Ruotsin Sars-2 varianteista statistiikkaa

https://www.folkhalsomyndigheten.se/publicerat-material/publikationsarkiv/h/helgenomsekvensering-av-svenska-sars-cov-2-som-orsakar-covid-19-del-5/

 https://www.folkhalsomyndigheten.se/smittskydd-beredskap/utbrott/aktuella-utbrott/covid-19/statistik-och-analyser/sars-cov-2-virusvarianter-av-sarskild-betydelse/

 

Den femte delen i rapportserien om genetisk karakterisering av SARS-CoV-2 i Sverige omfattar vecka 15 till 22, 2021. Övervakningsprogrammet för helgenomsekvensering av SARS-CoV-2 omfattar minst 10 procent av de positiva proverna per vecka och region.

I rapporten beskrivs förekomsten av virusvarianter av särskild betydelse enligt ECDCs definition; B.1.1.7 (alfa), B.1.1.7 med mutation E484K, B.1.351 (beta), P.1 (gamma) samt B.1.617.2 (delta).

Under rapportperioden har incidensen av covid-19 sjunkit markant i Sverige. B.1.1.7 (alfa) är fortsatt den dominerande genetiska gruppen. B.1.351 (beta), B.1.1.7 med E484K samt P.1 (gamma) förekommer fortsatt på låga nivåer. B.1.617.2 (delta) påvisas i en ökande andel av sekvenserade prover och förekommer både hos individer smittade utomlands och i Sverige. Den ökade förekomsten av inhemsk smitta med B.1.617.2 (delta) är delvis relaterad till ett antal regionala utbrott och skillnaderna i förekomst över landet är stora.

Suomen THL:n antamaa infoa Sars-2 virusvarianteista

 

Huolestuttavat virusmuunnokset 

Tällä hetkellä WHO:n nimeämiä VOC- eli variants of concern -linjoja on neljä:

• Alfa-muunnos (Britannian muunnos B.1.1.7)
• Beeta-muunnos (Etelä-Afrikan muunnos B.1.351)
• Gamma-muunnos (Brasilian muunnos P1)
• Delta-muunnos (Intian muunnos B.1.617.2. 

THL seuraa näitä linjoja ja alueellisesti ilmeneviä uusia virusmuunnoksia ja raportoi niistä säännöllisesti tilannekatsaussivulla.

Laboratorion sekvensoinneissa virusmuunnoslinjat voidaan erottaa niin sanotusta villityypin viruksesta eli pandemian alkuvaiheen viruksista piikkiproteiinin mutaatioiden avulla, jotka ovat taulukossa mainitut tunnusomaiset mutaatiot S-geenissä.

Huolestuttavat virusmuunnokset

Muunnos	Vaihtoehtoiset nimet	Ensimmäiset havainnot	Tunnusomaiset mutaatiot S-geenissä
Alfa	’Britannian muunnos’, B.1.1.7 ja B.1.1.7 + E484K, 20I/501Y.V1	UK 09/2020	H69/V70, 144, (E484K), N501Y, A570D, D614G, P681H, T716I, S982A, D1118H
Beeta	’Etelä-Afrikan muunnos’, B.1.351, 20H/501Y.V2	Etelä-Afrikka 08/2020	D80A, D215G, L241/A242/L243, K417N, E484K, N501Y, D614G, A701V
Gamma	’Brasilian P1 muunnos’, B.1.1.28.1, P1,  20J/501Y.V3	Japani ja Brasilia 12/2020	L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G H655Y, T1027I, V1176F
Delta	’Intian virusmuunnos’,  B.1.617.2, 21A/S:478K	Intia 10/2020	T19R, G142D, del157/158, L452R, T478K, D614G, P681R, D950N

Alfa-muunnos (Britannian virusmuunnos)

Britanniasta löydettiin joulukuussa 2020 linjan B.1.1.7 virusmuunnos, joka on todennäköisesti kehittynyt syksyllä 2020. Alfa-muunnokseksi nimetyn viruksen mutaatiot ovat geenissä, joka sisältää viruksen pinnalla sijaitsevan piikkiproteiinin valmistusohjeen. Piikkiproteiinin avulla koronavirus tunkeutuu ihmisen soluihin.

On arvioitu, että tämä virusmuunnos tarttuu helpommin kuin aiemmin kiertäneet viruslinjat.

