interest (VOI) and variants under monitoring (VUM)

Some countries continue to report high burdens of COVID-19, including increases in newly reported cases and, more importantly, increases in hospitalizations and deaths – the latter of which are considered more reliable indicators given the reductions in testing.
We present changes in epidemiological trends using a 28-day interval. Disaggregated data are still accessible on the WHO COVID-19 dashboard, where the full dataset is available for download. Global and national data on SARS-CoV-2 PCR percent positivity are available on WHO’s integrated dashboard provided by the Global Influenza Programme 

( Several countries are now being updated using data from the European Surveillance System (TESSy). As a result, for some of these countries, the numbers have been revised retrospectively, leading to reduced figures in certain instances. Consequently, the cumulative totals are now lower compared to the figures reported in the COVID-19 Weekly Epidemiological Update published on 22 June 2023).

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Figure 1. COVID-19 cases reported by WHO Region, and global deaths by 28-day intervals, as of 25 June 2023**
**See Annex 1: Data, table, and figure note

At the regional level, the number of newly reported 28-day cases decreased across all six WHO regions: the Eastern Mediterranean Region (-75%), the South-East Asia Region (-73%), the Region of the Americas (-66%), the European Region (-57%), the Western Pacific Region (-35%), and the African Region (-12%). 

The number of newly reported 28-day deaths decreased across five regions: the Region of the Americas (-68%), the Eastern Mediterranean Region (-63%), the European Region (-62%), the South-East Asia Region (-56%), and the Western Pacific Region (-43%); while newly reported deaths increased in the African Region (+20%).

 
At the country level, the highest numbers of new 28-day cases were reported from the Republic of Korea (371 513 new cases; -22%), Australia (111 543 new cases; -21%), Brazil (77 022 new cases; -41%), France (45 306 new cases; -55%), and Singapore (40 531 new cases; -56%). 

The highest numbers of new 28-day deaths were reported from Brazil (1055 new deaths; -10%), the Russian Federation (517 new deaths; -16%), Australia (343 new deaths; -53%), Italy (342 new deaths; -48%), and France (285 new deaths; -58%).

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 Hospitalizations and ICU admissions

At the global level, during the past 28 days (22 May 2023 to 18 June 2023), a total of 62 128 new hospitalizations and 2080 new intensive care unit (ICU) admissions were reported (Figure 4). This represents a 40% and 48% decrease in both hospitalizations and ICU admissions, respectively, compared to the previous 28 days (24 April 2023 to 21 May 2023). The presented hospitalization data are preliminary and might change as new data become available.
Furthermore, hospitalization data are subject to reporting delays. These data also likely include both hospitalizations with incidental cases of SARS-CoV-2 infection and those due to COVID-19 disease.
Globally, during the past 28 days, 40 (17%) countries reported data to WHO on new hospitalizations at least once
(Figure 5). 

The European Region had the highest proportion of countries reporting data on new hospitalizations (20 countries; 33%), followed by the Region of the Americas (eight countries; 14%), the African Region (four countries; 8%), the Eastern Mediterranean Region (three countries; 14%), the Western Pacific Region (three countries; 9%), and the South-East Asia Region (two countries; 20%). The proportion of countries that consistently ii reported new hospitalizations for the period was 10% (24 countries) (Table 2).
Among the 24 countries consistently reporting new hospitalizations, three (13%) countries registered an increase of 20% or greater in hospitalizations during the past 28 days compared to the previous 28-day period: Afghanistan (178 vs 33; +439%), Bangladesh (269 vs 104; +159%), and Malta (86 vs 35; +146%). The highest number of new hospitalizations was reported from the United States of America (27 065 vs 37 232; -27%), Ukraine (5744 vs 8853; -35%), and France (3634 vs 7642; -52%).
Across all six WHO regions, in the past 28 days, a total of 30 (13%) countries reported data to WHO on new ICU admissions at least once (Figure 5). The European Region had the highest proportion of countries reporting data on new ICU admissions (17 countries; 28%), followed by the Western Pacific Region (five countries; 14%), the Region of the Americas (four countries; 7%), the Eastern Mediterranean Region (two countries; 9%), the African Region (one country; 2%), and the South-East Asia Region (one country; 10%) The proportion of countries that consistently reported new ICU admissions for the period was 8% (18 countries) (Table 2).
Among the 18 countries consistently reporting new ICU admissions, two (11%) countries showed an increase of 20% or greater in new ICU admissions during the past 28 days compared to the previous 28-day period: Lithuania (19 vs 11; 73%) and Mexico (19 vs 14; +36%). The highest numbers of new ICU admissions were reported from France (438 vs 866; -49%), Australia (304 vs 325; -6%), and Ukraine (164 vs 280; -41%).
ii “Consistently” as used here refers to countries that submitted data for new hospitalizations and intensive care unit admissions for the four consecutive weeks that make up the 28-day period.

( Figures: Declining  skenario. Look maps in WHO link!)

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SARS-CoV-2 variants of interest (VOI)  and variants under monitoring (VUM)

Geographic spread and prevalence
Globally, from 29 May to 25 June 2023 (28 days), 13 152 SARS-CoV-2 sequences were shared through GISAID. WHO is currently tracking two variants of interest (VOIs), XBB.1.5 and XBB.1.16, along with six variants under monitoring (VUMs) and their descendent lineages. The VUMs are BA.2.75, CH.1.1, XBB, XBB.1.9.1, XBB.1.9.2, and XBB.2.3.

 

Globally, 114 countries have reported the detection of XBB.1.5 (VOI)  since its emergence. Its prevalence has been declining steadily. In epidemiological week 23 (5 to 11 June 2023), XBB.1.5 accounted for 19.8% of sequences, as compared to 32.1% in week 19 (8 to 14 May 2023). The updated risk assessment for XBB.1.5 presents supplementary laboratory and epidemiological evidence, which suggests that XBB.1.5 does not pose additional public health risks compared to other circulating variants.

 

XBB.1.16 (VOI)  has been reported from 89 countries. In week 23, XBB.1.16 (VOI)  accounted for 20.5% of sequences, an increase from 15.7% in week 19. Its prevalence has surpassed that of XBB.1.5 in week 23. An analysis of available data indicates that countries with a low prior prevalence of XBB.1.5 have experienced a significant increase in the prevalence of XBB.1.16, while

countries that had a high prevalence of XBB.1.5 have reported low circulation of XBB.1.16.

Table 3 shows the number of countries reporting the VOIs and VUMs and their prevalence from week 19 to week 23.

Table 3. Weekly prevalence of SARS-CoV-2 VOIs and VUMs, week 19

The VOI and the VUMs that have shown increasing trends during the last five weeks period are highlighted in orange, those that have remained stable are highlighted in blue, while those with decreasing trends are highlighted in green. Among the VUMs,
XBB, XBB.1.9.2, and XBB.2.3 have shown increasing trends in recent weeks. Overall, other VUMs show declining or stable trends during the same reporting period.

