Page semi-protected

Variants of SARS-CoV-2

From Wikipedia, the free encyclopedia

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

Part of a series on the
COVID-19 pandemic
Scientifically accurate atomic model of the external structure of SARS-CoV-2. Each "ball" is an atom.
  • COVID-19 (disease)
  • SARS-CoV-2 (virus)
Timeline
Locations
International response
hide
Medical response

Vaccines

Variants
Economic impact and recession
Impacts
SARS-CoV-2 (Wikimedia colors).svg COVID-19 portal
  • v
  • t
Positive, negative, and neutral mutations during the evolution of coronaviruses like SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), has many variants; some are believed, or have been believed, to be of particular importance due to their potential for increased transmissibility,[1] increased virulence, or reduced effectiveness of vaccines against them.[2][3]

Overview

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.[4]

The earliest available human virus genomes were collected from patients since 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 into B.1, which is the ancestor of the major global variants of concern, labeled in 2021 by the WHO as alpha, beta, gamma and delta.[5][6][7]

Early in the pandemic, there were few 'mutant' variant viruses because of the small number of people infected (i.e. there were fewer opportunities for escape mutants to emerge).[8] As time went on, SARS-CoV-2 started evolving to become more transmissible. Notably, the Alpha variant and the Delta variant are both more transmissible than the original virus identified around Wuhan in China.[9]

The following table presents information and relative risk level[10] for 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,[14][19] and neutralising antibody activity is retained by some monoclonal antibodies.[12][20][21]

Identification[19] 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 PHE variant[A] Nextstrain clade First outbreak Earliest sample[22] Designated VOC Notable mutations Transmissibility Hospitalisation Mortality From natural infection[B] From vaccination
Alpha B.1.1.7 VOC‑20DEC‑01 20I (V1) United Kingdom 20 Sep 2020[23] 18 Dec 2020[24] 69–70del, N501Y, P681H[25][26] +29% (24–33%)[27][C] +52% (47–57%)[D][C] +59% (44–74%)[D][C]
CFR 0.06% for <50 age group, 4.8% for >50 age group[29] 		Minimal reduction[12] Minimal reduction[12]
B.1.1.7 with E484K[E][13] VOC‑21FEB‑02 26 Jan 2021[30] 5 Feb 2021[31] E484K, 69–70del, N501Y, P681H[25][26] Considerably reduced[20] Considerably reduced[20]
Beta B.1.351 VOC‑20DEC‑02 20H (V2) South Africa May 2020 14 Jan 2021[32] K417N, E484K, N501Y[25] +25% (20–30%)[27] Under investigation Possibly increased[14][19] Reduced, T cell response elicited by D614G virus remains effective[12][19] Efficacy: reduced against symptomatic disease,[F] retained against severe disease[19]
Gamma P.1 VOC‑21JAN‑02 20J (V3) Brazil Nov 2020 15 Jan 2021[33][34] K417T, E484K, N501Y[25] +38% (29–48%)[27] Possibly increased[19] +50% (50% CrI, 20–90%)[G][I] Reduced[12] Retained by many[J]
Delta B.1.617.2 VOC‑21APR‑02 21A India Oct 2020 6 May 2021[37] L452R, T478K, P681R[38] +97% (76–117%)[27] +85% (39–147%) relative to Alpha[L] +137% (50–230%)[K]
CFR 0.04% for <50 age group unvaccinated, 6.5% for >50 age group unvaccinated[29] 		Reinfections happened, with smaller occurrence rate than vaccinated infections[M][41][42] Efficacy reduction for non-severe disease[19][42][N]

  Very high risk   High risk   Medium risk   Low risk   Unknown risk

  1. ^ Name format updated March 2021, changing year from 4 to 2 digits and month from 2 digits to 3 letters, for example, VOC-202101-02 to VOC-21JAN-02.[13]
  2. ^ Efficacy of natural infection against reinfection when available.
  3. ^ Jump up to: a b c B.1.1.7 with E484K assumed to only differ from B.1.1.7 on neutralising antibody activity.[15]
  4. ^ Jump up to: a b 23 November 2020 – 31 January 2021, England.[28]
  5. ^ B.1.1.7 with E484K has not received a WHO label; it is listed here with the same label as its parent lineage, B.1.1.7
  6. ^ Oxford-AstraZeneca, NovaVax.
  7. ^ The reported confidence or credible interval has a low probability, so the estimated value can only be understood as possible, not certain nor likely.
  8. ^ Jump up to: 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.
  9. ^ March 2020 – February 2021, Manaus.[35] Preliminary results from a study in the Southern Region of Brazil found lineage P.1 increases mortality for healthy young people much more. In groups without pre-existing conditions, the variant was found to increase mortality by 490% (220–985%) for men in the 20–39 age group, 465% (190–1003%) for women in the 20–39 age group and 670% (401–1083%) for women in the 40–59 age group.[36][H]
  10. ^ Except Pfizer–BioNTech.[14]
  11. ^ Jump up to: a b 7 February – 22 June 22, 2021, Ontario.[40]
  12. ^ 1 April – 6 June 2021, Scotland.[39] Another preliminary study in Ontario found that hospitalization by Delta increased by 120% relative to non-VOC lineages.[K][H]
  13. ^ 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.
  14. ^ Moderately reduced neutralisation with Covaxin.[43]

Nomenclature

SARS-CoV-2 corresponding nomenclatures[44] hide
PANGO lineages[45] Notes to PANGO lineages[46] Nextstrain clades,[47] 2021[48] GISAID clades Notable variants
A.1–A.6 19B S Contains "reference sequence" WIV04/2019[49]
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[38][50]
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[51] and Eta/B.1.525[12]
20G Predominant in US generally, Jan '21[51]
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]
20D
20J Includes Gamma/P.1 and Zeta/P.2[52][53]
20F
20I Includes Alpha/B.1.1.7 aka VOC-202012/01, VOC-20DEC-01 or 20I/501Y.V1
B.1.177 20E (EU1)[48] GV[b] Derived from 20A[48]
Tree diagram of lineages of SARS-CoV-2 according to the Pango nomenclature system.