Alfa-muunnoksen arvioidaan aiheuttaneen valtaosan Britannian uusista todetuista koronavirustapauksista ja sitä on havaittu monessa maassa ympäri maailmaa. Virusmuunnosta on todettu Suomessa joulukuusta 2020 alkaen ja kuten useimmissa Euroopan maista, siitä on tullut myös Suomessa vallitseva koronaviruslinja.

Alfa-muunnoksesta käytetään eri yhteyksissä tieteellisiä nimiä B.1.1.7, 202012/01 ja 20B/501Y.V1.

Beeta-muunnos (Etelä-Afrikan virusmuunnos)

Etelä-Afrikassa havaittu viruslinja B.1.351 kehittyi todennäköisesti syksyllä 2020. Myös Beeta-muunnos sisältää mutaatioita geenissä, jossa on viruksen pinnalla sijaitsevan piikkiproteiinin valmistusohje. Beeta-muunnoksen S-geenin mutaatiot eroavat kuitenkin Alfa-muunnoksen mutaatioista. 

On viitteitä siitä, että myös tämä virusmuunnos tarttuu aiempaa helpommin. Viruslinja on levinnyt useaan maahan ja sitä esiintyy myös Suomessa.

Beeta-muunnoksen tieteellisiä nimiä ovat B.1.351 ja 20C/501Y.V2.

Gamma-muunnos (Brasilian P1-virusmuunnos) 

P1-linjan virusmuunnos havaittiin ensimmäisen kerran Japanissa Brasiliasta palaavilla matkailijoilla maahantulotestauksen yhteydessä joulukuussa 2020. Brasiliassa Amazonien alueella Gamma-muunnoksen ensimmäiset havainnot ovat marraskuulta. Sen osuus kaikista viruslinjoista alueella nousi nopeasti ja jo tammikuussa valtaosa sekvensoiduista näytteistä osoittautui Gamma-muunnoskeksi. 

Vaikka tämä virusmuunnos ei ole läheistä sukua edellä mainituille virusmuunnoksille, on siihen syntynyt osittain samoja piikkiproteiinin mutaatioita kuin muihin VOC-linjoihin.

On viitteitä siitä, että Gamma-muunnos saattaa olla muita kantoja tartuttavampi. Ensimmäisen kerran sitä on todettu Suomessa helmikuussa 2021.

Gamma-muunnoksen tieteellisiä nimiä ovat P.1, B.1.1.28.1 ja 20J/501Y.V3.

Delta-muunnos (Intian virusmuunnos)

Linjan B.1.617.2 koronavirusmuunnos on syksyllä 2020 Intiassa ensimmäisen kerran havaittu ja siellä yleistynyt muunnos. Kolme alalinjaa B.1.617.1  (Kappa), B.1.617.2 (Delta) ja B.1.617.3 eroavat toisistaan sekä mutaatioprofiilin että maantieteellisen esiintyvyyden suhteen. Ainoastaan Delta-muunnosta pidetään nykyisen tiedon valossa huolestuttavana muunnoksena.

Delta-muunnoksen piikkiproteiinissa esiintyy useita mutaatioita, jotka ovat osittain samoja kuin muissa VOC- ja VOI-linjoissa havaitut mutaatiot. Näiden mutaatioiden yhteisvaikutusta koronavirusinfektioon tai vaikutusta koronavirusepidemiaan ei kuitenkaan tunneta, eikä voida luotettavasti ennustaa. 

Delta-muunnosta on tavattu Suomessa ensimmäisen kerran maaliskuussa matkustamiseen liittyvissä tapauksissa.

WHO on nostanut Delta-muunnoksen (B.1.617.2)  huolestuttavien virusmuunnosten joukkoon sen nykyisten tietojen mukaan suuremman tartuttavuuden ja leviämistehon takia. Tutkimus- ja seurantatietoa muunnoksen taudinaiheuttamiskyvystä, leviämistehosta ja torjuntakeinojen toimivuudesta on edelleen hyvin niukasti.

Tehostetun seurannan alaiset koronavirusmuunnokset

Tällä hetkellä WHO on nostanut kuusi koronavirusmuunnosta VOI-linjoiksi: 

Zeta, Z,  (P2); B.1.1.28.2.

Theta (P3); B.1.1.28.3.

Epsilon, E   (B.1.427/B.1.429); 

Eta, H  (B.1.525); 

Iota , I, (B.1.526) ja 

Kappa, K  (B.1.617). 

Näiden lisäksi ECDC on listannut VOI-linjoiksi 

B.1.620- ja 

B.1.621-linjat.

THL seuraa tehostetusti näitä virusmuunnoksia ja Suomessa alueellisesti ilmeneviä uusia linjoja, mutta ei raportoi niistä säännöllisesti. 