Table 3. Weekly prevalence of SARS-CoV-2 VOIs and VUMs, week 19 to week 23 of 2023
Lineage Countries§ Sequences§ 2023-19 2023-20 2023-21 2023-22 2023-23    2023 24
XBB.1.5*  114      242 397       32.16        29.66      24.81       22.26      19.79
XBB.1.16*  89       27 413        15.66        18.06     18.67        21.31      20.53
BA.2.75*  124      119 879          3.45           2.91      2.66          2.46         1.64
CH.1.1*     95         41 989          1.36          1.23       0.95          0.92         1.11
XBB*      130         62 221          4.75           5.01       5.61          5.82         6.37
XBB.1.9.1* 98       40 414         18.29        18.56     19.02       18.82        19.52
XBB.1.9.2* 79       20 604         10.32        10.52      12.03      12.15        12.18
XBB.2.3   * 60         5 769           2.79           3.38       4.23         4.31         4.06
Unassigned 91     146 918           0.99           1.09        1.46         2.52         4.70
Other+ 209        6 746 112          8.89           8.72        9.43         8.40         9.09
* Includes descendant lineages, except those individually specified elsewhere in the table. For example, XBB* does not include XBB.1.5, XBB.1.9.1, XBB.1.9.2, XBB.1.16, and XBB.2.3.
+ Others are other circulating lineages excluding the VOI, VUMs, BA.1*, BA.2*, BA.3*, BA.4*, BA.5*.
§ Number of countries and sequences are since the emergence of the variants
 

Additional resources
• Tracking SARS-CoV-2 Variants
• WHO statement on updated tracking system on SARS-CoV-2 variants of concern and variants of interest
• WHO XBB.1.5 Updated Risk Assessment, 20 June 2023
• WHO XBB.1.16 Updated Risk Assessment, 5 June 202

Lisäystä edelliseen taulukkoon 6.7. 2023 päivityksestä:Poimin numeooita esiin. Raportoivat maat vähentyneet edelleen pandemian käyrän laskiessa.

https://www.who.int/publications/m/item/weekly-epidemiological-update-on-covid-19---6-july-2023
Table 3. Weekly prevalence of SARS-CoV-2 VOIs and VUMs, epidemiological week 20 to week 24 of 2023. VOI variantit ovat edelleen samat  XBB.1.5* ja XBB.1.16*

 
Lin,             Cntr,§   Seqs§     2023-20 2023-21 2023-22 2023-23  2023-24
XBB.1.5*    115     250 410   30.14     26.66      22.56     21.12       16.26
XBB.1.16*   91        31 367   18.12     18.59     20.53      21.70       21.18
BA.2.75*   124       121 110    2.91       2.64       2.71         2.27         2.33
CH.1.1*       95         42 312    1.12       0.89       0.88         0.83         0.78
XBB*        130         63 467    4.95       5.61       5.80         6.68         7.46
XBB.1.9.1* 98        43 728   18.24    18.20      18.37       18.00       16.04
XBB.1.9.2* 82        22 645   10.26    11.43      12.70       11.85       12.68
XBB.2.3*    63         6 522      3.47      4.10        4.26        3.93         4.25
Unassigned 92      149 333     0.97      1.29        1.88        2.73          6.36
Other      +209   6 751 730     8.95      9.53        9.35        9.97        11.97
* Includes descendant lineages, except those individually specified elsewhere in the table. For example, XBB* does not include XBB.1.5, XBB.1.9.1,
XBB.1.9.2, XBB.1.16, and XBB.2.3.
+ Others are other circulating lineages excluding the VOI, VUMs, BA.1*, BA.2*, BA.3*, BA.4*, BA.5*.
§ Number of countries and sequences are since the emergence of the variants

STANFORD taulukoista tietoa Sars-Cov-2 virusvarianteista, rokotuksista ja neutroloivista vasta-aineista ja läpikäydyn infektion merkityksestä

 https://covdb.stanford.edu/susceptibility-data/table-vacc-neutral/

DUODECIM esittää tieteellisen päättelyn viruslääkkeiden merkityksestä Covid-19 infektion nykyvaiheessa kesällä 2023

 https://www.duodecimlehti.fi/lehti/2023/12/duo17701

DUODECIM lehden sivuilla 1023-1029  on lääketieteen kannalta loogisinta päättelyä   Sars-Cov-2  virusinfektionhoidossa käyttökelpoisimmista viruslääkkeistä.  Koksa tieteelliset päätelmät ovat  ajallisella viiveellä ainoastaan hankittavissa tutkimuksen heikkoudet ovat ainoastaan tässä aikaviiveessä, sillä  tulokset ovat niitä, joita on saatu ajalta ennen kuin omikron rehahti kasvamaan näitä nykyisiä  linjojaan ja niitten varianttien runsautta.  Artikkeli  antaa kuitenkin  runsaasti tutkimustulosta, josta voidaan  arvioida mitkä lääkkeet ovat vieläkin tehokkaita.  Ristiriitaista tietoa  on annettu artikkelissa  molnupiravirista eikä suota, sillä GITHUB-tietueen puolella taas on joskus mainittu  kroonikkopotilailla ilmenevien varianttien mutaatioiden johtuvan monlnupiraviirin vaikutuksesta. 

Varsinaiset viruslääkkeet remdesiviiri sekä nirmatrelviiri ja ritonaviiri ovat säilyttäneet tehonsa omikronkantojen viruksia vastaan. Monissa tutkimuksissa   oli kyse vertailusta rokottamattomien ja rokotettujen henkilöiden saamista hoitokuureista. Näistä  tutkimuksista heijastui  passiivisti esiin rokotuksen arvo. Toisaalta jos  kontrolliryhmät olivat lumelääkkeellä korostui minkä tahansa lääkeryhmän hoidollinen arvo jollain tavalla, esim. hieman lyhemmästä saraalassa hoitoajasta tai hieman lievemmästä taudista tai vähemmästä kuolleisuudesta.  

 Useimmat tutkimukset olivat tehty alku -VOC-varianttien aikana ( alfa, beeta, delta) eikä omikronin ja sen alalarianttien saati sitten alavarianttein rekombinaanttien  aikana.

Mikä sitten on viruksen wt- Wuhan viruksen luonnollinen vaellus ihmiskunnassa- Wuhanin viruksen kulku ja sen aiheuttamat luonnolliset vasta-aineet- sillä lie osuutensa siinä,että kuitenkin  pandemia on  sammumaan päin onhan siinä tekijöitä paljon enenmmän kuin niitä joita vastaan on tehty jokin vasta-aine tai rokote tai antiviruslääke.  Se on hyvin monipuolinen ja edelleen mielestni aika salaperäinen mikro-organismi. mutta  kaiketi ihmisessäkin on joitain salaperäisia tuntemattomia  esiingeneroituvia  antimikrobiaalisia  ominaisuuksia ihmiskunnan  pahan päivän varalle.