As of July 2021, no consistent nomenclature has been established for SARS-CoV-2.[55] Many organisations, including governments and news outlets, refer colloquially to concerning variants by the country in which they were first identified.[56][57][58] After months of discussions, the World Health Organization announced Greek-letter names for important strains on 31 May 2021,[59] so they could be easily referred to in a simple, easy to say, and non-stigmatising fashion.[60][61] This decision may have partially been taken because of criticism from governments on using country names to refer to variants of the virus, as it could cause discrimination towards locals of those countries.[62]

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

While there are many thousands of variants of SARS-CoV-2,[63] subtypes of the virus can be put into larger groupings such as lineages or clades.[c] Three main, generally used nomenclatures[55] have been proposed:

  • As of January 2021, GISAID—referring to SARS-CoV-2 as hCoV-19[46]—had identified eight global clades (S, O, L, V, G, GH, GR, and GV).[64]
  • In 2017, Hadfield et al. announced Nextstrain, intended "for real-time tracking of pathogen evolution".[65] 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.[66]
  • In 2020, Rambaut et al. of the Phylogenetic Assignment of Named Global Outbreak Lineages (PANGOLIN)[67] software team proposed in an article[45] "a dynamic nomenclature for SARS-CoV-2 lineages that focuses on actively circulating virus lineages and those that spread to new locations";[55] as of August 2021, 1340 lineages had been designated.[68][69]

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.[13] 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.[13]

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.[70]
  • One group (Sudhir Kumar et al.)[70] refers extensively to an NCBI reference genome (GenBankID:NC_045512; GISAID ID: EPI_ISL_402125),[71] this sample was collected on 26 December 2019,[72] although they also used the WIV04 GISAID reference genome (ID: EPI_ISL_402124),[73] in their analyses.[74]
  • 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".[49] WIV04/2019 was sampled from a symptomatic patient on 30 December 2019 and is widely used (especially by those collaborating with GISAID)[75] as a reference sequence.[49]

The variant first sampled and identified in Wuhan, China is considered by researchers to differ from the progenitor genome by three mutations.[70][76] Subsequently, many distinct lineages of SARS-CoV-2 have evolved.[68]

Criteria for notability

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".

Some of the potential consequences of emerging variants are the following:[25][77]

  • 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".[13][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".[12]

Variants of concern (WHO)

Listed below are the Variants of Concern (VOC) currently recognised by the World Health Organization.[11] Other organisations such as the CDC in the United States have at times used a slightly different list, but as of July 2021 their list matches that of the WHO.[12]

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.

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,[79] lineage B.1.1.7,[80] labelled Alpha variant by the WHO, was previously known as the first Variant Under Investigation in December 2020 (VUI – 202012/01)[81] and later notated as VOC-202012/01.[13] It is also known as 20I (V1),[22] 20I/501Y.V1[82] (formerly 20B/501Y.V1),[25][83][84] or 501Y.V1.[20] Since then, its prevalence odds have doubled every 6.5 days, the presumed generational interval.[85][86] It is correlated with a significant increase in the rate of COVID-19 infection in United Kingdom, associated partly with the N501Y mutation.[85] There had been some evidence that this variant had 40–80% increased transmissibility (with most estimates lying around the middle to higher end of this range),[87][88] and early analyses suggested an increase in lethality,[89][90] though more recent work has found no evidence of increased virulence.[91] As of May 2021, the Alpha variant has been detected in some 120 countries.[92]

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"[13] is of the same lineage in the Pango nomenclature system, but has an additional E484K mutation. As of 17 March 2021, there are 39 confirmed cases of VOC-21FEB-02 in the UK.[13] 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.[93][94][95] Other names for this variant include B.1.1.7+E484K[96] and B.1.1.7 Lineage with S:E484K.[97]

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),[22] 20H/501Y.V2[82] (formerly 20C/501Y.V2), 501Y.V2,[98] VOC-20DEC-02 (formerly VOC-202012/02), or lineage B.1.351,[25] was first detected in South Africa and reported by the country's health department.[99] 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.[100][101] 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.[99][100]

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,[99][102] K417N, and E484K.[103][104] The N501Y mutation has also been detected in the United Kingdom.[99][105]

Gamma (lineage P.1)

Main article: SARS-CoV-2 Gamma variant

The Gamma variant or lineage P.1, termed Variant of Concern 21JAN-02[13] (formerly VOC-202101/02) by Public Health England,[13] 20J (V3)[22] or 20J/501Y.V3[82] by Nextstrain, or just 501Y.V3,[20] 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.[106] On 12 January 2021, the Brazil-UK CADDE Centre confirmed 13 local cases of the new Gamma variant in the Amazon rainforest.[107] 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[14][108] 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.[107][108][109][110]: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 15–23 December 2020, followed by 52.2% during 15–31 December and 85.4% during 1–9 January 2021.[107] 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.[111]

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.[35][112][113]

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.[114] 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.[115]

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.[116][117] 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.[118]

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[22] or 21A/S:478K,[82] 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.[119][120][121][122][123] 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 as quickly as Alpha.[15][124][125] It carries L452R and P681R mutations in Spike;[38] 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.[126] 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.[127]

In June 2021, reports began to appear of a variant of Delta with the K417N mutation.[128] 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.[129] The variant, called "Delta with K417N" by Public Health England, includes two clades corresponding to the Pango lineages AY.1 and AY.2.[130] It has been nicknamed "Delta plus"[131] from "Delta plus K417N".[132] 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.[133] 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.[134]

Variants of interest (WHO)

Listed below are the Variants of Interest (VOI) which are, as of July 2021, recognised by the World Health Organization.[11] Other organisations such as the CDC in the United States may at times use a slightly different list.[12]

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[13] (previously VUI-202102/03) by Public Health England (PHE) and formerly known as UK1188,[13] 21D[22] or 20A/S:484K,[82] 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).[135] 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, it had been detected in 23 countries.[136][137][138] It has also been reported in Mayotte, the overseas department/region of France.[136] The first cases were detected in December 2020 in the UK and Nigeria, and as of 15 February, it had occurred in the highest frequency among samples in the latter country.[138] As of 24 February 56 cases were found in the UK.[13] Denmark, which sequences all its COVID-19 cases, found 113 cases of this variant from 14 January to 21 February, of which seven were directly related to foreign travel to Nigeria.[137]

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.[139]

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.[140] 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.[141]

Kappa (lineage B.1.617.1)

Main article: SARS-CoV-2 Kappa variant

The Kappa variant[11] is one of the three sublineages of lineage B.1.617. It is also known as lineage B.1.617.1, 21B[22] or 21A/S:154K,[82] and was first detected in India in December 2020.[142] By the end of March 2021, Kappa accounted for more than half of the sequences being submitted from India.[143] On 1 April 2021, it was designated a variant under investigation (VUI-21APR-01) by Public Health England.[37] It has the notable mutations L452R, E484Q, P681R.[144]

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.[11] It spread to at least 30 countries[145] around the world and, as of July 2021, it is unknown whether it is more infectious and resistant to vaccines than other strains.[146][147]

Former variants of interest

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[148] or CA VUI1,[149] 21C[22] or 20C/S:452R,[82] 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.[51][150] From March 17 to June 29, 2021, the CDC listed B.1.429 and the related B.1.427 as "variants of concern".[38][151][152][153] As of July 2021, Epsilon is no longer considered a variant of interest by the WHO,[11] as it was overtaken by Alpha.[141]

From September 2020 to January 2021, it was 19% to 24% more transmissible than earlier variants in California.[154] Neutralisation against it by antibodies from natural infections and vaccinations was moderately reduced,[155] but it remained detectable in most diagnostic tests.[156]

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.[157] It was not detected again until September when it reappeared among samples in California, but numbers remained very low until November.[158][159] 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.[150] In a joint press release by University of California, San Francisco, California Department of Public Health, and Santa Clara County Public Health Department,[160] 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%.[161] 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.[51] 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.[158][159] 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.[141]

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.[110] It evolved independently in Rio de Janeiro without being directly related to the Gamma variant from Manaus.[107] Though previously Zeta was labeled a variant of interest, as of July 2021, it is no longer considered as such by the WHO.[11]