Päivitetty:  4.6.2021

Viikkokatsaus (USA:n )seurattavista SARS-2 varianteista (25 .6. 2021)

 https://www.cdc.gov/coronavirus/2019-ncov/covid-data/covidview/index.html

The virus that causes COVID-19 is constantly changing through mutation, leading to new variants, including ones classified as variants of concern (VOCs). VOCs have the potential to spread more easily and quickly than other variants, which could lead to more cases of COVID-19. A recent CDC study found that the circulation of SARS-CoV-2 variants in the United States changed rapidly from December 2020 to May 2021, demonstrating how quickly a new variant can emerge, spread, and become the dominant strain.

Currently, several variants are found around the world, including in the United States. On June 15, 2021, the B.1.617.2 (Delta)* variant was classified as a VOC because it spreads from person to person more easily than other variants and may cause more severe disease. B.1.617.2 has been reported in 77 countries and in the United Kingdom has become the main variant in COVID-19 cases. In the United States, the proportion** of B.1.617.2 for the 2-week period ending June 19, 2021, is predicted to increase to 20.6% nationally and be higher in regions 2, 6, 7, 8, and 9.

The more a virus circulates in a population, the more opportunities it has to transform itself and can reduce the effectiveness of our vaccines. Recent studies have shown that the vaccines available in the United States are effective against variants currently circulating, including B.1.617.2. Vaccines interrupt the ability of the virus that causes COVID-19 to move between people and mutate, so it is important for everyone to get vaccinated as soon as they’re eligible. If you have questions or concerns about vaccines, please contact your healthcare professional, state or local health department, or local pharmacist or visit the CDC website. To find a place in your community to get a vaccine, visit Vaccines.gov or your local public health department website.

* To assist with public discussions of variants, the World Health Organizationexternal icon (WHO) recently proposed using labels consisting of the Greek Alphabet (e.g., Alpha, Beta, Gamma, Delta) as a practical way to discuss variants by non-scientific audiences. CDC supports WHO’s effort to a develop simple, non-stigmatizing variant naming system and is now indicating the WHO label for each key variant of interest (VOI) and variant of concern.

** The median time from specimen collection to sequence data reporting is about 3 weeks. As a result, weighted estimates for the most recent few weeks may be unstable or unavailable. CDC’s nowcast is a data projection tool that helps fill this gap by generating timely estimates of variant proportions for variants that are circulating in the United States. View nowcast estimates on CDC’s COVID Data Tracker website on the Variant Proportions page.

 

SARS-CoV-2 Variants

Multiple variants of the virus that causes COVID-19 are circulating globally and within the United States. To date, six variants have been classified as a variant of concern (VOC). Nowcast estimates* of SARS-CoV-2 cases caused by these VOCs for the two weeks ending June 19 are summarized here. Nationally, B.1.1.7 (Alpha) proportion is predicted to decrease to 52.2%;

 B.1.617.2 (Delta) proportion is predicted to increase to 20.6%; 

and P.1 (Gamma) proportion is predicted to increase to 16.4%. 

Nowcast estimates predict that B.1.1.7 (Alpha) proportions will be more than 50% in HHS regions 3, 4, 5, and 6. B.1.617.2 (Delta) is predicted to increase in all regions and to be more than 45% in regions 7 and 8. P.1 (Gamma) is predicted to be more than 20% in regions 1, 4, 5, and 10; and 

B.1.526 (Iota) is predicted to be more than 10% in regions 1, 2, and 3.

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

Updates on VOCs & VOIs

COVID-19 Weekly Epidemiological Updates

SARS-CoV-2 Variants, 31 December 2020

SARS-CoV-2 Variant – United Kingdom of Great Britain and Northern Ireland, 21 December 2020

SARS-CoV-2 mink-associated variant strain – Denmark, 3 December 2020

 

 

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/lineage	Nextstrain   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:
  • Variant of Interest
  • Variant of Concern
  • Variant of High Consequence
• 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 Interest (VOI) –  View current VOI in the United States that are being monitored and characterized

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

• Variants of High Consequence (VOHC) – Currently there are no SARS-CoV-2 variants that rise to the level of high consequence

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 Isolate^c: 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}

 

(*) = detected in some sequences but not all

a – Phylogenetic Assignment of Named Global Outbreak (PANGO) Lineages is software tool developed by members of the Rambaut Lab. The associated web application was developed by the Centre for Genomic Pathogen Surveillance in South Cambridgeshire and is intended to implement the dynamic nomenclature of SARS-CoV-2 lineages, known as the PANGO nomenclature.

b – Nextstrain, a collaboration between researchers in Seattle, USA and Basel, Switzerland, provides open-source tools for visualizing the genetics of outbreaks. The goal is to support public health surveillance by facilitating understanding of the spread and evolution of pathogens.

c – The Biodefense and Emerging Infections Research Resources (BEI Resources) is a NIAID-funded repository to provide reagents, tools, and information to the research community. The reference viruses proposed here facilitate the harmonization of information among all stakeholders in the COVID-19 pandemic research community. Please note that the reference viruses provided in the tables below are based on what is currently available through the BEI Resources.