Suomestakin mainitaan joitain sars-Cov-2 rekombinanttivariantteja GJ.1 ja FL alalinjoja

ESIMERKKI 1.  (GJ  alias XBB.2.3.3)

https://github.com/cov-lineages/pango-designation/issues/2059 

GJ.1 sublineage with ORF1b:V1110I, C1549T, and C7819G first detected in South Korea (164 GISAID seqs as of 2023-06-16; USA, China, Singapore, China, South Korea, Australia, Italy, Japan, New Zealand, Switzerland, Finland, Hong Kong, Philippines, Spain, Sweden, UK) #2059

 ESIMERKKI 2. FL.1.10 alalinjat selvittelyssä

https://github.com/cov-lineages/pango-designation/issues/2040

2 XBB.1.9.1* sublineages with S:E554K (Branch A with 61 seqs in 13 countries; Branch B with 49 seqs mainly in South Korea) #2040

( Github  text:  HynnSpylor )I propose 2 XBB.1.9.1* sublineages with S:E554K

Branch A: 61 seqs
Defining mutations: XBB.1.9.1>G23222A (S: E554K)

GISAID query: Spike_E554K, -Spike_A701V, G5720A, C11956T, -G2235A, -G2174A, -C12412T, -C230T (for excluding of convergent branch)
Earliest seq: 2023-02-15 (USA, EPI_ISL_17053663)
Most recent seq: 2023-05-19 (Finland, EPI_ISL_17763434)
Countries detected: Finland (20), USA (14), Spain (6), France (4), South Korea (4), Canada (3), Egypt (3), Switzerland (2), UK (1), Australia (1), Netherland (1), Austria (1), Croatia (1)

 Kommenttini: Eteläkorean alalija on jo merkattu FL.1.10.1.

 Suoemn alalinjassa on seuraavia  haarautumia  Spike E554K jälkeen: ORF8:A65V, ORF1ab: A2139V , ORF1ab: E931D.  Tällä haaralkla ei ole vielä ehkä  designaatiota. Muta se on joka tapauksesa  FL.1.10 alalinjoja  ja VUM variantteja, joita monitoroidaan XBB.1.9.1 ryhmästä Alias "FL" . 

ESIMERKKI 3. XBB.1.9.1 alalinja josa konvergoia mutaatio S:F490P.

Eniten on  löytynyt helmikuulta lähtien   Suomesta tätä FL alalinjaa: Sillä on joitain kasvuetuja verrattuna  FL linjaan. (Alias XBB.1.9.1)

https://github.com/cov-lineages/pango-designation/issues/2030

XBB.1.9.1 with S:F490P (170 seqs, 18 countries, mostly in Finland and around Europe) #2030

Transferred from sars-cov-2-variants/lineage-proposals#119

Defining mutations: (On XBB.1.9.1 Polytomy) > A20458G(ORF1b:I2331V) > T23030C(S:F490P) >
Query: A20458G, T23030C, C11956T
Earliest seq: 2023-02-16 (Finland, EPI_ISL_17077296)
Latest seq: 2023-05-15 (Austria, EPI_ISL_17715256)
Sampled in Countries: Finland (65), Sweden (22), Ireland (9), UK (7), Japan (5), Austria (4), USA (4), Spain (4, incl/ 1 from Canary Islands), France (4), Norway (1), Netherlands (1), Australia (1), Switzerland (1), Czech (1), Lithuania (1). 

• XBB acquired F490S (T23031C) from one of the donor BM.1.1.1, this further mutated T23030C turns S to P at residue 490.
• XBB.1.13 and XBB.1.36 are the other XBB* that has this convergent mutation.

HS maailman lintuinfluenssatilanteen näkymistä eläinkunnan puolella

 

Hanna Iittala STT

7:22

Ulkomaiset asiantuntijat varoittavat nopeasti tarttuvasta ja alati muuntuvasta lintuinfluenssaviruksesta, kertoo uutistoimisto AFP. Lintuinfluenssavirusta on havaittu maailmalla enemmän kuin koskaan.

Maailman terveysjärjestön WHO:n tutkija, yhdysvaltalainen Richard Webby kertoo AFP:lle, että virus on muuntunut entistä vaarallisemmaksi linnuille.

Virusta esiintyy Webbyn mukaan nyt myös vuoden ympäri. Aiemmin lintuinfluenssavirus H5N1 on aiheuttanut enimmäkseen kausiluonteisia epidemioita.

”Nyt on yhdentyyppinen H5-virus epidemisenä Euroopassa ja siirtynyt Etelä-Amerikkaan”, Terveyden ja hyvinvoinnin laitoksen (THL) johtava asiantuntija Niina Ikonen vahvistaa STT:lle.

Tämän hetken tautitilanteessa huolestuttavinta on AFP:n haastattelemien asiantuntijoiden mukaan se, että sairastuneiden nisäkkäiden määrä kasvaa koko ajan.

Etelä-Amerikassa sijaitseva Chile on tiedottanut, että kevään aikana lähes 9 000 merieläintä, kuten merileijonaa, pingviiniä ja delfiiniä on kuollut lintuinfluenssaan.

Maan viranomaisten mukaan eläimet ovat todennäköisesti saaneet viruksen syömällä sairasta lintua.

WHO:n tutkija Webby tietää kuitenkin muutaman tapauksen, joissa saattaa olla viitteitä viruksen tarttumisesta nisäkkäiden välillä: viime syksynä espanjalaisella minkkifarmilla ja tämän vuoden alkupuolella merileijonien välillä Etelä-Amerikan Perussa.

Ruokaviraston erityisasiantuntija Tiia Tuupanen ja erikoistutkija Niina Tammiranta Eläinten terveyden ja lääkitsemisen yksiköstä (ELL) lisäävät listalle vielä epäilyn kesällä 2022 hylkeistä Yhdysvalloissa.

Selkeät todisteet nisäkkäiden välisistä epäillyistä tartunnoista kuitenkin vielä puuttuvat. Suomessa on sairastunut lintuinfluenssaan aikaisemmin yksi ilves ja saukko.

Onko viruksesta sitten vaaraa ihmisille?

Britannian eläin- ja kasvinterveysviraston professori Ian Brown kertoo AFP:lle, että vaikka virus näyttää tulleen voimakkaammaksi linnuissa, se on yhä sopeutumaton ihmisiin.

Myös Euroopan tautikeskus on arvioinut, että tartuntariski ihmisväestölle on alhainen.

Terveyden ja hyvinvoinnin laitoksen mukaan lintujen influenssavirukset tarttuvat yleensä huonosti ihmiseen.

THL:n Ikosen mukaan on kuitenkin mahdollista, että yksittäisiä tartuntoja ihmisillä saatetaan todeta, jos altistuu tartunnan saaneelle linnulle.

”Tällä hetkellä Euroopassa luonnonvaraisissa linnuissa todetut influenssa A/H5 -virukset eivät ole muuntuneet ihmisiin herkemmin tarttuviksi. Euroopassa yksittäisiä tartuntoja on todettu ihmisillä, mutta heillä taudinkuva on ollut joko oireeton tai lieväoireinen”, Ikonen kertoo.

WHO:n tutkija Webby etsii parhaillaan näyttöä viruksen muuntumisesta. Hänen mukaansa lintuvirukset sitoutuvat yleensä eri reseptoreihin isäntäsoluissa kuin ihmisen virukset.

”Tarvitaan vain kaksi tai kolme pientä muutosta yhdessä virusproteiinissa, jotta se sopeutuisi paremmin ihmisiin”, hän kertoo AFP:lle.

