Tracking SARS-CoV-2 variants

Tracking SARS-CoV-2 variants
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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. Tracking SARS-CoV-2 variants

WHO, in collaboration with partners, expert networks, national authorities, institutions, and researchers has been monitoring and assessing the evolution of SARS-CoV-2 since January 2020. In late 2020, the emergence of variants that posed an increased risk to global public health prompted the characterization of specific Variants of Interest (VOIs) and Variants of Concern (VOCs), to prioritize 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 amino acid substitutions are identified, we can inform countries and the public about any changes that may be needed to respond 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.

Reducing transmission through established and proven disease control methods/measures, as well as avoiding introductions into animal populations, are crucial aspects of the global strategy to reduce the occurrence of mutations that have negative public health implications.

Current strategies and measures recommended by WHO continues to work against virus variants identified since the start of the pandemic. Evidence from multiple countries with the extensive transmission of VOCs has indicated that public health and social measures (PHSM), including infection prevention and control (IPC) measures, have been effective in reducing COVID-19 cases, hospitalizations and deaths. National and local authorities are encouraged to continue strengthening existing PHSM and IPC measures. Authorities are also encouraged to strengthen surveillance and sequencing capacities and apply a systematic approach to provide a representative indication of the extent of transmission of SARS-CoV-2 variants based on the local context, and to detect unusual epidemiological events.

Naming SARS-CoV-2 variants

The established nomenclature systems for naming and tracking SARS-CoV-2 genetic lineages by GISAIDNextstrain, and Pango are currently and will remain in use by scientists and 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-stigmatizing labels for VOI and VOC. At present, this expert group convened by WHO has recommended using letters of the Greek Alphabet, i.e., Alpha, Beta, Gamma, Delta which will be easier and more practical to be discussed by non-scientific audiences.

SARS-CoV-2 Variants, Working Definitions, and Actions Taken

Given the continuous evolution of the virus that leads to SARS-CoV-2 and the constant developments in our understanding of the impacts of variants, these working definitions may be periodically adjusted. When necessary, variants not otherwise meeting all criteria outlined in these definitions may be designated as VOIs/VOCs, and those posing a diminishing risk relative to other circulating variants may be reclassified, in consultation with the WHO Virus Evolution Working Group.

Variants of Concern (VOC)

Working definition:

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 ineffectiveness of public health and social measures or available diagnostics, vaccines, therapeutics.

 

Currently designated Variants of Concern:

WHO label  Pango  
lineage*
GISAID clade Next strain  
clade 
Additional amino acid changes monitored° Earliest documented  
samples 
Date of designation 
Alpha B.1.1.7 # GRY 20I (V1) +S:484K
+S:452R
The United Kingdom,
Sep-2020
18-Dec-2020
Beta B.1.351 GH/501Y.V2 20H (V2) +S: L18F South Africa,
May-2020
18-Dec-2020
Gamma P.1 GR/501Y.V3 20J (V3) +S:681H Brazil,
Nov-2020
11-Jan-2021
Delta B.1.617.2§ G/478K.V1 21A +S:417N India,
Oct-2020
VOI: 4-Apr-2021
VOC: 11-May-2021

 

*Includes all descendent lineages. The full list of Pango lineages can be found here: https://cov-lineages.org/lineage_list.html; for FAQ, visit: https://www.pango.network/faqs/

° only found in a subset of sequences

# includes all Q lineages (in the Pango nomenclature system, Q is an alias for B.1.1.7)

§ includes all AY lineages (in the Pango nomenclature system, AY is an alias for B.1.617.2); for more information on AY lineages, please visit: https://www.pango.network/new-ay-lineages/

 

Actions are taken by WHO and the Member States:

 

Primary actions by WHO for a potential VOC: 

  • Comparative assessment of variant characteristics and public health risks by WHO and the WHO Virus Evolution Working Group.
  • If determined necessary, coordinate additional laboratory investigations with the Member States and partners.
  • Communicate new designations and findings with the Member States and the public through established mechanisms.
  • Evaluate WHO guidance through established WHO mechanisms and update, if necessary.

 

 

Primary actions by a Member State, if a VOC is identified: 

  • Submit complete genome sequences and associated metadata to a publicly available database, such as GISAID.
  • Report initial cases/clusters associated with VOC infection to WHO through the IHR mechanism.
  • Where capacity exists and in coordination with the international community, perform field investigations and laboratory assessments to improve understanding of the potential impacts of the VOC on COVID-19 epidemiology, severity, the effectiveness of public health and social measures, diagnostic methods, immune responses, antibody neutralization, or other relevant characteristics.

 

Variants of Interest (VOI)

Working definition

A SARS-CoV-2 variant :

  • with genetic changes that are predicted or known to affect virus characteristics such as transmissibility, disease severity, immune escape, diagnostic or therapeutic escape; AND
  • Identified to cause significant community transmission or multiple COVID-19 clusters, in multiple countries with increasing relative prevalence alongside an increasing number of cases over time, or other apparent epidemiological impacts to suggest an emerging risk to global public health.

