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Variants of SARS-CoV-2

January 01, 1970

"New coronavirus variant" redirects here. For recent species of coronavirus, see Novel coronavirus and Coronavirus.

Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are viruses that, while similar to the original, have genetic changes that are of enough significance to lead virologists to label them separately. SARS-CoV-2 is the virus that causes coronavirus disease 2019 (COVID-19). Some have been stated, to be of particular importance due to their potential for increased transmissibility,[1] increased virulence, or reduced effectiveness of vaccines against them.[2][3] These variants contribute to the continuation of the COVID-19 pandemic.

Positive, negative, and neutral mutations during the evolution of coronaviruses like SARS-CoV-2.

As of May 2024, only Omicron is designated as a circulating variant of concern by the World Health Organization.[4][failed verification]

Overview

The origin of SARS-CoV-2 has not been identified.[5] However, the emergence of SARS-CoV-2 may have resulted from recombination events between a bat SARS-like coronavirus and a pangolin coronavirus through cross-species transmission.[6][7] The earliest available SARS-CoV-2 viral genomes were collected from patients in December 2019, and Chinese researchers compared these early genomes with bat and pangolin coronavirus strains to estimate the ancestral human coronavirus type; the identified ancestral genome type was labeled "S", and its dominant derived type was labeled "L" to reflect the mutant amino acid changes. Independently, Western researchers carried out similar analyses but labeled the ancestral type "A" and the derived type "B". The B-type mutated into further types including B.1, which is the ancestor of the major global variants of concern, labeled in 2021 by the WHO as alpha, beta, gamma, delta and omicron variants.[8][9][10]

Early in the pandemic, the relatively low number of infections (compared with later stages of the pandemic) resulted in fewer opportunities for mutation of the viral genome and, therefore, fewer opportunities for the occurrence of differentiated variants.[11] Since the occurrence of variants was rarer, the observation of S-protein mutations in the receptor-binding domain (RBD) region interacting with ACE2 was also not frequent.[12]

As time went on, the evolution of SARS-CoV-2's genome (by means of random mutations) led to mutant specimens of the virus (i.e., genetic variants), observed to be more transmissible, to be naturally selected. Notably, both the Alpha and the Delta variants were observed to be more transmissible than previously identified viral strains.[13]

Some SARS-CoV-2 variants are considered to be of concern as they maintain (or even increase) their replication fitness in the face of rising population immunity,[14] either by infection recovery or via vaccination. Some of the variants of concern show mutations in the RBD of the S-protein.[15]

The following table presents information and relative risk level[16] for currently and formerly circulating variants of concern (VOC).[a] The intervals assume a 95% confidence or credibility level, unless otherwise stated. Currently, all estimates are approximations due to the limited availability of data for studies. For Alpha, Beta, Gamma and Delta, there is no change in test accuracy,[20][25] and neutralising antibody activity is retained by some monoclonal antibodies.[18][26] PCR tests continue to detect the Omicron variant.[27]

Identification[25] Emergence Changes relative to previously circulating variants at the time and place of emergence Neutralising antibody activity (or efficacy when available)
WHO
label 		PANGO
lineage 		Nextstrain
clade 		First
outbreak 		Earliest
sample[28] 		Designated VOC Current circulation Notable mutations Transmissibility Hospitalisation Mortality From natural infection[A] From vaccination
Delta B.1.617.2 21A   India Oct 2020 6 May 2021[29] No L452R, T478K, P681R[30] +97% (76–117%)[31] +85% (39–147%) relative to Alpha[D] +137% (50–230%)[B] Reinfections happened, with smaller occurrence rate than vaccinated infections[E][34] Efficacy reduction for non-severe disease[25][34][F]
Omicron B.1.1.529 21K   South Africa 9 Nov 2021[36] 26 Nov 2021[27] Yes P681H, N440K, N501Y, S477N, many others[37] Possibly increased[38] −57% (59–61%) relative to Delta[39] −63% (69–74%) relative to Delta[39] Increased reinfection rate[38] Efficacy reduction against symptomatic disease, unknown for severe disease[38]
Alpha B.1.1.7 20I (V1)   United Kingdom 20 Sep 2020[40] 18 Dec 2020[41] No 69–70del, N501Y, P681H[42][43] +29% (24–33%)[31][G] +52% (47–57%)[H][G] +59% (44–74%)[H][G] Minimal reduction[18] Minimal reduction[18]
Gamma P.1 (B.1.1.28.1) 20J (V3)   Brazil Nov 2020 15 Jan 2021[45][46] No K417T, E484K, N501Y[42] +38% (29–48%)[31] Possibly increased[25] +50% (50% CrI, 20–90%)[I][J] Reduced[18] Retained by many[K]
Beta B.1.351 20H (V2)   South Africa May 2020 14 Jan 2021[47] No K417N, E484K, N501Y[42] +25% (20–30%)[31] Under investigation[when?] Possibly increased[20][25] Reduced, T cell response elicited by D614G virus remains effective[18][25] Efficacy reduction against symptomatic disease,[L] retained against severe disease[25]

  Very high risk   High risk   Medium risk   Low risk   Unknown risk

  1. ^ Efficacy of natural infection against reinfection when available.
  2. ^ a b 7 February – 22 June 22, 2021, Ontario. CFR 0.04% for <50 age group unvaccinated, 6.5% for >50 age group unvaccinated[33]
  3. ^ a b Differences may be due to different policies and interventions adopted in each area studied at different times, to the capacity of the local health system, or to different variants circulating at the time and place of the study.
  4. ^ 1 April – 6 June 2021, Scotland.[32] Another preliminary study in Ontario found that hospitalization by Delta increased by 120% relative to non-VOC lineages.[B][C]
  5. ^ The study in Israel tracked 46035 unvaccinated recovered and 46035 vaccinated people of the same age distribution, to compare their infection occurrence in the follow-up period. 640 infections in the vaccinated group and 108 infections in the recovered group were recorded.
  6. ^ Moderately reduced neutralisation with Covaxin.[35]
  7. ^ a b c B.1.1.7 with E484K assumed to only differ from B.1.1.7 on neutralising antibody activity.[21]
  8. ^ a b 23 November 2020 – 31 January 2021, England.[44] CFR 0.06% for <50 age group, 4.8% for >50 age group[33]
  9. ^ The reported confidence or credible interval has a low probability, so the estimated value can only be understood as possible, not certain nor likely.
  10. ^ March 2020 – February 2021, Manaus.[C]
  11. ^ Except Pfizer–BioNTech.[20]
  12. ^ Oxford-AstraZeneca, Novavax.

Nomenclature

See also: Colloquial names of SARS-CoV-2 variants
SARS-CoV-2 corresponding nomenclatures[48]
PANGO lineages[49] Notes to PANGO lineages[50] Nextstrain clades,[51] 2021[52] GISAID clades Notable variants
A.1–A.6 19B S Contains "reference sequence" WIV04/2019[53]
B.3–B.7, B.9, B.10, B.13–B.16 19A L
O[b]
B.2 V
B.1 B.1.5–B.1.72 20A G Lineage B.1 in the PANGO Lineages nomenclature system; includes Delta/B.1.617[30][54]
B.1.9, B.1.13, B.1.22, B.1.26, B.1.37 GH
B.1.3–B.1.66 20C Includes Epsilon/B.1.427/B.1.429/CAL.20C and Eta/B.1.525[18][55]
20G Predominant in US generally, Feb '21[55]
20H Includes Beta/B.1.351 aka 20H/501Y.V2 or 501.V2 lineage
B.1.1 20B GR Includes B.1.1.207[citation needed] and Lambda (lineage C.37)[56]
20D
20J Includes Gamma/P.1 and Zeta/P.2[57][58]
20F
20I Includes Alpha/B.1.1.7 aka VOC-202012/01, VOC-20DEC-01 or 20I/501Y.V1
B.1.177 20E (EU1)[52] GV[b] Derived from 20A[52]
 
Tree diagram of lineages of SARS-CoV-2 according to the Pango nomenclature system.

SARS-CoV-2 variants are grouped according to their lineage and component mutations.[14] Many organisations, including governments and news outlets, referred colloquially to concerning variants by the country in which they were first identified.[60][61][62] After months of discussions, the World Health Organization announced Greek-letter names for important strains on 31 May 2021,[63] so they could be easily referred to in a simple, easy to say, and non-stigmatising fashion.[64][65] This decision may have partially been taken because of criticism from governments on using country names to refer to variants of the virus; the WHO mentioned the potential for mentioning country names to cause stigma.[66] After using all the letters from Alpha to Mu (see below), in November 2021 the WHO skipped the next two letters of the Greek alphabet, Nu and Xi, and used Omicron, prompting speculation that Xi was skipped to avoid offending Chinese leader Xi Jinping.[67] The WHO gave as the explanation that Nu is too easily confounded with "new" and Xi is a common last name.[67] In the event that the WHO uses the entirety of the Greek alphabet, the agency considered naming future variants after constellations.[68]

 
Various SARS-CoV-2 variants that were reported officially by CDC, NIH, in May 2021 in relation to mutations L452R and E484K

Lineages and clades

While there are many thousands of variants of SARS-CoV-2,[69] subtypes of the virus can be put into larger groupings such as lineages or clades.[c] Three main, generally used nomenclatures[70] have been proposed:

  • As of January 2021, GISAID—referring to SARS-CoV-2 as hCoV-19[50]—had identified eight global clades (S, O, L, V, G, GH, GR, and GV).[71]
  • In 2017, Hadfield et al. announced Nextstrain, intended "for real-time tracking of pathogen evolution".[72] Nextstrain has later been used for tracking SARS-CoV-2, identifying 13 major clades[d] (19A–B, 20A–20J and 21A) as of June 2021.[73]
  • In 2020, Rambaut et al. of the Phylogenetic Assignment of Named Global Outbreak Lineages (PANGOLIN)[74] software team proposed in an article[49] "a dynamic nomenclature for SARS-CoV-2 lineages that focuses on actively circulating virus lineages and those that spread to new locations";[70] as of August 2021, 1340 lineages had been designated.[75][76]

Each national public health institute may also institute its own nomenclature system for the purposes of tracking specific variants. For example, Public Health England designated each tracked variant by year, month and number in the format [YYYY] [MM]/[NN], prefixing 'VUI' or 'VOC' for a variant under investigation or a variant of concern respectively.[19] This system has now been modified and now uses the format [YY] [MMM]-[NN], where the month is written out using a three-letter code.[19]

Classification of variants

Variants that appear to meet one or more specific criteria considered during the COVID-19 pandemic may be labeled "variants of interest" or "variants under investigation" ('VUI') pending verification and validation of these properties. Once validated, variants of interest /VUI may be renamed "variants of concern" by monitoring organizations, such as the CDC in the US.[77][78][79] A related category is "variant of high consequence", used by the CDC if there is clear evidence that the effectiveness of prevention or intervention measures for a particular variant is substantially reduced.[80]

Reference sequence

As it is currently not known when the index case or "patient zero" occurred, the choice of reference sequence for a given study is relatively arbitrary, with different notable research studies' choices varying as follows:

  • The earliest sequence, Wuhan-1, was collected on 24 December 2019.[81]
  • One group (Sudhir Kumar et al.)[81] refers extensively to an NCBI reference genome (GenBankID:NC_045512; GISAID ID: EPI_ISL_402125),[82] this sample was collected on 26 December 2019,[83] although they also used the WIV04 GISAID reference genome (ID: EPI_ISL_402124),[84] in their analyses.[85]
  • According to another source (Zhukova et al.), the sequence WIV04/2019, belonging to the GISAID S clade / PANGO A lineage / Nextstrain 19B clade, is thought to most closely reflect the sequence of the original virus infecting humans—known as "sequence zero".[53] WIV04/2019 was sampled from a symptomatic patient on 30 December 2019 and is widely used (especially by those collaborating with GISAID)[86] as a reference sequence.[53]

The variant first sampled and identified in Wuhan, China is considered by researchers to differ from the progenitor genome by three mutations.[81][87] Subsequently, many distinct lineages of SARS-CoV-2 have evolved.[75]

Notability criteria

Viruses generally acquire mutations over time, giving rise to new variants. When a new variant appears to be growing in a population, it can be labelled as an "emerging variant". In the case of SARS-CoV-2, new lineages often differ from one another by just a few nucleotides.[14]

Some of the potential consequences of emerging variants are the following:[42][88]

  • Increased transmissibility
  • Increased morbidity
  • Increased mortality
  • Ability to evade detection by diagnostic tests
  • Decreased susceptibility to antiviral drugs (if and when such drugs are available)
  • Decreased susceptibility to neutralising antibodies, either therapeutic (e.g., convalescent plasma or monoclonal antibodies) or in laboratory experiments
  • Ability to evade natural immunity (e.g., causing reinfections)
  • Ability to infect vaccinated individuals
  • Increased risk of particular conditions such as multisystem inflammatory syndrome or long COVID.
  • Increased affinity for particular demographic or clinical groups, such as children or immunocompromised individuals.

Variants that appear to meet one or more of these criteria may be labelled "variants under investigation" or "variants of interest" pending verification and validation of these properties. The primary characteristic of a variant of interest is that it shows evidence that demonstrates it is the cause of an increased proportion of cases or unique outbreak clusters; however, it must also have limited prevalence or expansion at national levels, or the classification would be elevated to a "variant of concern".[19][78] If there is clear evidence that the effectiveness of prevention or intervention measures for a particular variant is substantially reduced, that variant is termed a "variant of high consequence".[18]

Variants of concern (WHO)

Listed below are the variants of concern (VOC) recognised by the World Health Organization as of October 2022.[17] Other organisations such as the CDC in the United States have at times used a slightly different list; for example, the CDC has de-escalated the Delta variant on 14 April 2022,[18] while the WHO did so on 7 June 2022.

 
False-colour transmission electron micrograph of a B.1.1.7 variant coronavirus. The variant's increased transmissibility is believed to be due to changes in structure of the spike proteins, shown here in green.

Omicron

Main article: SARS-CoV-2 Omicron variant

Lineage B.1.1.529

The Omicron variant, known as lineage B.1.1.529, was declared a variant of concern by the World Health Organization on 26 November 2021.[89]

The variant has a large number of mutations, of which some are concerning. Some evidence shows that this variant has an increased risk of reinfection. Studies are underway to evaluate the exact impact on transmissibility, mortality, and other factors.[90]

Named Omicron by the WHO,[89][91] it was identified in November 2021 in Botswana and South Africa;[92] one case had travelled to Hong Kong,[93][4][94] one confirmed case was identified in Israel in a traveler returning from Malawi,[95] along with two who returned from South Africa and one from Madagascar.[96] Belgium confirmed the first detected case in Europe on 26 November 2021 in an individual who had returned from Egypt on 11 November.[97] Indian SARS-CoV-2 Genomics Consortium (INSACOG) in its January 2022 bulletin noted that Omicron is in community transmission in India where new cases have been rising exponentially.[98]

BA. sublineages

According to the WHO, BA.1, BA.1.1, and BA.2 were the most common sublineages of Omicron globally as of February 2022.[99] BA.2 contains 28 unique genetic changes, including four in its spike protein, compared to BA.1, which had already acquired 60 mutations since the ancestral Wuhan strain, including 32 in the spike protein.[100] BA.2 is more transmissible than BA.1.[101] It was causing most cases in England by mid-March 2022, and by the end of March, BA.2 became dominant in the US.[102][100] As of May 2022, the sublineages BA.1 to BA.5 including all their descendants are classified as variants of concern by the WHO,[4] the CDC,[18] and the ECDC[103] (with the latter excluding BA.3).