Maailman lintuinfluenssatilannetta parantaisi WHO:n Webbyn mukaan siipikarjan rokottaminen. Hänen tietojensa mukaan Kiina, Egypti ja Vietnam ovat jo rokottamiseen ryhtyneet.

Yhdysvallat on aloittanut linnuille sopivan rokotevaihtoehdon etsimisen tämän vuoden huhtikuussa. Ranska toivoo aloittavansa siipikarjan rokottamisen aikaisintaan tänä syksynä.

Jotkut maat ovat myös vastustaneet rokotuskampanjoita. Britannian johtava eläinlääkintäasiantuntija Christine Middlemiss on esittänyt epäilyksensä siipikarjan rokottamisesta, koska virus muuntuu koko ajan.

Suomessa siipikarjan ja muiden lintujen rokottaminen lintuinfluenssaa vastaan on kielletty, koska Suomessa ei esiinny lintuinfluenssaa siinä määrin, että rokottamisella katsottaisiin saavutettavan hyötyä, kertoo Ruokaviraston erityisasiantuntija Hanna Lounela.

WHO:n eläintautijärjestön pääjohtaja Monique Eloit kannustaa maailman maita nostamaan lintuinfluenssa-asian pöydälle.

”Nykyään tiedämme, että lintuinfluenssapandemia ei ole kuvitelmaa, vaan voi pian olla totta”, Eloit sanoi AFP:n mukaan.

Suomessa todettiin tämän vuoden ensimmäinen lintuinfluenssatapaus Heinolan lintuhoitolassa varpushaukalla.

Lisäksi Salossa 13. kesäkuuta löydetyn parikymmenpäisen naurulokkiyhdyskunnan kuolema johtui Ruokaviraston mukaan lintuinfluenssasta. Kuolinsyyksi on varmistunut korkeapatogeeninen eli suuren taudin aiheuttamiskyvyn omaava H5N1-tyypin lintuinfluenssa.

Kyseessä on tämän vuoden ensimmäinen Suomessa todettu, lintuinfluenssan aiheuttama luonnonvaraisten lokkien joukkokuolema.

Ruokaviraston mukaan lähes kaikki Suomessa tavatut lintuinfluenssatapaukset on tavattu luonnonvaraisissa linnuissa. Viime vuonna Suomessa todetuista tapauksista 24 oli luonnonvaraisissa linnuissa.

Vuonna 2022 Suomessa todettiin pääsääntöisesti H5N1-tyypin lintuinfluenssaa. Lisäksi todettiin yksi tapaus korkeapatogeenista H5N5-tyypin lintuinfluenssaa.

Uusia designaatioita ilmestynyt GITHUB listoihin tag/v1.21 nyt näinä hetkinä!

 https://github.com/cov-lineages/pango-designation/releases/tag/v1.21

 

Detaljia Sars-Cov-2 spike-mutaation mahdollisista vaikutuksista :Esimerkkinä D796Y, Y796H, Y796D. Löytyi Abstrakti asiasta ,

 

XBB.1.9.1 with S:Y796H (85 seqs, 19 countries) #1870

https://github.com/cov-lineages/pango-designation/issues/1870

 

Open

aviczhl2 opened this issue Apr 10, 2023 · 6 comments

" Y796H pops up every now and then, and I think it was one of the mutations seen in Ravi Gupta's early study that followed an immunocompromised patient with a chronic infection. Seems it was something of an antibody-evasion mutation that imposed a slight cost in infectivity. https://www.nature.com/articles/s41586-021-03291-y

Toinen tuore uutinen GITHUB sivulta . VUM-variantilla XBB.1.9.1 Alias "FL" on havaittu aika iso määrittämätön alalinja

https://github.com/cov-lineages/pango-designation/issues/2065 

Quite large undesignated branch of XBB.1.9.1 with Orf1b:V1132I circulating in Philippines #2065

FedeGueli ( Commented 1 h ag): 

" Hi corneliusroemer , InfrPopGen,  looking at samples uploaded from Philippines yesterday i would  highlight that an entire new branch of XBB.1.9.1 has been formed now defined by Orf1b:V1132I"

 

Sitaatti klo 20:27  Ruotsin aikaa, 21.6. 2023 .

Tuore GITHUB-uutinen : VUM -varianttien selvittelyä: Runsaita löytöjä rekombinanttialalinjasta linjasta XBB.2.3.2

Kaksi tuntia sitten  nettiin: Ruotsin aika 20:14, 21.6. 2023  -.

Huge Branch (1500 seqs，70%+ of parent, increased to about 85% recently and still growing) of XBB.2.3.2 that we need to classify: XBB.2.3.2*+G24193A #2064

ttps://github.com/cov-lineages/pango-designation/issues/2064

XBC.1.6.3 alalinjaselvittelyjä

 https://github.com/cov-lineages/pango-designation/issues/2056

xbc.1.6.3 with ORF1a:T1597I and ORF1a:A2123V (183 seq.) mostly Australia #2056

FedeGueli  in MAY:  "  It is the main branch of XBC.1.6.3 could have some advantage although not totally clear as today. Lets wait until the end of the month to have a clearer picture".

 

FedeGueli 2 weeks ago: " I think if it there is any , the one to monitor is the Orf1a:A2123V is 80% of the proposed branch and the one growing".

Omikron-delta-omikron tyyppinen XBC rekombinantti koostuu BA.2* /B.1.617.2*/BA.2* varianttiosista ja alalinjat XBC.1.6* vaikuttavat lisääntyvän.

https://github.com/cov-lineages/pango-designation/issues/2057 

Designaation ovat jo  saaneet jo alalinja XBC.1.6.1, XBC.1.6.2 , XBC.1.6.3 ja XBC.1.6.4 , vaan vielä löytyy lisää XBC.1.6 linjalle  alalinjoja ja  selvitellään niiden kasvuedellytyksiä. 

Otan sitaattia  GITHUB- tekstistä.  

To monitor new XBC.1.6 branches appearing and growing in MAY 2023 #2057

FedeGueli  commented Jun 16, 2023 •

After the recent designation of XBC.1.6.4 i am noticing new branches with very recent samples collected during May. i would like to share them with corneliusroemer , i suppose he is aware of them but better to have a reminder here , looking at how fast XBC.1.6 is growing as share of total sequences in Australia: XBC.1.6 > G3671A (ORF1a:E1136K) Gisaid : G3671A ,C12733T > 76 seqs (63 of them collected in May) XBC.1.6 > T8707C, C26735T Gisaid : C26735T, C10156T,T8707C > 51 seqs (31 of them collected in May) XBC.1.6 > C1594T Gisaid C1594T,C12733T,C2334T, G3606T > 50 seqs ( 28 seqs of the, collected in May) XBC.1.6 > C10833T (ORF1a:A3523V) Gisaid: C12733T,G3606T,C10833T 32 seqs (23 seqs out of 30 collected in May

 to fast comparing all of them to parental XBC.1.6:
https://cov-spectrum.org/explore/Australia/AllSamples/Past3M/variants?nextcladePangoLineage=XBC.1.6*&nucMutations1=G3671A%2CC12733T&nucMutations2=C26735T%2CC10156T%2CT8707C&nucMutations3=C1594T%2CC12733T%2CC2334T%2CG3606T&nucMutations4=C12733T%2CG3606T%2CC10833T&analysisMode=CompareToBaseline&

 

WHO tiedotus A(H5N1) lintuviruksesta: Kahdella siipikarjatyöntekijällä Englannissa seulonnassa positiivinen A H5N1, oireettomia.

