Variants of SARS-CoV-2
From Wikipedia the free encyclopedia
|Part of a series on the|
There are many variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19). Some are believed, or have been stated, to be of particular importance due to their potential for increased transmissibility, increased virulence, or reduced effectiveness of vaccines against them. These variants contribute to the continuation of the COVID-19 pandemic.
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. 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.
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. 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.
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.
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, either by infection recovery or via vaccination. Some of the variants of concern show mutations in the RBD of the S-protein.
The following table presents information and relative risk level 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, and neutralising antibody activity is retained by some monoclonal antibodies. PCR tests continue to detect the Omicron variant.
|Identification||Emergence||Changes relative to previously circulating variants at the time and place of emergence||Neutralising antibody activity (or efficacy when available)|
|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 ||No||L452R, T478K, P681R ||+97% (76–117%) ||+85% (39–147%) relative to Alpha ||+137% (50–230%) ||Reinfections happened, with smaller occurrence rate than vaccinated infections ||Efficacy reduction for non-severe disease|
|Omicron||B.1.1.529||21K||South Africa||9 Nov 2021 ||26 Nov 2021 ||Yes||P681H, N440K, N501Y, S477N, many others ||Possibly increased ||−57% (59–61%) relative to Delta||−63% (69–74%) relative to Delta||Increased reinfection rate ||Efficacy reduction against symptomatic disease, unknown for severe disease|
|Alpha||B.1.1.7||20I (V1)||United Kingdom||20 Sep 2020 ||18 Dec 2020 ||No||69–70del, N501Y, P681H ||+29% (24–33%) ||+52% (47–57%) ||+59% (44–74%) ||Minimal reduction ||Minimal reduction|
|Gamma||P.1 (B.188.8.131.52)||20J (V3)||Brazil||Nov 2020||15 Jan 2021 ||No||K417T, E484K, N501Y ||+38% (29–48%) ||Possibly increased ||+50% (50% CrI, 20–90%) ||Reduced ||Retained by many|
|Beta||B.1.351||20H (V2)||South Africa||May 2020||14 Jan 2021 ||No||K417N, E484K, N501Y ||+25% (20–30%) ||Under investigation[when?]||Possibly increased ||Reduced, T cell response elicited by D614G virus remains effective ||Efficacy reduction against symptomatic disease,[L] retained against severe disease|
Very high risk High risk Medium risk Low risk Unknown risk
- Efficacy of natural infection against reinfection when available.
- 7 February – 22 June 22, 2021, Ontario. CFR 0.04% for <50 age group unvaccinated, 6.5% for >50 age group unvaccinated
- 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. 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.
- B.1.1.7 with E484K assumed to only differ from B.1.1.7 on neutralising antibody activity.
- 23 November 2020 – 31 January 2021, England. CFR 0.06% for <50 age group, 4.8% for >50 age group
- 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.
- Oxford-AstraZeneca, Novavax.
|PANGO lineages||Notes to PANGO lineages||Nextstrain clades, 2021||GISAID clades||Notable variants|
|A.1–A.6||19B||S||Contains "reference sequence" WIV04/2019|
|B.3–B.7, B.9, B.10, B.13–B.16||19A||L|
|B.1||B.1.5–B.1.72||20A||G||Lineage B.1 in the PANGO Lineages nomenclature system; includes Delta/|
|B.1.9, B.1.13, B.1.22, B.1.26, B.1.37||GH|
|20G||Predominant in US generally, Feb '21|
|B.1.1||20B||GR||Includes B.1.1.207 and Lambda (lineage C.37)|
|B.1.177||20E (EU1)||GV[b]||Derived from 20A|
SARS-CoV-2 variants are grouped according to their lineage and component mutations. Many organisations, including governments and news outlets, referred colloquially to concerning variants by the country in which they were first identified. After months of discussions, the World Health Organization announced Greek-letter names for important strains on 31 May 2021, so they could be easily referred to in a simple, easy to say, and non-stigmatising fashion. 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. 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. The WHO gave as the explanation that Nu is too easily confounded with "new" and Xi is a common last name. In the event that the WHO uses the entirety of the Greek alphabet, the agency considered naming future variants after constellations.
Lineages and clades
While there are many thousands of variants of SARS-CoV-2, subtypes of the virus can be put into larger groupings such as lineages or clades.[c] Three main, generally used nomenclatures have been proposed:
- As of January 2021[update], GISAID—referring to SARS-CoV-2 as hCoV-19—had identified eight global clades (S, O, L, V, G, GH, GR, and GV).
- In 2017, Hadfield et al. announced Nextstrain, intended "for real-time tracking of pathogen evolution". 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].
- In 2020, Rambaut et al. of the Phylogenetic Assignment of Named Global Outbreak Lineages (PANGOLIN) software team proposed in an article "a dynamic nomenclature for SARS-CoV-2 lineages that focuses on actively circulating virus lineages and those that spread to new locations"; as of August 2021[update], 1340 lineages had been designated.
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. 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.
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. 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.
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.
- One group (Sudhir Kumar et al.) refers extensively to an NCBI reference genome (GenBankID:NC_045512; GISAID ID: EPI_ISL_402125), this sample was collected on 26 December 2019, although they also used the WIV04 GISAID reference genome (ID: EPI_ISL_402124), in their analyses.
- 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". WIV04/2019 was sampled from a symptomatic patient on 30 December 2019 and is widely used (especially by those collaborating with GISAID) as a reference sequence.
The variant first sampled and identified in Wuhan, China is considered by researchers to differ from the progenitor genome by three mutations. Subsequently, many distinct lineages of SARS-CoV-2 have evolved.
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.
- 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". 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".
Variants of concern (WHO)
Listed below are the variants of concern (VOC) recognised by the World Health Organization as of October 2022[update]. 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, while the WHO did so on 7 June 2022.
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.
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.
Named Omicron by the WHO, it was identified in November 2021 in Botswana and South Africa; one case had travelled to Hong Kong, one confirmed case was identified in Israel in a traveler returning from Malawi, along with two who returned from South Africa and one from Madagascar. Belgium confirmed the first detected case in Europe on 26 November 2021 in an individual who had returned from Egypt on 11 November. 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.
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]. 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. BA.2 is more transmissible than BA.1. It was causing most cases in England by mid-March 2022, and by the end of March, BA.2 became dominant in the US. 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, the CDC, and the ECDC (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 year end 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.
On 22 December 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.
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.
|Pango lineage||GISAID clade||Nextstrain clade||Relation to circulating VOCs||First documented||Notable features|
|BF.7||GRA||22B||BA.5 sublineage||24-01-2022||BA.5 + S:R346T|
|BQ.1||GRA||22E||BA.5 sublineage||07-02-2022||BQ.1 and BQ.1.1: BA.5 + S:R346T, S:K444T, S:N460K|
|BA.2.75||GRA||22D||BA.2 sublineage||31-12-2021||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: BA.2.75 + S:L452R, S:F486S
|XBB||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||13-08-2022||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: XBB + S:F486P
Variants of interest (WHO)
Listed below are the Variants of Interest (VOI) which are recognised by the World Health Organization. Other organisations such as the CDC in the United States may at times use a slightly different list.