Further sublineages emerging in 2022

During 2022, a number of further new strains emerged in different localities, including XBB.1.5, which evolved from the XBB strain of Omicron. The first case involving XBB in England was detected from a specimen sample taken on 10 September 2022 and further cases have since been identified in most English regions. By the end of the year, XBB.1.5 accounted for 40.5% of new cases across the US, and was the dominant strain; variant of concern BQ.1 was running at 18.3% and BQ.1.1 represented 26.9% of new cases, while the BA.5 strain was in decline, at 3.7%. At this stage, it was uncommon in many other countries, for example in the UK it was represented about 7% of new cases, according to UKHSA sequencing data.[104]

On 22 December 2022, the European Centre for Disease Control wrote in a summary that XBB strains accounted for circa 6.5% of new cases in five EU countries with sufficient volume of sequencing or genotyping to provide estimates.[104]

Further sublineages emerging in 2023: EG.5 "Eris", BA.2.86, and JN.1 "Pirola"

During 2023, SARS-CoV-2 continued to circulate in the global population and to evolve, with a number of new strains hitting the headlines. Testing, sequencing and reporting rates reduced.[105]

EG.5, a subvariant of XBB.1.9.2, (nicknamed "Eris" by some media[106]) emerged in February 2023.[107] On 6 August 2023, the UK Health Security Agency reported the EG.5 strain was responsible for one in seven new cases in the UK during the third week of July.[108]

Main article: BA.2.86

BA.2.86 was first detected in a sample from 24 July 2023, and was designated as a variant under monitoring by the World Health Organization on 17 August 2023.[109]

"JN.1" redirects here. For other uses, see JN1 (disambiguation).

JN.1 (sometimes referred to as "Pirola"), a subvariant of BA.2.86 Omicron, emerged during August 2023 in Luxembourg. By December 2023, it had been detected in 12 countries, including the UK and US.[110][111] On 19 December, JN.1 was declared by the WHO to be a variant of interest independently of its parent strain BA.2.86, but overall risk for public health was determined as low.[112] With JN.1 accounting for some 60% of cases in Singapore, in December 2023, Singapore and Indonesia recommended wearing masks at airports.[113] The CDC estimated that the variant accounted for 44% of cases in the US on 22 December 2023 and 62% of cases on 5 January 2024.[114]

As of 9 February 2024, JN.1 was estimated by the WHO to be the most prevalent variant of SARS-CoV-2 (70–90% prevalence in four out of six global regions; insufficient data in the East Mediterranean and African regions). The general level of population immunity and immunity from XBB.1.5 booster versions of the COVID-19 vaccine was expected to provide some protection (cross-reactivity) to JN.1.[115]

Variant of concern lineages under monitoring (WHO)

On 25 May 2022, the World Health Organization introduced a new category for potentially concerning sublineages of widespread variants of concern, called VOC lineages under monitoring (VOC-LUMs). This decision was made to reflect that already in February 2022, over 98% of all sequenced samples belonged to the Omicron family, and there has been significant evolution within this family.[4]

As of 10 February 2023[116]
Pango lineage GISAID clade Nextstrain clade Relation to circulating VOCs First documented Notable features
BF.7 GRA 22B BA.5 sublineage 2022-01-24 BA.5 + S:R346T
BQ.1 GRA 22E BA.5 sublineage 2022-02-07 BQ.1 and BQ.1.1: BA.5 + S:R346T, S:K444T, S:N460K
BA.2.75 GRA 22D BA.2 sublineage 2021-12-31 BA.2.75: BA.2 + S:K147E, S:W152R, S:F157L, S:I210V, S:G257S, S:D339H, S:G446S, S:N460K, S:Q493R reversion
CH.1.1 GRA 22D BA.2 sublineage 2022-07-20 BA.2.75 + S:L452R, S:F486S
XBB GRA 22F Recombinant of BA.2.10.1 and BA.2.75 sublineages, i.e. BJ1 and BM.1.1.1, with a breakpoint in S1 2022-08-13 BA.2+ S:V83A, S:Y144-, S:H146Q, S:Q183E, S:V213E, S:G252V, S:G339H, S:R346T, S:L368I, S:V445P, S:G446S, S:N460K, S:F486S, S:F490S
XBB.1.5 GRA 23A Recombinant of BA.2.10.1 and BA.2.75 sublineages, i.e. BJ1 and BM.1.1.1, with a breakpoint in S1 2022-01-05 XBB + S:F486P
XBF GRA Recombinant of BA.5.2.3 and CJ.1 (BA.2.75.3 sublineage) 2022-07-20 BA.5 + S:K147E, S:W152R, S:F157L, S:I210V, S:G257S, S:G339H, S:R346T, S:G446S, S:N460K, S:F486P, S:F490S
JN.1 GRA 24A BA.2.86 sublineage; genetic features include S:L455S 2023-08-25 As of 9 February 2024: most prevalent variant; low risk expected

Variants of interest (WHO)

Listed below are the Variants of Interest (VOI) which are recognised by the World Health Organization.[17] Other organisations such as the CDC in the United States may at times use a slightly different list.[18]

As of 15 March 2023,[117] The WHO defines a VOI as a variant "with genetic changes that are predicted or known to affect virus characteristics such as transmissibility, virulence, antibody evasion, susceptibility to therapeutics and detectability" and that it is circulating more than other variants in over one WHO region to such an extent that a global public health risk can be suggested.[118] Furthermore, the update stated that "VOIs will be referred to using established scientific nomenclature systems such as those used by Nextstrain and Pango".[118]

As of 20 December 2023, the WHO lists XBB.1.5, XBB.1.16, EG.5, BA.2.86 and JN.1 as circulating variants of interest.[119]

Variants under monitoring (WHO)

Listed below are Variants under Monitoring (VUM) which are recognised by the WHO. VUM's are defined as variants with genetic changes suspected to affect virus characteristics and some indication of posing a future risk, but with unclear evidence of phenotypic or epidemiological impact, requiring enhanced monitoring and repeat assessment after new evidence.[17]

As of 21 November 2023, the WHO lists DV.7, XBB, XBB.1.9.1, XBB.1.9.2, XBB.2.3 as circulating variants under monitoring.[4]

Previously circulating and formerly monitored variants (WHO)

The WHO defines a previously circulating variant as a variant that "has demonstrated to no longer pose a major added risk to global public health compared to other circulating SARS-CoV-2 variants", but should still be monitored.[4]

On 15 March 2023, the WHO released an update on the tracking system of VOCs, announcing that only VOCs will be assigned Greek letters.[117]

Previously circulating variants of concern (VOC)

The variants listed below had previously been designated as variants of concern, but were displaced by other variants. As of May 2022, the WHO lists the following under "previously circulating variants of concern":[4]

Alpha (lineage B.1.1.7)

Main article: SARS-CoV-2 Alpha variant

First detected in October 2020 during the COVID-19 pandemic in the United Kingdom from a sample taken the previous month in Kent,[120] lineage B.1.1.7,[121] labelled Alpha variant by the WHO, was previously known as the first Variant Under Investigation in December 2020 (VUI – 202012/01)[122] and later notated as VOC-202012/01.[19] It is also known as 20I (V1),[28] 20I/501Y.V1[123] (formerly 20B/501Y.V1),[42][124][125] or 501Y.V1.[126] From October to December 2020, its prevalence doubled every 6.5 days, the presumed generational interval.[127][128] It is correlated with a significant increase in the rate of COVID-19 infection in United Kingdom, associated partly with the N501Y mutation.[127] There was some evidence that this variant had 40–80% increased transmissibility (with most estimates lying around the middle to higher end of this range),[129][130] and early analyses suggested an increase in lethality,[131][132] though later work found no evidence of increased virulence.[133] As of May 2021, the Alpha variant had been detected in some 120 countries.[134]

On 16 March 2022, the WHO has de-escalated the Alpha variant and its subvariants to "previously circulating variants of concern".[135][136]

B.1.1.7 with E484K

Variant of Concern 21FEB-02 (previously written as VOC-202102/02), described by Public Health England (PHE) as "B.1.1.7 with E484K"[19] is of the same lineage in the Pango nomenclature system, but has an additional E484K mutation. As of 17 March 2021, there were 39 confirmed cases of VOC-21FEB-02 in the UK.[19] On 4 March 2021, scientists reported B.1.1.7 with E484K mutations in the state of Oregon. In 13 test samples analysed, one had this combination, which appeared to have arisen spontaneously and locally, rather than being imported.[137][138][139] Other names for this variant include B.1.1.7+E484K[140] and B.1.1.7 Lineage with S:E484K.[141]

Beta (lineage B.1.351)

Main article: SARS-CoV-2 Beta variant

On 18 December 2020, the 501.V2 variant, also known as 501.V2, 20H (V2),[28] 20H/501Y.V2[123] (formerly 20C/501Y.V2), 501Y.V2,[142] VOC-20DEC-02 (formerly VOC-202012/02), or lineage B.1.351,[42] was first detected in South Africa and reported by the country's health department.[143] It has been labelled as Beta variant by WHO. Researchers and officials reported that the prevalence of the variant was higher among young people with no underlying health conditions, and by comparison with other variants it is more frequently resulting in serious illness in those cases.[144][145] The South African health department also indicated that the variant may be driving the second wave of the COVID-19 epidemic in the country due to the variant spreading at a more rapid pace than other earlier variants of the virus.[143][144]

Scientists noted that the variant contains several mutations that allow it to attach more easily to human cells because of the following three mutations in the receptor-binding domain (RBD) in the spike glycoprotein of the virus: N501Y,[143][146] K417N, and E484K.[147][148] The N501Y mutation has also been detected in the United Kingdom.[143][149]

On 16 March 2022, the WHO has de-escalated the Beta variant and its subvariants to "previously circulating variants of concern".[135][136]

Gamma (lineage P.1)

Main article: SARS-CoV-2 Gamma variant

The Gamma variant or lineage P.1, termed Variant of Concern 21JAN-02[19] (formerly VOC-202101/02) by Public Health England,[19] 20J (V3)[28] or 20J/501Y.V3[123] by Nextstrain, or just 501Y.V3,[126] was detected in Tokyo on 6 January 2021 by the National Institute of Infectious Diseases (NIID). It has been labelled as Gamma variant by WHO. The new variant was first identified in four people who arrived in Tokyo having travelled from the Brazilian Amazonas state on 2 January 2021.[150] On 12 January 2021, the Brazil-UK CADDE Centre confirmed 13 local cases of the new Gamma variant in the Amazon rainforest.[151] This variant of SARS-CoV-2 has been named lineage P.1 (although it is a descendant of B.1.1.28, the name B.1.1.28.1[20][152] is not permitted and thus the resultant name is P.1), and has 17 unique amino acid changes, 10 of which in its spike protein, including the three concerning mutations: N501Y, E484K and K417T.[151][152][153][154]: Figure 5 

The N501Y and E484K mutations favour the formation of a stable RBD-hACE2 complex, thus, enhancing the binding affinity of RBD to hACE2. However, the K417T mutation disfavours complex formation between RBD and hACE2, which has been demonstrated to reduce the binding affinity.[1]

The new variant was absent in samples collected from March to November 2020 in Manaus, Amazonas state, but it was detected for the same city in 42% of the samples from 15 to 23 December 2020, followed by 52.2% during 15–31 December and 85.4% during 1–9 January 2021.[151] A study found that infections by Gamma can produce nearly ten times more viral load compared to persons infected by one of the other lineages identified in Brazil (B.1.1.28 or B.1.195). Gamma also showed 2.2 times higher transmissibility with the same ability to infect both adults and older persons, suggesting P.1 and P.1-like lineages are more successful at infecting younger humans irrespective of sex.[155]

A study of samples collected in Manaus between November 2020 and January 2021, indicated that the Gamma variant is 1.4–2.2 times more transmissible and was shown to be capable of evading 25–61% of inherited immunity from previous coronavirus diseases, leading to the possibility of reinfection after recovery from an earlier COVID-19 infection. As for the fatality ratio, infections by Gamma were also found to be 10–80% more lethal.[156][157][158]

A study found that people fully vaccinated with Pfizer or Moderna have significantly decreased neutralisation effect against Gamma, although the actual impact on the course of the disease is uncertain. A pre-print study by the Oswaldo Cruz Foundation published in early April found that the real-world performance of people with the initial dose of the Sinovac's Coronavac Vaccine had approximately 50% efficacy rate. They expected the efficacy to be higher after the 2nd dose. As of July 2021, the study is ongoing.[159]

Preliminary data from two studies indicate that the Oxford–AstraZeneca vaccine is effective against the Gamma variant, although the exact level of efficacy has not yet been released.[160][161] Preliminary data from a study conducted by Instituto Butantan suggest that CoronaVac is effective against the Gamma variant as well, and as of July 2021 has yet to be expanded to obtain definitive data.[162]

On 16 March 2022, the WHO has de-escalated the Gamma variant and its subvariants to "previously circulating variants of concern".[135][136]

Delta (lineage B.1.617.2)

Main article: SARS-CoV-2 Delta variant

The Delta variant, also known as B.1.617.2, G/452R.V3, 21A[28] or 21A/S:478K,[123] was a globally dominant variant that spread to at least 185 countries.[163] It was first discovered in India. Descendant of lineage B.1.617, which also includes the Kappa variant under investigation, it was first discovered in October 2020 and has since spread internationally.[164][165][166][167][168] On 6 May 2021, British scientists declared B.1.617.2 (which notably lacks mutation at E484Q) as a "variant of concern", labelling it VOC-21APR-02, after they flagged evidence that it spreads more quickly than the original version of the virus and could spread quicker or as quickly as Alpha.[169][21][170][171] It carries L452R and P681R mutations in Spike;[30] unlike Kappa it carries T478K but not E484Q.