Avian Influenza A(H5N1) - United Kingdom of Great Britain and Northern Ireland

30 May 2023

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Situation at a glance

In mid-May, the United Kingdom of Great Britain and Northern Ireland reported to the World Health Organization (WHO) the detection of avian influenza A(H5) virus in a poultry worker at a farm in England where poultry was infected with high pathogenicity avian influenza (HPAI) A(H5N1) viruses. Another detection was reported in a second individual performing culling operations on the farm. Both detections were later confirmed by additional testing as A(H5N1). Both cases were asymptomatic and detected as part of an ongoing enhanced surveillance study of asymptomatic workers exposed to poultry infected with avian influenza.

All the workers at this farm and their contacts have been identified; none of the contacts have reported symptoms, and no other influenza cases have been identified. The United Kingdom Health Security Agency (UKHSA) has not detected evidence of human-to-human transmission.

Based on the available information, WHO considers these as sporadic detections of avian influenza viruses among humans with no evidence of person-to-person transmission to date. Thus, the likelihood of international disease spread through humans is considered to be low.

Given the widespread circulation in birds and the constantly evolving nature of influenza viruses, WHO stresses the importance of global surveillance to detect virological, epidemiological and clinical changes associated with circulating influenza viruses which may affect human (or animal) health.

Description of the situation

In late April, the UKHSA was notified by the Animal and Plant Health Protection Agency (APHA) of an outbreak of HPAI (H5N1) on a poultry farm in England, United Kingdom. The human cases were detected through an ongoing enhanced surveillance study of asymptomatic workers exposed to poultry infected with avian influenza.

The UKHSA Rapid Investigation Team were deployed to the farm in early May 2023 to recruit exposed participants for the study. Of the 24 eligible persons, one tested positive for influenza A (with no detection of human seasonal subtypes H1 or H3) on the first sample self-taken at the premises. Two further nasopharyngeal samples collected from the same person tested negative for influenza A by a UKHSA regional laboratory and by the UKHSA national influenza reference laboratory. The participant remained clinically asymptomatic throughout.

An update from the United Kingdom authorities to WHO in mid-May 2023, notified of an additional case from the same farm as influenza A(H5) positive on two separate samples. This second person was a poultry culler exposed to infected birds at the same farm. The poultry culler worked on the farm in early May using personal protective equipment (PPE). The case was clinically assessed and remains asymptomatic. The case was treated with oseltamivir and was negative on respiratory sampling taken on the last day of isolation.

Sequencing later confirmed the virus detected in both individuals as A(H5N1). All samples from these two individuals were negative for seasonal influenza viruses. All other study participants remain well and have tested negative for influenza A on their samples to date. Follow-up of contacts has been completed. The affected farm is one of the first recruited in the ongoing enhanced surveillance study of asymptomatic workers exposed to poultry infected with avian influenza.

Work to determine whether these are infections or not (i.e., could instead be due to transient mucosal contamination of the nose with virus particles) is underway, though it may be difficult to reach a conclusion.

Epidemiology of disease

Animal influenza viruses normally circulate in animals but can also infect humans. Infections in humans have primarily been acquired through direct contact with infected animals or contaminated environments.

Depending on the host type, influenza A viruses can be classified as avian influenza, swine influenza, or other types of animal influenza viruses.

Avian, swine, and other animal influenza virus infections in humans may cause disease ranging from mild upper respiratory tract infection to more severe disease and may be fatal. Conjunctivitis, gastrointestinal symptoms, encephalitis and encephalopathy have also been reported.

Laboratory tests are required to diagnose human infection with influenza. WHO periodically updates technical guidance protocols for the detection of zoonotic influenza using molecular methods, e.g. Reverse transcription polymerase chain reaction (RT-PCR). Evidence suggests that some antiviral drugs, notably neuraminidase inhibitors (oseltamivir, zanamivir), can reduce the duration of viral replication and improve prospects of survival in some cases.

In 2023, Europe has been experiencing a large epidemic of A(H5N1) viruses in birds, with outbreaks reported in domestic birds, wild birds, and mammals across 24 countries. Outbreaks in wild and domestic birds continue to be reported through May 2023.

Public health response

The United Kingdom implemented the following public health measures:

Coordination and response: Since late April 2023, the standard measures for control of avian influenza in England were applied in the affected poultry farm. Situational assessment and response to human detection was coordinated by UKHSA and Public Health Scotland and undertaken by local health protection and National Health Service clinical services.

Surveillance: A follow-up response including passive and active surveillance of exposed workers was undertaken for the first detection. For the second detected case, close contacts were offered chemoprophylaxis, swabbing, and were requested to self-isolate for ten days since their last exposure, reporting information about their health conditions. This second case was isolated until the negative swab result.

Laboratory: Further samples have been obtained from the second case for analysis in a reference laboratory in Scotland. Virus characterization and genomic analysis are in process by the Respiratory Virus Unit, UKHSA/Scottish reference laboratory.

Infection prevention and control: In the affected farms, measures related to the control of the outbreak have been undertaken, including on-site slaughter of the birds, the destruction of contaminated materials that could carry the virus, and cleaning and disinfection of the facilities. All participants involved in the culling process wore personal protective equipment.

As per standard practice for confirmed infected poultry premises in the United Kingdom, a ten-kilometre surveillance zone, and a three-kilometre protection zone were declared by the United Kingdom Department for Environment, Food and Rural Affairs around the infected premises. The zone will remain in place for at least 21 days after preliminary cleansing and disinfection completion. It will not be lifted until surveillance activities, including clinical inspections of all commercial premises in the zone, have been undertaken.

WHO risk assessment

The two reported individuals with influenza A(H5N1) detection in their samples have remained asymptomatic and tested negative for influenza in their most recent samples to date. Their close contacts were asymptomatic and the follow-up period has been completed.

Both cases were detected as part of an ongoing enhanced surveillance study of asymptomatic workers exposed to poultry infected with avian influenza. In these cases, detections may have resulted from either transient respiratory tract contamination (with no virus replication) or asymptomatic infection. Further testing (e.g., serology) is needed to confirm infection.

Whenever avian influenza viruses are circulating in birds, humans who are exposed to these birds or their environments are at risk of infection.

Sporadic human cases and transient contaminations of humans are rare, but not unexpected in such contexts. Thus far, there is no evidence of person-to-person transmission in this incident.

Although both reported cases were asymptomatic in this instance, previous A(H5N1) infections have resulted in severe infections in humans.

Based on the available information, WHO assesses that the risk for the general population posed by this virus is low, and for occupationally exposed persons it is low to moderate.

WHO advice

The reports of these events do not change the current WHO recommendations on public health measures and surveillance of influenza.

