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lördag 26 juni 2021

Päivityksiä huolestuttavista ja seurattavista Sars-2 virusmutanteista (VOC ja VOI)

Updates on VOCs & VOIs

 

 

Sars-2 varianttien seurannasta ja nimityksestä

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

Tracking SARS-CoV-2 variants

 

All viruses, including SARS-CoV-2, the virus that causes COVID-19, change over time. Most changes have little to no impact on the virus’ properties. However, some changes may affect the virus’s properties, such as how easily it spreads, the associated disease severity, or the performance of vaccines, therapeutic medicines, diagnostic tools, or other public health and social measures. 

WHO, in collaboration with partners, expert networks, national authorities, institutions and researchers have been monitoring and assessing the evolution of SARS-CoV-2 since January 2020. During late 2020, the emergence of variants that posed an increased risk to global public health prompted the characterisation of specific Variants of Interest (VOIs) and Variants of Concern (VOCs), in order to prioritise global monitoring and research, and ultimately to inform the ongoing response to the COVID-19 pandemic.  

WHO and its international networks of experts are monitoring changes to the virus so that if significant mutations are identified, we can inform countries and the public about any changes needed to react to the variant, and prevent its spread. Globally, systems have been established and are being strengthened to detect “signals” of potential VOIs or VOCs and assess these based on the risk posed to global public health. National authorities may choose to designate other variants of local interest/concern. 

Current strategies and measures recommended by WHO continue to work against virus variants identified since the start of the pandemic. 

Naming SARS-CoV-2 variants

The established nomenclature systems for naming and tracking SARS-CoV-2 genetic lineages by GISAID, Nextstrain and Pango are currently and will remain in use by scientists and in scientific research. To assist with public discussions of variants, WHO convened a group of scientists from the WHO Virus Evolution Working Group, the WHO COVID-19 reference laboratory network, representatives from GISAID, Nextstrain, Pango and additional experts in virological, microbial nomenclature and communication from several countries and agencies to consider easy-to-pronounce and non-stigmatising labels for VOI and VOC. At the present time, this expert group convened by WHO has recommended using labeled using letters of the Greek Alphabet, i.e., Alpha, Beta, Gamma, which will be easier and more practical to discussed by non-scientific audiences. 

 

SARS-CoV-2 Variants of Concern and Variants of Interest, updated 15 June 2021

Variants of Concern 

A SARS-CoV-2 variant that meets the definition of a VOI (see below) and, through a comparative assessment, has been demonstrated to be associated with one or more of the following changes at a degree of global public health significance: 

  • Increase in transmissibility or detrimental change in COVID-19 epidemiology; or 
  • Increase in virulence or change in clinical disease presentation; or 
  • Decrease in effectiveness of public health and social measures or available diagnostics, vaccines, therapeutics.  

WHO label 

Pango  
lineage 
GISAID clade/lineageNextstrain  
clade 
Earliest documented  
samples 
Date of designation 

Alpha 

B.1.1.7 

GRY (formerly GR/501Y.V1) 

20I (V1) 

United Kingdom,  
Sep-2020 

18-Dec-2020

Beta 
B.1.351  GH/501Y.V2  20H (V2)South Africa,  
May-2020 
18-Dec-2020
Gamma 
P.1  GR/501Y.V3  20J (V3) Brazil,  
Nov-2020 
11-Jan-2021
Delta 
B.1.617.2   G/478K.V1  21A India,  
Oct-2020 
VOI: 4-Apr-2021 
VOC: 11-May-2021

 

Variants of Interest 

 

WHO label  Pango  
lineage 
GISAID clade/lineage Nextstrain  
clade 
Earliest documented  
samples 
Date of designation 
Epsilon  B.1.427/B.1.429   GH/452R.V1  21C  United States of America,   
Mar-2020 
5-Mar-2021 
Zeta  P.2  GR/484K.V2 20B/S.484K  Brazil,  
Apr-2020 
17-Mar-2021 
Eta  B.1.525  G/484K.V3  21D Multiple countries, 
Dec-2020 
17-Mar-2021 
Theta  P.3  GR/1092K.V1  21E  Philippines,  
Jan-2021 
24-Mar-2021 
Iota  B.1.526   GH/253G.V1 21F  United States of America,  
Nov-2020 
24-Mar-2021 
Kappa  B.1.617.1   G/452R.V3  21B  
India,  
Oct-2020  
4-Apr-2021 

Lambda

C.37

GR/452Q.V1

20D

Peru, Dec-2020

14-Jun-2021

A SARS-CoV-2 isolate is a Variant of Interest (VOI) if, compared to a reference isolate, its genome has mutations with established or suspected phenotypic implications, and either:  

  • has been identified to cause community transmission/multiple COVID-19 cases/clusters, or has been detected in multiple countries; OR  
  • is otherwise assessed to be a VOI by WHO in consultation with the WHO SARS-CoV-2 Virus Evolution Working Group. 