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.[162]

On 13 March, the Department of Health confirmed the mutations constitutes a variant which was designated as lineage P.3.[163] 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.[164] On 12 March it was announced that Theta had also been detected in Japan.[165][166] On 17 March, the United Kingdom confirmed its first two cases,[167] where PHE termed it VUI-21MAR-02.[13] On 30 April 2021, Malaysia detected 8 cases of the Theta variant in Sarawak.[168]

As of July 2021, Theta is no longer considered a variant of interest by the WHO.[11]

Other notable variants

R.1

R.1 is designated as a variant of interest by the National Institute of Infectious Diseases in Japan.[169] It has the E484K mutation on the receptor binding domain and the W152L mutation on the N Terminal Domain, both of which may have implications for immune escape.[170] It has been found in 30 countries with 7,057 cases in Japan,[169] and 1,249 cases in the United States.[171] A small study in the U.S. found that the Pfizer-Biontech vaccine was 94% effective against hospitalisation and death from R.1 during an outbreak.[172] In Japan, cases of R.1 continue to appear.[169]

Lineage B.1.1.207

Lineage B.1.1.207 was first sequenced in August 2020 in Nigeria;[173] the implications for transmission and virulence are unclear but it has been listed as an emerging variant by the US Centers for Disease Control.[25] 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.[173] As of May 2021, lineage B.1.1.207 has been detected in 10 countries.[174]

Lineage B.1.620

In March 2021, Linage B.1.620 was discovered in Lithuania. It was named lineage B.1.620,[175] also known as the 'Lithuanian strain'. It is found in Central Africa as well as North America.[176] Apart from Lithuania, other European countries including France and Belgium have also found presence of this variant.[175] This lineage has 23 mutations and deletions compared to the reference strain, some of which are unique mutations. The lineage contains an E484K mutation.[176][177] D614G, a mutation present in most circulating strain, is also found in this variant.[178] Other notable mutations include P681H and S477N.[176]

Additional variants

  • 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.[179][180] 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.[181]
  • Lineage B.1.1.318 was designated by PHE as a VUI (VUI-21FEB-04,[13] previously VUI-202102/04) on 24 February 2021. 16 cases of it have been detected in the UK.[13][182] 155 cases were detected in the province of Ontario, Canada between May 30 and June 26, 2021.[183]
  • 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.[184]
  • Lineage B.1.621, a new coronavirus variant which was first discovered in Colombia, is also under investigation as of late July 2021.[185] This lineage contains the E484K mutation. It is listed by ECDC as a variant of interest.[186]
  • Lineage C.1.2 was identified in May 2021 when it accounted for 0.2% (2/1054) of genomes sequenced in South Africa, rising in June to 1.6% (25/2177), and in July to 2.0% (26/1326), similar to the increases of the early detection of the Beta and Delta variants. In June 2021 it was detected in England and China, and as of 13 August 2021 it had also been detected in Portugal, Switzerland, Democratic Republic of the Congo (DRC), Mauritius, and New Zealand.[187][188][189] C.1.2 contains multiple substitutions (C136F, R190S, D215G, Y449H, N484K, N501Y, H655Y, N679K and T859N) and deletions (Y144del, L242-A243del) within the spike protein.[187]

Notable missense mutations

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

N440K

The name of the mutation, N440K, refers to an exchange whereby the asparagine (N) is replaced by lysine (K) at position 440.[190]

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).[191] It is involved in current rapid surges of Covid cases in India.[192] India has the largest proportion of N440K mutated variants followed by the US and Germany.[193]

L452R

The name of the mutation, L452R, refers to an exchange whereby the leucine (L) is replaced by arginine (R) at position 452.[190]

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 class of cells 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.[120]

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[194] and the Biotech Company Innophore[195] have shown in a recent publication that structurally, the position S477 shows the highest flexibility among them.[196]

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[197] referenced this amino acid exchange as relevant regarding future vaccine design in a preprint published in February 2021.[198]

E484Q

The name of the mutation, E484Q, refers to an exchange whereby the glutamic acid (E) is replaced by glutamine (Q) at position 484.[190]

The Kappa variant circulating in India has E484Q. These variants were initially (but misleadingly) referred to as a "double mutant".[199] E484Q may enhance ACE2 receptor binding ability, and may reduce vaccine-stimulated antibodies' ability to attach to this altered spike protein.[120]

E484K

The name of the mutation, E484K, refers to an exchange whereby the glutamic acid (E) is replaced by lysine (K) at position 484.[190] It is nicknamed "Eeek".[200]

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[201][202]) from at least one form of monoclonal antibody against SARS-CoV-2, indicating there may be a "possible change in antigenicity".[203] The Gamma variant (lineage P.1),[107] the Zeta variant (lineage P.2, also known as lineage B.1.1.28.2)[110] and the Beta variant (501.V2) exhibit this mutation.[203] A limited number of lineage B.1.1.7 genomes with E484K mutation have also been detected.[30] Monoclonal and serum-derived antibodies are reported to be from 10 to 60 times less effective in neutralising virus bearing the E484K mutation.[204][205] 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.[206][207]

N501Y

N501Y denotes a change from asparagine (N) to tyrosine (Y) in amino-acid position 501.[208] N501Y has been nicknamed "Nelly".[200]

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.[26] 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,[203][107] 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.[209][210]

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.[211]

D614G is a missense mutation that affects the spike protein of SARS-CoV-2. From early appearances in Eastern China, the frequency of this mutation in the global viral population has increased during the pandemic.[212] G (glycine) has replaced D (aspartic acid) at position 614 in many countries, especially in Europe though more slowly in China and the rest of East Asia, supporting the hypothesis that G increases the transmission rate, which is consistent with higher viral titres and infectivity in vitro.[49] Researchers with the PANGOLIN tool nicknamed this mutation "Doug".[200]

In July 2020, it was reported that the more infectious D614G SARS-CoV-2 variant had become the dominant form in the pandemic.[213][214][215][216] PHE confirmed that the D614G mutation had a "moderate effect on transmissibility" and was being tracked internationally.[208][217]

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.[218]

Variants containing the D614G mutation are found in the G clade by GISAID[49] and the B.1 clade by the PANGOLIN tool.[49]

P681H

Logarithmic Prevalence of P681H in 2020 according to sequences in the GISAID database[211]

The name of the mutation, P681H, refers to an exchange whereby the proline (P) is replaced by histidine (H) at position 681.[211]

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.[211][219]

P681R

The name of the mutation, P681R, refers to an exchange whereby the proline (P) is replaced by arginine (R) at position 681.[190]

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.[120]

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.[220] 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.[221]

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.[222][223] These reports also referred to samples collected from the Benteng Lahad Datu cluster.[222][223] 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.[223]

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.[222] In GISAID, the prevalence of this mutation is found to be about 0.18%. of cases.[222]

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.[224]

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, BBIBP-CorV § Effectiveness, Sputnik V COVID-19 vaccine § Effectiveness, CoronaVac § Effectiveness, Covaxin § Efficacy, ZF2001 § Efficacy, and Abdala (vaccine) § Efficacy
World Health Organization video describing how variants proliferate in unvaccinated areas.