Due to the constantly evolving nature of influenza viruses, and their widespread circulation in birds, WHO continues to stress the importance of global surveillance to detect and monitor virological, epidemiological, and clinical changes associated with emerging or circulating influenza viruses that may affect human (or animal birds and mammals) health and timely virus sharing for risk assessment.

When avian influenza viruses are circulating in an area, people involved in high-risk activities such as sampling infected birds or non-human mammals, culling, and disposing of infected animals, eggs, litters, and cleaning of contaminated premises should be trained on the proper use of and provided with appropriate PPE. All persons involved in these tasks should be registered and monitored closely by local health authorities for at least seven days following the last day of contact with infected animals or their environments. Those who develop respiratory symptoms should be rapidly sampled. Testing of asymptomatic exposed individuals could also be considered on a case-by-case basis, depending on available resources and objectives.

In the case of a confirmed or suspected human infection caused by a novel influenza virus with pandemic potential, including a variant virus (infection with a swine influenza A virus), a thorough epidemiologic investigation (even while awaiting the confirmatory laboratory results) of history of exposure to animals, of travel, and contact tracing should be conducted. The epidemiologic investigation should include early identification of unusual respiratory events that could signal person-to-person transmission of the novel virus. 

Clinical specimens collected from the case should be tested and sent to a WHO Collaboration Centre for further characterization. 

WHO recommends that all people involved in work with poultry or birds should have a seasonal influenza vaccination to reduce the risk of potential recombination events.

Travellers to countries with known outbreaks of animal influenza should avoid farms, contact with animals in live animal markets, entering areas where animals may be slaughtered, or contact with any surfaces that appear to be contaminated with animal faeces. 

General precautions include regular hand washing and following good food safety and good food hygiene practices. Should infected individuals from affected areas travel internationally, their infection may be detected in another country during travel or after arrival. If this were to occur, further community-level spread is considered unlikely as this virus has not acquired the ability to transmit easily among humans. 

All human infections caused by a novel influenza subtype are notifiable under the International Health Regulations (IHR) and State Parties to the IHR (2005) are required to immediately notify WHO of any laboratory-confirmed case of a recent human infection caused by an influenza A virus with the potential to cause a pandemic. Evidence of illness is not required for this report.

WHO does not recommend any restrictions on travel and/or trade for the United Kingdom based on available information on this event.

Further information

1. UK Health Security Agency (UKHSA). Avian flu detected in 2 individuals taking part in testing programme.
2. UK Health Security Agency (UKHSA). Management of contacts of highly pathogenic avian influenza H5N1 during the 2022 to 2023 avian influenza season
3. World Health Organization. Health topics, Influenza (avian and other zoonotic)
4. World Health Organization. Fact sheets, Influenza (Avian and other zoonotic)
5. World Health Organization. Influenza at the human-animal interface summary and assessment, 24 April 2023
6. World Health Organization. Cumulative number of confirmed human cases for avian influenza A(H5N1) reported to WHO, 2003-2023, 24 April 2023.
7. EFSA (European Food Safety Authority), ECDC (European Centre for Disease Prevention and Control), EURL (European Reference Laboratory for Avian Influenza), Adlhoch C, Fusaro A, Gonzales JL, Kuiken T, Mirinaviciute G, Niqueux É, Stahl K, Staubach C, Terregino C, Broglia A, Kohnle L and Baldinelli F, 2023. Scientific report: Avian influenza overview March–April 2023. EFSA Journal 2023;21(5):8039, 45 pp. https://doi.org/10.2903/j.efsa.2023.8039
8. Institute for International Cooperation in Animal and Biologics. The Centre for Food Security And Public Health. Highly pathogenic avian influenza
9. WHO information for molecular diagnosis of influenza virus - update

Citable reference: World Health Organization (30 May 2023). Disease Outbreak News; Avian Influenza A (H5N1) – United Kingdom of Great Britain and Northern Ireland. Available at https://www.who.int/emergencies/disease-outbreak-news/item/2023-DON468

 

Lintuinfluenssauutinen HPAI H5N1 Suomen Salosta, ensimmäinen lokkilintujen joukkokuolema

 https://www.hs.fi/kotimaa/turku/art-2000009666634.html

Salossa kuolleiden 20 naurulokin kuolinsyyksi on varmistunut korkeapatogeeninen H5N1-tyypin lintuinfluenssa, Ruokavirasto tiedottaa. Naurulokit löytyivät samalta rannalta Halikon kunnasta 13. kesäkuuta. Lintuinfluenssa todettiin lintujen elinnäytteistä Ruokaviraston tutkimuksissa. Kyseessä on ensimmäinen Suomessa todettu lintuinfluenssan aiheuttama luonnonvaraisten lokkien joukkokuolema. Yhdellä lokeista oli neurologisia oireita ja se lopetettiin paikan päällä. Lintujen joukkokuolemia on ilmennyt tänä keväänä eri puolilla Eurooppaa. Myös toukokuun lopussa Hollolassa kuolleesta varpushaukasta todettiin korkeapatogeenista lintuinfluenssaa.

Ruokavirasto suosittelee, että Salon alueella lintuja pidetään sisällä tai muutoin varmistetaan, että luonnonvaraiset linnut eivät pääse tekemisiin siipikarjan ja vankeudessa pidettävien lintujen tai niille tarjottavan rehun ja veden kanssa. Ruokavirasto muistuttaa samalla tautisuojauksen tärkeydestä siipikarjatilojen ja muiden lintujen pitopaikoissa lintuinfluenssatartuntojen estämiseksi.

Lintuinfluenssa leviää herkästi luonnonvaraisista linnuista siipikarjaan ja muihin lintuihin. Se voi levitä myös pidempiä matkoja esimerkiksi ihmisten tai viruksella saastuneiden välineiden mukana. Lintuinfluenssavirukset tarttuvat huonosti ihmiseen, ja tartunta vaatii yleensä läheisen kontaktin sairastuneeseen villilintuun, siipikarjaan tai niiden eritteisiin.

”Vain muutamalla ihmisellä Euroopassa on todettu lintuinfluenssa, eikä heillä esiintynyt vakavia oireita. Kuolleeseen lintuun ei kuitenkaan pidä koskea paljain käsin, ja taudilta tulee suojautua, jos tietää sen tarttuneen omiin lintuihin”, eläintautien valvonnan erityisasiantuntija Hanna Lounela kertoo HS:lle.

Jos siipikarjassa tai muissa linnuissa havaitaan lintuinfluenssaan viittaavia oireita, normaalista poikkeavaa kuolleisuutta tai muutoksia tuotannossa, on asiasta ilmoitettava heti kunnan- tai läänineläinlääkärille. Veden ja rehun kulutuksen tai munantuotannon väheneminen voivat olla merkkejä lintuinfluenssatartunnasta. Myös luonnonvaraisten lintujen joukkokuolemista ja yksittäisistä kuolleista petolinnuista tulee ilmoittaa kunnan- tai läänineläinlääkärille.