Variants under monitoring (WHO)
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.
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.
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":
Alpha (lineage B.1.1.7)
First detected in October 2020 during the COVID-19 pandemic in the United Kingdom from a sample taken the previous month in Kent, lineage B.1.1.7, labelled Alpha variant by the WHO, was previously known as the first Variant Under Investigation in December 2020 (VUI – 202012/01) and later notated as VOC-202012/01. It is also known as 20I (V1), 20I/501Y.V1 (formerly 20B/501Y.V1), or 501Y.V1. From October to December 2020, its prevalence doubled every 6.5 days, the presumed generational interval. It is correlated with a significant increase in the rate of COVID-19 infection in United Kingdom, associated partly with the N501Y mutation. 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), and early analyses suggested an increase in lethality, though later work found no evidence of increased virulence. As of May 2021, the Alpha variant had been detected in some 120 countries.
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" 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. 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. Other names for this variant include B.1.1.7+E484K and B.1.1.7 Lineage with S:E484K.
Beta (lineage B.1.351)
On 18 December 2020, the 501.V2 variant, also known as 501.V2, 20H (V2), 20H/501Y.V2 (formerly 20C/501Y.V2), 501Y.V2, VOC-20DEC-02 (formerly VOC-202012/02), or lineage B.1.351, was first detected in South Africa and reported by the country's health department. 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. 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.
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, K417N, and E484K. The N501Y mutation has also been detected in the United Kingdom.
Gamma (lineage P.1)
The Gamma variant or lineage P.1, termed Variant of Concern 21JAN-02 (formerly VOC-202101/02) by Public Health England, 20J (V3) or 20J/501Y.V3 by Nextstrain, or just 501Y.V3, 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. On 12 January 2021, the Brazil-UK CADDE Centre confirmed 13 local cases of the new Gamma variant in the Amazon rainforest. 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.184.108.40.206 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.: 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.
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. 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.
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.
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.
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. 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.
Delta (lineage B.1.617.2)
The Delta variant, also known as B.1.617.2, G/452R.V3, 21A or 21A/S:478K, was a globally dominant variant that spread to at least 185 countries. 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. 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. It carries L452R and P681R mutations in Spike; 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. 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.
In June 2021, reports began to appear of a variant of Delta with the K417N mutation. 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. The variant, called "Delta with K417N" by Public Health England, includes two clades corresponding to the Pango lineages AY.1 and AY.2. It has been nicknamed "Delta plus" from "Delta plus K417N". The name of the mutation, K417N, refers to an exchange whereby lysine (K) is replaced by asparagine (N) at position 417. 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. 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. 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.
Previously circulating variants of interest (VOI)
|Pango lineage||GISAID clade||Nextstrain clade||Earliest samples||Date of VOI||Date of designation||Country of sampling||Notes|
Epsilon (lineages B.1.429, B.1.427, CAL.20C)
The Epsilon variant or lineage B.1.429, also known as CAL.20C or CA VUI1, 21C or 20C/S:452R, 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. From 17 March to 29 June 2021, the CDC listed B.1.429 and the related B.1.427 as "variants of concern". As of July 2021, Epsilon is no longer considered a variant of interest by the WHO, as it was overtaken by Alpha.
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, but it remained detectable in most diagnostic tests.
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. It was not detected again until September when it reappeared among samples in California, but numbers remained very low until November. 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. In a joint press release by University of California, San Francisco, California Department of Public Health, and Santa Clara County Public Health Department, 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%. 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. 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. 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.
Zeta (lineage P.2)
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. It evolved independently in Rio de Janeiro without being directly related to the Gamma variant from Manaus. Though previously Zeta was labeled a variant of interest, as of July 2021, it is no longer considered as such by the WHO.
Eta (lineage B.1.525)
The Eta variant or lineage B.1.525, also called VUI-21FEB-03 (previously VUI-202102/03) by Public Health England (PHE) and formerly known as UK1188, 21D or 20A/S:484K, 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). 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. It has also been reported in Mayotte, the overseas department/region of France. 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. As of 24 February 56 cases were found in the UK. 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.
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.
Theta (lineage P.3)
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.
On 13 March, the Department of Health confirmed the mutations constitutes a variant which was designated as lineage P.3. 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. On 12 March it was announced that Theta had also been detected in Japan. On 17 March, the United Kingdom confirmed its first two cases, where PHE termed it VUI-21MAR-02. On 30 April 2021, Malaysia detected 8 cases of the Theta variant in Sarawak.
As of July 2021, Theta is no longer considered a variant of interest by the WHO.
Iota (lineage B.1.526)
In November 2020, a mutant variant was discovered in New York City, which was named lineage B.1.526. 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.
Kappa (lineage B.1.617.1)
The Kappa variant is one of the three sublineages of lineage B.1.617. It is also known as lineage B.1.617.1, 21B or 21A/S:154K, and was first detected in India in December 2020. By the end of March 2021, Kappa accounted for more than half of the sequences being submitted from India. On 1 April 2021, it was designated a variant under investigation (VUI-21APR-01) by Public Health England. It has the notable mutations L452R, E484Q, P681R.
Lambda (lineage C.37)
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. It spread to at least 30 countries around the world and, as of July 2021[update], it is unknown whether it is more infectious and resistant to vaccines than other strains. On 16 March 2022, the WHO has de-escalated the Lambda variant to "previously circulating variants of concern".
Mu (lineage B.1.621)
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. There have been outbreaks in South America and Europe. On 16 March 2022, the WHO has de-escalated the Mu variant and its subvariants to "previously circulating variants of concern".
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.
|Pango lineage||GISAID clade||Nextstrain clade||Earliest samples||Date of VUM||Date of designation||Country of sampling|
|B.1.640||GH/490R||2021-09||2021-11-22||Republic of Congo|
Other notable variants
Lineage B.1.1.207 was first sequenced in August 2020 in Nigeria; the implications for transmission and virulence are unclear but it has been listed as an emerging variant by the US Centers for Disease Control. 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. As of May 2021, lineage B.1.1.207 has been detected in 10 countries.
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.
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.
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. 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.
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".
Lineage B.1.640.2 (also known as the IHU variant) was detected in October 2021 by researchers at the Institut Hospitalo-Universitaire (IHU) in Marseille. They found the variant in a traveler who returned to France from Cameroon and reportedly infected 12 people. 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. 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. 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.
In March 2022, researchers reported SARS-CoV-2 variant recombinant viruses that contain elements of Delta and Omicron – Deltacron (also called "Deltamicron"). 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 – will be able to compete with Omicron and whether that would be detrimental to health.
Notable missense mutations
There have been a number of missense mutations observed of SARS-CoV-2.
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.
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).
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.
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). It was involved in rapid surges of COVID-19 cases in India in May 2021. India has the largest proportion of N440K mutated variants followed by the US and Germany.
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.
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.
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.
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 and the Biotech Company Innophore have shown in a recent publication that structurally, the position S477 shows the highest flexibility among them.