SARS-2 virusvarianttien aikakautta

KEYS POINTS

( sitaatti tehty 23.6. 2021. https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html

  • Genetic variants of SARS-CoV-2 have been emerging and circulating around the world throughout the COVID-19 pandemic.
  • Viral mutations and variants in the United States are routinely monitored through sequence-based surveillance, laboratory studies, and epidemiological investigations.
  • A US government interagency group developed a Variant Classification scheme that defines three classes of SARS-CoV-2 variants:
  • The B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.427 (Epsilon), B.1.429 (Epsilon), and B.1.617.2 (Delta) variants circulating in the United States are classified as variants of concern.
  • To date, no variants of high consequence have been identified in the United States.
  • Laboratory studies suggest specific monoclonal antibody treatments may be less effective for treating cases of COVID-19 caused by variants with certain substitutions or combinations of substitutions in the spike protein.
    • L452R is present in B.1.526.1, B.1.427 (Epsilon), and B.1.429 (Epsilon) lineages, as well as the B.1.617 (Kappa, Delta) lineages and sub-lineages.
    • E484K is present in B.1.525 (Eta), P.2 (Zeta), P.1 (Gamma), and B.1.351 (Beta), but only some strains of B.1.526 (Iota) and B.1.1.7 (Alpha).
    • The combination of K417N, E484K, and N501Y substitutions is present in B.1.351 (Beta).
    • The combination of K417T, E484K, and N501Y substitutions is present in P.1 (Gamma).

Viruses constantly change through mutation. A variant has one or more mutations that differentiate it from other variants in circulation. As expected, multiple variants of SARS-CoV-2 have been documented in the United States and globally throughout this pandemic. To inform local outbreak investigations and understand national trends, scientists compare genetic differences between viruses to identify variants and how they are related to each other.

Variant classifications

The US Department of Health and Human Services (HHS) established a SARS-CoV-2 Interagency Group (SIG) to improve coordination among the Centers for Disease Control and Prevention (CDC), National Institutes of Health (NIH), Food and Drug Administration (FDA), Biomedical Advanced Research and Development Authority (BARDA), and Department of Defense (DoD). This interagency group is focused on the rapid characterization of emerging variants and actively monitors their potential impact on critical SARS-CoV-2 countermeasures, including vaccines, therapeutics, and diagnostics.

  • Variants of Concern (VOC) – View current VOC in the United States that are being closely monitored and characterized by federal agencies

Variant of Interest

A variant with specific genetic markers that have been associated with changes to receptor binding, reduced neutralization by antibodies generated against previous infection or vaccination, reduced efficacy of treatments, potential diagnostic impact, or predicted increase in transmissibility or disease severity.

Possible attributes of a variant of interest:

  • Specific genetic markers that are predicted to affect transmission, diagnostics, therapeutics, or immune escape
  • Evidence that it is the cause of an increased proportion of cases or unique outbreak clusters
  • Limited prevalence or expansion in the US or in other countries

A variant of interest might require one or more appropriate public health actions, including enhanced sequence surveillance, enhanced laboratory characterization, or epidemiological investigations to assess how easily the virus spreads to others, the severity of disease, the efficacy of therapeutics and whether currently authorized vaccines offer protection.

Current variants of interest in the United States that are being monitored and characterized are listed in the table below. The table will be updated when a new variant of interest is identified.