Lokkilinnut, Laridae,

Pikkulokki, Dvärgmås, Larus minutus, Laridae

Naurulokki, Skrattmås. Larus ridibundus , Laridae

Varpushaukka, Sparvhöl, Accipiter nisus,  Accipitridae

Sars-Cov-2 varianttien monitorointi jatkuu. Kasvava VOI varianttilinja XBB.1.16 saa alalinjoja edelleen.

 Eräs  alalinja on merkattu kodilla "FU" Alias XBB.1.16.1 .

Tämä  alalinja  FU.1 omaa  aminohapposubstituution Spike T547I. 

Sitten on havaittu  tälläkin FU.1 linjajlla runsasta alalinjaa, mutta   ei näytä olevan aminohapposubstituutiota, joten niitä on vaikea  hahmotella, kun ei vielä tiedetä, onko  kliinisiä merkityksiä, jotka poikkeaisivat  emolinjasta niin selvästi, että pitäisi merkata erikseen.

FU.1.1 linja on merkattu eri linjakseen pelkän nukelotidsimutaation perusteella. FU.1.1 ( nuc T3802C mutaatio).

Sitten  on lytynyt lisää alalinjaa FU.1 emolle (parent lineage) ja niitä tulee pitkin maapalloa GISAID tietueeseen , Nyt on koossa jo 1061 sekvenssiä linjaa,  jossa on nuc  A460G  mutaatio,  eikä vieläkään ole tunnistuksmerkiksi  aminohappomutaatiota. Tästä ollaan keskustelemasa.  Osa tutkijoista haluasi jo merkata tämän omaksi linjakseen ja joku tutkija vielä jarruttaisi, koska sitten alkaisi olla  usea linja pelkän synonyymisen mutaation perusteella   tunnistettu omana linjanaan Tietysti se on tutkijoille  kai yksinkertainen peruste sekin. 

Asista keskustellaan täss GITHUB kohdassa: Issue #2037.

 https://github.com/cov-lineages/pango-designation/issues/2037

Siteeraan vain  paikkakuntien nimet  ja maat  missä  tätä  linjaehdotusta  on popahtanut esiin:

China 642+3:
Shanghai 526, 88 imported: 6 HK, 7 Macao, 2 TW; 30 Thailand, 7 S. Korea, 4 UAE, 4 Singapore, 4 Japan, 4 Vietnam, 4 Malaysia, 3 Egypt, 2 US, 2 UK, 1 Deutschland, 1 Algeria, 1 Sweden, 1 Switzerland, 1 India, 1 NZ, 3 travelling info unavailable.
Hubei 24: 5 Jingzhou, 4 Huanggang, 3 Huangshi, 3 Ezhou, 2 Jingzhou, 2 Xiangyang, 1 Wuhan, 1 Xiaogan, 1 Enshi, 1 Shiyan and 1 Xianning.
Fujian 24: 12 Fuzhou, 3 Longyan, 3 Sanming, 2 Amoy, 2 Nanping, 1 Zhangzhou and 1 Quanzhou.
Anhui 21: 8 Hefei, 6 Bozhou, 5 Lu'an and 2 Fuyang.
Guangdong 12: 7 Shenzhen, 2 Guangzhou, 1 Meizhou, 1 Zhanjiang and 1 Dongguan.
Yunnan 9, city not assigned.
Sichuan 8: 2 Yibin, 2 Luzhou, 1 Neijiang, 1 Ya'an, 1 Guangyuan, 1 Liangshan.
Xinjiang 5: 3 Aksu, 1 Urumqi, 1 Kizilsu.
Jiangsu 4: 2 Zhenjiang, 1 Wuxi, 1 Changzhou.
Taiwan 3, all from Mainland.
Henan 2: 1 Hebi and 1 Xinyang.
Qinghai 2, all in Xining.
Beijing 1, Zhejiang 1(Hangzhou?), Heilongjiang 1, Shanxi 1(Jincheng), Liaoning 1(Chaoyang).

US 14: 1 from Deutschland, 1 from China Mainland, 2 from Taiwan, 1 from South Korea, 1 from Greece, 6 Airport Screening, 2 local cases in Washington State
South Korea 9: 4 from China, 2 from Switzerland, 1 from Turkey.
Japan 6, 5 Imported, at least 3 from China.
Australia 3(NSW 2, SA 1)
NZ 2(Auckland & Waitemata)
Singapore 2, all Local.
Austria 1(Vienna)
France 1(Occitanie)
Canada 1(Ontario)

Muistiin  19.6. 2023 

Spike P521S mutaatiosta Sars-Cov-2 rekombinanttivariantissa XBB.1.16.1 (VOI-variantti)

 https://github.com/cov-lineages/pango-designation/issues/1942

B.1.16.1 Sublineage with S:P521S, ORF1a:L681F #1942

ryhisner opened this issue Apr 22, 2023 · 2 comments

Labels

monitor currently too small, watch for future developments Recommend if grows An interesting lineage that should be prioritised for designation if it continues to grow at all reviewed XBB proposed sublineage of XBB

Comments

Description Sub-lineage of: XBB.1.16.1 Earliest sequence: 2023-3-16, France — EPI_ISL_17497793 2nd-Earliest Sequence: 2023-4-1, Belgium — EPI_ISL_17484410 Most recent sequence: 2023-4-3, France — EPI_ISL_17524580 Countries circulating: France (3), Australia (2), Belgium (1) Number of Sequences: 6 GISAID AA Query: Spike_T547I, Spike_P521S, NSP2_L401F GISAID Nucleotide Query: C2306T, C23123T, C23202T CovSpectrum Query: Nextcladepangolineage:XBB.1.16* & C2306T & C23123T & C23202T Substitutions on top of XBB.1.16.1: Spike: P521S ORF1a: L681F Nucleotide: C2306T, C23123T Evidence According to CovSpectrum Collection 42, created & run by Andrew Urquhart, after XBB.1.16 and XBB.1.16.1, the fastest-growing variants (as measured by low CI growth advantage) with ≥250 sequences are XBB.2.3.2, EU.1 (XBB.1.5.26.1), EU.1.1 (XBB.1.5.26.1.1), and XBB.2.3. All of these lineages possess S:P521S. This mutation has not been noticeably advantageous previously, but the same could be said for S:K478R/Q/N. Whether due to epistasis with other XBB* + S:S486P mutations or due to some change in population immunity, S:P521S seems now to confer some degree of benefit. Furthermore, other mutations at the same site have appeared in other XBB* lineages, mainly S:P521Q and S:P521S. Notably, the four sequences from France and Belgium all have the 2-nucleotide extended homology (A28877T, G28878C) for the TRS-B of N*, the novel sgRNA created by the 3-nucleotide N:203-204 mutations that has been in every B.1 lineage since it first emerged in 2020, and which one early study found to mess with host-cell interferon expression and increase viral loads. https://www.nature.com/articles/s41467-022-28287-8   ,,,,,,,,,,,,,,,,,         Tällä VOI variantilla XBB,1,16,1,  on muitakin  alalinjaehdokkaita.  on alalinja XBB.1.16.1 1 merkitään FU.1. Se taas  omaa alalinjoja, joka on suuri ryhmä ja parhaillaan sen fylogeneetistä puuta  ollaan selvittämässä. FU.1.1 ja FU.2 ovat jo saaneet designaationsa.  Esim seuraava  FU.1 alalinja odottaa selvitystään: https://github.com/cov-lineages/pango-designation/issues/2037

Tämä taas

Vertailen taulukoita . Viikon 20 prevalenssi tiedot lisätty edellisen (Viikot 14-18) taulukon tietoihin.