On 3 June 2021, Public Health England reported that twelve of the 42 deaths from the Delta variant in England were among the fully vaccinated, and that it was spreading almost twice as fast as the Alpha variant.[172] Also on 11 June, Foothills Medical Centre in Calgary, Canada reported that half of their 22 cases of the Delta variant occurred among the fully vaccinated.[173]

In June 2021, reports began to appear of a variant of Delta with the K417N mutation.[174] The mutation, also present in the Beta and Gamma variants, raised concerns about the possibility of reduced effectiveness of vaccines and antibody treatments and increased risk of reinfection.[175] The variant, called "Delta with K417N" by Public Health England, includes two clades corresponding to the Pango lineages AY.1 and AY.2.[176] It has been nicknamed "Delta plus"[177] from "Delta plus K417N".[178] The name of the mutation, K417N, refers to an exchange whereby lysine (K) is replaced by asparagine (N) at position 417.[179] On 22 June, India's Ministry of Health and Family Welfare declared the "Delta plus" variant of COVID-19 a variant of concern, after 22 cases of the variant were reported in India.[180] After the announcement, leading virologists said there was insufficient data to support labelling the variant as a distinct variant of concern, pointing to the small number of patients studied.[181] In the UK in July 2021, AY.4.2 was identified. Alongside those previously mentioned it also gained the nickname 'Delta Plus', on the strength of its extra mutations, Y145H and A222V. These are not unique to it, but distinguish it from the original Delta variant.[182]

On 7 June 2022, the WHO has de-escalated the Delta variant and its subvariants to "previously circulating variants of concern".[136][183]

Previously circulating variants of interest (VOI)

Pango lineage GISAID clade Nextstrain clade Earliest samples Date of VOI Date of designation Country of sampling Notes
P.2 GR/484K.V2 20B/S.484K 2020-04 2021-07-06 2021-08-17 Zeta variant
P.3 GR/1092K.V1 21E 2021-01 2021-07-06 2021-08-17 Theta variant
B.1.427
B.1.429		 GH/452R.V1 21C 2020-03 2021-07-06 2021-11-09 Epsilon variant
B.1.617.1 G/452R.V3 21B 2020-10 2021-09-20 Kappa variant
B.1.526 GH/253G.V1 21F 2020-11 2021-09-20 Iota variant
B.1.525 G/484K.V3 21D 2020-12 2021-09-20 Eta variant
C.37 GR/452Q.V1 21G 2020-12 2021-06-14 2022-03-09 Lambda variant
B.1.621 GH 21H 2021-01 2021-08-30 2022-03-09 Mu variant

Epsilon (lineages B.1.429, B.1.427, CAL.20C)

Main article: SARS-CoV-2 Epsilon variant

The Epsilon variant or lineage B.1.429, also known as CAL.20C[184] or CA VUI1,[185] 21C[28] or 20C/S:452R,[123] is defined by five distinct mutations (I4205V and D1183Y in the ORF1ab gene, and S13I, W152C, L452R in the spike protein's S-gene), of which the L452R (previously also detected in other unrelated lineages) was of particular concern.[55][186] From 17 March to 29 June 2021, the CDC listed B.1.429 and the related B.1.427 as "variants of concern".[30][187][188][189] As of July 2021, Epsilon is no longer considered a variant of interest by the WHO,[17] as it was overtaken by Alpha.[190]

From September 2020 to January 2021, it was 19% to 24% more transmissible than earlier variants in California. Neutralisation against it by antibodies from natural infections and vaccinations was moderately reduced,[191] but it remained detectable in most diagnostic tests.[192]

Epsilon (CAL.20C) was first observed in July 2020 by researchers at the Cedars-Sinai Medical Center, California, in one of 1,230 virus samples collected in Los Angeles County since the start of the COVID-19 epidemic.[193] It was not detected again until September when it reappeared among samples in California, but numbers remained very low until November.[194][195] In November 2020, the Epsilon variant accounted for 36 per cent of samples collected at Cedars-Sinai Medical Center, and by January 2021, the Epsilon variant accounted for 50 per cent of samples.[186] In a joint press release by University of California, San Francisco, California Department of Public Health, and Santa Clara County Public Health Department,[196] the variant was also detected in multiple counties in Northern California. From November to December 2020, the frequency of the variant in sequenced cases from Northern California rose from 3% to 25%.[197] In a preprint, CAL.20C is described as belonging to clade 20C and contributing approximately 36% of samples, while an emerging variant from the 20G clade accounts for some 24% of the samples in a study focused on Southern California. Note, however, that in the US as a whole, the 20G clade predominates, as of January 2021.[55] Following the increasing numbers of Epsilon in California, the variant has been detected at varying frequencies in most US states. Small numbers have been detected in other countries in North America, and in Europe, Asia and Australia.[194][195] After an initial increase, its frequency rapidly dropped from February 2021 as it was being outcompeted by the more transmissible Alpha. In April, Epsilon remained relatively frequent in parts of northern California, but it had virtually disappeared from the south of the state and had never been able to establish a foothold elsewhere; only 3.2% of all cases in the United States were Epsilon, whereas more than two-thirds were Alpha.[190]

Zeta (lineage P.2)

Main article: SARS-CoV-2 Zeta variant

Zeta variant or lineage P.2, a sub-lineage of B.1.1.28 like Gamma (P.1), was first detected in circulation in the state of Rio de Janeiro; it harbours the E484K mutation, but not the N501Y and K417T mutations.[154] It evolved independently in Rio de Janeiro without being directly related to the Gamma variant from Manaus.[151] Though previously Zeta was labeled a variant of interest, as of July 2021, it is no longer considered as such by the WHO.[17]

Eta (lineage B.1.525)

Main article: SARS-CoV-2 Eta variant

The Eta variant or lineage B.1.525, also called VUI-21FEB-03[19] (previously VUI-202102/03) by Public Health England (PHE) and formerly known as UK1188,[19] 21D[28] or 20A/S:484K,[123] does not carry the same N501Y mutation found in Alpha, Beta and Gamma, but carries the same E484K-mutation as found in the Gamma, Zeta, and Beta variants, and also carries the same ΔH69/ΔV70 deletion (a deletion of the amino acids histidine and valine in positions 69 and 70) as found in Alpha, N439K variant (B.1.141 and B.1.258) and Y453F variant (Cluster 5).[198] Eta differs from all other variants by having both the E484K-mutation and a new F888L mutation (a substitution of phenylalanine (F) with leucine (L) in the S2 domain of the spike protein). As of 5 March 2021, it had been detected in 23 countries.[199][200][201] It has also been reported in Mayotte, the overseas department/region of France.[199] The first cases were detected in December 2020 in the UK and Nigeria, and as of 15 February 2021, it had occurred in the highest frequency among samples in the latter country.[201] As of 24 February 56 cases were found in the UK.[19] Denmark, which sequences all its COVID-19 cases, found 113 cases of this variant from 14 January to 21 February 2021, of which seven were directly related to foreign travel to Nigeria.[200]

As of July 2021, UK experts are studying it to ascertain how much of a risk it could be. It is currently regarded as a "variant under investigation", but pending further study, it may become a "variant of concern". Ravi Gupta, from the University of Cambridge said in a BBC interview that lineage B.1.525 appeared to have "significant mutations" already seen in some of the other newer variants, which means their likely effect is to some extent more predictable.[202]

Theta (lineage P.3)

Main article: SARS-CoV-2 Theta variant

On 18 February 2021, the Department of Health of the Philippines confirmed the detection of two mutations of COVID-19 in Central Visayas after samples from patients were sent to undergo genome sequencing. The mutations were later named as E484K and N501Y, which were detected in 37 out of 50 samples, with both mutations co-occurrent in 29 out of these.[203]

On 13 March, the Department of Health confirmed the mutations constitutes a variant which was designated as lineage P.3.[204] On the same day, it also confirmed the first COVID-19 case caused by the Gamma variant in the country. The Philippines had 98 cases of the Theta variant on 13 March.[205] On 12 March it was announced that Theta had also been detected in Japan.[206][207] On 17 March, the United Kingdom confirmed its first two cases,[208] where PHE termed it VUI-21MAR-02.[19] On 30 April 2021, Malaysia detected 8 cases of the Theta variant in Sarawak.[209]

As of July 2021, Theta is no longer considered a variant of interest by the WHO.[17]

Iota (lineage B.1.526)

Main article: SARS-CoV-2 Iota variant

In November 2020, a mutant variant was discovered in New York City, which was named lineage B.1.526.[210] As of 11 April 2021, the variant has been detected in at least 48 U.S. states and 18 countries. In a pattern mirroring Epsilon, Iota was initially able to reach relatively high levels in some states, but by May 2021 it was outcompeted by the more transmissible Delta and Alpha.[190]

Kappa (lineage B.1.617.1)

Main article: SARS-CoV-2 Kappa variant

The Kappa variant[17] is one of the three sublineages of lineage B.1.617. It is also known as lineage B.1.617.1, 21B[28] or 21A/S:154K,[123] and was first detected in India in December 2020.[211] By the end of March 2021, Kappa accounted for more than half of the sequences being submitted from India.[212] On 1 April 2021, it was designated a variant under investigation (VUI-21APR-01) by Public Health England.[29] It has the notable mutations L452R, E484Q, P681R.[213]

Lambda (lineage C.37)

Main article: SARS-CoV-2 Lambda variant

The Lambda variant, also known as lineage C.37, was first detected in Peru in August 2020 and was designated by the WHO as a variant of interest on 14 June 2021.[17] It spread to at least 30 countries[214] around the world and, as of July 2021, it is unknown whether it is more infectious and resistant to vaccines than other strains.[215][216] On 16 March 2022, the WHO has de-escalated the Lambda variant to "previously circulating variants of concern".[135][136]

Mu (lineage B.1.621)

Main article: SARS-CoV-2 Mu variant

The Mu variant, also known as lineage B.1.621, was first detected in Colombia in January 2021 and was designated by the WHO as a variant of interest on 30 August 2021.[17] There have been outbreaks in South America and Europe.[217][218] On 16 March 2022, the WHO has de-escalated the Mu variant and its subvariants to "previously circulating variants of concern".[135][136]

Formerly monitored variants (WHO)

The variants listed below were once listed under variants under monitoring, but were reclassified due to either no longer circulating at a significant level, not having had a significant impact on the situation, or scientific evidence of the variant not having concerning properties.[4]

As of 26 May 2022[4]
Pango lineage GISAID clade Nextstrain clade Earliest samples Date of VUM Date of designation Country of sampling
AV.1 GR 2021-03 2021-05-26 2021-07-21   UK
AT.1 GR 2021-01 2021-06-09 2021-07-21   Russia
R.1 GR 2021-01 2021-04-07 2021-11-09   Japan
B.1.466.2 GH 2020-11 2021-04-28 2021-11-09   Indonesia
B.1.1.519 GR 20B/S.732A 2020-11 2021-06-02 2021-11-09 Multiple countries
C.36.3 GR 2021-01 2021-06-16 2021-11-09 Multiple countries
B.1.214.2 G 2020-11 2021-06-30 2021-11-09 Multiple countries
B.1.1.523 GR 2020-05 2021-07-14 2021-11-09 Multiple countries
B.1.619 G 2020-05 2021-07-14 2021-11-09 Multiple countries
B.1.620 G 20A/S.126A 2020-11 2021-07-14 2021-11-09   Lithuania
B.1.1.318

AZ.5

GR 2021-01 2021-06-02   England
C.1.2 GR 2021-05 2021-09-01   South Africa
B.1.630 GH 2021-03 2021-10-12   Dominican Republic
B.1.640 GH/490R 2021-09 2021-11-22   Republic of Congo
XD 2022-01 2022-03-09   France

Other notable variants

Lineage B.1.1.207 was first sequenced in August 2020 in Nigeria;[219] the implications for transmission and virulence are unclear but it has been listed as an emerging variant by the US Centers for Disease Control.[42] Sequenced by the African Centre of Excellence for Genomics of Infectious Diseases in Nigeria, this variant has a P681H mutation, shared in common with the Alpha variant. It shares no other mutations with the Alpha variant and as of late December 2020 this variant accounts for around 1% of viral genomes sequenced in Nigeria, though this may rise.[219] As of May 2021, lineage B.1.1.207 has been detected in 10 countries.[220]

Lineage B.1.1.317, while not considered a variant of concern, is noteworthy in that Queensland Health forced 2 people undertaking hotel quarantine in Brisbane, Australia to undergo an additional 5 days' quarantine on top of the mandatory 14 days after it was confirmed they were infected with this variant.[221]

Lineage B.1.616, being identified in Brittany, Western France in early January 2021 and designated by WHO as "Variant under investigation" in March 2021, was reported to be difficult to detect from nasopharyngeal swab sampling method of coronavirus detection, and detection of the virus needs to rely on samples from lower respiratory tract.[citation needed]

Lineage B.1.618 was first isolated in October 2020. It has the E484K mutation in common with several other variants, and showed significant spread in April 2021 in West Bengal, India.[222][223] As of 23 April 2021, the PANGOLIN database showed 135 sequences detected in India, with single-figure numbers in each of eight other countries worldwide.[224]

In July 2021, scientists reported in a preprint which was published in a journal in February 2022, the detection of anomalous unnamed unknown-host SARS-CoV-2 lineages via wastewater surveillance in New York City. They hypothesized that "these lineages are derived from unsampled human COVID-19 infections or that they indicate the presence of a non-human animal reservoir".[225][226]

Lineage B.1.640.2 (also known as the IHU variant[227]) was detected in October 2021 by researchers at the Institut Hospitalo-Universitaire (IHU) in Marseille.[228] They found the variant in a traveler who returned to France from Cameroon and reportedly infected 12 people.[229][230] The B.1.640 lineage, which includes B.1.640.2, was designated a variant under monitoring (VUM) by the World Health Organization (WHO) on 22 November 2021.[231] However, the WHO has reported that lineage B.1.640.2 has spread much slower than the Omicron variant, and so is of relatively little concern.[230][232] According to a preprint study, lineage B.1.640.2 has two already known spike protein mutations – E484K and N501Y – among a total of 46 nucleotide substitutions and 37 deletions.[229][233][234]

In March 2022, researchers reported SARS-CoV-2 variant recombinant viruses that contain elements of Delta and Omicron – Deltacron (also called "Deltamicron").[235][236][237][238][239] Recombination occurs when a virus combines parts from a related virus with its genetic sequence as it assembles copies of itself. It is unclear whether Deltacron – which is not to be confused with "Deltacron" reported in January albeit the first detection was also in January[239][240] – will be able to compete with Omicron and whether that would be detrimental to health.[241]

In July 2023, Professor Lawrence Young, a virologist at Warwick University announced a super mutated Delta variant from a swab of an Indonesian case with 113 unique mutations, with 37 affecting the spike protein.[242]

Notable missense mutations

There have been a number of missense mutations observed of SARS-CoV-2.

del 69-70

The name of the mutation, del 69-70, or 69-70 del, or other similar notations, refers to the deletion of amino acid at position 69 to 70. The mutation is found in the Alpha variant, and could lead to "spike gene target failure" and result in false negative result in PCR virus test.[243]

RSYLTPGD246-253N

Otherwise referred to as del 246-252, or other various similar expression, refer to the deletion of amino acid from the position of 246 to 252, in the N-terminal domain of spike protein, accompanied with a replacement of the aspartic acid (D) at the position 253 for asparagine (N).[244][245]

The 7 amino acid deletion mutation is currently described as unique in the Lambda variant, and have been attributed to as one of the cause of the strain's increased capability to escape from neutralizing antibodies according to preprint paper.[246]

N440K

The name of the mutation, N440K, refers to an exchange whereby the asparagine (N) is replaced by lysine (K) at position 440.[247]

This mutation has been observed in cell cultures to be 10 times more infective compared to the previously widespread A2a strain (A97V substitution in RdRP sequence) and 1000 times more in the lesser widespread A3i strain (D614G substitution in Spike and a and P323L substitution in RdRP).[248] It was involved in rapid surges of COVID-19 cases in India in May 2021.[249] India has the largest proportion of N440K mutated variants followed by the US and Germany.[250]

G446V

The name of the mutation, G446V, refers to an exchange whereby the glycine (G) is replaced by valine (V) at position 446.[247]

The mutation, identified in Japan among inbound travelers starting from May, and among 33 samples from individuals related to 2020 Tokyo Olympic Games and 2020 Tokyo Paralympic Games, are said to be possible to impact affinity of multiple monoclonal antibody, although its clinical impact against the use of antibody medicine is still yet to be known.[251]

L452R

The name of the mutation, L452R, refers to an exchange whereby the leucine (L) is replaced by arginine (R) at position 452.[247]

L452R is found in both the Delta and Kappa variants which first circulated in India, but have since spread around the world. L452R is a relevant mutation in this strain that enhances ACE2 receptor binding ability and can reduce vaccine-stimulated antibodies from attaching to this altered spike protein.