 

Variant of Concern

A variant for which there is evidence of an increase in transmissibility, more severe disease (e.g.,  increased hospitalizations or deaths), significant reduction in neutralization by antibodies generated during previous infection or vaccination, reduced effectiveness of treatments or vaccines, or diagnostic detection failures.

Possible attributes of a variant of concern:

In addition to the possible attributes of a variant of interest

• Evidence of impact on diagnostics, treatments, or vaccines
  • Widespread interference with diagnostic test targets
  • Evidence of substantially decreased susceptibility to one or more class of therapies
  • Evidence of significant decreased neutralization by antibodies generated during previous infection or vaccination
  • Evidence of reduced vaccine-induced protection from severe disease
• Evidence of increased transmissibility
• Evidence of increased disease severity

Variants of concern might require one or more appropriate public health actions, such as notification to WHO under the International Health Regulations, reporting to CDC, local or regional efforts to control spread, increased testing, or research to determine the effectiveness of vaccines and treatments against the variant. Based on the characteristics of the variant, additional considerations may include the development of new diagnostics or the modification of vaccines or treatments.

Current variants of concern in the United States that are being closely monitored and characterized by federal agencies are included in the table below. The table will be updated when a new variant of concern is identified.

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Selected Characteristics of SARS-CoV-2 Variants of Concern

B.1.1.7 (Pango lineageexternal icon)^a

Spike Protein Substitutions: 69del, 70del, 144del, (E484K*), (S494P*), N501Y, A570D, D614G, P681H, T716I, S982A, D1118H (K1191N*)

Name (Nextstrainexternal icon)^b: 20I/501Y.V1

WHO Label: Alpha

First Identified: United Kingdom

BEI Reference Isolate^c: NR-54000external icon

Attributes:

• ~50% increased transmission ⁵
• Potential increased severity based on hospitalizations and case fatality rates ⁶
• No impact on susceptibility to EUA monoclonal antibody treatments ^7,14
• Minimal impact on neutralization by convalescent and post-vaccination sera ^{8,9,10,11,12,13,19}

B.1.351 (Pango lineageexternal icon)^a

Spike Protein Substitutions: D80A, D215G, 241del, 242del, 243del, K417N, E484K, N501Y, D614G, A701V

Name (Nextstrainexternal icon)^b: 20H/501.V2

WHO Label: Beta

First Identified: South Africa

BEI Reference Isolate^c: NR-55282external icon

Attributes:

• ~50% increased transmission¹⁶
• Significantly reduced susceptibility to the combination of bamlanivimab and etesevimab monoclonal antibody treatment,⁷ but other EUA monoclonal antibody treatments are available ¹⁴
• Reduced neutralization by convalescent and post-vaccination sera ^{8,12,18,19,20}

B.1.427 (Pango lineageexternal icon)^a

Spike Protein Substitutions: L452R, D614G

Name (Nextstrainexternal icon)^b: 20C/S:452R

WHO Label: Epsilon

First Identified: United States-(California)

Attributes:

• ~20% increased transmission ²¹
• Modest decrease in susceptibility to the combination of bamlanivimab and etesevimab; however, the clinical implications of this decrease are not known.⁷ Alternative monoclonal antibody treatments are available.¹⁴
• Reduced neutralization by convalescent and post-vaccination sera ²¹

B.1.429 (Pango lineageexternal icon)^a

Spike Protein Substitutions: S13I, W152C, L452R, D614G

Name (Nextstrainexternal icon)^b: 20C/S:452R

WHO Label: Epsilon

First Identified: United States-(California)

Attributes:

• ~20% increased transmission ²¹
• Reduced susceptibility to the combination of bamlanivimab and etesevimab; however, the clinical implications of this decrease are not known.⁷ Alternative monoclonal antibody treatments are available.¹⁴
• Reduced neutralization by convalescent and post-vaccination sera ²¹