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 referenced this amino acid exchange as relevant regarding future vaccine design in a preprint published in February 2021.
The Kappa variant circulating in India has E484Q. These variants were initially (but misleadingly) referred to as a "double mutant". E484Q may enhance ACE2 receptor binding ability, and may reduce vaccine-stimulated antibodies' ability to attach to this altered spike protein.
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) from at least one form of monoclonal antibody against SARS-CoV-2, indicating there may be a "possible change in antigenicity". The Gamma variant (lineage P.1), the Zeta variant (lineage P.2, also known as lineage B.220.127.116.11) and the Beta variant (501.V2) exhibit this mutation. A limited number of lineage B.1.1.7 genomes with E484K mutation have also been detected. Monoclonal and serum-derived antibodies are reported to be from 10 to 60 times less effective in neutralising virus bearing the E484K mutation. 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.
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.
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. 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. Variants with N501Y include Gamma, Alpha (VOC 20DEC-01), Beta, and COH.20G/501Y (identified in Columbus, Ohio). 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.
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.
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. 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. Researchers with the PANGOLIN tool nicknamed this mutation "Doug".
In July 2020, it was reported that the more infectious D614G SARS-CoV-2 variant had become the dominant form in the pandemic. PHE confirmed that the D614G mutation had a "moderate effect on transmissibility" and was being tracked internationally.
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.
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. 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."
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. The frequency of such mutation being recorded has increased from late 2020 to early 2021.
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.
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.
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. 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.
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. These reports also referred to samples collected from the Benteng Lahad Datu cluster. 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.
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. In GISAID, the prevalence of this mutation is found to be about 0.18%. of cases.
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.
Differential vaccine effectiveness
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. 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. The emergence of vaccine-resistant variants is more likely in a highly vaccinated population with uncontrolled transmission.
Immune evasion by variants
In June 2022, researchers, health organizations and regulators were discussing, investigating (including with preliminary laboratory studies and trials) and partly recommending COVID-19 vaccine boosters that mix the original vaccine formulation with Omicron-adjusted parts – such as spike proteins of a specific Omicron subvariant – to better prepare the immune system to recognize a wide variety of variants amid substantial and ongoing immune evasion by Omicron (and other SARS-CoV-2 variants).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. The United States Food and Drug Administration (FDA) has authorized the bivalent vaccines for use in the USA .
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. 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.
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". As of January 2021[update], more than half of all genomic sequencing of COVID-19 was carried out in the UK.
Incubation theory for multiple mutated variants
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, with the same deletions in surface antigens repeatedly recurring in different patients.
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. 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.
In early November 2020, Cluster 5, also referred to as ΔFVI-spike by the Danish State Serum Institute (SSI), 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.
The WHO stated that cluster 5 had a "moderately decreased sensitivity to neutralising antibodies". 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. 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.
- RaTG13, the second closest known relative to SARS-CoV-2
- Pandemic prevention § Surveillance and mapping
- COVID-19 vaccine § Effectiveness
- Based on various trackers and periodic reports.
- In another source, GISAID name a set of 7 clades without the O clade but including a GV clade.
- According to the WHO, "Lineages or clades can be defined based on viruses that share a phylogenetically determined common ancestor".
- As of January 2021[update], at least one of the following criteria must be met in order to count as a clade in the Nextstrain system (quote from source):
- A clade reaches >20% global frequency for 2 or more months
- A clade reaches >30% regional frequency for 2 or more months
- A VOC ('variant of concern') is recognized (applies currently [6 January 2021] to 501Y.V1 and 501Y.V2)
- Produces S gene target failure (SGTF) in TaqPath.
- Detectable by the TIB MolBiol assay using the melting curve method.
- Shahhosseini N, Babuadze GG, Wong G, Kobinger GP (April 2021). "Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern". Microorganisms. 9 (5): 926. doi:10.3390/microorganisms9050926. PMC 8146828. PMID 33925854. S2CID 233460887.
- "Coronavirus variants and mutations: The science explained". BBC News. 6 January 2021. Archived from the original on 22 February 2021. Retrieved 2 February 2021.
- Kupferschmidt K (15 January 2021). "New coronavirus variants could cause more reinfections, require updated vaccines". Science. doi:10.1126/science.abg6028. S2CID 234141081. Archived from the original on 22 February 2021. Retrieved 2 February 2021.
- Tracking SARS-CoV-2 variants. www.who.int, accessed 26 May 2022. Updated frequently.
- Shahhosseini N, Wong G, Kobinger GP, Chinikar S (June 2021). "SARS-CoV-2 spillover transmission due to recombination event". Gene Reports. 23: 101045. doi:10.1016/j.genrep.2021.101045. PMC 7884226. PMID 33615041.
- "The rise and fall of the lab leak hypothesis for the origin of SARS-CoV-2 | Science-Based Medicine". sciencebasedmedicine.org. 1 August 2022. Retrieved 4 November 2022.
- Tang, Xiaolu; Wu, Changcheng; Li, Xiang; Song, Yuhe (3 March 2020). "On the origin and continuing evolution of SARS-CoV-2". National Science Review. 7 (6): 1012–1023. doi:10.1093/nsr/nwaa036. PMC 7107875. PMID 34676127.
- Forster, Peter; Forster, Lucy; Renfrew, Colin; Forster, Michael (8 April 2020). "Phylogenetic network analysis of SARS-CoV-2 genomes". Proceedings of the National Academy of Sciences. 117 (17): 9241–9243. Bibcode:2020PNAS..117.9241F. doi:10.1073/pnas.2004999117. ISSN 0027-8424. PMC 7196762. PMID 32269081.
- Rambaut, A; Holmes, EC; OToole, A; Hill, V; McCrone, JT; Ruis, C; du Plessis, L; Pybus, OG (15 July 2020). "A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology". Nature Microbiology. 5 (11): 1403–1407. doi:10.1038/s41564-020-0770-5. PMC 7610519. PMID 32669681.
- Tregoning, John S.; Flight, Katie E.; Higham, Sophie L.; Wang, Ziyin; Pierce, Benjamin F. (9 August 2021). "Progress of the COVID-19 vaccine effort: viruses, vaccines and variants versus efficacy, effectiveness and escape". Nature Reviews Immunology. 21 (10): 626–636. doi:10.1038/s41577-021-00592-1. PMC 8351583. PMID 34373623.
- Piplani, Sakshi; Singh, Puneet Kumar; Winkler, David A.; Petrovsky, Nikolai (December 2021). "In silico comparison of SARS-CoV-2 spike protein-ACE2 binding affinities across species and implications for virus origin". Scientific Reports. 11 (1): 13063. Bibcode:2021NatSR..1113063P. doi:10.1038/s41598-021-92388-5. PMC 8225877. PMID 34168168.
- Gallagher J (12 June 2021). "Covid: Is there a limit to how much worse variants can get?". BBC. Archived from the original on 15 June 2021. Retrieved 12 June 2021.