Selected Characteristics of SARS-CoV-2 Variants of Interest

B.1.525 (Pango lineageexternal icon)a

Spike Protein Substitutions: A67V, 69del, 70del, 144del, E484K, D614G, Q677H, F888L

Name (Nextstrainexternal icon)b: 20A/S:484K

WHO Label: Eta

First Identified: United Kingdom/Nigeria – December 2020

Attributes:

  • Potential reduction in neutralization by some EUA monoclonal antibody treatments 7, 14
  • Potential reduction in neutralization by convalescent and post-vaccination sera 22

B.1.526 (Pango lineageexternal icon)a

Spike Protein Substitutions: (L5F*), T95I, D253G, (S477N*), (E484K*), D614G, (A701V*)

Name (Nextstrainexternal icon)b: 20C/S:484K

WHO Label: Iota

First Identified: United States (New York) – November 2020

BEI Reference Isolatec: NR-55359external icon

Attributes:

  • Reduced susceptibility to the combination of bamlanivimab and etesevimab monoclonal antibody treatment; however, the clinical implications of this are not known.7 Alternative monoclonal antibody treatments are available.14
  • Reduced neutralization by convalescent and post-vaccination sera 22, 24

B.1.526.1 (Pango lineageexternal icon)a

Spike Protein Substitutions: D80G, 144del, F157S, L452R, D614G, (T791I*), (T859N*), D950H

Name (Nextstrainexternal icon)b: 20C

First Identified: United States (New York) – October 2020

Attributes:

  • Potential reduction in neutralization by some EUA monoclonal antibody treatments 7, 14
  • Potential reduction in neutralization by convalescent and post-vaccination sera22

B.1.617 (Pango lineageexternal icon)a

Spike Protein Substitutions: L452R, E484Q, D614G

Name (Nextstrainexternal icon)b: 20A

First Identified: India – February 2021

Attributes:

  • Potential reduction in neutralization by some EUA monoclonal antibody treatments 7, 14
  • Reduced neutralization by post-vaccination sera 25, 26

B.1.617.1 (Pango lineageexternal icon)a

Spike Protein Substitutions: (T95I), G142D, E154K, L452R, E484Q, D614G, P681R, Q1071H

Name (Nextstrainexternal icon)b: 20A/S:154K

WHO Label: Kappa

First Identified: India – December 2020

Attributes:

  • Potential reduction in neutralization by some EUA monoclonal antibody treatments 7, 14
  • Potential reduction in neutralization by post-vaccination sera 26

B.1.617.3 (Pango lineageexternal icon)a

Spike Protein Substitutions: T19R, G142D, L452R, E484Q, D614G, P681R, D950N

Name (Nextstrainexternal icon)b: 20A

First Identified: India – October 2020

Attributes:

  • Potential reduction in neutralization by some EUA monoclonal antibody treatments 7, 14
  • Potential reduction in neutralization by post-vaccination sera 26

P.2 (Pango lineageexternal icon)a

Spike Protein Substitutions: E484K, (F565L*), D614G, V1176F

Name (Nextstrainexternal icon)b: 20J

WHO Label: Zeta

First Identified: Brazil – April 2020

Attributes:

  • Potential reduction in neutralization by some EUA monoclonal antibody treatments 7, 14
  • Reduced neutralization by post-vaccination sera 22, 23

 

måndag 14 juni 2021

Koronavirusrokotusten aikaa.

 Kun  tiedot koronavirus Sars-2:n genomista alkoivat tulla, katselin sitä rakeennetta geeni geeniltä  2020 vuoden aikana, mutta  kun  etsi erilaisiaterapiamuotoja  viruksen moninaista  työkaluarsenaalia  vastaan , huomaa lopulta , että lähtökohta  tiedon hankkimiseen pitää sittenkin  keskittää  rokotuksen kehittelyn ja  rokotekohteen etsintään.  Tähän taan olennaisesti liittyy  ajan mittaan tulevien  virusvarianttien  tutkiminen ja niitä koskevien artikkeleiden löytäminen.  Nyt kun rokotteistakin alkaa seuloutua  tehokkaimpia  ja relevanteimpia esiin, eri  kansat  koettavat hankkia  kukin mahdollisuuksiensa mukaan rokotesuojaa.  Sain  oman  mRNA- perusteisen  rokotteeni Ruotsin puolella  viime kuun alkupäivinä ja  toisen anoksen tulen saamaan juhannuksen aikoihin. Tämä on sitä Pfizerin rokotetta. 

COVAX- ohjelmassa koetetaan saada  kaikille valtioille 20%:inen  rokotekattavuus.  Skandinaviassa lienee nyt rokotettujen määrät  ainakin  40% ellei jo ylikin.  