B.1.617.2 (Pango lineageexternal icon)^a

Spike Protein Substitutions: T19R, (G142D*), 156del, 157del, R158G, L452R, T478K, D614G, P681R, D950N

Name (Nextstrainexternal icon)^b: 20A/S:478K

WHO Label: Delta

First Identified: India

Attributes:

• Increased transmissibility²⁹
• Potential reduction in neutralization by some EUA monoclonal antibody treatments ^{7, 14}
• Potential reduction in neutralization by post-vaccination sera ²¹

P.1 (Pango lineageexternal icon)^a

Spike Protein Substitutions: L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I

Name (Nextstrainexternal icon)^b: 20J/501Y.V3

WHO Label: Gamma

First Identified: Japan/Brazil

BEI Reference Isolate^c: NR-54982external icon

Attributes:

• Significantly reduced susceptibility to the combination of bamlanivimab and etesevimab monoclonal antibody treatment,⁷ but other EUA monoclonal antibody treatments are available ¹⁴
• Reduced neutralization by convalescent and post-vaccination sera ¹⁵

Variant of High Consequence

A variant of high consequence has clear evidence that prevention measures or medical countermeasures (MCMs) have significantly reduced effectiveness relative to previously circulating variants.

Possible attributes of a variant of high consequence:

In addition to the possible attributes of a variant of concern

• Impact on Medical Countermeasures (MCM)
  • Demonstrated failure of diagnostics
  • Evidence to suggest a significantly reduction in vaccine effectiveness, a disproportionately high number of vaccine breakthrough cases, or very low vaccine-induced protection against severe disease
  • Significantly reduced susceptibility to multiple Emergency Use Authorization (EUA) or approved therapeutics
  • More severe clinical disease and increased hospitalizations

A variant of high consequence would require notification to WHO under the International Health Regulations, reporting to CDC, an announcement of strategies to prevent or contain transmission, and recommendations to update treatments and vaccines.

Currently there are no SARS-CoV-2 variants that rise to the level of high consequence.

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Treatment considerations for healthcare providers

Substitutions of Concern for SARS-CoV-2 Monoclonal Antibody Therapies

In the United States, there are three anti-SARS-CoV-2 monoclonal antibody treatments with FDA Emergency Use Authorization (EUA) for the treatment of COVID-19: bamlanivimab plus etesevimabexternal icon, casirivimab plus imdevimab,external icon, and sotrovimabexternal icon.

CDC’s national genomic surveillance program identifies new and emerging SARS-CoV-2 variants to determine implications for COVID-19 diagnostics, treatments, or vaccines authorized for use in the United States. Sequences with similar genetic changes are grouped into lineages, and multiple lineages can have the same substitutions. For example, the E484K substitution is found in lineages B.1.351, P.1, B.1.526, and many others. Genomic surveillance efforts provide the capability to detect viruses that have reduced susceptibility to treatments more quickly.

In laboratory studies, SARS-CoV-2 variants that contain certain substitutions in the spike protein cause a marked reduction in susceptibility to bamlanivimab and may have reduced sensitivity to etesevimab and casirivimab. The L452R substitution found in the B.1.427 and B.1.429 lineages has been shown to cause a significant reduction in susceptibility to bamlanivimab and a modest decrease in susceptibility to the combination of bamlanivimab and etesevimab, although the clinical implications of this modest decrease are not known. ⁷ The E484K substitution found in the B.1.351, P.1, and B.1.526 lineages also results in a marked reduction in susceptibility to bamlanivimab, as well as the combination of bamlanivimab and etesevimab.⁷  Laboratory studies also suggest that the K417N and K417T substitutions, which are present in the B.1.351 and P.1 variants, respectively, along with the E484K mutation, reduces virus susceptibility to casirivimab, although the combination of casirivimab and imdevimab appears to retain activity.¹⁴ There is no reported reduction in susceptibility of variants to sotrovimab.²⁸

The table below shows the national and regional unweighted proportions of SARS-CoV-2 that contain the L452R or E484K substitution, individually, as well as the unweighted proportions of SARS-CoV-2 that contain the combination of K417N, E484K, and N501Y substitutions or the combination of K417T, E484K, and N501Y substitutions. As new data become available, additional substitutions may be added to the table below. The national and regional proportions provided in the table below will be updated weekly.

Resources

Monoclonal Antibody COVID-19 Infusionexternal icon

Statement on Anti-SARS-CoV-2 Monoclonal Antibodies EUA | COVID-19 Treatment Guidelines (nih.gov)external icon

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.