- Tao, Kaiming; Tzou, Philip L.; Nouhin, Janin; Gupta, Ravindra K.; de Oliveira, Tulio; Kosakovsky Pond, Sergei L.; Fera, Daniela; Shafer, Robert W. (17 September 2021). "The biological and clinical significance of emerging SARS-CoV-2 variants". Nature Reviews Genetics. 22 (12): 757–773. doi:10.1038/s41576-021-00408-x. PMC 8447121. PMID 34535792.
- Hendy, Mohamed; Kaufman, Samuel; Ponga, Mauricio (December 2021). "Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations". Scientific Reports. 11 (1): 21735. Bibcode:2021NatSR..1121735H. doi:10.1038/s41598-021-01081-0. PMC 8571385. PMID 34741079.
- "SARS-CoV-2 variants: risk assessment framework" (PDF). GOV.UK. Government Digital Service. Public Health England. 22 May 2021. GOV-8426. Archived (PDF) from the original on 27 May 2021. Retrieved 22 June 2021.
- "Tracking SARS-CoV-2 variants". who.int. World Health Organization. Archived from the original on 18 June 2021. Retrieved 22 June 2021. Updated frequently.
- "SARS-CoV-2 Variant Classifications and Definitions". CDC.gov. Centers for Disease Control and Prevention. 11 February 2020. Archived from the original on 29 June 2021. Retrieved 18 June 2021. Updated frequently.
- "Variants: distribution of cases data". Public Health England. Government Digital Service. Archived from the original on 7 June 2021. Retrieved 16 February 2021. Updated frequently. Data up to 19 May 2021 included in the 2 July 2021 update.
- "Living Evidence – SARS-CoV-2 variants". Agency for Clinical Innovation. nsw.gov.au. Ministry of Health (New South Wales). 23 July 2021. Archived from the original on 16 April 2021. Retrieved 22 March 2021. Updated frequently.
- "SARS-CoV-2 variants of concern". ECDC.eu. European Centre for Disease Prevention and Control. Archived from the original on 16 June 2021. Retrieved 12 May 2021. Updated frequently.
- "Coronavirus Disease (COVID-19) Situation Reports". who.int. World Health Organization. Archived from the original on 26 January 2020. Retrieved 14 June 2021. Updated frequently.
- "Investigation of SARS-CoV-2 variants: technical briefings". GOV.UK. Government Digital Service. Public Health England. Retrieved 18 November 2021. Updated frequently.
- "Investigation of SARS-CoV-2 variants of concern: variant risk assessments". GOV.UK. Government Digital Service. Public Health England. Archived from the original on 19 June 2021. Retrieved 19 June 2021. Updated frequently.
- Weekly epidemiological update on COVID-19 – 20 July 2021 (Situation report). World Health Organization. 20 July 2021. Archived from the original on 23 July 2021. Retrieved 24 July 2021.
- Planas D, Veyer D, Baidaliuk A, Staropoli I, Guivel-Benhassine F, Rajah MM, et al. (27 May 2021). "Reduced sensitivity of infectious SARS-CoV-2 variant B.1.617.2 to monoclonal antibodies and sera from convalescent and vaccinated individuals". bioRxiv 10.1101/2021.05.26.445838.
- "Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern". World Health Organization. 26 November 2021. Retrieved 26 November 2021.
- Weekly epidemiological update on COVID-19 – 22 June 2021 (Situation report). World Health Organization. 22 June 2021. Archived from the original on 29 June 2021. Retrieved 26 June 2021.
- SARS-CoV-2 variants of concern and variants under investigation in England, technical briefing 10 (PDF) (Briefing). Public Health England. 7 May 2021. GOV-8226. Archived (PDF) from the original on 8 May 2021. Retrieved 6 June 2021.
- "SARS-CoV-2 Variant Classifications and Definitions". CDC.gov. Centers for Disease Control and Prevention. 29 June 2021. Archived from the original on 16 June 2021. Retrieved 19 February 2021. Frequently updated.
- Campbell F, Archer B, Laurenson-Schafer H, Jinnai Y, Konings F, Batra N, et al. (June 2021). "Increased transmissibility and global spread of SARS-CoV-2 variants of concern as at June 2021". Euro Surveillance. 26 (24): 2100509. doi:10.2807/1560-7917.ES.2021.26.24.2100509. PMC 8212592. PMID 34142653.
- Sheikh A, McMenamin J, Taylor B, Robertson C (June 2021). "SARS-CoV-2 Delta VOC in Scotland: demographics, risk of hospital admission, and vaccine effectiveness". Lancet. 397 (10293): 2461–2462. doi:10.1016/S0140-6736(21)01358-1. PMC 8201647. PMID 34139198.
- "SARS-CoV-2 variants of concern and variants under investigation in England Technical Briefing 21" (PDF). Public Health England. 20 August 2021. p. 16 and 22. Archived (PDF) from the original on 29 August 2021. Retrieved 29 August 2021.
- Risk assessment for SARS-CoV-2 variant Delta (PDF) (Assessment). Public Health England. 23 July 2021. Archived (PDF) from the original on 25 July 2021. Retrieved 24 July 2021.
- Yadav PD, Sapkal GN, Abraham P, Ella R, Deshpande G, Patil DY, et al. (May 2021). "Neutralization of variant under investigation B.1.617 with sera of BBV152 vaccinees". Clinical Infectious Diseases. Oxford University Press. 74 (ciab411): 366–368. bioRxiv 10.1101/2021.04.23.441101. doi:10.1093/cid/ciab411. PMID 33961693.
- Callaway, Ewen (25 November 2021). "Heavily mutated coronavirus variant puts scientists on alert". Nature. 600 (7887): 21. doi:10.1038/d41586-021-03552-w. PMID 34824381. S2CID 244660616.
- SARS-CoV-2 variants of concern and variants under investigation in England, technical briefing 29 (PDF) (Briefing). Public Health England. 26 November 2021. GOV-10481. Archived (PDF) from the original on 27 November 2021. Retrieved 26 November 2021.
- Risk assessment for SARS-CoV-2 variant Omicron (PDF) (Assessment). Public Health England. 22 December 2021. GOV-10869. Retrieved 23 December 2021.
- Nyberg, Tommy; Ferguson, Neil M.; Nash, Sophie G.; Webster, Harriet H.; Flaxman, Seth; Andrews, Nick; Hinsley, Wes; Bernal, Jamie Lopez; Kall, Meaghan; Bhatt, Samir; Blomquist, Paula (16 March 2022). "Comparative analysis of the risks of hospitalisation and death associated with SARS-CoV-2 omicron (B.1.1.529) and delta (B.1.617.2) variants in England: a cohort study". The Lancet. 399 (10332): 1303–1312. doi:10.1016/S0140-6736(22)00462-7. ISSN 0140-6736. PMC 8926413. PMID 35305296.
- Rambaut A, Loman N, Pybus O, Barclay W, Barrett J, Carabelli A, et al. (18 December 2020). "Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations". Virological. Archived from the original on 21 December 2020. Retrieved 14 June 2021.
- Investigation of novel SARS-COV-2 variant, technical briefing 1 (PDF) (Briefing). Public Health England. 21 December 2020. Archived (PDF) from the original on 15 June 2021. Retrieved 6 June 2021.