L452R, some studies show, could even make the coronavirus resistant to T cells, that are necessary to target and destroy virus-infected cells. They are different from antibodies that are useful in blocking coronavirus particles and preventing it from proliferating.[165]

Y453F

The name of the mutation, Y453F, refers to an exchange whereby the tyrosine (Y) is replaced by phenylalanine (F) at position 453. The mutation have been found potentially linked to the spread of SARS-CoV-2 among minks in the Netherlands in 2020.[252]

S477G/N

A highly flexible region in the receptor binding domain (RBD) of SARS-CoV-2, starting from residue 475 and continuing up to residue 485, was identified using bioinformatics and statistical methods in several studies. The University of Graz[253] and the Biotech Company Innophore[254] have shown in a recent publication that structurally, the position S477 shows the highest flexibility among them.[255]

At the same time, S477 is hitherto the most frequently exchanged amino acid residue in the RBDs of SARS-CoV-2 mutants. By using molecular dynamics simulations of RBD during the binding process to hACE2, it has been shown that both S477G and S477N strengthen the binding of the SARS-COV-2 spike with the hACE2 receptor. The vaccine developer BioNTech[256] referenced this amino acid exchange as relevant regarding future vaccine design in a preprint published in February 2021.[257]

E484Q

The name of the mutation, E484Q, refers to an exchange whereby the glutamic acid (E) is replaced by glutamine (Q) at position 484.[247]

The Kappa variant circulating in India has E484Q. These variants were initially (but misleadingly) referred to as a "double mutant".[258] E484Q may enhance ACE2 receptor binding ability, and may reduce vaccine-stimulated antibodies' ability to attach to this altered spike protein.[165]

E484K

The name of the mutation, E484K, refers to an exchange whereby the glutamic acid (E) is replaced by lysine (K) at position 484.[247] It is nicknamed "Eeek".[259]

E484K has been reported to be an escape mutation (i.e., a mutation that improves a virus's ability to evade the host's immune system[260][261]) from at least one form of monoclonal antibody against SARS-CoV-2, indicating there may be a "possible change in antigenicity".[262] The Gamma variant (lineage P.1),[151] the Zeta variant (lineage P.2, also known as lineage B.1.1.28.2)[154] and the Beta variant (501.V2) exhibit this mutation.[262] A limited number of lineage B.1.1.7 genomes with E484K mutation have also been detected.[263] Monoclonal and serum-derived antibodies are reported to be from 10 to 60 times less effective in neutralising virus bearing the E484K mutation.[264][265] On 2 February 2021, medical scientists in the United Kingdom reported the detection of E484K in 11 samples (out of 214,000 samples), a mutation that may compromise current vaccine effectiveness.[266][267]

F490S

F490S denotes a change from phenylalanine (F) to serine (S) in amino-acid position 490.[268]

It is one of the mutation found in Lambda, and have been associated with reduced susceptibility to antibody generated by those who were infected with other strains, meaning antibody treatment against people infected with strains carrying such mutation would be less effective.[269]

N501Y

N501Y denotes a change from asparagine (N) to tyrosine (Y) in amino-acid position 501.[270] N501Y has been nicknamed "Nelly".[259]

This change is believed by PHE to increase binding affinity because of its position inside the spike glycoprotein's receptor-binding domain, which binds ACE2 in human cells; data also support the hypothesis of increased binding affinity from this change.[43] Molecular interaction modelling and the free energy of binding calculations has demonstrated that the mutation N501Y has the highest binding affinity in variants of concern RBD to hACE2.[1] Variants with N501Y include Gamma,[262][151] Alpha (VOC 20DEC-01), Beta, and COH.20G/501Y (identified in Columbus, Ohio).[1] This last became the dominant form of the virus in Columbus in late December 2020 and January and appears to have evolved independently of other variants.[271][272]

N501S

N501S denotes a change from asparagine (N) to serine (S) in amino-acid position 501.[273]

As of September 2021, there are 8 cases of patients around the world infected with Delta variant which feature this N501S mutation. As it is considered a mutation similar to N501Y, it is suspected to have similar characteristics as N501Y mutation, which is believed to increase the infectivity of the virus, however the exact effect is unknown yet.[274]

D614G

 
Prevalence of mutation D614G across all reported GISAID strains during the course of 2020. Convergence with unity closely matches the upper limb of the logistics curve.[275]

D614G is a missense mutation that affects the spike protein of SARS-CoV-2. From early appearances in Eastern China early in 2020, the frequency of this mutation in the global viral population increased early on during the pandemic.[276] G (glycine) quickly replaced D (aspartic acid) at position 614 in Europe, though more slowly in China and the rest of East Asia, supporting the hypothesis that G increased the transmission rate, which is consistent with higher viral titres and infectivity in vitro.[53] Researchers with the PANGOLIN tool nicknamed this mutation "Doug".[259]

In July 2020, it was reported that the more infectious D614G SARS-CoV-2 variant had become the dominant form in the pandemic.[277][278][279][280] PHE confirmed that the D614G mutation had a "moderate effect on transmissibility" and was being tracked internationally.[270][281]

The global prevalence of D614G correlates with the prevalence of loss of smell (anosmia) as a symptom of COVID-19, possibly mediated by higher binding of the RBD to the ACE2 receptor or higher protein stability and hence higher infectivity of the olfactory epithelium.[282]

Variants containing the D614G mutation are found in the G clade by GISAID[53] and the B.1 clade by the PANGOLIN tool.[53]

Q677P/H

The name of the mutation, Q677P/H, refers to an exchange whereby the glutamine (Q) is replaced by proline (P) or histidine (H) at position 677.[247] There are several sub-lineages containing the Q677P mutation; six of these, which also contain various different combinations of other mutations, are referred to by names of birds. One of the earlier ones noticed for example is known as "Pelican," while the most common of these as of early 2021 was provisionally named "Robin 1."[283]

The mutation has been reported in multiple lineages circulating inside the United States as of late 2020 and also some lineages outside the country. 'Pelican' was first detected in Oregon, and as of early 2021 'Robin 1' was found often in the Midwestern United States, while another Q667H sub-lineage, 'Robin 2', was found mostly in the southeastern United States.[283] The frequency of such mutation being recorded has increased from late 2020 to early 2021.[284]

P681H

 
Logarithmic Prevalence of P681H in 2020 according to sequences in the GISAID database[275]

The name of the mutation, P681H, refers to an exchange whereby the proline (P) is replaced by histidine (H) at position 681.[275]

In January 2021, scientists reported in a preprint that the mutation P681H, a characteristic feature of the Alpha variant and lineage B.1.1.207 (identified in Nigeria), is showing a significant exponential increase in worldwide frequency, thus following a trend to be expected in the lower limb of the logistics curve. This may be compared with the trend of the now globally prevalent D614G.[275][285]

P681R

The name of the mutation, P681R, refers to an exchange whereby the proline (P) is replaced by arginine (R) at position 681.[247]

Indian SARS-CoV-2 Genomics Consortium (INSACOG) found that other than the two mutations E484Q and L452R, there is also a third significant mutation, P681R in lineage B.1.617. All three concerning mutations are on the spike protein, the operative part of the coronavirus that binds to receptor cells of the body.[165]

A701V

According to initial media reports, the Malaysian Ministry of Health announced on 23 December 2020 that it had discovered a mutation in the SARS-CoV-2 genome which they designated as A701B(sic), among 60 samples collected from the Benteng Lahad Datu cluster in Sabah. The mutation was characterised as being similar to the one found recently at that time in South Africa, Australia, and the Netherlands, although it was uncertain if this mutation was more infectious or aggressive[clarification needed] than before.[286] The provincial government of Sulu in neighbouring Philippines temporarily suspended travel to Sabah in response to the discovery of 'A701B' due to uncertainty over the nature of the mutation.[287]

On 25 December 2020, the Malaysian Ministry of Health described a mutation A701V as circulating and present in 85% of cases (D614G was present in 100% of cases) in Malaysia.[288][289] These reports also referred to samples collected from the Benteng Lahad Datu cluster.[288][289] The text of the announcement was mirrored verbatim on the Facebook page of Noor Hisham Abdullah, Malay Director-General of Health, who was quoted in some of the news articles.[289]

The A701V mutation has the amino acid alanine (A) substituted by valine (V) at position 701 in the spike protein. Globally, South Africa, Australia, Netherlands and England also reported A701V at about the same time as Malaysia.[288] In GISAID, the prevalence of this mutation is found to be about 0.18%. of cases.[288]

On 14 April 2021, the Malaysian Ministry of Health reported that the third wave, which had started in Sabah, has involved the introduction of variants with D614G and A701V mutations.[290]

Recombinant variants

The British government has reported a number of recombinant variants of SARS-CoV-2.[291] These recombinant lineages have been given the Pango lineage identifiers XD, XE, and XF.[292]

XE is a recombinant lineage of Pango lineages BA.1 and BA.2.[293] As of March 2022 XE was believed to have a growth rate 9.8% greater than BA.2.[291]

Differential vaccine effectiveness

See also: Oxford–AstraZeneca COVID-19 vaccine § Effectiveness, Pfizer–BioNTech COVID-19 vaccine § Effectiveness, Moderna COVID-19 vaccine § Effectiveness, Janssen COVID-19 vaccine § Efficacy, Novavax COVID-19 vaccine § Efficacy, Sinopharm BIBP COVID-19 vaccine § Effectiveness, Sputnik V COVID-19 vaccine § Effectiveness, CoronaVac § Effectiveness, Covaxin § Efficacy, ZF2001 § Efficacy, Abdala (vaccine) § Efficacy, SCB-2019 § Efficacy, and COVID-19 vaccine clinical research § Variants

The interplay between the SARS-CoV-2 virus and its human hosts was initially natural but then started being altered by the rising availability of vaccines seen in 2021.[294] The potential emergence of a SARS-CoV-2 variant that is moderately or fully resistant to the antibody response elicited by the COVID-19 vaccines may necessitate modification of the vaccines.[295] The emergence of vaccine-resistant variants is more likely in a highly vaccinated population with uncontrolled transmission.[296]

As of February 2021, the US Food and Drug Administration believed that all FDA authorized vaccines remained effective in protecting against circulating strains of SARS-CoV-2.[295]

Immune evasion by variants

This section is an excerpt from COVID-19 vaccine § Immune evasion by variants.[edit]
In contrast to other investigated prior variants, the SARS-CoV-2 Omicron variant[297][298][299][300][301] and its BA.4/5 subvariants[302] have evaded immunity induced by vaccines, which may lead to breakthrough infections despite recent vaccination. Nevertheless, vaccines are thought to provide protection against severe illness, hospitalizations, and deaths due to Omicron.[303]

Vaccine adjustments

This section is an excerpt from SARS-CoV-2 Omicron variant § Vaccine adjustments.[edit]

In June 2022, Pfizer and Moderna developed bivalent vaccines to protect against the SARS-CoV-2 wild-type and the Omicron variant. The bivalent vaccines are well-tolerated and offer immunity to Omicron superior to previous mRNA vaccines.[304] In September 2022, the United States Food and Drug Administration (FDA) authorized the bivalent vaccines for use in the US.[305][306][307]

In June 2023, the FDA advised manufacturers that the 2023–2024 formulation of the COVID-19 vaccines for use in the US be updated to be a monovalent COVID-19 vaccine using the XBB.1.5 lineage of the Omicron variant.[308][309]

Data and methods

Modern DNA sequencing, where available, may permit rapid detection (sometimes known as 'real-time detection') of genetic variants that appear in pathogens during disease outbreaks.[310] Through use of phylogenetic tree visualisation software, records of genome sequences can be clustered into groups of identical genomes all containing the same set of mutations. Each group represents a 'variant', 'clade', or 'lineage', and comparison of the sequences allows the evolutionary path of a virus to be deduced. For SARS-CoV-2, until March 2021, over 330,000 viral genomic sequences had been generated by molecular epidemiology studies across the world.[311]

New variant detection and assessment

On 26 January 2021, the British government said it would share its genomic sequencing capabilities with other countries in order to increase the genomic sequencing rate and trace new variants, and announced a "New Variant Assessment Platform".[312] As of January 2021, more than half of all genomic sequencing of COVID-19 was carried out in the UK.[313]

Wastewater surveillance was demonstrated to be one technique to detect SARS-CoV-2 variants[226] and to track their rise for studying related ongoing infection dynamics.[314][315][316]

Testing

Whether one or more mutations visible in RT-PCR tests can be used reliably to identify a variant depends on the prevalence of other variants currently circulating in the same population.[317][318]

Mutations used to identify variants of concern in commercial test assays[319]
Mutation Alpha Beta Gamma Delta Omicron
Δ69–70[e]          
ins214EPE[f]          
S371L/S373P[f]          
N501Y          
E484K          
E484A[f]          
L452R          
nsp6:Δ106–108          

Incubation theory for multiple mutated variants

See also: Antigenic escape and Escape mutation

Researchers have suggested that multiple mutations can arise in the course of the persistent infection of an immunocompromised patient, particularly when the virus develops escape mutations under the selection pressure of antibody or convalescent plasma treatment,[320][321] with the same deletions in surface antigens repeatedly recurring in different patients.[322]

Cross-species transmission

Further information: Impact of the COVID-19 pandemic on animals and List of animals that can get SARS-CoV-2

There is a risk that COVID-19 could transfer from humans to other animal populations and could combine with other animal viruses to create yet more variants that are dangerous to humans.[323] Reverse zoonosis spillovers may cause reservoirs for mutating variants that spill back to humans – another possible source for variants of concern, in addition to immunocompromised people.[324]

Cluster 5

Main article: Cluster 5

In early November 2020, Cluster 5, also referred to as ΔFVI-spike by the Danish State Serum Institute (SSI),[325] was discovered in Northern Jutland, Denmark. It is believed to have been spread from minks to humans via mink farms. On 4 November 2020, it was announced that the mink population in Denmark would be culled to prevent the possible spread of this mutation and reduce the risk of new mutations happening. A lockdown and travel restrictions were introduced in seven municipalities of Northern Jutland to prevent the mutation from spreading, which could compromise national or international responses to the COVID-19 pandemic. By 5 November 2020, some 214 mink-related human cases had been detected.[326]

The WHO stated that cluster 5 had a "moderately decreased sensitivity to neutralising antibodies".[327] SSI warned that the mutation could reduce the effect of COVID-19 vaccines under development, although it was unlikely to render them useless. Following the lockdown and mass-testing, SSI announced on 19 November 2020 that cluster 5 in all probability had become extinct.[328] As of 1 February 2021, authors to a peer-reviewed paper, all of whom were from the SSI, assessed that cluster 5 was not in circulation in the human population.[329]

See also

Notes

  1. ^ Based on various trackers[17][18][19][20][21] and periodic reports.[22][23][24]
  2. ^ a b In another source, GISAID name a set of 7 clades without the O clade but including a GV clade.[59]
  3. ^ According to the WHO, "Lineages or clades can be defined based on viruses that share a phylogenetically determined common ancestor".[70]
  4. ^ As of January 2021, at least one of the following criteria must be met in order to count as a clade in the Nextstrain system (quote from source):[52]
    1. A clade reaches >20% global frequency for 2 or more months
    2. A clade reaches >30% regional frequency for 2 or more months
    3. A VOC ('variant of concern') is recognized (applies currently [6 January 2021] to 501Y.V1 and 501Y.V2)
  5. ^ Produces S gene target failure (SGTF) in TaqPath.
  6. ^ a b c Detectable by the TIB MolBiol assay using the melting curve method.