The interplay between the SARS-CoV-2 virus and its human hosts was initially natural but is now being altered by the prompt availability of vaccines.[225] 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.[226] The emergence of vaccine-resistant variants is more likely in a highly vaccinated population with uncontrolled transmission.[227] Trials indicate many vaccines developed for the initial strain have lower efficacy for some variants against symptomatic COVID-19.[228] 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.[226]

Alpha (lineage B.1.1.7)

Further information: SARS-CoV-2 Alpha variant

Limited evidence from various preliminary studies reviewed by the WHO has indicated retained efficacy/effectiveness against disease from Alpha with the Oxford–AstraZeneca vaccine, Pfizer–BioNTech and Novavax, with no data for other vaccines yet. Relevant to how vaccines can end the pandemic by preventing asymptomatic infection, they have also indicated retained antibody neutralization against Alpha with most of the widely distributed vaccines (Sputnik V, Pfizer–BioNTech, Moderna, CoronaVac, BBIBP-CorV, Covaxin), minimal to moderate reduction with the Oxford–AstraZeneca and no data for other vaccines yet.[229]

Early results suggest protection to the variant from the Pfizer-BioNTech and Moderna vaccines.[230][231]

One study indicated that the Oxford–AstraZeneca COVID-19 vaccine had an efficacy of 42–89% against Alpha, versus 71–91% against other variants.[232]

Preliminary data from a clinical trial indicates that the Novavax vaccine is ~96% effective for symptoms against the original variant and ~86% against Alpha.[233]

Beta (lineage B.1.351)

Further information: SARS-CoV-2 Beta variant

Limited evidence from various preliminary studies reviewed by the WHO have indicated reduced efficacy/effectiveness against disease from Beta with the Oxford–AstraZeneca vaccine (possibly substantial), Novavax (moderate), Pfizer–BioNTech and Janssen (minimal), with no data for other vaccines yet. Relevant to how vaccines can end the pandemic by preventing asymptomatic infection, they have also indicated possibly reduced antibody neutralization against Beta with most of the widely distributed vaccines (Oxford–AstraZeneca, Sputnik V, Janssen, Pfizer–BioNTech, Moderna, Novavax; minimal to substantial reduction) except CoronaVac and BBIBP-CorV (minimal to modest reduction), with no data for other vaccines yet.[229]

Moderna has launched a trial of a vaccine to tackle the Beta variant or lineage B.1.351.[234] On 17 February 2021, Pfizer announced neutralization activity was reduced by two-thirds for this variant, while stating that no claims about the efficacy of the vaccine in preventing illness for this variant could yet be made.[235] Decreased neutralizing activity of sera from patients vaccinated with the Moderna and Pfizer-BioNTech vaccines against Beta was later confirmed by several studies.[231][236] On 1 April 2021, an update on a Pfizer/BioNTech South African vaccine trial stated that the vaccine was 100% effective so far (i.e., vaccinated participants saw no cases), with six of nine infections in the placebo control group being the Beta variant.[237]

In January 2021, Johnson & Johnson, which held trials for its Janssen vaccine in South Africa, reported the level of protection against moderate to severe COVID-19 infection was 72% in the United States and 57% in South Africa.[238]

On 6 February 2021, the Financial Times reported that provisional trial data from a study undertaken by South Africa's University of the Witwatersrand in conjunction with Oxford University demonstrated reduced efficacy of the Oxford–AstraZeneca COVID-19 vaccine against the variant.[239] The study found that in a sample size of 2,000 the AZD1222 vaccine afforded only "minimal protection" in all but the most severe cases of COVID-19.[240] On 7 February 2021, the Minister for Health for South Africa suspended the planned deployment of about a million doses of the vaccine whilst they examine the data and await advice on how to proceed.[240][241]

In March 2021, it was reported that the "preliminary efficacy" of the Novavax vaccine (NVX-CoV2373) against Beta for mild, moderate, or severe COVID-19[242] for HIV-negative participants is 51%.[medical citation needed]

Gamma (lineage P.1)

Further information: SARS-CoV-2 Gamma variant

Limited evidence from various preliminary studies reviewed by the WHO have indicated likely retained efficacy/effectiveness against disease from Gamma with CoronaVac and BBIBP-CorV, with no data for other vaccines yet. Relevant to how vaccines can end the pandemic by preventing asymptomatic infection, they have also indicated retained antibody neutralization against Gamma with Oxford–AstraZeneca and CoronaVac (no to minimal reduction) and slightly reduced neutralization with Pfizer–BioNTech and Moderna (minimal to moderate reduction), with no data for other vaccines yet.[229]

The Gamma variant or lineage P.1 variant (also known as 20J/501Y.V3), initially identified in Brazil, seems to partially escape vaccination with the Pfizer-BioNTech vaccine.[236]

Delta (lineage B.1.617.2)

Further information: SARS-CoV-2 Delta variant

Limited evidence from various preliminary studies reviewed by the WHO have indicated likely retained efficacy/effectiveness against disease from Delta with the Oxford–AstraZeneca vaccine and Pfizer–BioNTech, with no data for other vaccines yet. Relevant to how vaccines can end the pandemic by preventing asymptomatic infection, they have also indicated reduced antibody neutralization against Delta with single-dose Oxford–AstraZeneca (substantial reduction), Pfizer–BioNTech and Covaxin (modest to moderate reduction), with no data for other vaccines yet.[229]

Mutations present in the spike protein in the B.1.617 lineage are associated with reduced antibody neutralization in laboratory experiments.[243][244]

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.[245] 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, over 330,000 viral genomic sequences have been generated by molecular epidemiology studies across the world.[246]

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".[247] As of January 2021, more than half of all genomic sequencing of COVID-19 was carried out in the UK.[248]

Testing

On 11 June 2021, Public Health England introduced a rules-based decision algorithm to distinguish between variants in RT-PCR results. The system is reviewed weekly. In particular, the rules require that specific mutations in the S gene[249] be present for each variant (P681R for Delta, K417N for Beta and K417T for Gamma); the confirmation status of the test is dependent also on other requirements for the detection or non-detection of presence or absence of these mutations and the mutations N501Y and E484K. Where the result is 'undetermined', two categories are possible: with or without E484K.[clarification needed].[250]

Incubation theory for multiply 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,[251][252] with the same deletions in surface antigens repeatedly recurring in different patients.[253]

Cross-species transmission

Further information: Impact of the COVID-19 pandemic on animals

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),[254] was discovered in Northern Jutland, Denmark, and 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.[255]

The WHO has stated that cluster 5 has a "moderately decreased sensitivity to neutralising antibodies".[256] 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.[257] 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.[258]

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.[259]

See also

  • RaTG13, the closest known relative to SARS-CoV-2
  • Pandemic prevention § Surveillance and mapping