- "Emerging SARS-CoV-2 Variants". CDC.gov (Science brief). Centers for Disease Control and Prevention. 28 January 2021. Archived from the original on 15 May 2021. Retrieved 4 January 2021. This article incorporates text from this source, which is in the public domain.
- Chand et al. (2020), p. 6, Potential impact of spike variant N501Y.
- Nyberg T, Twohig KA, Harris RJ, Seaman SR, Flannagan J, Allen H, et al. (June 2021). "Risk of hospital admission for patients with SARS-CoV-2 variant B.1.1.7: cohort analysis". BMJ. 373: n1412. arXiv:2104.05560. doi:10.1136/bmj.n1412. PMC 8204098. PMID 34130987. S2CID 235187479.
- "Confirmed cases of COVID-19 variants identified in UK". GOV.UK. Public Health England. 15 January 2021. Archived from the original on 7 May 2021. Retrieved 5 March 2021.
- Horby P, Barclay W, Gupta R, Huntley C (27 January 2021). NERVTAG paper: note on variant P.1 (Note). Public Health England. Archived from the original on 6 June 2021. Retrieved 6 June 2021.
- Horby P, Barclay W, Huntley C (13 January 2021). NERVTAG paper: brief note on SARS-CoV-2 variants (Note). Public Health England. Archived from the original on 6 June 2021. Retrieved 6 June 2021.
- This table is an adaptation and expansion of Alm et al., figure 1.
- Rambaut A, Holmes EC, O'Toole Á, Hill V, McCrone JT, Ruis C, et al. (November 2020). "A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology". Nature Microbiology. 5 (11): 1403–1407. doi:10.1038/s41564-020-0770-5. PMC 7610519. PMID 32669681. S2CID 220544096. Cited in Alm et al.
- Alm E, Broberg EK, Connor T, Hodcroft EB, Komissarov AB, Maurer-Stroh S, et al. (The WHO European Region sequencing laboratories and GISAID EpiCoV group) (August 2020). "Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020". Euro Surveillance. 25 (32). doi:10.2807/1560-7917.ES.2020.25.32.2001410. PMC 7427299. PMID 32794443.
- "Nextclade" (What are the clades?). nextstrain.org. Archived from the original on 19 January 2021. Retrieved 19 January 2021.
- Bedford T, Hodcroft B, Neher RA (6 January 2021). "Updated Nextstrain SARS-CoV-2 clade naming strategy". nextstrain.org. Archived from the original on 18 January 2021. Retrieved 19 January 2021.
- Zhukova A, Blassel L, Lemoine F, Morel M, Voznica J, Gascuel O (November 2020). "Origin, evolution and global spread of SARS-CoV-2". Comptes Rendus Biologies. 344: 57–75. doi:10.5802/crbiol.29. PMID 33274614.
- "Genomic epidemiology of novel coronavirus – Global subsampling (Filtered to B.1.617)". nextstrain.org. Archived from the original on 13 July 2021. Retrieved 5 May 2021.
- Zhang W, Davis B, Chen SS, Martinez JS, Plummer JT, Vail E (2021). "Emergence of a Novel SARS-CoV-2 Variant in Southern California". JAMA. 325 (13): 1324–1326. doi:10.1001/jama.2021.1612. ISSN 0098-7484. PMC 7879386. PMID 33571356. Retrieved 2 October 2021.
- What are the clades? clades.nextstrain.org, accessed 29 November 2021
- "PANGO lineages-Lineage B.1.1.28". cov-lineages.org. Archived from the original on 24 February 2021. Retrieved 4 February 2021.[failed verification]
- "Variant: 20J/501Y.V3". covariants.org. 1 April 2021. Archived from the original on 23 March 2021. Retrieved 6 April 2021.
- "clade tree (from 'Clade and lineage nomenclature')". GISAID. 4 July 2020. Archived from the original on 9 January 2021. Retrieved 7 January 2021.
- "Don't call it the 'British variant.' Use the correct name: B.1.1.7". STAT. 9 February 2021. Archived from the original on 4 June 2021. Retrieved 12 February 2021.
- Flanagan R (2 February 2021). "Why the WHO won't call it the 'U.K. variant', and you shouldn't either". CTV News. Archived from the original on 1 May 2021. Retrieved 12 February 2021.
- For a list of sources using names referring to the country in which the variants were first identified, see, for example, Talk:South African COVID variant and Talk:U.K. Coronavirus variant.
- "Today, @WHO announces new, easy-to-say labels for #SARSCoV2 Variants of Concern (VOCs) & Interest (VOIs)". Archived from the original on 7 July 2021. Retrieved 7 July 2021.
- Branswell H (31 May 2021). "The name game for coronavirus variants just got a little easier". Stat News. Archived from the original on 17 June 2021. Retrieved 28 June 2021.
- World Health Organization (15 January 2021). "Statement on the sixth meeting of the International Health Regulations (2005) Emergency Committee regarding the coronavirus disease (COVID-19) pandemic". Archived from the original on 7 February 2021. Retrieved 18 January 2021.
- "Covid: WHO renames UK and other variants with Greek letters". BBC News. 31 May 2021. Archived from the original on 31 May 2021. Retrieved 7 July 2021.
- "WHO skipped two Greek alphabet letters in naming coronavirus variant". The Associated Press. 27 November 2021.
- "New COVID variants could be named after constellations once Greek alphabet is used up". Sky News. 8 August 2021. Retrieved 30 November 2021.
- Koyama T, Platt D, Parida L (July 2020). "Variant analysis of SARS-CoV-2 genomes". Bulletin of the World Health Organization. 98 (7): 495–504. doi:10.2471/BLT.20.253591. PMC 7375210. PMID 32742035.
We detected in total 65776 variants with 5775 distinct variants.
- WHO Headquarters (8 January 2021). "3.6 Considerations for virus naming and nomenclature". SARS-CoV-2 genomic sequencing for public health goals: Interim guidance, 8 January 2021. World Health Organization. p. 6. Archived from the original on 23 January 2021. Retrieved 2 February 2021.
- "Global phylogeny, updated by Nextstrain". GISAID. 18 January 2021. Archived from the original on 20 January 2021. Retrieved 19 January 2021.
- Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C, et al. (December 2018). Kelso J (ed.). "Nextstrain: real-time tracking of pathogen evolution". Bioinformatics. 34 (23): 4121–4123. doi:10.1093/bioinformatics/bty407. PMC 6247931. PMID 29790939.
- "Nextstrain COVID-19". Nextstrain. Archived from the original on 21 January 2021. Retrieved 1 June 2021.
- "cov-lineages/pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages". Github. Archived from the original on 15 February 2021. Retrieved 2 January 2021.
- "Lineage descriptions". cov-lineages.org. Pango team. Archived from the original on 4 June 2021. Retrieved 24 December 2020.
- Rambaut A, Holmes EC, O'Toole Á, Hill V, McCrone JT, Ruis C, et al. (March 2021). "Addendum: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology". Nature Microbiology. 6 (3): 415. doi:10.1038/s41564-021-00872-5. PMC 7845574. PMID 33514928.