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January 01, 1970
variants, sars, coronavirus, variant, redirects, here, recent, species, coronavirus, novel, coronavirus, coronavirus, variants, severe, acute, respiratory, syndrome, coronavirus, sars, viruses, that, while, similar, original, have, genetic, changes, that, enou. New coronavirus variant redirects here For recent species of coronavirus see Novel coronavirus and Coronavirus Variants of severe acute respiratory syndrome coronavirus 2 SARS CoV 2 are viruses that while similar to the original have genetic changes that are of enough significance to lead virologists to label them separately SARS CoV 2 is the virus that causes coronavirus disease 2019 COVID 19 Some have been stated to be of particular importance due to their potential for increased transmissibility 1 increased virulence or reduced effectiveness of vaccines against them 2 3 These variants contribute to the continuation of the COVID 19 pandemic source source source source source source source source Positive negative and neutral mutations during the evolution of coronaviruses like SARS CoV 2 As of May 2024 update only Omicron is designated as a circulating variant of concern by the World Health Organization 4 failed verification Contents 1 Overview 2 Nomenclature 2 1 Lineages and clades 2 2 Classification of variants 3 Reference sequence 4 Notability criteria 5 Variants of concern WHO 5 1 Omicron 5 1 1 Lineage B 1 1 529 5 1 2 BA sublineages 5 1 3 Further sublineages emerging in 2022 5 1 4 Further sublineages emerging in 2023 EG 5 Eris BA 2 86 and JN 1 Pirola 6 Variant of concern lineages under monitoring WHO 7 Variants of interest WHO 8 Variants under monitoring WHO 9 Previously circulating and formerly monitored variants WHO 9 1 Previously circulating variants of concern VOC 9 1 1 Alpha lineage B 1 1 7 9 1 1 1 B 1 1 7 with E484K 9 1 2 Beta lineage B 1 351 9 1 3 Gamma lineage P 1 9 1 4 Delta lineage B 1 617 2 9 2 Previously circulating variants of interest VOI 9 2 1 Epsilon lineages B 1 429 B 1 427 CAL 20C 9 2 2 Zeta lineage P 2 9 2 3 Eta lineage B 1 525 9 2 4 Theta lineage P 3 9 2 5 Iota lineage B 1 526 9 2 6 Kappa lineage B 1 617 1 9 2 7 Lambda lineage C 37 9 2 8 Mu lineage B 1 621 9 3 Formerly monitored variants WHO 10 Other notable variants 11 Notable missense mutations 11 1 del 69 70 11 2 RSYLTPGD246 253N 11 3 N440K 11 4 G446V 11 5 L452R 11 6 Y453F 11 7 S477G N 11 8 E484Q 11 9 E484K 11 10 F490S 11 11 N501Y 11 12 N501S 11 13 D614G 11 14 Q677P H 11 15 P681H 11 16 P681R 11 17 A701V 12 Recombinant variants 13 Differential vaccine effectiveness 13 1 Immune evasion by variants 13 1 1 Vaccine adjustments 14 Data and methods 14 1 New variant detection and assessment 14 2 Testing 15 Incubation theory for multiple mutated variants 16 Cross species transmission 16 1 Cluster 5 17 See also 18 Notes 19 References 20 Further reading 21 External linksOverviewThe origin of SARS CoV 2 has not been identified 5 However the emergence of SARS CoV 2 may have resulted from recombination events between a bat SARS like coronavirus and a pangolin coronavirus through cross species transmission 6 7 The earliest available SARS CoV 2 viral genomes were collected from patients in December 2019 and Chinese researchers compared these early genomes with bat and pangolin coronavirus strains to estimate the ancestral human coronavirus type the identified ancestral genome type was labeled S and its dominant derived type was labeled L to reflect the mutant amino acid changes Independently Western researchers carried out similar analyses but labeled the ancestral type A and the derived type B The B type mutated into further types including B 1 which is the ancestor of the major global variants of concern labeled in 2021 by the WHO as alpha beta gamma delta and omicron variants 8 9 10 Early in the pandemic the relatively low number of infections compared with later stages of the pandemic resulted in fewer opportunities for mutation of the viral genome and therefore fewer opportunities for the occurrence of differentiated variants 11 Since the occurrence of variants was rarer the observation of S protein mutations in the receptor binding domain RBD region interacting with ACE2 was also not frequent 12 As time went on the evolution of SARS CoV 2 s genome by means of random mutations led to mutant specimens of the virus i e genetic variants observed to be more transmissible to be naturally selected Notably both the Alpha and the Delta variants were observed to be more transmissible than previously identified viral strains 13 Some SARS CoV 2 variants are considered to be of concern as they maintain or even increase their replication fitness in the face of rising population immunity 14 either by infection recovery or via vaccination Some of the variants of concern show mutations in the RBD of the S protein 15 The following table presents information and relative risk level 16 for currently and formerly circulating variants of concern VOC a The intervals assume a 95 confidence or credibility level unless otherwise stated Currently all estimates are approximations due to the limited availability of data for studies For Alpha Beta Gamma and Delta there is no change in test accuracy 20 25 and neutralising antibody activity is retained by some monoclonal antibodies 18 26 PCR tests continue to detect the Omicron variant 27 Identification 25 Emergence Changes relative to previously circulating variants at the time and place of emergence Neutralising antibody activity or efficacy when available WHOlabel PANGOlineage Nextstrainclade Firstoutbreak Earliestsample wbr 28 Designated VOC Current circulation Notable mutations Transmissibility Hospitalisation Mortality From natural infection A From vaccination Delta B 1 617 2 21A nbsp India Oct 2020 6 May 2021 wbr 29 No L452R T478K P681R wbr 30 97 76 117 wbr 31 85 39 147 relative to Alpha wbr D 137 50 230 wbr B Reinfections happened with smaller occurrence rate than vaccinated infections wbr E 34 Efficacy reduction for non severe disease wbr 25 34 F Omicron B 1 1 529 21K nbsp South Africa 9 Nov 2021 wbr 36 26 Nov 2021 wbr 27 Yes P681H N440K N501Y S477N many others wbr 37 Possibly increased wbr 38 57 59 61 relative to Delta 39 63 69 74 relative to Delta 39 Increased reinfection rate wbr 38 Efficacy reduction against symptomatic disease unknown for severe disease wbr 38 Alpha B 1 1 7 20I V1 nbsp United Kingdom 20 Sep 2020 wbr 40 18 Dec 2020 wbr 41 No 69 70del N501Y P681H wbr 42 43 29 24 33 wbr 31 G 52 47 57 wbr H G 59 44 74 wbr H G Minimal reduction wbr 18 Minimal reduction wbr 18 Gamma P 1 B 1 1 28 1 20J V3 nbsp Brazil Nov 2020 15 Jan 2021 wbr 45 46 No K417T E484K N501Y wbr 42 38 29 48 wbr 31 Possibly increased wbr 25 50 50 CrI 20 90 wbr I J Reduced wbr 18 Retained by many wbr K Beta B 1 351 20H V2 nbsp South Africa May 2020 14 Jan 2021 wbr 47 No K417N E484K N501Y wbr 42 25 20 30 wbr 31 Under investigation when Possibly increased wbr 20 25 Reduced T cell response elicited by D614G virus remains effective wbr 18 25 Efficacy reduction against symptomatic disease L retained against severe disease wbr 25 Very high risk High risk Medium risk Low risk Unknown risk Efficacy of natural infection against reinfection when available a b 7 February 22 June 22 2021 Ontario CFR 0 04 for lt 50 age group unvaccinated 6 5 for gt 50 age group unvaccinated 33 a b Differences may be due to different policies and interventions adopted in each area studied at different times to the capacity of the local health system or to different variants circulating at the time and place of the study 1 April 6 June 2021 Scotland 32 Another preliminary study in Ontario found that hospitalization by Delta increased by 120 relative to non VOC lineages B C The study in Israel tracked 46035 unvaccinated recovered and 46035 vaccinated people of the same age distribution to compare their infection occurrence in the follow up period 640 infections in the vaccinated group and 108 infections in the recovered group were recorded Moderately reduced neutralisation with Covaxin wbr 35 a b c B 1 1 7 with E484K assumed to only differ from B 1 1 7 on neutralising antibody activity 21 a b 23 November 2020 31 January 2021 England 44 CFR 0 06 for lt 50 age group 4 8 for gt 50 age group 33 The reported confidence or credible interval has a low probability so the estimated value can only be understood as possible not certain nor likely March 2020 February 2021 Manaus C Except Pfizer BioNTech 20 Oxford AstraZeneca Novavax NomenclatureSee also Colloquial names of SARS CoV 2 variants SARS CoV 2 corresponding nomenclatures 48 PANGO lineages 49 Notes to PANGO lineages 50 Nextstrain clades 51 2021 52 GISAID clades Notable variants A 1 A 6 19B S Contains reference sequence WIV04 2019 53 B 3 B 7 B 9 B 10 B 13 B 16 19A L O b B 2 V B 1 B 1 5 B 1 72 20A G Lineage B 1 in the PANGO Lineages nomenclature system includes Delta wbr B 1 617 30 54 B 1 9 B 1 13 B 1 22 B 1 26 B 1 37 GH B 1 3 B 1 66 20C Includes Epsilon wbr B 1 427 wbr B 1 429 wbr CAL 20C and Eta wbr B 1 525 18 55 20G Predominant in US generally Feb 21 55 20H Includes Beta wbr B 1 351aka 20H 501Y V2 or 501 V2 lineage B 1 1 20B GR Includes B 1 1 207 citation needed and Lambda lineage C 37 56 20D 20J Includes Gamma wbr P 1 and Zeta wbr P 2 57 58 20F 20I Includes Alpha wbr B 1 1 7aka VOC 202012 01 VOC 20DEC 01 or 20I 501Y V1 B 1 177 20E EU1 52 GV b Derived from 20A 52 nbsp Tree diagram of lineages of SARS CoV 2 according to the Pango nomenclature system SARS CoV 2 variants are grouped according to their lineage and component mutations 14 Many organisations including governments and news outlets referred colloquially to concerning variants by the country in which they were first identified 60 61 62 After months of discussions the World Health Organization announced Greek letter names for important strains on 31 May 2021 63 so they could be easily referred to in a simple easy to say and non stigmatising fashion 64 65 This decision may have partially been taken because of criticism from governments on using country names to refer to variants of the virus the WHO mentioned the potential for mentioning country names to cause stigma 66 After using all the letters from Alpha to Mu see below in November 2021 the WHO skipped the next two letters of the Greek alphabet Nu and Xi and used Omicron prompting speculation that Xi was skipped to avoid offending Chinese leader Xi Jinping 67 The WHO gave as the explanation that Nu is too easily confounded with new and Xi is a common last name 67 In the event that the WHO uses the entirety of the Greek alphabet the agency considered naming future variants after constellations 68 nbsp Various SARS CoV 2 variants that were reported officially by CDC NIH in May 2021 in relation to mutations L452R and E484K Lineages and clades While there are many thousands of variants of SARS CoV 2 69 subtypes of the virus can be put into larger groupings such as lineages or clades c Three main generally used nomenclatures 70 have been proposed As of January 2021 update GISAID referring to SARS CoV 2 as hCoV 19 50 had identified eight global clades S O L V G GH GR and GV 71 In 2017 Hadfield et al announced Nextstrain intended for real time tracking of pathogen evolution 72 Nextstrain has later been used for tracking SARS CoV 2 identifying 13 major clades d 19A B 20A 20J and 21A as of June 2021 update 73 In 2020 Rambaut et al of the Phylogenetic Assignment of Named Global Outbreak Lineages PANGOLIN 74 software team proposed in an article 49 a dynamic nomenclature for SARS CoV 2 lineages that focuses on actively circulating virus lineages and those that spread to new locations 70 as of August 2021 update 1340 lineages had been designated 75 76 Each national public health institute may also institute its own nomenclature system for the purposes of tracking specific variants For example Public Health England designated each tracked variant by year month and number in the format YYYY MM NN prefixing VUI or VOC for a variant under investigation or a variant of concern respectively 19 This system has now been modified and now uses the format YY MMM NN where the month is written out using a three letter code 19 Classification of variants Variants that appear to meet one or more specific criteria considered during the COVID 19 pandemic may be labeled variants of interest or variants under investigation VUI pending verification and validation of these properties Once validated variants of interest VUI may be renamed variants of concern by monitoring organizations such as the CDC in the US 77 78 79 A related category is variant of high consequence used by the CDC if there is clear evidence that the effectiveness of prevention or intervention measures for a particular variant is substantially reduced 80 Reference sequenceAs it is currently not known when the index case or patient zero occurred the choice of reference sequence for a given study is relatively arbitrary with different notable research studies choices varying as follows The earliest sequence Wuhan 1 was collected on 24 December 2019 81 One group Sudhir Kumar et al 81 refers extensively to an NCBI reference genome GenBankID NC 045512 GISAID ID EPI ISL 402125 82 this sample was collected on 26 December 2019 83 although they also used the WIV04 GISAID reference genome ID EPI ISL 402124 84 in their analyses 85 According to another source Zhukova et al the sequence WIV04 2019 belonging to the GISAID S clade PANGO A lineage Nextstrain 19B clade is thought to most closely reflect the sequence of the original virus infecting humans known as sequence zero 53 WIV04 2019 was sampled from a symptomatic patient on 30 December 2019 and is widely used especially by those collaborating with GISAID 86 as a reference sequence 53 The variant first sampled and identified in Wuhan China is considered by researchers to differ from the progenitor genome by three mutations 81 87 Subsequently many distinct lineages of SARS CoV 2 have evolved 75 Notability criteriaViruses generally acquire mutations over time giving rise to new variants When a new variant appears to be growing in a population it can be labelled as an emerging variant In the case of SARS CoV 2 new lineages often differ from one another by just a few nucleotides 14 Some of the potential consequences of emerging variants are the following 42 88 Increased transmissibility Increased morbidity Increased mortality Ability to evade detection by diagnostic tests Decreased susceptibility to antiviral drugs if and when such drugs are available Decreased susceptibility to neutralising antibodies either therapeutic e g convalescent plasma or monoclonal antibodies or in laboratory experiments Ability to evade natural immunity e g causing reinfections Ability to infect vaccinated individuals Increased risk of particular conditions such as multisystem inflammatory syndrome or long COVID Increased affinity for particular demographic or clinical groups such as children or immunocompromised individuals Variants that appear to meet one or more of these criteria may be labelled variants under investigation or variants of interest pending verification and validation of these properties The primary characteristic of a variant of interest is that it shows evidence that demonstrates it is the cause of an increased proportion of cases or unique outbreak clusters however it must also have limited prevalence or expansion at national levels or the classification would be elevated to a variant of concern 19 78 If there is clear evidence that the effectiveness of prevention or intervention measures for a particular variant is substantially reduced that variant is termed a variant of high consequence 18 Variants of concern WHO This section needs to be updated Please help update this article to reflect recent events or newly available information May 2023 Listed below are the variants of concern VOC recognised by the World Health Organization as of October 2022 update 17 Other organisations such as the CDC in the United States have at times used a slightly different list for example the CDC has de escalated the Delta variant on 14 April 2022 18 while the WHO did so on 7 June 2022 nbsp False colour transmission electron micrograph of a B 1 1 7 variant coronavirus The variant s increased transmissibility is believed to be due to changes in structure of the spike proteins shown here in green Omicron Main article SARS CoV 2 Omicron variant Lineage B 1 1 529 The Omicron variant