Notes

  1. ^ Based on various trackers[11][12][13][14][15] and periodic reports.[16][17][18]
  2. ^ Jump up to: a b In another source, GISAID name a set of 7 clades without the O clade but including a GV clade.[54]
  3. ^ According to the WHO, "Lineages or clades can be defined based on viruses that share a phylogenetically determined common ancestor".[55]
  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):[48]
    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)

References

  1. ^ Jump up to: a b c d 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.
  2. ^ "Coronavirus variants and mutations: The science explained". BBC News. 6 January 2021. Retrieved 2 February 2021.
  3. ^ Kupferschmidt K (15 January 2021). "New coronavirus variants could cause more reinfections, require updated vaccines". Science. doi:10.1126/science.abg6028. Retrieved 2 February 2021.
  4. ^ 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.
  5. ^ 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.
  6. ^ 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. doi:10.1073/pnas.2004999117. ISSN 0027-8424. PMC 7196762. PMID 32269081.
  7. ^ 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.
  8. ^ 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. doi:10.1038/s41577-021-00592-1. PMC 8351583. PMID 34373623.
  9. ^ Gallagher J (12 June 2021). "Covid: Is there a limit to how much worse variants can get?". BBC.
  10. ^ "SARS-CoV-2 variants: risk assessment framework" (PDF). GOV.UK. Government Digital Service. Public Health England. 22 May 2021. GOV-8426.
  11. ^ Jump up to: a b c d e f g h "Tracking SARS-CoV-2 variants". who.int. World Health Organization. Updated frequently.
  12. ^ Jump up to: a b c d e f g h i j "SARS-CoV-2 Variant Classifications and Definitions". CDC.gov. Centers for Disease Control and Prevention. 11 February 2020. Updated frequently.
  13. ^ Jump up to: a b c d e f g h i j k l m n o p q "Variants: distribution of cases data". Public Health England. Government Digital Service. Updated frequently. Data up to 19 May 2021 included in the 2 July 2021 update.
  14. ^ Jump up to: a b c d e "Living Evidence – SARS-CoV-2 variants". Agency for Clinical Innovation. nsw.gov.au. Ministry of Health (New South Wales). 23 July 2021. Updated frequently.
  15. ^ Jump up to: a b c "SARS-CoV-2 variants of concern". ECDC.eu. European Centre for Disease Prevention and Control. Updated frequently.
  16. ^ "Coronavirus Disease (COVID-19) Situation Reports". who.int. World Health Organization. Updated frequently.
  17. ^ "Investigation of SARS-CoV-2 variants of concern: technical briefings". GOV.UK. Government Digital Service. Public Health England. Updated frequently.
  18. ^ "Investigation of SARS-CoV-2 variants of concern: variant risk assessments". GOV.UK. Government Digital Service. Public Health England. Updated frequently.
  19. ^ Jump up to: a b c d e f g Weekly epidemiological update on COVID-19 - 20 July 2021 (Situation report). World Health Organization. 20 July 2021. Retrieved 24 July 2021.
  20. ^ Jump up to: a b c d e 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).
  21. ^ 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.
  22. ^ Jump up to: a b c d e f g h Weekly epidemiological update on COVID-19 - 22 June 2021 (Situation report). World Health Organization. 22 June 2021. Retrieved 26 June 2021.
  23. ^ 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. Retrieved 14 June 2021.
  24. ^ Investigation of novel SARS-COV-2 variant, technical briefing 1 (PDF) (Briefing). Public Health England. 21 December 2020. Retrieved 6 June 2021.
  25. ^ Jump up to: a b c d e f g h "Emerging SARS-CoV-2 Variants". CDC.gov (Science brief). Centers for Disease Control and Prevention. 28 January 2021. Retrieved 4 January 2021. Public Domain This article incorporates text from this source, which is in the public domain.
  26. ^ Jump up to: a b c Chand et al. (2020), p. 6, Potential impact of spike variant N501Y.
  27. ^ Jump up to: a b c d 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.
  28. ^ 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. doi:10.1136/bmj.n1412. PMC 8204098. PMID 34130987. S2CID 235187479.
  29. ^ Jump up to: a b "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. Retrieved 29 August 2021.
  30. ^ Jump up to: a b Investigation of novel SARS-CoV-2 variant 202012/01, technical briefing 5 (PDF) (Briefing). Public Health England. 2 February 2021. GW-1905. Retrieved 14 June 2021.
  31. ^ Investigation of SARS-CoV-2 variants of concern in England, technical briefing 6 (PDF) (Briefing). Public Health England. 13 February 2021. GW-1934. Retrieved 6 June 2021.
  32. ^ Horby P, Barclay W, Huntley C (13 January 2021). NERVTAG paper: brief note on SARS-CoV-2 variants (Note). Public Health England. Retrieved 6 June 2021.
  33. ^ "Confirmed cases of COVID-19 variants identified in UK". GOV.UK. Public Health England. 15 January 2021.
  34. ^ Horby P, Barclay W, Gupta R, Huntley C (27 January 2021). NERVTAG paper: note on variant P.1 (Note). Public Health England. Retrieved 6 June 2021.
  35. ^ Jump up to: a b 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. 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.
  36. ^ Freitas AR, Lemos DR, Beckedorff OA, Cavalcanti LP, Siqueira AM, Mello RC, et al. (19 April 2021). "The increase in the risk of severity and fatality rate of covid-19 in southern Brazil after the emergence of the Variant of Concern (VOC) SARS-CoV-2 P.1 was greater among young adults without pre-existing risk conditions". medRxiv (Preprint). doi:10.1101/2021.04.13.21255281. S2CID 233295278. Female 20 to 39 years old, with no pre-existing risk conditions, were at risk of death 5.65 times higher in February (95% CI, 2.9-11.03; p <0.0001) and in the age group of 40 and 59 years old, this risk was 7.7 times higher (95% CI, 5.01-11.83; p <0.0001) comparing with November–December. ... The heterogeneity observed between the age groups was greater when we analysed the subgroup of the population without preexisting risk conditions where we found that the CFR in the female sex in the second wave was 1.95 times (95% CI, 1.38-2.76) the CFR of the first wave in the population over 85 years old and was 7.7 times (95% CI, 5.01-11.83; p < 0.0001) in the population between 40 and 59 years old. In the male population without previous diseases, the CFR in the second wave was 2.18 (95% CI, 1.62-2.93) times the CFR of the first wave in the population over 85 years old and 5.9 (95% CI, 3.2-10.85; p < 0, 0001) higher in the range between 20 and 39 years old.
  37. ^ Jump up to: a b 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. Retrieved 6 June 2021.