- "Variants: distribution of cases data". GOV.UK. 28 January 2021. At "Differences between a Variant of Concern and Variant Under Investigation". Retrieved 19 February 2021.
SARS-CoV-2 variants, if considered to have concerning epidemiological, immunological, or pathogenic properties, are raised for formal investigation. At this point they are designated Variant Under Investigation (VUI) with a year, month, and number. Following a risk assessment with the relevant expert committee, they may be designated Variant of Concern (VOC)
- Griffiths E, Tanner J, Knox N, Hsiao W, Van Domselaar G (15 January 2021). CanCOGeN Interim Recommendations for Naming, Identifying, and Reporting SARS-CoV-2 Variants of Concern (PDF). CanCOGeN (nccid.ca) (Report). 1.0. Archived (PDF) from the original on 17 April 2021.
- Investigation of SARS-CoV-2 variants of concern in EnglandTechnical briefing 6 13 February 2021 (See section: Nomenclature of variants in the UK, P.3) assets.publishing.service.gov.uk, accessed 27 February 2021
- CDC (11 February 2020). "Cases, Data, and Surveillance". Centers for Disease Control and Prevention. Retrieved 16 March 2021.
- Kumar S, Tao Q, Weaver S, Sanderford M, Caraballo-Ortiz MA, Sharma S, et al. (May 2021). "An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic". Molecular Biology and Evolution. 38 (8): 3046–3059. doi:10.1093/molbev/msab118. PMC 8135569. PMID 33942847.
- Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, et al. (March 2020). "A new coronavirus associated with human respiratory disease in China". Nature. 579 (7798): 265–269. Bibcode:2020Natur.579..265W. doi:10.1038/s41586-020-2008-3. PMC 7094943. PMID 32015508.
- Chiara M, Horner DS, Gissi C, Pesole G (May 2021). "Comparative Genomics Reveals Early Emergence and Biased Spatiotemporal Distribution of SARS-CoV-2". Molecular Biology and Evolution. 38 (6): 2547–2565. doi:10.1093/molbev/msab049. PMC 7928790. PMID 33605421.
- Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, et al. (March 2020). "A pneumonia outbreak associated with a new coronavirus of probable bat origin". Nature. 579 (7798): 270–273. Bibcode:2020Natur.579..270Z. doi:10.1038/s41586-020-2012-7. PMC 7095418. PMID 32015507.
- Okada P, Buathong R, Phuygun S, Thanadachakul T, Parnmen S, Wongboot W, et al. (February 2020). "Early transmission patterns of coronavirus disease 2019 (COVID-19) in travellers from Wuhan to Thailand, January 2020". Euro Surveillance. 25 (8). doi:10.2807/1560-7917.ES.2020.25.8.2000097. PMC 7055038. PMID 32127124.
- "Official hCoV-19 Reference Sequence". www.gisaid.org. Archived from the original on 6 May 2021. Retrieved 14 May 2021.
- "The ancestor of SARS-CoV-2's Wuhan strain was circulating in late October 2019". News Medical. Archived from the original on 24 July 2021. Retrieved 10 May 2020.
Journal reference: Kumar, S. et al. (2021). An evolutionary portrait...
- IDSA Contributor "COVID "Mega-variant" and eight criteria for a template to assess all variants". Science Speaks: Global ID News. 2 February 2021. Archived from the original on 21 April 2021. Retrieved 20 February 2021.
- "Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern". www.who.int. Retrieved 26 November 2021.
- Callaway, Ewen (25 November 2021). "Heavily mutated coronavirus variant puts scientists on alert". Nature. 600 (7887): 21. doi:10.1038/d41586-021-03552-w. PMID 34824381. S2CID 244660616.
- Fernando, Michael James and Christine. "World experts hold special meeting on worrying new COVID-19 variant in South Africa: Latest updates". USA Today.
- "outbreak.info". outbreak.info. Retrieved 26 November 2021.
- Covid: New heavily mutated variant B.1.1.529 in South Africa raises concern, 25 November 2021, BBC News, accessed 25 November 2021
- Whiteside, Philip (30 November 2021). "COVID-19: How the spread of Omicron went from patient zero to all around the globe". Sky News. Retrieved 3 January 2022.
- @BNODesk (26 November 2021). "Statement from Israel's health ministry reporting 1 confirmed case of new coronavirus variant B.1.1.529" (Tweet). Retrieved 26 November 2021 – via Twitter.
- 14:30 4 מאומתים לווריאנט החדש התגלו בארץ, רה"מ יקיים מסיבת עיתונאים translated: "...Verified for the new strain 4 verified for the new variant were discovered in the country...", m.ynet.co.il, accessed 26 November 2021
- "Belgium detects first case of new COVID-19 variant in Europe". Reuters. 26 November 2021. Retrieved 26 November 2021.
- "INSACOG WEEKLY BULLETIN" (PDF). dbtindia.gov.in. 10 January 2022. Retrieved 24 January 2022.
- "Statement on Omicron sublineage BA.2". www.who.int. Retrieved 4 April 2022.
- Schmidt, Charles. "What We Know About Omicron's BA.2 Variant So Far". Scientific American. Retrieved 4 April 2022.
- "Covid infections rising again across UK - ONS". BBC News. 11 March 2022.
- Jessica Rendall (29 March 2022). "BA.2 is Now the Dominant COVID Variant in US, CDC Data Shows".
- ECDC (12 May 2022). "Changes to list of SARS-CoV-2 variants of concern, variants of interest, and variants under monitoring" (PDF).
- Peter Russell (6 January 2023). "Omicron XBB.1.5: What Do We Know So Far?". Retrieved 8 January 2023.
- "Covid: Ireland, Italy, Belgium and Netherlands ban flights from UK". BBC News. 20 December 2020. Archived from the original on 21 December 2020. Retrieved 23 December 2020.
- Chand M, Hopkins S, Dabrera G, Achison C, Barclay W, Ferguson N, et al. (21 December 2020). Investigation of novel SARS-COV-2 variant: Variant of Concern 202012/01 (PDF) (Report). Public Health England. Archived (PDF) from the original on 22 February 2021. Retrieved 23 December 2020.
- "PHE investigating a novel strain of COVID-19". Public Health England (PHE). 14 December 2020.
- Weekly epidemiological update on COVID-19 for 8 June 2021 (Situation report). World Health Organization. 8 June 2021. Archived from the original on 15 June 2021. Retrieved 14 June 2021.
- Rambaut A, Loman N, Pybus O, Barclay W, Barrett J, Carabelli A, et al. (2020). Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations (Report). Written on behalf of COVID-19 Genomics Consortium UK. Archived from the original on 22 February 2021. Retrieved 20 December 2020.
- Kupferschmidt K (20 December 2020). "Mutant coronavirus in the United Kingdom sets off alarms but its importance remains unclear". Science Mag. Archived from the original on 21 December 2020. Retrieved 21 December 2020.