known as lineage B 1 1 529 was declared a variant of concern by the World Health Organization on 26 November 2021 89 The variant has a large number of mutations of which some are concerning Some evidence shows that this variant has an increased risk of reinfection Studies are underway to evaluate the exact impact on transmissibility mortality and other factors 90 Named Omicron by the WHO 89 91 it was identified in November 2021 in Botswana and South Africa 92 one case had travelled to Hong Kong 93 4 94 one confirmed case was identified in Israel in a traveler returning from Malawi 95 along with two who returned from South Africa and one from Madagascar 96 Belgium confirmed the first detected case in Europe on 26 November 2021 in an individual who had returned from Egypt on 11 November 97 Indian SARS CoV 2 Genomics Consortium INSACOG in its January 2022 bulletin noted that Omicron is in community transmission in India where new cases have been rising exponentially 98 BA sublineages According to the WHO BA 1 BA 1 1 and BA 2 were the most common sublineages of Omicron globally as of February 2022 update 99 BA 2 contains 28 unique genetic changes including four in its spike protein compared to BA 1 which had already acquired 60 mutations since the ancestral Wuhan strain including 32 in the spike protein 100 BA 2 is more transmissible than BA 1 101 It was causing most cases in England by mid March 2022 and by the end of March BA 2 became dominant in the US 102 100 As of May 2022 update the sublineages BA 1 to BA 5 including all their descendants are classified as variants of concern by the WHO 4 the CDC 18 and the ECDC 103 with the latter excluding BA 3 Further sublineages emerging in 2022 During 2022 a number of further new strains emerged in different localities including XBB 1 5 which evolved from the XBB strain of Omicron The first case involving XBB in England was detected from a specimen sample taken on 10 September 2022 and further cases have since been identified in most English regions By the end of the year XBB 1 5 accounted for 40 5 of new cases across the US and was the dominant strain variant of concern BQ 1 was running at 18 3 and BQ 1 1 represented 26 9 of new cases while the BA 5 strain was in decline at 3 7 At this stage it was uncommon in many other countries for example in the UK it was represented about 7 of new cases according to UKHSA sequencing data 104 On 22 December 2022 the European Centre for Disease Control wrote in a summary that XBB strains accounted for circa 6 5 of new cases in five EU countries with sufficient volume of sequencing or genotyping to provide estimates 104 Further sublineages emerging in 2023 EG 5 Eris BA 2 86 and JN 1 Pirola During 2023 SARS CoV 2 continued to circulate in the global population and to evolve with a number of new strains hitting the headlines Testing sequencing and reporting rates reduced 105 EG 5 a subvariant of XBB 1 9 2 nicknamed Eris by some media 106 emerged in February 2023 107 On 6 August 2023 the UK Health Security Agency reported the EG 5 strain was responsible for one in seven new cases in the UK during the third week of July 108 Main article BA 2 86 BA 2 86 was first detected in a sample from 24 July 2023 and was designated as a variant under monitoring by the World Health Organization on 17 August 2023 109 JN 1 redirects here For other uses see JN1 disambiguation JN 1 sometimes referred to as Pirola a subvariant of BA 2 86 Omicron emerged during August 2023 in Luxembourg By December 2023 it had been detected in 12 countries including the UK and US 110 111 On 19 December JN 1 was declared by the WHO to be a variant of interest independently of its parent strain BA 2 86 but overall risk for public health was determined as low 112 With JN 1 accounting for some 60 of cases in Singapore in December 2023 Singapore and Indonesia recommended wearing masks at airports 113 The CDC estimated that the variant accounted for 44 of cases in the US on 22 December 2023 and 62 of cases on 5 January 2024 114 As of 9 February 2024 update JN 1 was estimated by the WHO to be the most prevalent variant of SARS CoV 2 70 90 prevalence in four out of six global regions insufficient data in the East Mediterranean and African regions The general level of population immunity and immunity from XBB 1 5 booster versions of the COVID 19 vaccine was expected to provide some protection cross reactivity to JN 1 115 Variant of concern lineages under monitoring WHO On 25 May 2022 the World Health Organization introduced a new category for potentially concerning sublineages of widespread variants of concern called VOC lineages under monitoring VOC LUMs This decision was made to reflect that already in February 2022 over 98 of all sequenced samples belonged to the Omicron family and there has been significant evolution within this family 4 As of 10 February 2023 update 116 Pango lineage GISAID clade Nextstrain clade Relation to circulating VOCs First documented Notable features BF 7 GRA 22B BA 5 sublineage 2022 01 24 BA 5 S R346T BQ 1 GRA 22E BA 5 sublineage 2022 02 07 BQ 1 and BQ 1 1 BA 5 S R346T S K444T S N460K BA 2 75 GRA 22D BA 2 sublineage 2021 12 31 BA 2 75 BA 2 S K147E S W152R S F157L S I210V S G257S S D339H S G446S S N460K S Q493R reversion CH 1 1 GRA 22D BA 2 sublineage 2022 07 20 BA 2 75 S L452R S F486S XBB GRA 22F Recombinant of BA 2 10 1 and BA 2 75 sublineages i e BJ1 and BM 1 1 1 with a breakpoint in S1 2022 08 13 BA 2 S V83A S Y144 S H146Q S Q183E S V213E S G252V S G339H S R346T S L368I S V445P S G446S S N460K S F486S S F490S XBB 1 5 GRA 23A Recombinant of BA 2 10 1 and BA 2 75 sublineages i e BJ1 and BM 1 1 1 with a breakpoint in S1 2022 01 05 XBB S F486P XBF GRA Recombinant of BA 5 2 3 and CJ 1 BA 2 75 3 sublineage 2022 07 20 BA 5 S K147E S W152R S F157L S I210V S G257S S G339H S R346T S G446S S N460K S F486P S F490S JN 1 GRA 24A BA 2 86 sublineage genetic features include S L455S 2023 08 25 As of 9 February 2024 update most prevalent variant low risk expectedVariants of interest WHO Listed below are the Variants of Interest VOI which are recognised by the World Health Organization 17 Other organisations such as the CDC in the United States may at times use a slightly different list 18 As of 15 March 2023 update 117 The WHO defines a VOI as a variant with genetic changes that are predicted or known to affect virus characteristics such as transmissibility virulence antibody evasion susceptibility to therapeutics and detectability and that it is circulating more than other variants in over one WHO region to such an extent that a global public health risk can be suggested 118 Furthermore the update stated that VOIs will be referred to using established scientific nomenclature systems such as those used by Nextstrain and Pango 118 As of 20 December 2023 update the WHO lists XBB 1 5 XBB 1 16 EG 5 BA 2 86 and JN 1 as circulating variants of interest 119 Variants under monitoring WHO Listed below are Variants under Monitoring VUM which are recognised by the WHO VUM s are defined as variants with genetic changes suspected to affect virus characteristics and some indication of posing a future risk but with unclear evidence of phenotypic or epidemiological impact requiring enhanced monitoring and repeat assessment after new evidence 17 As of 21 November 2023 update the WHO lists DV 7 XBB XBB 1 9 1 XBB 1 9 2 XBB 2 3 as circulating variants under monitoring 4 Previously circulating and formerly monitored variants WHO The WHO defines a previously circulating variant as a variant that has demonstrated to no longer pose a major added risk to global public health compared to other circulating SARS CoV 2 variants but should still be monitored 4 On 15 March 2023 the WHO released an update on the tracking system of VOCs announcing that only VOCs will be assigned Greek letters 117 Previously circulating variants of concern VOC The variants listed below had previously been designated as variants of concern but were displaced by other variants As of May 2022 update the WHO lists the following under previously circulating variants of concern 4 Alpha lineage B 1 1 7 Main article SARS CoV 2 Alpha variant First detected in October 2020 during the COVID 19 pandemic in the United Kingdom from a sample taken the previous month in Kent 120 lineage B 1 1 7 121 labelled Alpha variant by the WHO was previously known as the first Variant Under Investigation in December 2020 VUI 202012 01 122 and later notated as VOC 202012 01 19 It is also known as 20I V1 28 20I 501Y V1 123 formerly 20B 501Y V1 42 124 125 or 501Y V1 126 From October to December 2020 its prevalence doubled every 6 5 days the presumed generational interval 127 128 It is correlated with a significant increase in the rate of COVID 19 infection in United Kingdom associated partly with the N501Y mutation 127 There was some evidence that this variant had 40 80 increased transmissibility with most estimates lying around the middle to higher end of this range 129 130 and early analyses suggested an increase in lethality 131 132 though later work found no evidence of increased virulence 133 As of May 2021 the Alpha variant had been detected in some 120 countries 134 On 16 March 2022 the WHO has de escalated the Alpha variant and its subvariants to previously circulating variants of concern 135 136 B 1 1 7 with E484K Variant of Concern 21FEB 02 previously written as VOC 202102 02 described by Public Health England PHE as B 1 1 7 with E484K 19 is of the same lineage in the Pango nomenclature system but has an additional E484K mutation As of 17 March 2021 there were 39 confirmed cases of VOC 21FEB 02 in the UK 19 On 4 March 2021 scientists reported B 1 1 7 with E484K mutations in the state of Oregon In 13 test samples analysed one had this combination which appeared to have arisen spontaneously and locally rather than being imported 137 138 139 Other names for this variant include B 1 1 7 E484K 140 and B 1 1 7 Lineage with S E484K 141 Beta lineage B 1 351 Main article SARS CoV 2 Beta variant On 18 December 2020 the 501 V2 variant also known as 501 V2 20H V2 28 20H 501Y V2 123 formerly 20C 501Y V2 501Y V2 142 VOC 20DEC 02 formerly VOC 202012 02 or lineage B 1 351 42 was first detected in South Africa and reported by the country s health department 143 It has been labelled as Beta variant by WHO Researchers and officials reported that the prevalence of the variant was higher among young people with no underlying health conditions and by comparison with other variants it is more frequently resulting in serious illness in those cases 144 145 The South African health department also indicated that the variant may be driving the second wave of the COVID 19 epidemic in the country due to the variant spreading at a more rapid pace than other earlier variants of the virus 143 144 Scientists noted that the variant contains several mutations that allow it to attach more easily to human cells because of the following three mutations in the receptor binding domain RBD in the spike glycoprotein of the virus N501Y 143 146 K417N and E484K 147 148 The N501Y mutation has also been detected in the United Kingdom 143 149 On 16 March 2022 the WHO has de escalated the Beta variant and its subvariants to previously circulating variants of concern 135 136 Gamma lineage P 1 Main article SARS CoV 2 Gamma variant The Gamma variant or lineage P 1 termed Variant of Concern 21JAN 02 19 formerly VOC 202101 02 by Public Health England 19 20J V3 28 or 20J 501Y V3 123 by Nextstrain or just 501Y V3 126 was detected in Tokyo on 6 January 2021 by the National Institute of Infectious Diseases NIID It has been labelled as Gamma variant by WHO The new variant was first identified in four people who arrived in Tokyo having travelled from the Brazilian Amazonas state on 2 January 2021 150 On 12 January 2021 the Brazil UK CADDE Centre confirmed 13 local cases of the new Gamma variant in the Amazon rainforest 151 This variant of SARS CoV 2 has been named lineage P 1 although it is a descendant of B 1 1 28 the name B 1 1 28 1 20 152 is not permitted and thus the resultant name is P 1 and has 17 unique amino acid changes 10 of which in its spike protein including the three concerning mutations N501Y E484K and K417T 151 152 153 154 Figure 5 The N501Y and E484K mutations favour the formation of a stable RBD hACE2 complex thus enhancing the binding affinity of RBD to hACE2 However the K417T mutation disfavours complex formation between RBD and hACE2 which has been demonstrated to reduce the binding affinity 1 The new variant was absent in samples collected from March to November 2020 in Manaus Amazonas state but it was detected for the same city in 42 of the samples from 15 to 23 December 2020 followed by 52 2 during 15 31 December and 85 4 during 1 9 January 2021 151 A study found that infections by Gamma can produce nearly ten times more viral load compared to persons infected by one of the other lineages identified in Brazil B 1 1 28 or B 1 195 Gamma also showed 2 2 times higher transmissibility with the same ability to infect both adults and older persons suggesting P 1 and P 1 like lineages are more successful at infecting younger humans irrespective of sex 155 A study of samples collected in Manaus between November 2020 and January 2021 indicated that the Gamma variant is 1 4 2 2 times more transmissible and was shown to be capable of evading 25 61 of inherited immunity from previous coronavirus diseases leading to the possibility of reinfection after recovery from an earlier COVID 19 infection As for the fatality ratio infections by Gamma were also found to be 10 80 more lethal 156 157 158 A study found that people fully vaccinated with Pfizer or Moderna have significantly decreased neutralisation effect against Gamma although the actual impact on the course of the disease is uncertain A pre print study by the Oswaldo Cruz Foundation published in early April found that the real world performance of people with the initial dose of the Sinovac s Coronavac Vaccine had approximately 50 efficacy rate They expected the efficacy to be higher after the 2nd dose As of July 2021 the study is ongoing 159 Preliminary data from two studies indicate that the Oxford AstraZeneca vaccine is effective against the Gamma variant although the exact level of efficacy has not yet been released 160 161 Preliminary data from a study conducted by Instituto Butantan suggest that CoronaVac is effective against the Gamma variant as well and as of July 2021 has yet to be expanded to obtain definitive data 162 On 16 March 2022 the WHO has de escalated the Gamma variant and its subvariants to previously circulating variants of concern 135 136 Delta lineage B 1 617 2 Main article SARS CoV 2 Delta variant The Delta variant also known as B 1 617 2 G 452R V3 21A 28 or 21A S 478K 123 was a globally dominant variant that spread to at least 185 countries 163 It was first discovered in India Descendant of lineage B 1 617 which also includes the Kappa variant under investigation it was first discovered in October 2020 and has since spread internationally 164 165 166 167 168 On 6 May 2021 British scientists declared B 1 617 2 which notably lacks mutation at E484Q as a variant of concern labelling it VOC 21APR 02 after they flagged evidence that it spreads more quickly than the original version of the virus and could spread quicker or as quickly as Alpha 169 21 170 171 It carries L452R and P681R mutations in Spike 30 unlike Kappa it carries T478K but not E484Q On 3 June 2021 Public Health England reported that twelve of the 42 deaths from the Delta variant in England were among the fully vaccinated and that it was spreading almost twice as fast as the Alpha variant 172 Also on 11 June Foothills Medical Centre in Calgary Canada reported that half of their 22 cases of the Delta variant occurred among the fully vaccinated 173 In June 2021 reports began to appear of a variant of Delta with the K417N mutation 174 The mutation also present in the Beta and Gamma variants raised concerns about the possibility of reduced effectiveness of vaccines and antibody treatments and increased risk of reinfection 175 The variant called Delta with K417N by Public Health England includes two clades corresponding to the Pango lineages AY 1 and AY 2 176 It has been nicknamed Delta plus 177 from Delta plus K417N 178 The name of the mutation K417N refers to an exchange whereby lysine K is replaced by asparagine N at position 417 179 On 22 June India s Ministry of Health and Family Welfare