  38. ^ Jump up to: a b c d "SARS-CoV-2 Variant Classifications and Definitions". CDC.gov. Centers for Disease Control and Prevention. 29 June 2021. Frequently updated.
  39. ^ 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.
  40. ^ Fisman D, Tuite A (12 July 2021). "Progressive Increase in Virulence of Novel SARS-CoV-2 Variants in Ontario, Canada". medRxiv (Preprint). doi:10.1101/2021.07.05.21260050. S2CID 235756602.
  41. ^ Gazit S (25 August 2021). "Comparing SARS-CoV-2 natural immunity to vaccine-induced immunity: reinfections versus breakthrough infections" (PDF). medRxiv.
  42. ^ Jump up to: a b Risk assessment for SARS-CoV-2 variant Delta (PDF) (Assessment). Public Health England. 23 July 2021. Retrieved 24 July 2021.
  43. ^ 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 (ciab411). bioRxiv 10.1101/2021.04.23.441101. doi:10.1093/cid/ciab411. PMID 33961693.
  44. ^ This table is an adaptation and expansion of Alm et al., figure 1.
  45. ^ Jump up to: a b 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.
  46. ^ Jump up to: a b 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.
  47. ^ "Nextclade" (What are the clades?). nextstrain.org. Archived from the original on 19 January 2021. Retrieved 19 January 2021.
  48. ^ Jump up to: a b c d Bedford T, Hodcroft B, Neher RA (6 January 2021). "Updated Nextstrain SARS-CoV-2 clade naming strategy". nextstrain.org. Retrieved 19 January 2021.
  49. ^ Jump up to: a b c d e f 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.
  50. ^ "Genomic epidemiology of novel coronavirus – Global subsampling (Filtered to B.1.617)". nextstrain.org. Retrieved 5 May 2021.
  51. ^ Jump up to: a b c d Zhang W, Davis B, Chen SS, Martinez JS, Plummer JT, Vail E (2021). "Emergence of a novel SARS-CoV-2 strain in Southern California, USA". medRxiv. doi:10.1101/2021.01.18.21249786. S2CID 231646931.
  52. ^ "PANGO lineages-Lineage B.1.1.28". cov-lineages.org. Retrieved 4 February 2021.[failed verification]
  53. ^ "Variant: 20J/501Y.V3". covariants.org. 1 April 2021. Retrieved 6 April 2021.
  54. ^ "clade tree (from 'Clade and lineage nomenclature')". GISAID. 4 July 2020. Retrieved 7 January 2021.
  55. ^ Jump up to: a b c d 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. Retrieved 2 February 2021.
  56. ^ "Don't call it the 'British variant.' Use the correct name: B.1.1.7". STAT. 9 February 2021. Retrieved 12 February 2021.
  57. ^ Flanagan R (2 February 2021). "Why the WHO won't call it the 'U.K. variant', and you shouldn't either". CTV News. Retrieved 12 February 2021.
  58. ^ 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.
  59. ^ "Today, @WHO announces new, easy-to-say labels for #SARSCoV2 Variants of Concern (VOCs) & Interest (VOIs)". Retrieved 7 July 2021.
  60. ^ Branswell H (31 May 2021). "The name game for coronavirus variants just got a little easier". Stat News. Retrieved 28 June 2021.
  61. ^ 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". Retrieved 18 January 2021.
  62. ^ "Covid: WHO renames UK and other variants with Greek letters". BBC News. 31 May 2021. Retrieved 7 July 2021.
  63. ^ 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.
  64. ^ "Global phylogeny, updated by Nextstrain". GISAID. 18 January 2021. Retrieved 19 January 2021.
  65. ^ 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.
  66. ^ "Nextstrain COVID-19". Nextstrain. Retrieved 1 June 2021.
  67. ^ "cov-lineages/pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages". Github. Retrieved 2 January 2021.
  68. ^ Jump up to: a b "Lineage descriptions". cov-lineages.org. Pango team.
  69. ^ 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.
  70. ^ Jump up to: a b c 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.
  71. ^ 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.
  72. ^ 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.
  73. ^ 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.
  74. ^ 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.
  75. ^ "Official hCoV-19 Reference Sequence". www.gisaid.org. Retrieved 14 May 2021.
  76. ^ "The ancestor of SARS-CoV-2's Wuhan strain was circulating in late October 2019". News Medical. Retrieved 10 May 2020. Journal reference: Kumar, S. et al. (2021). An evolutionary portrait...
  77. ^ IDSA Contributor (2 February 2021). "COVID "Mega-variant" and eight criteria for a template to assess all variants". Science Speaks: Global ID News. Retrieved 20 February 2021.
  78. ^ 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). Retrieved 25 February 2021.
  79. ^ "Covid: Ireland, Italy, Belgium and Netherlands ban flights from UK". BBC News. 20 December 2020.
  80. ^ 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. Retrieved 23 December 2020.
  81. ^ "PHE investigating a novel strain of COVID-19". Public Health England (PHE). 14 December 2020.
  82. ^ Jump up to: a b c d e f g Weekly epidemiological update on COVID-19 for 8 June 2021 (Situation report). World Health Organization. 8 June 2021.
  83. ^ 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. Retrieved 20 December 2020.
  84. ^ Kupferschmidt K (20 December 2020). "Mutant coronavirus in the United Kingdom sets off alarms but its importance remains unclear". Science Mag. Retrieved 21 December 2020.
  85. ^ Jump up to: a b "New evidence on VUI-202012/01 and review of the public health risk assessment". Knowledge Hub. 15 December 2020.
  86. ^ "COG-UK Showcase Event". Retrieved 25 December 2020 – via YouTube.
  87. ^ 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.
  88. ^ 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.
  89. ^ 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.
  90. ^ Gallagher J (22 January 2021). "Coronavirus: UK variant 'may be more deadly'". BBC News. Retrieved 22 January 2021.
  91. ^ 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. doi:10.1016/S1473-3099(21)00170-5. PMC 8041359. PMID 33857406.
  92. ^ "PANGO lineages Lineage B.1.1.7". cov-lineages.org. 15 May 2021.
  93. ^ 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. Retrieved 6 March 2021.
  94. ^ 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.
  95. ^ "B.1.1.7 Lineage with S:E484K Report". outbreak.info. 5 March 2021. Retrieved 7 March 2021.
  96. ^ 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.
  97. ^ "B.1.1.7 Lineage with S:E484K Report". outbreak.info.
  98. ^ 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.
  99. ^ Jump up to: a b c d "South Africa announces a new coronavirus variant". The New York Times. 18 December 2020. Retrieved 20 December 2020.
  100. ^ Jump up to: a b Wroughton L, Bearak M (18 December 2020). "South Africa coronavirus: Second wave fueled by new strain, teen 'rage festivals'". The Washington Post. Retrieved 20 December 2020.