- Collier DA, De Marco A, Ferreira IA, Meng B, Datir RP, Walls AC, et al. (May 2021). "Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies". Nature (Published). 593 (7857): 136–141. doi:10.1038/s41586-021-03412-7. PMID 33706364.
We therefore generated pseudoviruses that carried the B.1.1.7 spike mutations with or without the additional E484K substitution and tested these against sera obtained after the first and second dose of the BNT162b2 mRNA vaccine as well as against convalescent sera. After the second vaccine dose, we observed a considerable loss of neutralising activity for the pseudovirus with the B.1.1.7 spike mutations and E484K (Fig. 3d, e). The mean fold change for the E484K-containing B.1.1.7 spike variant was 6.7 compared with 1.9 for the B.1.1.7 variant, relative to the wild-type spike protein (Fig. 3a–c and Extended Data Fig. 5). Similarly, when we tested a panel of convalescent sera with a range of neutralisation titres (Fig. 1f, g and Extended Data Fig. 5), we observed additional loss of activity against the mutant B.1.1.7 spike with E484K, with fold change of 11.4 relative to the wild-type spike protein (Fig. 3f, g and Extended Data Fig. 5).
- "New evidence on VUI-202012/01 and review of the public health risk assessment". Knowledge Hub. 15 December 2020. Archived from the original on 21 December 2020. Retrieved 25 December 2020.
- "COG-UK Showcase Event". Archived from the original on 14 June 2021. Retrieved 25 December 2020 – via YouTube.
- Davies NG, Abbott S, Barnard RC, Jarvis CI, Kucharski AJ, Munday JD, et al. (April 2021). "Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England". Science. 372 (6538): eabg3055. doi:10.1126/science.abg3055. PMC 8128288. PMID 33658326.
- Volz E, Mishra S, Chand M, Barrett JC, Johnson R, Geidelberg L, et al. (May 2021). "Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England". Nature. 593 (7858): 266–269. Bibcode:2021Natur.593..266V. doi:10.1038/s41586-021-03470-x. PMID 33767447.
- Horby P, Huntley C, Davies N, Edmunds J, Ferguson N, Medley G, Hayward A, Cevik M, Semple C (11 February 2021). "NERVTAG paper on COVID-19 variant of concern B.1.1.7: NERVTAG update note on B.1.1.7 severity (2021-02-11)" (PDF). GOV.UK. Archived (PDF) from the original on 13 April 2021. Retrieved 26 February 2021.
- Gallagher J (22 January 2021). "Coronavirus: UK variant 'may be more deadly'". BBC News. Archived from the original on 23 May 2021. Retrieved 22 January 2021.
- Frampton D, Rampling T, Cross A, Bailey H, Heaney J, Byott M, et al. (April 2021). "Genomic characteristics and clinical effect of the emergent SARS-CoV-2 B.1.1.7 lineage in London, UK: a whole-genome sequencing and hospital-based cohort study". The Lancet. Infectious Diseases. 21 (9): 1246–1256. doi:10.1016/S1473-3099(21)00170-5. PMC 8041359. PMID 33857406.
- "PANGO lineages Lineage B.1.1.7". cov-lineages.org. 15 May 2021. Archived from the original on 16 June 2021. Retrieved 15 May 2021.
- "Tracking SARS-CoV-2 variants (updated 2022-03-16)". www.who.int. 16 March 2022. Archived from the original on 17 March 2022. Retrieved 17 March 2022.
- "Tracking SARS-CoV-2 variants (updated 2022-03-07)". www.who.int. 7 March 2022. Archived from the original on 15 March 2022. Retrieved 21 May 2022.
- Mandavilli A (5 March 2021). "In Oregon, Scientists Find a Virus Variant With a Worrying Mutation – In a single sample, geneticists discovered a version of the coronavirus first identified in Britain with a mutation originally reported in South Africa". The New York Times. Archived from the original on 6 March 2021. Retrieved 6 March 2021.
- Chen RE, Zhang X, Case JB, Winkler ES, Liu Y, VanBlargan LA, et al. (April 2021). "Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies". Nature Medicine. 27 (4): 717–726. doi:10.1038/s41591-021-01294-w. PMC 8058618. PMID 33664494.
- "B.1.1.7 Lineage with S:E484K Report". outbreak.info. 5 March 2021. Archived from the original on 7 March 2021. Retrieved 7 March 2021.
- Moustafa AM, Bianco C, Denu L, Ahmed A, Neide B, Everett J, et al. (21 April 2021). "Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania". bioRxiv 10.1101/2021.04.21.440801.
- "B.1.1.7 Lineage with S:E484K Report". outbreak.info. Archived from the original on 3 July 2021. Retrieved 28 May 2021.
- Risk related to the spread of new SARS-CoV-2 variants of concern in the EU/EEA – first update (Risk assessment). European Centre for Disease Prevention and Control. 2 February 2021. Archived from the original on 25 March 2021. Retrieved 22 March 2021.
- "South Africa announces a new coronavirus variant". The New York Times. 18 December 2020. Archived from the original on 21 December 2020. Retrieved 20 December 2020.
- Wroughton L, Bearak M (18 December 2020). "South Africa coronavirus: Second wave fueled by new strain, teen 'rage festivals'". The Washington Post. Archived from the original on 27 December 2020. Retrieved 20 December 2020.
- Mkhize Z (18 December 2020). "Update on Covid-19 (18th December 2020)" (Press release). South Africa. COVID-19 South African Online Portal. Archived from the original on 4 May 2021. Retrieved 23 December 2020.
Our clinicians have also warned us that things have changed and that younger, previously healthy people are now becoming very sick.
- Abdool Karim, Salim S. (19 December 2020). "The 2nd Covid-19 wave in South Africa:Transmissibility & a 501.V2 variant, 11th slide". www.scribd.com. Archived from the original on 6 January 2021. Retrieved 23 December 2020.
- Lowe D (22 December 2020). "The New Mutations". In the Pipeline. American Association for the Advancement of Science. Archived from the original on 29 January 2021. Retrieved 23 December 2020.
I should note here that there's another strain in South Africa that is bringing on similar concerns. This one has eight mutations in the Spike protein, with three of them (K417N, E484K and N501Y) that may have some functional role.
- "Statement of the WHO Working Group on COVID-19 Animal Models (WHO-COM) about the UK and South African SARS-CoV-2 new variants" (PDF). World Health Organization. 22 December 2020. Archived (PDF) from the original on 4 May 2021. Retrieved 23 December 2020.
- "Novel mutation combination in spike receptor binding site" (Press release). GISAID. 21 December 2020. Archived from the original on 22 February 2021. Retrieved 23 December 2020.
- "Japan finds new coronavirus variant in travelers from Brazil". Japan Today. Japan. 11 January 2021. Archived from the original on 11 January 2021. Retrieved 14 January 2021.
- Faria NR, Claro IM, Candido D, Moyses Franco LA, Andrade PS, Coletti TM, et al. (12 January 2021). "Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings". CADDE Genomic Network. virological.org. Archived from the original on 20 May 2021. Retrieved 23 January 2021.