 

Currently designated Variants of Interest:

WHO label  Pango  
lineage*
GISAID clade Next strain  
clade 
Earliest documented  
samples 
Date of designation 
Lambda C.37 GR/452Q.V1 21G Peru, Dec-2020 14-Jun-2021
Mu B.1.621 GH 21H Colombia, Jan-2021 30-Aug-2021

*includes all descendent lineages. The full list of Pango lineages can be found here:https://cov-lineages.org/lineage_list.html; for FAQ, visit: https://www.pango.network/faqs/

 

Actions are taken by WHO and the Member States:

Primary actions by a Member State, if a new potential VOI is identified: 

  • Inform WHO through established WHO Country or Regional Office reporting channels with supporting information about VOI-associated cases (person, place, time, clinical, and other relevant characteristics).
  • Submit complete genome sequences and associated metadata to a publicly available database, such as GISAID.
  • Perform field investigations to improve understanding of the potential impacts of the VOI on COVID-19 epidemiology, severity, the effectiveness of public health and social measures, or other relevant characteristics.
  • Perform laboratory assessments according to capacity or contact WHO for support to conduct laboratory assessments on the impact of the VOI on relevant topics.

 

Primary actions by WHO for a potential VOI: 

  • Comparative assessment of variant characteristics and public health risks by WHO.
  • If determined necessary, coordinated laboratory investigations with the Member States and partners.
  • Review global epidemiology of VOI.
  • Monitor and track the global spread of VOI

 

Tracking SARS-CoV-2 variants

Reclassifying VOIs/ VOCs

A previously designated Variant of Interest (VOI) or Variant of Concern (VOC) has conclusively demonstrated to no longer pose a major added risk to global public health compared to other circulating SARS-CoV-2 variants, can be reclassified.

This is undertaken through a critical expert assessment, in collaboration with the WHO Virus Evolution Working Group of several criteria, such as the observed incidence/relative prevalence of variant detections among sequenced samples over time and between geographical locations, the presence/absence of other risk factors, and any ongoing impact on control measures.

Variants Under Monitoring (VUM, formerly called “Alerts for Further Monitoring”)

Working definition

A SARS-CoV-2 variant with genetic changes that are suspected to affect virus characteristics with some indication that it may pose a future risk, but evidence of phenotypic or epidemiological impact is currently unclear, requiring enhanced monitoring and repeat assessment pending new evidence.

Note: It is expected that our understanding of the impacts of these variants may fast evolve, and designated Variants under Monitoring may be readily added/removed; therefore, WHO labels will not be assigned at this time. Former VOIs/VOCs may, however, be monitored for an extended period under this category, and will maintain their assigned WHO label until further notice.

Currently designated Variants Under Monitoring (Tracking SARS-CoV-2 variants)

Pango  
lineage* 
GISAID clade Next strain  
clade 
Earliest documented  
samples 
Date of designation 
B.1.427§
B.1.429
GH/452R.V1 21C The United States of America,
Mar-2020
VOI: 5-Mar-2021
VUM: 6-Jul-2021
R.1 GR
Multiple countries,
Jan-2021
07-Apr-2021
B.1.466.2 GH Indonesia,
Nov-2020
28-Apr-2021
B.1.1.318 GR Multiple countries,
Jan-2021
02-Jun-2021
B.1.1.519 GR 20B/S.732A Multiple countries,
Nov-2020
02-Jun-2021
C.36.3
GR Multiple countries,
Jan-2021
16-Jun-2021
B.1.214.2 G Multiple countries, Nov-2020 30-Jun-2021
B.1.1.523 GR Multiple countries, May-2020 14-July-2021
B.1.619 G 20A/S.126A Multiple countries, May-2020 14-July-2021
B.1.620 G Multiple countries, November 2020 14-July-2021
C.1.2 GR South Africa, May 2021 01-Sep-2021
B.1.617.1§ G/452R.V3 21B India, Oct-2020
VOI: 4-Apr-2021
VUM: 20-Sep-2021
B.1.526§ GH/253G.V1 21F
The United States of America,
Nov-2020
VOI: 24-Mar-2021
VUM: 20-Sep-2021
B.1.525§ G/484K.V3 21D Multiple countries,
Dec-2020
VOI:17-Mar-2021
VUM: 20-Sep-2021

*includes all descendent lineages. The full list of Pango lineages can be found here: https://cov-lineages.org/lineage_list.html; for FAQ, please visit: https://www.pango.network/faqs/

§Former VOIs currently designated as VUMs: Kappa: B.1.617.1; Iota: B.1.526; Eta: B.1.525; Epsilon: B.1.427/B.1.429. Former VOIs no longer designated as VUMs: Zeta: P.2; Theta: P.3

Tracking SARS-CoV-2 variants

Member State Actions:

  • Enhance efforts towards a more representative picture of circulating variants in the country. Submit complete genome sequences and associated metadata to a publicly available database, such as GISAID.
  • Perform field investigations to improve understanding of the characteristics of the VUM on COVID-19 epidemiology (infectivity, neutralization, severity, etc.).
  • Conduct laboratory investigations to understand the phenotypic implications of the VUM
  • Monitor spread of VUM and interaction with other circulating variants for the potential to outcompeting or thrive in the presence of a known dominant VOC/VOI

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