  101. ^ Mkhize Z (18 December 2020). "Update on Covid-19 (18th December 2020)" (Press release). South Africa. COVID-19 South African Online Portal. 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.
  102. ^ 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.
  103. ^ Lowe D (22 December 2020). "The New Mutations". In the Pipeline. American Association for the Advancement of Science. 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.
  104. ^ "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. Retrieved 23 December 2020.
  105. ^ "Novel mutation combination in spike receptor binding site" (Press release). GISAID. 21 December 2020. Retrieved 23 December 2020.
  106. ^ "Japan finds new coronavirus variant in travelers from Brazil". Japan Today. Japan. 11 January 2021. Retrieved 14 January 2021.
  107. ^ Jump up to: a b c d e f 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. Retrieved 23 January 2021.
  108. ^ Jump up to: a b "P.1". cov-lineages.org. Pango team. 1 July 2021.
  109. ^ 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. Retrieved 25 January 2021.
  110. ^ Jump up to: a b c 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.
  111. ^ 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. Retrieved 2 March 2021.
  112. ^ 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. Retrieved 3 March 2021.
  113. ^ 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. Retrieved 3 March 2021.
  114. ^ Garcia-Beltran WF, Lam EC, St Denis K, Nitido AD, Garcia ZH, Hauser BM, et al. (February 2021). "Circulating SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity". medRxiv. doi:10.1101/2021.02.14.21251704. PMC 7899476. PMID 33619506.
  115. ^ Sofia Moutinho (4 May 2021). "Chinese COVID-19 vaccine maintains protection in variant-plagued Brazil". Science. doi:10.1126/science.abi9414.
  116. ^ Gaier R (5 March 2021). "Exclusive: Oxford study indicates AstraZeneca effective against Brazil variant, source says". Reuters. Rio de Janeiro. Retrieved 9 March 2021.
  117. ^ "Exclusive: Oxford study indicates AstraZeneca effective against Brazil variant, source says". Reuters. Rio de Janeiro. 8 March 2021. Retrieved 9 March 2021.
  118. ^ 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. Retrieved 9 March 2021.
  119. ^ "PANGO lineages". cov-lineages.org. Retrieved 18 April 2021.
  120. ^ Jump up to: a b c d Koshy J (8 April 2021). "Coronavirus | Indian 'double mutant' strain named B.1.617". The Hindu.
  121. ^ "India's variant-fuelled second wave coincided with spike in infected flights landing in Canada". Toronto Sun. 10 April 2021. Retrieved 10 April 2021.
  122. ^ "Weekly epidemiological update on COVID-19". World Health Organization. 11 May 2021. Retrieved 12 May 2021.
  123. ^ "COVID strain first detected in India found in 53 territories: WHO".
  124. ^ "British scientists warn over Indian coronavirus variant". Reuters. 7 May 2021. Retrieved 7 May 2021.
  125. ^ "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. Retrieved 15 May 2021.
  126. ^ 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. Retrieved 26 June 2021.
  127. ^ 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. Retrieved 12 June 2021.
  128. ^ Schraer R (4 June 2021). "'Nepal variant': What's the mutation stopping green list trips to Portugal?". BBC News. Retrieved 18 June 2021.
  129. ^ Acharya B, Jamkhandikar S (23 June 2021). "Explainer: What is the Delta variant of coronavirus with K417N mutation?". Reuters. Retrieved 23 June 2021.
  130. ^ 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. Retrieved 26 June 2021.
  131. ^ Sharma M. "New 'Delta Plus' variant of SARS-CoV-2 identified; here's what we know so far". India Today. Retrieved 16 June 2021.
  132. ^ Cutler S (18 June 2021). "'Nepal variant': what we've learned so far". The Conversation. Retrieved 18 June 2021.
  133. ^ "India says new COVID variant is a concern". Reuters. Bengaluru. 22 June 2021. Retrieved 23 June 2021.
  134. ^ Biswas S (23 June 2021). "Delta plus: Scientists say too early to tell risk of Covid-19 variant". BBC News. Retrieved 23 June 2021.
  135. ^ "Delta-PCR-testen" [The Delta PCR Test] (in Danish). Statens Serum Institut. 25 February 2021. Retrieved 27 February 2021.
  136. ^ Jump up to: a b "GISAID hCOV19 Variants (see menu option 'G/484K.V3 (B.1.525)')". GISAID. Retrieved 4 March 2021.
  137. ^ Jump up to: a b "Status for udvikling af SARS-CoV-2 Variants of Concern (VOC) i Danmark" [Status of development of SARS-CoV-2 Variants of Concern (VOC) in Denmark] (in Danish). Statens Serum Institut. 27 February 2021. Retrieved 27 February 2021.
  138. ^ Jump up to: a b "B.1.525 international lineage report". cov-lineages.org. Pango team. 19 May 2021.
  139. ^ Roberts M (16 February 2021). "Another new coronavirus variant seen in the UK". BBC News. Retrieved 16 February 2021.
  140. ^ Mandavilli A (24 February 2021). "A New Coronavirus Variant Is Spreading in New York, Researchers Report". The New York Times.
  141. ^ Jump up to: a b c Zimmer C, Mandavilli A (14 May 2021). "How the United States Beat the Variants, for Now". The New York Times. Retrieved 17 May 2021.
  142. ^ Weekly epidemiological update on COVID-19 - 27 April 2021 (Situation report). World Health Organization. 27 April 2021. Retrieved 14 June 2021.
  143. ^ Le Page M (4 June 2021). "Indian covid-19 variant (B.1.617)". New Scientist. Retrieved 8 June 2021.
  144. ^ Nuki P, Newey S (16 April 2021). "Arrival of India's 'double mutation' adds to variant woes, but threat posed remains unclear". The Telegraph. ISSN 0307-1235. Retrieved 17 April 2021.
  145. ^ "Covid 19 coronavirus: Ultra-contagious Lambda variant detected in Australia".
  146. ^ "COVID-19: Lambda variant may be more resistant to vaccines than other strains".
  147. ^ "Lambda variant: What is the new strain of Covid detected in the UK?".
  148. ^ "Southern California COVID-19 Strain Rapidly Expands Global Reach". Cedars-Sinai Newsroom. Los Angeles. 11 February 2021. Retrieved 17 March 2021.
  149. ^ Latif AA, Mullen JL, Alkuzweny M, Tsueng G, Cano M, Haag E, et al. (The Center for Viral Systems Biology). "B.1.429 Lineage Report". outbreak.info. Retrieved 28 May 2021.
  150. ^ Jump up to: a b "New California Variant May Be Driving Virus Surge There, Study Suggests". The New York Times. 19 January 2021.
  151. ^ Azad A (17 March 2021). "Coronavirus strains first detected in California are officially 'variants of concern,' CDC says". CNN. Retrieved 6 June 2021.
  152. ^ Shen X, Tang H, Pajon R, Smith G, Glenn GM, Shi W, et al. (June 2021). "Neutralization of SARS-CoV-2 Variants B.1.429 and B.1.351". The New England Journal of Medicine. 384 (24): 2352–2354. doi:10.1056/NEJMc2103740. PMC 8063884. PMID 33826819.