- "P.1". cov-lineages.org. Pango team. 1 July 2021. Archived from the original on 9 June 2021. Retrieved 7 March 2021.
- Covid-19 Genomics UK Consortium (15 January 2021). "COG-UK Report on SARS-CoV-2 Spike mutations of interest in the UK" (PDF). www.cogconsortium.uk. Archived (PDF) from the original on 16 April 2021. Retrieved 25 January 2021.
- Voloch CM, da Silva Francisco R, de Almeida LG, Cardoso CC, Brustolini OJ, Gerber AL, et al. (March 2021). "Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil". Journal of Virology. 95 (10). doi:10.1128/jvi.00119-21. PMC 8139668. PMID 33649194.
- Nascimento V, Souza V (25 February 2021). "COVID-19 epidemic in the Brazilian state of Amazonas was driven by long-term persistence of endemic SARS-CoV-2 lineages and the recent emergence of the new Variant of Concern P.1". Research Square. doi:10.21203/rs.3.rs-275494/v1. Archived from the original on 1 March 2021. Retrieved 2 March 2021.
- Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DD, Mishra S, et al. (May 2021). "Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil". Science. 372 (6544): 815–821. Bibcode:2021Sci...372..815F. doi:10.1126/science.abh2644. ISSN 0036-8075. PMC 8139423. PMID 33853970.
Within this plausible region of parameter space, P.1 can be between 1.7 and 2.4 times more transmissible (50% BCI, 2.0 median, with a 99% posterior probability of being >1) than local non-P1 lineages and can evade 21 to 46% (50% BCI, 32% median, with a 95% posterior probability of being able to evade at least 10%) of protective immunity elicited by previous infection with non-P.1 lineages, corresponding to 54 to 79% (50% BCI, 68% median) cross-immunity ... We estimate that infections are 1.2 to 1.9 times more likely (50% BCI, median 1.5, 90% posterior probability of being >1) to result in mortality in the period after the emergence of P.1, compared with before, although posterior estimates of this relative risk are also correlated with inferred cross-immunity. More broadly, the recent epidemic in Manaus has strained the city's health care system, leading to inadequate access to medical care. We therefore cannot determine whether the estimated increase in relative mortality risk is due to P.1 infection, stresses on the Manaus health care system, or both. Detailed clinical investigations of P.1 infections are needed.
- Andreoni M, Londoño E, Casado L (3 March 2021). "Brazil's Covid Crisis Is a Warning to the Whole World, Scientists Say – Brazil is seeing a record number of deaths, and the spread of a more contagious coronavirus variant that may cause reinfection". The New York Times. Archived from the original on 3 March 2021. Retrieved 3 March 2021.
- Zimmer C (1 March 2021). "Virus Variant in Brazil Infected Many Who Had Already Recovered From Covid-19 – The first detailed studies of the so-called P.1 variant show how it devastated a Brazilian city. Now scientists want to know what it will do elsewhere". The New York Times. Archived from the original on 3 March 2021. Retrieved 3 March 2021.
- Sofia Moutinho (4 May 2021). "Chinese COVID-19 vaccine maintains protection in variant-plagued Brazil". Science. doi:10.1126/science.abi9414. S2CID 234804602. Archived from the original on 16 June 2021. Retrieved 4 May 2021.
- Gaier R (5 March 2021). "Exclusive: Oxford study indicates AstraZeneca effective against Brazil variant, source says". Reuters. Rio de Janeiro. Archived from the original on 9 March 2021. Retrieved 9 March 2021.
- "Exclusive: Oxford study indicates AstraZeneca effective against Brazil variant, source says". Reuters. Rio de Janeiro. 8 March 2021. Archived from the original on 9 March 2021. Retrieved 9 March 2021.
- Simões E, Gaier R (8 March 2021). "CoronaVac e Oxford são eficazes contra variante de Manaus, dizem laboratórios" [CoronaVac and Oxford are effective against Manaus variant, say laboratories]. UOL Notícias (in Portuguese). Reuters Brazil. Archived from the original on 8 March 2021. Retrieved 9 March 2021.
- "Delta Globally Dominant Covid Strain, Now Spread To 185 Countries: WHO". 22 September 2021.
- "PANGO lineages". cov-lineages.org. Archived from the original on 3 June 2021. Retrieved 18 April 2021.
- Koshy J (8 April 2021). "Coronavirus | Indian 'double mutant' strain named B.1.617". The Hindu. Archived from the original on 26 May 2021. Retrieved 10 April 2021.
- "India's variant-fuelled second wave coincided with spike in infected flights landing in Canada". Toronto Sun. 10 April 2021. Archived from the original on 2 June 2021. Retrieved 10 April 2021.
- "Weekly epidemiological update on COVID-19". World Health Organization. 11 May 2021. Archived from the original on 11 May 2021. Retrieved 12 May 2021.
- "COVID strain first detected in India found in 53 territories: WHO". www.aljazeera.com. Archived from the original on 19 June 2021. Retrieved 27 May 2021.
- Mishra, Swapnil; Mindermann, Sören; Sharma, Mrinank; Whittaker, Charles; Mellan, Thomas A.; Wilton, Thomas; Klapsa, Dimitra; Mate, Ryan; Fritzsche, Martin; Zambon, Maria; Ahuja, Janvi (1 September 2021). "Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England". EClinicalMedicine. 39: 101064. doi:10.1016/j.eclinm.2021.101064. ISSN 2589-5370. PMC 8349999. PMID 34401689.
- "British scientists warn over Indian coronavirus variant". Reuters. 7 May 2021. Archived from the original on 22 May 2021. Retrieved 7 May 2021.
- "expert reaction to VUI-21APR-02/B.1.617.2 being classified by PHE as a variant of concern". Science Media Centre. 7 May 2021. Archived from the original on 13 July 2021. Retrieved 15 May 2021.
- SARS-CoV-2 variants of concern and variants under investigation in England, technical briefing 14 (PDF) (Briefing). Public Health England. 3 June 2021. GOV-8530. Archived (PDF) from the original on 4 July 2021. Retrieved 26 June 2021.
- Pearson H, Pullen L, Dao C (11 June 2021). "AHS breaks down vaccination data of COVID-19 Delta variant outbreak at Calgary hospital". Global News. Archived from the original on 12 June 2021. Retrieved 12 June 2021.
- Schraer R (4 June 2021). "'Nepal variant': What's the mutation stopping green list trips to Portugal?". BBC News. Archived from the original on 19 June 2021. Retrieved 18 June 2021.
- Acharya B, Jamkhandikar S (23 June 2021). "Explainer: What is the Delta variant of coronavirus with K417N mutation?". Reuters. Archived from the original on 23 June 2021. Retrieved 23 June 2021.
- SARS-CoV-2 variants of concern and variants under investigation in England, technical briefing 17 (PDF) (Briefing). Public Health England. 25 June 2021. GOV-8576. Archived (PDF) from the original on 25 June 2021. Retrieved 26 June 2021.
- Sharma M. "New 'Delta Plus' variant of SARS-CoV-2 identified; here's what we know so far". India Today. Archived from the original on 17 June 2021. Retrieved 16 June 2021.