Nyt viime päivinä olen katsellut  varianttien luokittelua VOC, VOI, VUI,  VHC. Very High Concern- ryhmään ei tällä hetkellä lueta  mitään nykyvarianteista.  Vaikutavimmat VOC- ryhmäläiset  on alettu nietä kreikkalaisin krijaimin Alfa,Beta, Gamma ja Delta. Lisäksi on  tarkkailtavien  variantein joukossa  epsilonista Kappaan asti merkattuja  linjoja. 

thl.fi  ja CDC  antavat  tarkkoja luetteloja näistä varianteista

Varianttien nimityksistä  PANGOLIN järjestelmässä on pitkä luettelonsa joista  osa  on jo hiipuneita variantteja.  Tällaisen listan löytin tänään.https://gifhub.com/cov-lineages/pango-designation/blob/master/lineage-notes.txt

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

Sitten  löysin erään varianttipuun, jossa A =  The Root of the pandemic. Etsin yhden variantin merkitystä, ja  näin löysin Brasilialaisten VOC varianttien  kaavakuvan ja puun. Brasiliassa on ollutkovin  suuri kuolemanaalto. Myös Venäällä on nyt menossa    paha kuolemanaalto  pandemiasta. 

 

www.isbtweb.org/fileadmin/user_upload/Silvano_Wendel_SARS-CoV-2_Variants_in_Brazil_TTID_meeting_SW_Final_Mar_2021.pdf

Monissa maissa on  parin kolmen aallon jälkeistä   rauhallisempaa vaihetta kuten  nyt Skandinaviassa ,jossa eräitä rajoittavia sääntöjä jo voidaan  asteittan helpottaa. Yhteiskunnan liikkuvuus ja ekonomiset rattaat alkavat pikku hiljaa normalisoitua.

Olen ollut pitkiä  ajanjaksoja  näinä pandemian päivinä Tanskan puolellatyttäreni ja tyttärentyttäreni luona.Hil

jaiseloa. Maskin käyttöä ulkona kaupassa käydessä tai  tarhaan  lasta viedessä. Emme ole  olleet missään erityisessä  monipäisten joukkojen tilaisuuksissa pandemian aikana. Joulukirkossa käytiin  Tanskan suomalaisten kanssa.

måndag 22 februari 2021

Suomessa on muokattu Tartuntatautilakia ja uusi laki asettuu voimaan tänään 22.2. 2021.

H5N8 A-influenssaviruksen alaluokan lintuvirus tarttunut kanoista ihmiseen Venäjällä

 Tätä lintuvirusta esiintyy monin paikoin eri maissa,esim Tanskassa. Nyt on tulut TIETO VENÄJÄLTÄ, että  siipikarjasta on tarttunut ihmisiin ( n=7)  tätä virusta. 
Otan esiin netistä  tietoja edellisistä purkauksista ja  H5N8 viruksen luonteesta. 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5037296/
Voi olla , että rokote tulee olemaan tässäkin paras keino jos pandemia tulee. Saattaa olla resistenssiäperinteisille  influenssaviruslääkkeille.

Muistiin 22.2. 2021. 


Ps.  nyt kun on coronaviruspandemia ja kolmatta aaltoa ollaan odottamassa, kirjoitan  covid-19 ja Satrs-2  asiasta vain Facebookiin   uutisvirtaan. Vaikka saattaisi olla hyvä ottaa tietoja talteen myös tähän blogiin.

torsdag 15 oktober 2020

INO1 entsyymi. Inositolin synteesi linkkiytynee galaktoosin metaboliaan.

 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2788023/

 

 

Ihmisellä  geeni tunnetaan nimellä ISYNA1, sijainti19p13.11. 

Tämä on inositolia sisältävien yhdisteiden  metaboliassa tahtia rajoittava  entsyymi. Sen tehtävät on konvertoida glukoosi-6-fosfaattia myoinositoli-1-fosfaatiksi  (MIP) , siitä taas impaasi-entsyymit voivat  saada aikaan   myoinositolia mI. Sanon tätäsokeria "haisokeriksi"!. Hai käyttää tätä sokeria energiansa  kehittämiseen. Myös ihmisaivojen   harmaissa soluissa on inositolilipidien   kehittämää energia järjestelmää .  Glukoosin aueella toimii  ATP ja GTP, galaktoosin alueella UTP ja tämä  inositoli  alkaa CTP alueella synteesejään.  mutta   metabolinen tie yhtyy lopulta  jälleen ATP ja GTP  teihin, joitten  toimintaa   tämä  vahvistaa.