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fredag 17 mars 2023

WHO päivittänyt VOC, VOI, VUM asioita ja tehostanut nykyisin kiertävien omikronvirusten tapahtumia ja tilanteen hahmotusta

 https://www.who.int/

 Latest News Viimeisimmät uutiset  Sars-Cov-2 viruksen seurannasta 

https://www.who.int/news/item/16-03-2023-statement-on-the-update-of-who-s-working-definitions-and-tracking-system-for-sars-cov-2-variants-of-concern-and-variants-of-interest

 https://covid19.who.int/

Pandemian tilanne globaaleina käyrinä 

Statement on the update of WHO’s working definitions and tracking system for SARS-CoV-2 variants of concern and variants of interest

 
16 March 2023
Statement
Reading time: 2 min (477 words)

WHO has updated its tracking system and working definitions for variants of SARS-CoV-2, the virus that causes COVID-19, to better correspond to the current global variant landscape, to independently evaluate Omicron sublineages in circulation, and classify new variants more clearly when required.

SARS-CoV-2 continues to evolve. Since the beginning of the COVID-19 pandemic, multiple variants of concern (VOCs) and variants of interest (VOIs) have been designated by WHO based on their assessed potential for expansion and replacement of prior variants, for causing new waves with increased circulation, and for the need for adjustments to public health actions.

Based on comparisons of antigenic cross reactivity using animal sera, replication studies in experimental models of the human respiratory tract, and evidence from clinical and epidemiological studies in humans, there is consensus among experts in WHO’s Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG-VE) that compared to previous variants, Omicron represents the most divergent VOC seen to date. Since its emergence, Omicron viruses have continued to evolve genetically and antigenically with an expanding range of sublineages, which so far have all been characterized by properties of evasion of existing population immunity and a preference to infect the upper respiratory tract (versus lower respiratory tract), as compared to pre-Omicron VOCs.

The Omicron viruses account for over 98% of the publicly available sequences since February 2022 and constitute the genetic background from which new SARS-CoV-2 variants will likely emerge, although the emergence of variants derived from previously circulating VOCs or of completely new variants remains possible. The previous system classified all Omicron sublineages as part of the Omicron VOC and thus did not have the granularity needed to compare new descendent lineages with altered phenotypes to the Omicron parent lineages (BA.1, BA.2, BA.4/BA.5). Therefore, from 15 March 2023, the WHO variant tracking system will consider the classification of Omicron sublineages independently as variants under monitoring (VUMs), VOIs, or VOCs.

WHO is also updating the working definitions for VOCs and VOIs. The main update consists in making the VOC definition more specific, to include major SARS-CoV-2 evolutionary steps that require major public health interventions. For the updated definitions, please visit the WHO variant tracking website.

In addition, going forward, WHO will assign Greek labels for VOCs, and will no longer do so for VOIs.

With these changes factored in, Alpha, Beta, Gamma, Delta as well as the Omicron parent lineage (B.1.1.529) are considered previously circulating VOCs. WHO has now classified XBB.1.5 as a VOI. 

WHO will also continue to issue regular risk assessments for both VOIs and VOCs (see latest risk assessment for XBB.1.5).

WHO emphasizes that these changes do not imply that the circulation of Omicron viruses no longer pose a threat to public health. Rather, the changes have been made in order to better identify additional or new threats over and above those posed by the current Omicron viruses in circulation.


onsdag 15 mars 2023

Lintuinfluenssaa 58 ihmisessä AH5N1 Kambodjassa vuodesta 2003 laskien. Mortaliteetti 68%

 https://www.who.int/emergencies/disease-outbreak-news/item/2023-DON445

Description of the cases

On 23 February 2023, the IHR NFP of Cambodia notified WHO of a confirmed case of human infection with avian influenza A (H5N1) virus. The case was an 11-year-old girl from Prey Veng province, in the south of Cambodia. On 16 February 2023, the case developed symptoms and received treatment at a local hospital. On 21 February 2023, the case was admitted to the National Pediatric Hospital with severe pneumonia. A sample was collected the same day through the severe acute respiratory infection (SARI) sentinel system and tested positive for avian influenza A (H5N1) virus by the reverse transcriptase-polymerase chain reaction (RT-PCR) at the National Institute of Public Health on the same day. The sample was also sent to Institute Pasteur Cambodia, the National Influenza Center, which confirmed the finding. The patient died on 22 February 2023. Cambodia shared the genetic sequence data of the virus from the index case through the publicly accessible database GISAID. Virus sequencing shows the H5N1 virus belongs to clade 2.3.2.1c, and similar to the 2.3.2.1c clade viruses circulating in poultry in southeast Asia since 2014.

A total of twelve close contacts (eight asymptomatic close contacts and four symptomatic who met the suspected case definition) of the index case were identified and samples were collected and tested. Laboratory investigations confirmed the second case on 23 February 2023, the father of the index child. The father, who is asymptomatic, is in isolation at the referral hospital. The eleven other samples tested negative for A (H5N1) and SARS-CoV-2.