declared the Delta plus variant of COVID 19 a variant of concern after 22 cases of the variant were reported in India 180 After the announcement leading virologists said there was insufficient data to support labelling the variant as a distinct variant of concern pointing to the small number of patients studied 181 In the UK in July 2021 AY 4 2 was identified Alongside those previously mentioned it also gained the nickname Delta Plus on the strength of its extra mutations Y145H and A222V These are not unique to it but distinguish it from the original Delta variant 182 On 7 June 2022 the WHO has de escalated the Delta variant and its subvariants to previously circulating variants of concern 136 183 Previously circulating variants of interest VOI Pango lineage GISAID clade Nextstrain clade Earliest samples Date of VOI Date of designation Country of sampling Notes P 2 GR 484K V2 20B S 484K 2020 04 2021 07 06 2021 08 17 Zeta variant P 3 GR 1092K V1 21E 2021 01 2021 07 06 2021 08 17 Theta variant B 1 427B 1 429 GH 452R V1 21C 2020 03 2021 07 06 2021 11 09 Epsilon variant B 1 617 1 G 452R V3 21B 2020 10 2021 09 20 Kappa variant B 1 526 GH 253G V1 21F 2020 11 2021 09 20 Iota variant B 1 525 G 484K V3 21D 2020 12 2021 09 20 Eta variant C 37 GR 452Q V1 21G 2020 12 2021 06 14 2022 03 09 Lambda variant B 1 621 GH 21H 2021 01 2021 08 30 2022 03 09 Mu variant Epsilon lineages B 1 429 B 1 427 CAL 20C Main article SARS CoV 2 Epsilon variant The Epsilon variant or lineage B 1 429 also known as CAL 20C 184 or CA VUI1 185 21C 28 or 20C S 452R 123 is defined by five distinct mutations I4205V and D1183Y in the ORF1ab gene and S13I W152C L452R in the spike protein s S gene of which the L452R previously also detected in other unrelated lineages was of particular concern 55 186 From 17 March to 29 June 2021 the CDC listed B 1 429 and the related B 1 427 as variants of concern 30 187 188 189 As of July 2021 Epsilon is no longer considered a variant of interest by the WHO 17 as it was overtaken by Alpha 190 From September 2020 to January 2021 it was 19 to 24 more transmissible than earlier variants in California Neutralisation against it by antibodies from natural infections and vaccinations was moderately reduced 191 but it remained detectable in most diagnostic tests 192 Epsilon CAL 20C was first observed in July 2020 by researchers at the Cedars Sinai Medical Center California in one of 1 230 virus samples collected in Los Angeles County since the start of the COVID 19 epidemic 193 It was not detected again until September when it reappeared among samples in California but numbers remained very low until November 194 195 In November 2020 the Epsilon variant accounted for 36 per cent of samples collected at Cedars Sinai Medical Center and by January 2021 the Epsilon variant accounted for 50 per cent of samples 186 In a joint press release by University of California San Francisco California Department of Public Health and Santa Clara County Public Health Department 196 the variant was also detected in multiple counties in Northern California From November to December 2020 the frequency of the variant in sequenced cases from Northern California rose from 3 to 25 197 In a preprint CAL 20C is described as belonging to clade 20C and contributing approximately 36 of samples while an emerging variant from the 20G clade accounts for some 24 of the samples in a study focused on Southern California Note however that in the US as a whole the 20G clade predominates as of January 2021 55 Following the increasing numbers of Epsilon in California the variant has been detected at varying frequencies in most US states Small numbers have been detected in other countries in North America and in Europe Asia and Australia 194 195 After an initial increase its frequency rapidly dropped from February 2021 as it was being outcompeted by the more transmissible Alpha In April Epsilon remained relatively frequent in parts of northern California but it had virtually disappeared from the south of the state and had never been able to establish a foothold elsewhere only 3 2 of all cases in the United States were Epsilon whereas more than two thirds were Alpha 190 Zeta lineage P 2 Main article SARS CoV 2 Zeta variant Zeta variant or lineage P 2 a sub lineage of B 1 1 28 like Gamma P 1 was first detected in circulation in the state of Rio de Janeiro it harbours the E484K mutation but not the N501Y and K417T mutations 154 It evolved independently in Rio de Janeiro without being directly related to the Gamma variant from Manaus 151 Though previously Zeta was labeled a variant of interest as of July 2021 it is no longer considered as such by the WHO 17 Eta lineage B 1 525 Main article SARS CoV 2 Eta variant The Eta variant or lineage B 1 525 also called VUI 21FEB 03 19 previously VUI 202102 03 by Public Health England PHE and formerly known as UK1188 19 21D 28 or 20A S 484K 123 does not carry the same N501Y mutation found in Alpha Beta and Gamma but carries the same E484K mutation as found in the Gamma Zeta and Beta variants and also carries the same DH69 DV70 deletion a deletion of the amino acids histidine and valine in positions 69 and 70 as found in Alpha N439K variant B 1 141 and B 1 258 and Y453F variant Cluster 5 198 Eta differs from all other variants by having both the E484K mutation and a new F888L mutation a substitution of phenylalanine F with leucine L in the S2 domain of the spike protein As of 5 March 2021 it had been detected in 23 countries 199 200 201 It has also been reported in Mayotte the overseas department region of France 199 The first cases were detected in December 2020 in the UK and Nigeria and as of 15 February 2021 it had occurred in the highest frequency among samples in the latter country 201 As of 24 February 56 cases were found in the UK 19 Denmark which sequences all its COVID 19 cases found 113 cases of this variant from 14 January to 21 February 2021 of which seven were directly related to foreign travel to Nigeria 200 As of July 2021 UK experts are studying it to ascertain how much of a risk it could be It is currently regarded as a variant under investigation but pending further study it may become a variant of concern Ravi Gupta from the University of Cambridge said in a BBC interview that lineage B 1 525 appeared to have significant mutations already seen in some of the other newer variants which means their likely effect is to some extent more predictable 202 Theta lineage P 3 Main article SARS CoV 2 Theta variant On 18 February 2021 the Department of Health of the Philippines confirmed the detection of two mutations of COVID 19 in Central Visayas after samples from patients were sent to undergo genome sequencing The mutations were later named as E484K and N501Y which were detected in 37 out of 50 samples with both mutations co occurrent in 29 out of these 203 On 13 March the Department of Health confirmed the mutations constitutes a variant which was designated as lineage P 3 204 On the same day it also confirmed the first COVID 19 case caused by the Gamma variant in the country The Philippines had 98 cases of the Theta variant on 13 March 205 On 12 March it was announced that Theta had also been detected in Japan 206 207 On 17 March the United Kingdom confirmed its first two cases 208 where PHE termed it VUI 21MAR 02 19 On 30 April 2021 Malaysia detected 8 cases of the Theta variant in Sarawak 209 As of July 2021 Theta is no longer considered a variant of interest by the WHO 17 Iota lineage B 1 526 Main article SARS CoV 2 Iota variant In November 2020 a mutant variant was discovered in New York City which was named lineage B 1 526 210 As of 11 April 2021 the variant has been detected in at least 48 U S states and 18 countries In a pattern mirroring Epsilon Iota was initially able to reach relatively high levels in some states but by May 2021 it was outcompeted by the more transmissible Delta and Alpha 190 Kappa lineage B 1 617 1 Main article SARS CoV 2 Kappa variant The Kappa variant 17 is one of the three sublineages of lineage B 1 617 It is also known as lineage B 1 617 1 21B 28 or 21A S 154K 123 and was first detected in India in December 2020 211 By the end of March 2021 Kappa accounted for more than half of the sequences being submitted from India 212 On 1 April 2021 it was designated a variant under investigation VUI 21APR 01 by Public Health England 29 It has the notable mutations L452R E484Q P681R 213 Lambda lineage C 37 Main article SARS CoV 2 Lambda variant The Lambda variant also known as lineage C 37 was first detected in Peru in August 2020 and was designated by the WHO as a variant of interest on 14 June 2021 17 It spread to at least 30 countries 214 around the world and as of July 2021 update it is unknown whether it is more infectious and resistant to vaccines than other strains 215 216 On 16 March 2022 the WHO has de escalated the Lambda variant to previously circulating variants of concern 135 136 Mu lineage B 1 621 Main article SARS CoV 2 Mu variant The Mu variant also known as lineage B 1 621 was first detected in Colombia in January 2021 and was designated by the WHO as a variant of interest on 30 August 2021 17 There have been outbreaks in South America and Europe 217 218 On 16 March 2022 the WHO has de escalated the Mu variant and its subvariants to previously circulating variants of concern 135 136 Formerly monitored variants WHO The variants listed below were once listed under variants under monitoring but were reclassified due to either no longer circulating at a significant level not having had a significant impact on the situation or scientific evidence of the variant not having concerning properties 4 As of 26 May 2022 update 4 Pango lineage GISAID clade Nextstrain clade Earliest samples Date of VUM Date of designation Country of sampling AV 1 GR 2021 03 2021 05 26 2021 07 21 nbsp UK AT 1 GR 2021 01 2021 06 09 2021 07 21 nbsp Russia R 1 GR 2021 01 2021 04 07 2021 11 09 nbsp Japan B 1 466 2 GH 2020 11 2021 04 28 2021 11 09 nbsp Indonesia B 1 1 519 GR 20B S 732A 2020 11 2021 06 02 2021 11 09 Multiple countries C 36 3 GR 2021 01 2021 06 16 2021 11 09 Multiple countries B 1 214 2 G 2020 11 2021 06 30 2021 11 09 Multiple countries B 1 1 523 GR 2020 05 2021 07 14 2021 11 09 Multiple countries B 1 619 G 2020 05 2021 07 14 2021 11 09 Multiple countries B 1 620 G 20A S 126A 2020 11 2021 07 14 2021 11 09 nbsp Lithuania B 1 1 318 AZ 5 GR 2021 01 2021 06 02 nbsp England C 1 2 GR 2021 05 2021 09 01 nbsp South Africa B 1 630 GH 2021 03 2021 10 12 nbsp Dominican Republic B 1 640 GH 490R 2021 09 2021 11 22 nbsp Republic of Congo XD 2022 01 2022 03 09 nbsp FranceOther notable variantsLineage B 1 1 207 was first sequenced in August 2020 in Nigeria 219 the implications for transmission and virulence are unclear but it has been listed as an emerging variant by the US Centers for Disease Control 42 Sequenced by the African Centre of Excellence for Genomics of Infectious Diseases in Nigeria this variant has a P681H mutation shared in common with the Alpha variant It shares no other mutations with the Alpha variant and as of late December 2020 this variant accounts for around 1 of viral genomes sequenced in Nigeria though this may rise 219 As of May 2021 lineage B 1 1 207 has been detected in 10 countries 220 Lineage B 1 1 317 while not considered a variant of concern is noteworthy in that Queensland Health forced 2 people undertaking hotel quarantine in Brisbane Australia to undergo an additional 5 days quarantine on top of the mandatory 14 days after it was confirmed they were infected with this variant 221 Lineage B 1 616 being identified in Brittany Western France in early January 2021 and designated by WHO as Variant under investigation in March 2021 was reported to be difficult to detect from nasopharyngeal swab sampling method of coronavirus detection and detection of the virus needs to rely on samples from lower respiratory tract citation needed Lineage B 1 618 was first isolated in October 2020 It has the E484K mutation in common with several other variants and showed significant spread in April 2021 in West Bengal India 222 223 As of 23 April 2021 the PANGOLIN database showed 135 sequences detected in India with single figure numbers in each of eight other countries worldwide 224 In July 2021 scientists reported in a preprint which was published in a journal in February 2022 the detection of anomalous unnamed unknown host SARS CoV 2 lineages via wastewater surveillance in New York City They hypothesized that these lineages are derived from unsampled human COVID 19 infections or that they indicate the presence of a non human animal reservoir 225 226 Lineage B 1 640 2 also known as the IHU variant 227 was detected in October 2021 by researchers at the Institut Hospitalo Universitaire IHU in Marseille 228 They found the variant in a traveler who returned to France from Cameroon and reportedly infected 12 people 229 230 The B 1 640 lineage which includes B 1 640 2 was designated a variant under monitoring VUM by the World Health Organization WHO on 22 November 2021 231 However the WHO has reported that lineage B 1 640 2 has spread much slower than the Omicron variant and so is of relatively little concern 230 232 According to a preprint study lineage B 1 640 2 has two already known spike protein mutations E484K and N501Y among a total of 46 nucleotide substitutions and 37 deletions 229 233 234 In March 2022 researchers reported SARS CoV 2 variant recombinant viruses that contain elements of Delta and Omicron Deltacron also called Deltamicron 235 236 237 238 239 Recombination occurs when a virus combines parts from a related virus with its genetic sequence as it assembles copies of itself It is unclear whether Deltacron which is not to be confused with Deltacron reported in January albeit the first detection was also in January 239 240 will be able to compete with Omicron and whether that would be detrimental to health 241 In July 2023 Professor Lawrence Young a virologist at Warwick University announced a super mutated Delta variant from a swab of an Indonesian case with 113 unique mutations with 37 affecting the spike protein 242 Notable missense mutationsThere have been a number of missense mutations observed of SARS CoV 2 del 69 70 The name of the mutation del 69 70 or 69 70 del or other similar notations refers to the deletion of amino acid at position 69 to 70 The mutation is found in the Alpha variant and could lead to spike gene target failure and result in false negative result in PCR virus test 243 RSYLTPGD246 253N Otherwise referred to as del 246 252 or other various similar expression refer to the deletion of amino acid from the position of 246 to 252 in the N terminal domain of spike protein accompanied with a replacement of the aspartic acid D at the position 253 for asparagine N 244 245 The 7 amino acid deletion mutation is currently described as unique in the Lambda variant and have been attributed to as one of the cause of the strain s increased capability to escape from neutralizing antibodies according to preprint paper 246 N440K The name of the mutation N440K refers to an exchange whereby the asparagine N is replaced by lysine K at position 440 247 This mutation has been observed in cell cultures to be 10 times more infective compared to the previously widespread A2a strain A97V substitution in RdRP sequence and 1000 times more in the lesser widespread A3i strain D614G substitution in Spike and a and P323L substitution in RdRP 248 It was involved in rapid surges of COVID 19 cases in India in May 2021 249 India has the largest proportion of N440K mutated variants followed by the US and Germany 250 G446V The name of the mutation G446V refers to an exchange whereby the glycine G is replaced by valine V at position 446 247 The mutation identified in Japan among inbound travelers starting from May and among 33 samples from individuals related to 2020 Tokyo Olympic Games and 2020 Tokyo Paralympic Games are said to be possible to impact affinity of multiple monoclonal antibody although its clinical impact against the use of antibody medicine is still yet to be known 251 L452R The name of the mutation L452R refers to an exchange whereby the leucine L is replaced by arginine R at position 452 247 L452R is found in both the Delta and Kappa variants which first circulated in India but have since spread around the world L452R is a relevant mutation in this strain that enhances ACE2 receptor binding ability and can reduce vaccine stimulated