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:

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:
 * 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."


 * 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

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
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

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