As of 25 February 2023, a total of 58 cases of human infection with avian influenza A (H5N1) virus have been reported in Cambodia since 2003, including 38 deaths (CFR 66%); nine cases and seven deaths between 2003 to 2009 and 47 cases and 30 deaths between 2010 to 2014 were reported. 

Muistiin 15.3. 2023   KAndidaattirokotteita  rokotepankkiin, kerrottiin WHO mediakonferenssissa. 

 

 

onsdag 8 mars 2023

Eph reseptori-Efriini-signaloinnin merkitys monille viruksille

 https://www.sciencedirect.com/science/article/pii/S1043661820313463?via%3Dihub

Eph
erythropoietin-producing human hepatocellular receptors
Ephrin
Eph family receptor interacting proteins

 

Artikkeli mainitsee  18 virusta, jotka tavalla tai toisella käyttävät  ihmiskudosten solujen  Eph-Ephrin-signalointijärjestelmää. Arvellaan, että myös Sars-Cov-2 hyödyntäisi tätä järjestelmää.

CABYV
Cucurbit aphid borne yellows virus
CeV
Cedar virus
EBV
Epstein-Barr virus
HBV
Hepatitis B virus
HCV
Hepatitis C virus
HeV
Hendra virus
HIV
Human immunodeficiency virus
HNV
Henipavirus
IAPE
Intracisternal A-type Particles elements with an Envelope
IAV
Influenza A virus
IPNV
Infectious pancreatic necrosis virus
KSHV
Kaposi’s sarcoma-assicated virus
MojV
Mòjiāng virus
NiV
Nipah virus
PEDV
Porcine epidemic diarrhoea virus
RRV
Rhesus monkey rhadinovirus
RSV
Respiratory syncytial virus
SIV
Simian immunodeficiency virus
TuYV
Turnip yellow virus

 

söndag 5 mars 2023

BA.1.18 alalinja , yksittäinen, kroonikosta.

aviczhl2 commented Mar 4, 2023

First sequence: EPI_ISL_16751977(France) 2022.12.28
Most Recent Sequence: EPI_ISL_17050958(France) 2023.2.5

GISAID query: Spike_T22I,Spike_E132Q,Spike_V987F
Genome:
EPI_ISL_16751721-16751722, EPI_ISL_16751789, EPI_ISL_16751791,
EPI_ISL_16751977, EPI_ISL_16868993, EPI_ISL_16869007,
EPI_ISL_17050958

Mutations on top of BA.1.18:
C3486A, A7986G, G21956C, G24521T, C26029A, C11750T, C22664A, A5405G, G5572T, T6905G, T7322C, C12623T, A22964G, G25677T, G28209T, C21627T, G22599C, T5406C, G7252T, T22846C, A28612T, C24337T

S: T22I, R346T, I468V, E132Q,L368I,V987F
orf1a: I1714A, L2329F, M1769I, S2214A, Y2353H, P4120S, A1074D, Q2574R, L3829F
orf3a:L95F,Q213K
orf8:E106stop

 

fredag 3 mars 2023

BA.5.2 linjasta tulee myös kuin kankaankudontana varianttia. Uusi linja CP.1 esimerkkinä. Alias BA.5.2.6.7

 https://github.com/cov-lineages/pango-designation/issues/1473

Jokseenkin paljon kohesiivista konservatiivisuutta ja koosapitävää voimaa  täytyy  variantissa olla, kun näin  hienoja käyriä - kuin kangaspuilla  tehtynä-  saa niistä  aikaan. Katso linkistä. 

"CP" , alias BA.5.2.6 

CP.7 = " BA.5.6.2.7" 

Olen nimittäin sitä mieltä että suurin osa   koronavirusvarianteista on kuin pyramideja, jotka koettavat  lähteä liikkeelle  ja  keskenään muodostua  yhteismatgeriaaleistaan uusiksi pyramidiksi kaikkine aminohappo- ja nukleotidiresursseineen;  osin on kuin stoikkasmia niiden  ilmenemismuodot , ehkä vain  harvoin näin hienoja  viruksen ahkerasti tekemiä   "kankaspuuvalmisteita"  näkyy  käyrissä.  tietysti riippuu myös  havaitsevien laboratorioiden  kapasiteeteista ja saaduista näytemääristä näitten luonnon kasvunihmeiden  paljastaminen.

Myös BA.5.1 diversiteetistä on tullut uusi designaatio kuten EQ.1 (alias BA.5.1.33.1)

https://github.com/cov-lineages/pango-designation/issues/1522


Muistiin 3.3. 2023. Huomasin eilen että BA.5.1 diversiteetissä on myös myös paljon materiaalia selvitettävänä. Tässä EQ.1 tapauksessa  on alternatiivi luenta Orf 9 tapahtunut ja esiinty Orf9b. Niitä on tulossa muitakin sen kaltaisia alalinjoja kuten #1677 GITHUB asiassa mainitaan.