antibodies from attaching to this altered spike protein L452R some studies show could even make the coronavirus resistant to T cells that are necessary to target and destroy virus infected cells They are different from antibodies that are useful in blocking coronavirus particles and preventing it from proliferating 165 Y453F The name of the mutation Y453F refers to an exchange whereby the tyrosine Y is replaced by phenylalanine F at position 453 The mutation have been found potentially linked to the spread of SARS CoV 2 among minks in the Netherlands in 2020 252 S477G N A highly flexible region in the receptor binding domain RBD of SARS CoV 2 starting from residue 475 and continuing up to residue 485 was identified using bioinformatics and statistical methods in several studies The University of Graz 253 and the Biotech Company Innophore 254 have shown in a recent publication that structurally the position S477 shows the highest flexibility among them 255 At the same time S477 is hitherto the most frequently exchanged amino acid residue in the RBDs of SARS CoV 2 mutants By using molecular dynamics simulations of RBD during the binding process to hACE2 it has been shown that both S477G and S477N strengthen the binding of the SARS COV 2 spike with the hACE2 receptor The vaccine developer BioNTech 256 referenced this amino acid exchange as relevant regarding future vaccine design in a preprint published in February 2021 257 E484Q The name of the mutation E484Q refers to an exchange whereby the glutamic acid E is replaced by glutamine Q at position 484 247 The Kappa variant circulating in India has E484Q These variants were initially but misleadingly referred to as a double mutant 258 E484Q may enhance ACE2 receptor binding ability and may reduce vaccine stimulated antibodies ability to attach to this altered spike protein 165 E484K The name of the mutation E484K refers to an exchange whereby the glutamic acid E is replaced by lysine K at position 484 247 It is nicknamed Eeek 259 E484K has been reported to be an escape mutation i e a mutation that improves a virus s ability to evade the host s immune system 260 261 from at least one form of monoclonal antibody against SARS CoV 2 indicating there may be a possible change in antigenicity 262 The Gamma variant lineage P 1 151 the Zeta variant lineage P 2 also known as lineage B 1 1 28 2 154 and the Beta variant 501 V2 exhibit this mutation 262 A limited number of lineage B 1 1 7 genomes with E484K mutation have also been detected 263 Monoclonal and serum derived antibodies are reported to be from 10 to 60 times less effective in neutralising virus bearing the E484K mutation 264 265 On 2 February 2021 medical scientists in the United Kingdom reported the detection of E484K in 11 samples out of 214 000 samples a mutation that may compromise current vaccine effectiveness 266 267 F490S F490S denotes a change from phenylalanine F to serine S in amino acid position 490 268 It is one of the mutation found in Lambda and have been associated with reduced susceptibility to antibody generated by those who were infected with other strains meaning antibody treatment against people infected with strains carrying such mutation would be less effective 269 N501Y N501Y denotes a change from asparagine N to tyrosine Y in amino acid position 501 270 N501Y has been nicknamed Nelly 259 This change is believed by PHE to increase binding affinity because of its position inside the spike glycoprotein s receptor binding domain which binds ACE2 in human cells data also support the hypothesis of increased binding affinity from this change 43 Molecular interaction modelling and the free energy of binding calculations has demonstrated that the mutation N501Y has the highest binding affinity in variants of concern RBD to hACE2 1 Variants with N501Y include Gamma 262 151 Alpha VOC 20DEC 01 Beta and COH 20G 501Y identified in Columbus Ohio 1 This last became the dominant form of the virus in Columbus in late December 2020 and January and appears to have evolved independently of other variants 271 272 N501S N501S denotes a change from asparagine N to serine S in amino acid position 501 273 As of September 2021 there are 8 cases of patients around the world infected with Delta variant which feature this N501S mutation As it is considered a mutation similar to N501Y it is suspected to have similar characteristics as N501Y mutation which is believed to increase the infectivity of the virus however the exact effect is unknown yet 274 D614G nbsp Prevalence of mutation D614G across all reported GISAID strains during the course of 2020 Convergence with unity closely matches the upper limb of the logistics curve 275 D614G is a missense mutation that affects the spike protein of SARS CoV 2 From early appearances in Eastern China early in 2020 the frequency of this mutation in the global viral population increased early on during the pandemic 276 G glycine quickly replaced D aspartic acid at position 614 in Europe though more slowly in China and the rest of East Asia supporting the hypothesis that G increased the transmission rate which is consistent with higher viral titres and infectivity in vitro 53 Researchers with the PANGOLIN tool nicknamed this mutation Doug 259 In July 2020 it was reported that the more infectious D614G SARS CoV 2 variant had become the dominant form in the pandemic 277 278 279 280 PHE confirmed that the D614G mutation had a moderate effect on transmissibility and was being tracked internationally 270 281 The global prevalence of D614G correlates with the prevalence of loss of smell anosmia as a symptom of COVID 19 possibly mediated by higher binding of the RBD to the ACE2 receptor or higher protein stability and hence higher infectivity of the olfactory epithelium 282 Variants containing the D614G mutation are found in the G clade by GISAID 53 and the B 1 clade by the PANGOLIN tool 53 Q677P H The name of the mutation Q677P H refers to an exchange whereby the glutamine Q is replaced by proline P or histidine H at position 677 247 There are several sub lineages containing the Q677P mutation six of these which also contain various different combinations of other mutations are referred to by names of birds One of the earlier ones noticed for example is known as Pelican while the most common of these as of early 2021 was provisionally named Robin 1 283 The mutation has been reported in multiple lineages circulating inside the United States as of late 2020 and also some lineages outside the country Pelican was first detected in Oregon and as of early 2021 Robin 1 was found often in the Midwestern United States while another Q667H sub lineage Robin 2 was found mostly in the southeastern United States 283 The frequency of such mutation being recorded has increased from late 2020 to early 2021 284 P681H nbsp Logarithmic Prevalence of P681H in 2020 according to sequences in the GISAID database 275 The name of the mutation P681H refers to an exchange whereby the proline P is replaced by histidine H at position 681 275 In January 2021 scientists reported in a preprint that the mutation P681H a characteristic feature of the Alpha variant and lineage B 1 1 207 identified in Nigeria is showing a significant exponential increase in worldwide frequency thus following a trend to be expected in the lower limb of the logistics curve This may be compared with the trend of the now globally prevalent D614G 275 285 P681R The name of the mutation P681R refers to an exchange whereby the proline P is replaced by arginine R at position 681 247 Indian SARS CoV 2 Genomics Consortium INSACOG found that other than the two mutations E484Q and L452R there is also a third significant mutation P681R in lineage B 1 617 All three concerning mutations are on the spike protein the operative part of the coronavirus that binds to receptor cells of the body 165 A701V According to initial media reports the Malaysian Ministry of Health announced on 23 December 2020 that it had discovered a mutation in the SARS CoV 2 genome which they designated as A701B sic among 60 samples collected from the Benteng Lahad Datu cluster in Sabah The mutation was characterised as being similar to the one found recently at that time in South Africa Australia and the Netherlands although it was uncertain if this mutation was more infectious or aggressive clarification needed than before 286 The provincial government of Sulu in neighbouring Philippines temporarily suspended travel to Sabah in response to the discovery of A701B due to uncertainty over the nature of the mutation 287 On 25 December 2020 the Malaysian Ministry of Health described a mutation A701V as circulating and present in 85 of cases D614G was present in 100 of cases in Malaysia 288 289 These reports also referred to samples collected from the Benteng Lahad Datu cluster 288 289 The text of the announcement was mirrored verbatim on the Facebook page of Noor Hisham Abdullah Malay Director General of Health who was quoted in some of the news articles 289 The A701V mutation has the amino acid alanine A substituted by valine V at position 701 in the spike protein Globally South Africa Australia Netherlands and England also reported A701V at about the same time as Malaysia 288 In GISAID the prevalence of this mutation is found to be about 0 18 of cases 288 On 14 April 2021 the Malaysian Ministry of Health reported that the third wave which had started in Sabah has involved the introduction of variants with D614G and A701V mutations 290 Recombinant variantsThe British government has reported a number of recombinant variants of SARS CoV 2 291 These recombinant lineages have been given the Pango lineage identifiers XD XE and XF 292 XE is a recombinant lineage of Pango lineages BA 1 and BA 2 293 As of March 2022 update XE was believed to have a growth rate 9 8 greater than BA 2 291 Differential vaccine effectivenessSee also Oxford AstraZeneca COVID 19 vaccine Effectiveness Pfizer BioNTech COVID 19 vaccine Effectiveness Moderna COVID 19 vaccine Effectiveness Janssen COVID 19 vaccine Efficacy Novavax COVID 19 vaccine Efficacy Sinopharm BIBP COVID 19 vaccine Effectiveness Sputnik V COVID 19 vaccine Effectiveness CoronaVac Effectiveness Covaxin Efficacy ZF2001 Efficacy Abdala vaccine Efficacy SCB 2019 Efficacy and COVID 19 vaccine clinical research Variants The interplay between the SARS CoV 2 virus and its human hosts was initially natural but then started being altered by the rising availability of vaccines seen in 2021 294 The potential emergence of a SARS CoV 2 variant that is moderately or fully resistant to the antibody response elicited by the COVID 19 vaccines may necessitate modification of the vaccines 295 The emergence of vaccine resistant variants is more likely in a highly vaccinated population with uncontrolled transmission 296 As of February 2021 the US Food and Drug Administration believed that all FDA authorized vaccines remained effective in protecting against circulating strains of SARS CoV 2 295 Immune evasion by variants This section is an excerpt from COVID 19 vaccine Immune evasion by variants edit In contrast to other investigated prior variants the SARS CoV 2 Omicron variant 297 298 299 300 301 and its BA 4 5 subvariants 302 have evaded immunity induced by vaccines which may lead to breakthrough infections despite recent vaccination Nevertheless vaccines are thought to provide protection against severe illness hospitalizations and deaths due to Omicron 303 Vaccine adjustments This section is an excerpt from SARS CoV 2 Omicron variant Vaccine adjustments edit In June 2022 Pfizer and Moderna developed bivalent vaccines to protect against the SARS CoV 2 wild type and the Omicron variant The bivalent vaccines are well tolerated and offer immunity to Omicron superior to previous mRNA vaccines 304 In September 2022 the United States Food and Drug Administration FDA authorized the bivalent vaccines for use in the US 305 306 307 In June 2023 the FDA advised manufacturers that the 2023 2024 formulation of the COVID 19 vaccines for use in the US be updated to be a monovalent COVID 19 vaccine using the XBB 1 5 lineage of the Omicron variant 308 309 Data and methodsModern DNA sequencing where available may permit rapid detection sometimes known as real time detection of genetic variants that appear in pathogens during disease outbreaks 310 Through use of phylogenetic tree visualisation software records of genome sequences can be clustered into groups of identical genomes all containing the same set of mutations Each group represents a variant clade or lineage and comparison of the sequences allows the evolutionary path of a virus to be deduced For SARS CoV 2 until March 2021 over 330 000 viral genomic sequences had been generated by molecular epidemiology studies across the world 311 New variant detection and assessment On 26 January 2021 the British government said it would share its genomic sequencing capabilities with other countries in order to increase the genomic sequencing rate and trace new variants and announced a New Variant Assessment Platform 312 As of January 2021 update more than half of all genomic sequencing of COVID 19 was carried out in the UK 313 Wastewater surveillance was demonstrated to be one technique to detect SARS CoV 2 variants 226 and to track their rise for studying related ongoing infection dynamics 314 315 316 Testing Whether one or more mutations visible in RT PCR tests can be used reliably to identify a variant depends on the prevalence of other variants currently circulating in the same population 317 318 Mutations used to identify variants of concern in commercial test assays 319 Mutation Alpha Beta Gamma Delta Omicron D69 70 e nbsp nbsp nbsp nbsp nbsp ins214EPE f nbsp nbsp nbsp nbsp nbsp S371L S373P f nbsp nbsp nbsp nbsp nbsp N501Y nbsp nbsp nbsp nbsp nbsp E484K nbsp nbsp nbsp nbsp nbsp E484A f nbsp nbsp nbsp nbsp nbsp L452R nbsp nbsp nbsp nbsp nbsp nsp6 D106 108 nbsp nbsp nbsp nbsp nbsp Incubation theory for multiple mutated variantsSee also Antigenic escape and Escape mutation Researchers have suggested that multiple mutations can arise in the course of the persistent infection of an immunocompromised patient particularly when the virus develops escape mutations under the selection pressure of antibody or convalescent plasma treatment 320 321 with the same deletions in surface antigens repeatedly recurring in different patients 322 Cross species transmissionFurther information Impact of the COVID 19 pandemic on animals and List of animals that can get SARS CoV 2 There is a risk that COVID 19 could transfer from humans to other animal populations and could combine with other animal viruses to create yet more variants that are dangerous to humans 323 Reverse zoonosis spillovers may cause reservoirs for mutating variants that spill back to humans another possible source for variants of concern in addition to immunocompromised people 324 Cluster 5 Main article Cluster 5 In early November 2020 Cluster 5 also referred to as DFVI spike by the Danish State Serum Institute SSI 325 was discovered in Northern Jutland Denmark It is believed to have been spread from minks to humans via mink farms On 4 November 2020 it was announced that the mink population in Denmark would be culled to prevent the possible spread of this mutation and reduce the risk of new mutations happening A lockdown and travel restrictions were introduced in seven municipalities of Northern Jutland to prevent the mutation from spreading which could compromise national or international responses to the COVID 19 pandemic By 5 November 2020 some 214 mink related human cases had been detected 326 The WHO stated that cluster 5 had a moderately decreased sensitivity to neutralising antibodies 327 SSI warned that the mutation could reduce the effect of COVID 19 vaccines under development although it was unlikely to render them useless Following the lockdown and mass testing SSI announced on 19 November 2020 that cluster 5 in all probability had become extinct 328 As of 1 February 2021 authors to a peer reviewed paper all of whom were from the SSI assessed that cluster 5 was not in circulation in the human population 329 See also nbsp COVID 19 portal nbsp Medicine portal nbsp Viruses portal nbsp Pandemics portal GX P2V is a mutant strain of COVID 19 that is deadly to hACE2 humanized mice RaTG13 the second closest known relative to SARS CoV 2 Pandemic prevention Surveillance and mapping 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