Download 8.6. 2023 sisältää paljon selventäviä käyriä ja tekstejä: Kts WHO linkistä.
Figure 7. Top three SARS-CoV-2 variants (including non-VOIs/VUMs) by WHO region, epidemiological week 16 to week 20 of 2023
Figure 8. The number and percentage of SARS-CoV-2 sequences, from 1 January to 21 May 2023
Figure 8. Panel A shows the number, and Panel B the percentage, of all circulating variants since January 2023. Omicron sister-lineages and additional Omicron VOC descendent lineages under further monitoring are shown. BA.1*, BA.2*, BA.3*, BA.4* and BA.5* (* indicates inclusion of descendent lineages) include all BA.1, BA.2, BA.3, BA.4 and BA.5 pooled descendent lineages, except currently circulating variants shown individually. The
Unassigned category includes lineages pending for a PANGO lineage name, whereas the Other category includes lineages that are assigned but not listed in the legend. Source: SARS- CoV-2 sequence data and metadata from GISAID, from 1 January 2023 to 21 May 2023.)Among the VUMs, XBB, XBB.1.9.1, XBB.1.9.2, and XBB.2.3 have shown increasing trends

Edellinen  taulukko  kuuakuden takaa: + viikko 20 lisättynä.  uudet  sekvenssimäärät punaisella.
Table 2. Weekly prevalence of SARS-CoV-2 VOIs and VUMs, week 14 to week 18 of 2023 + w.20
Lineage  Countries§   Sequences§    2023-14, 2023-15, 2023-16, 2023-17, 2023-18, 2023-20
XBB.1.5* (VOI) 116 c.  240,457  seq   50.44      49.44     46.41     45.65          41.57    30.28%.
XBB.1.16* (VOI) 65 c.   16,368   seq     6.92       8.55     10.01     10.73          13.17     16,81%.
BA.2.75*           123  c.111,956  seq      3.28      2.84       2.42        1.00            1.17         1,19%
CH.1.1*               92 c.  46,871  seq      3.85       3.77      3.15        2.86            2.26          1,96%
BQ.1*                150 c. 411,412  seq      3.73       2.83      2.06        1.42            0.75         0.34%
XBB*                 127 c.  64,360 seq      6.28       6.76       7.21       9.02          10.80          5,27%
XBB.1.9.1*          90  c.  31,583  seq   10.57      11.93      13.34    14.79          15.65       18,19%
XBB.1.9.2*         64  c.    8,426  seq     2.65        3.25        4.14      4.77            5.15          6,63%
XBB.2.3*             55  c.   6,359  seq     1.95        2.18        2.52      2.88           3.59           7,09%
Unassigned       103 c.  149,639 seq     2.13      1.26        0.93      0.03            -                   1,4%
Other+            207c.  6.724,206 seq    6.14      6.40        7.28      8.16             7.94           10,47%
Includes descendant lineages, except those individually specified elsewhere in the table. For example, XBB* does not include XBB.1.5, XBB.1.9.1,XBB.1.9.2, XBB.1.16, and XBB.2.3.
+ Others are other circulating lineages excluding the VOI, VUMs, BA.1*, BA.2*, BA.3*, BA.4*, BA.5*.
§ Countries and sequences are since the emergence of the variants

 
SARS-CoV-2 variants of interest and variants under monitoring
Geographic spread and prevalence
Globally, from 8 May to 4 June 2023 (28 days), 17 523 SARS-CoV-2 sequences were shared through GISAID. WHO is currently tracking two variants of interest (VOIs), XBB.1.5 and XBB.1.16, along with seven variants under monitoring
(VUMs) and their descendent lineages. The VUMs are BA.2.75, CH.1.1, BQ.1, XBB, XBB.1.9.1, XBB.1.9.2 and XBB.2.3.

There has been an increase in the number of countries reporting the two VOIs.

 Between 10 April and 7 May 2023 (28 days), 61 countries reported XBB.1.5 sequences, a cumulative total of 116 countries as of 21 May 2023 (Figure 6A,

 
Table 2). During the same 28-day period, 51 countries reported XBB.1.16 sequences, bringing the cumulative total to 65 countries (Figure 6B, Table 2).

 While XBB.1.5 remains dominant globally, its prevalence has been declining steadily. In epidemiological week 20 (15 to 21 May 2023), XBB.1.5 accounted for 30.3% of sequences, a decline from 46.2% in week 16 (17 to 23 April 2023).

  Globally, XBB.1.16 continues to rise in prevalence, accounting for 16.8% of
sequences in week 20 compared to 10.2% in week 16.

 

 

 

( Kuukausi sitten : Asetan Viikon 20 tähän yläpuolelle  mukaan. ja korjaan uudet arvot  viikolta 20 punaisella : 

Table 2. Weekly prevalence of SARS-CoV-2 VOIs and VUMs, week 14 to week 18 of 2023
Lineage  Countries§   Sequences§    2023-14, 2023-15, 2023-16, 2023-17, 2023-18
XBB.1.5* (VOI) 113 c.  227033 seq   50.44      49.44     46.41     45.65          41.57
XBB.1.16* (VOI) 58 c.   11857  seq     6.92       8.55     10.01     10.73          13.17
BA.2.75*           123  c.111031  seq      3.28      2.84       2.42        1.00            1.17
CH.1.1*               91 c.  45949  seq      3.85       3.77      3.15        2.86            2.26
BQ.1*                149 c. 410340  seq      3.73       2.83      2.06        1.42            0.75
XBB*                 127 c.   67073 seq      6.28       6.76       7.21       9.02          10.80
XBB.1.9.1*          84  c.  26149  seq   10.57      11.93      13.34    14.79          15.65
XBB.1.9.2*          58  c.    6805  seq     2.65        3.25        4.14      4.77            5.15
XBB.2.3*             52  c.    3657  seq     1.95        2.18        2.52      2.88           3.59
Unassigned       103 c.  149154 seq     2.13      1.26        0.93      0.03            -
Other+               207c.  6710043 seq    6.14      6.40        7.28      8.16             7.94
* Includes descendant lineages, except those individually specified elsewhere in the table. For example, XBB* does not include XBB.1.5, XBB.1.9.1,
XBB.1.9.2, XBB.1.16, and XBB.2.3.
+ Others are other circulating lineages excluding the VOI, VUMs, BA.1*, BA.2*, BA.3*, BA.4*, BA.5*.
§ Countries and sequences are since the emergence of the variants
Additional resources
• Tracking SARS-CoV-2 Variants
• WHO statement on updated tracking system on SARS-CoV-2 variants of concern and variants of interest
• WHO XBB.1.16 Initial Risk Assessment, 17 April 2023
• WHO XBB.1.5 rapid risk assessment, 24 February 2023