SARS-CoV-2 Variants

Virus variants - General

VUI - Variant Under Investigation
VOC - Variant Of Concern


World Health Organization Tracking SARS-CoV-2 variants (31 May 2021)
Variant of interest:

" 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."

Variant of concern:

"A SARS-CoV-2 variant that meets the definition of a VOI ... 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. "

Public Health England (16 Feb 2021) Guidance for investigating and managing individuals with a possible or confirmed SARS-CoV-2 Variant of Concern or Variant Under Investigation, GOV.UK.

Public Health England: Latest genomically confirmed case numbers of Covid-19 variants

COVID-19 Genomics UK (COG-UK) News and Updates

SARS-CoV-2 lineages - Visualisation of global virus lineages and reports of new variants (UK, South African and Brazilian)

Nextstrain.org SARS-CoV-2 genomic data (Global data)

Microreact SARS-CoV-2 genomic data visualisation (COG-UK)


Eric Topol. Summary table of UK, SA and Brazil variants (Twitter).

Florian Krammer. Vaccine-variant tweetorial

Variants of concern

Wikipedia page contains a nice summary table.

Alpha variant of concern B.1.1.7 first identified in UK

Russell P. (23 Dec 2020) New Variant of SARS-CoV-2 FAQs. Medscape UK.

Increased hazard of death in community-tested cases of SARS-CoV-2 Variant of Concern 202012/01 Nicholas G. Davies, Christopher I. Jarvis, CMMID COVID-19 Working Group, W. John Edmunds, Nicholas P. Jewell, Karla Diaz-Ordaz, Ruth H. Keogh medRxiv 2021.02.01.21250959; doi: https://doi.org/10.1101/2021.02.01.21250959


New and Emerging Respiratory Virus Threats Advisory Group (21 Jan 2021) NERVTAG note on B.1.1.7 severity - discusses B117 and mortality/disease severity

Baker L. (19 Dec 2020) Independent SAGE scientists share update as new mutation triggers today’s lockdown announcements. Healthcare Newsdesk.

Muik A et al. (19 Jan 2021) Neutralization of SARS-CoV-2 lineage B.1.1.7 pseudovirus by BNT162b2 vaccine-elicited human sera. bioRxiv 2021.01.18.426984; doi: https://doi.org/10.1101/2021.01.18.426984 "These data, together with the combined immunity involving humoral and cellular effectors induced by this vaccine, make it unlikely that the B.1.1.7 lineage will escape BNT162b2-mediated protection."

Twitter discussion(s)
Dr Eric Feigl-Ding: B117 and ?decrease in Pfizer vaccine efficacy


Beta variant of concern B.1.351 first identified in South Africa

Wibmer CK et al. (19 January 2021) SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma bioRxiv 2021.01.18.427166; doi: https://doi.org/10.1101/2021.01.18.427166


Twitter discussion(s)
Dr Eric Feigl-Ding: B1135 and ?decrease in Pfizer vaccine efficacy

Gamma variant of concern P.1 first identified in Brazil

Faria et al. (Jan 12 2021) Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings.

Delta variant of concern B.1.617.2 first identified in India

Planas, D., Veyer, D., Baidaliuk, A. et al. (8 July 2021) Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization. Nature (2021). https://doi.org/10.1038/s41586-021-03777-9

Public Health England. (14 May 2021) JCVI advice to mitigate impact of B1.617.2 variant

Public Health England (22 May 2021) Vaccines highly effective against B.1.617.2 variant after 2 doses

The study found that, for the period from 5 April to 16 May:
  • the Pfizer-BioNTech vaccine was 88% effective against symptomatic disease from the B.1.617.2 variant 2 weeks after the second dose, compared to 93% effectiveness against the B.1.1.7 variant
  • 2 doses of the AstraZeneca vaccine were 60% effective against symptomatic disease from the B.1.617.2 variant compared to 66% effectiveness against the B.1.1.7 variant
  • both vaccines were 33% effective against symptomatic disease from B.1.617.2, 3 weeks after the first dose compared to around 50% effectiveness against the B.1.1.7 variant

Other

Lambda variant of interest C.37 first identified in South America

Acevedo et al. (1 July 2021) Infectivity and immune escape of the new SARS-CoV-2 variant of interest Lambda (pre-print) medRxiv. doi: https://doi.org/10.1101/2021.06.28.21259673

The UK "Liverpool" variant under investigation Jan 2021 VUI202102/01

Public Health England (10 Feb 2021). PHE statement on Variant of Concern and new Variant Under Investigation. GOV.UK.

The UK "Bristol" variant Jan 2021 VOC202102/02 - mixed South African and UK mutations

Public Health England (21 Jan 2020) Investigation of novel SARS-CoV-2 variant Variant of Concern 202012/01: Technical briefing 5.

The spike protein mutation E484K (found in VOC 202012/02 B1.351 and VOC 202101/02 P1) has been detected in 11 B1.1.7 sequences. Preliminary information suggests more than one acquisition event.


The Danish mink variant

Lassaunière R. et al. (Nov 2020) Working paper on SARS-CoV-2 spike mutations arising in Danish mink, their spread to humans and neutralization data. From Statens Serum Institute