  153. ^ "SARS-CoV-2 Variant Classifications and Definitions: Updated June 23, 2021". CDC.gov. Centers for Disease Control and Prevention. 23 June 2021. Archived from the original on 29 June 2021.
  154. ^ Deng X, Garcia-Knight MA, Khalid MM, Servellita V, Wang C, Morris MK, et al. (March 2021). "Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation". medRxiv (Preprint). doi:10.1101/2021.03.07.21252647. PMC 7987058. PMID 33758899.
  155. ^ Wadman M (23 February 2021). "California coronavirus strain may be more infectious – and lethal". Science News. doi:10.1126/science.abh2101. Retrieved 17 March 2021.
  156. ^ Ho C (28 February 2021). "Do coronavirus tests work on variants?". San Francisco Chronicle. Retrieved 24 June 2021.
  157. ^ "Local COVID-19 Strain Found in Over One-Third of Los Angeles Patients". news wise (Press release). California: Cedars Sinai Medical Center. 19 January 2021. Retrieved 3 March 2021.
  158. ^ Jump up to: a b "B.1.429". Rambaut Group, University of Edinburgh. PANGO Lineages. 15 February 2021. Retrieved 16 February 2021.
  159. ^ Jump up to: a b "B.1.429 Lineage Report". Scripps Research. outbreak.info. 15 February 2021. Retrieved 16 February 2021.
  160. ^ "COVID-19 Variant First Found in Other Countries and States Now Seen More Frequently in California". California Department of Public Health. Retrieved 30 January 2021.
  161. ^ Weise E, Weintraub K. "New strains of COVID swiftly moving through the US need careful watch, scientists say". USA Today. Retrieved 30 January 2021.
  162. ^ "DOH confirms detection of 2 SARS-CoV-2 mutations in Region 7". ABS-CBN News. 18 February 2021. Retrieved 13 March 2021.
  163. ^ Santos E (13 March 2021). "DOH reports COVID-19 variant 'unique' to PH, first case of Brazil variant". CNN Philippines. Retrieved 17 March 2021.
  164. ^ "DOH confirms new COVID-19 variant first detected in PH, first case of Brazil variant". ABS-CBN News. 13 March 2021. Retrieved 13 March 2021.
  165. ^ "PH discovered new COVID-19 variant earlier than Japan, expert clarifies". CNN Philippines. 13 March 2021. Retrieved 17 March 2021.
  166. ^ "Japan detects new coronavirus variant from traveler coming from PH". CNN Philippines. 13 March 2021. Retrieved 21 March 2021.
  167. ^ "UK reports 2 cases of COVID-19 variant first detected in Philippines". ABS-CBN. 17 March 2021. Retrieved 21 March 2021.
  168. ^ "Covid-19: Sarawak detects variant reported in the Philippines". 30 April 2021. Retrieved 30 April 2021.
  169. ^ Jump up to: a b c "Infectious Disease Weekly Report". National Institute of Infectious Diseases. Retrieved 19 July 2021.
  170. ^ Hirotsu Y, Omata M (June 2021). "Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan". PLOS Pathogens. 17 (6): e1009619. doi:10.1371/journal.ppat.1009619. PMC 8238201. PMID 34097716.
  171. ^ search R.1 on "Near real-time visualization of SARS-CoV-2 (hCoV-19) genomic variation". Covizu. Retrieved 19 July 2021.
  172. ^ Cavanaugh AM, Fortier S, Lewis P, Arora V, Johnson M, George K, et al. (April 2021). "COVID-19 Outbreak Associated with a SARS-CoV-2 R.1 Lineage Variant in a Skilled Nursing Facility After Vaccination Program - Kentucky, March 2021". MMWR. Morbidity and Mortality Weekly Report. 70 (17): 639–643. doi:10.15585/mmwr.mm7017e2. PMC 8084128. PMID 33914720.
  173. ^ Jump up to: a b "Detection of SARS-CoV-2 P681H Spike Protein Variant in Nigeria". Virological. 23 December 2020. Retrieved 1 January 2021.
  174. ^ "Lineage B.1.1.207". cov-lineages.org. Pango team. Retrieved 11 March 2021.
  175. ^ Jump up to: a b "pango-designation issue #54". github.com/cov-lineages. 4 July 2021.
  176. ^ Jump up to: a b c "COVID-19: African variant reveals sequencing lag".
  177. ^ "Unidentified coronavirus strain found in eastern Lithuania". www.lrt.lt. 20 April 2021. Retrieved 6 May 2021.
  178. ^ "The travel-related origin and spread of SARS-CoV-2 B.1.620 strain". 11 May 2021.
  179. ^ "New coronavirus variant found in West Bengal". www.thehindu.com. Retrieved 23 April 2021.
  180. ^ "What is the new 'triple mutant variant' of Covid-19 virus found in Bengal? How bad is it?". www.indiatoday.in. Retrieved 23 April 2021.
  181. ^ "PANGO lineages Lineage B.1.618". cov-lineages.org. Retrieved 23 April 2021.
  182. ^ "Latest update: New Variant Under Investigation designated in the UK". GOV.UK. 4 March 2021. Retrieved 5 March 2021.
  183. ^ "SARS-CoV-2 Whole Genome Sequencing in Ontario, July 14, 2021" (PDF). Public Health Ontario. Retrieved 19 July 2021.
  184. ^ "Queensland travellers have hotel quarantine extended after Russian variant of coronavirus detected". www.abc.net.au. 3 March 2021. Retrieved 3 March 2021.
  185. ^ "A New Covid Variant Is Being Investigated In The U.K. After Being Detected In Countries Including The U.S. And Japan". www.forbes.com. 23 July 2021. Retrieved 5 August 2021.
  186. ^ "SARS-CoV-2 variants of concern as of 11 May 2021". www.ecdc.europa.eu. 11 May 2021. Retrieved 13 May 2021.
  187. ^ Jump up to: a b Scheepers, Cathrine; et al. (24 August 2021). "The continuous evolution of SARS-CoV-2 in South Africa: a new lineage with rapid accumulation of mutations of concern and global detection". medRxiv (preprint). doi:10.1101/2021.08.20.21262342. Retrieved 30 August 2021.
  188. ^ "Detection and frequency of the C.1.2 mutated SARS-COV-2 lineage in South Africa". National Institute for Communicable Diseases. 30 August 2021. Retrieved 31 August 2021.
  189. ^ Joffre, Tzvi (29 August 2021). "New COVID variant detected in South Africa, most mutated variant so far". The Jerusalem Post. Retrieved 30 August 2021.
  190. ^ Jump up to: a b c d e Greenwood M (15 January 2021). "What Mutations of SARS-CoV-2 are Causing Concern?". News Medical Lifesciences. Retrieved 16 January 2021.
  191. ^ Tandel D, Gupta D, Sah V, Harshan KH (30 April 2021). "N440K variant of SARS-CoV-2 has Higher Infectious Fitness". bioRxiv 10.1101/2021.04.30.441434.
  192. ^ Bhattacharjee S (3 May 2021). "COVID-19 | A.P. strain at least 15 times more virulent". The Hindu.
  193. ^ "Hyderabad: Mutant N440K 10 times more infectious than parent strain".
  194. ^ "University of Graz". www.uni-graz.at. Retrieved 22 February 2021.
  195. ^ "Coronavirus SARS-CoV-2 (formerly known as Wuhan coronavirus and 2019-nCoV) – what we can find out on a structural bioinformatics level". Innophore. 23 January 2020. Retrieved 22 February 2021.
  196. ^ Singh A, Steinkellner G, Köchl K, Gruber K, Gruber CC (February 2021). "Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2". Scientific Reports. 11 (1): 4320. Bibcode:2021NatSR..11.4320S. doi:10.1038/s41598-021-83761-5. PMC 7900180. PMID 33619331.
  197. ^ "BioNTech: We aspire to individualize cancer medicine". BioNTech. Retrieved 22 February 2021.
  198. ^ Schroers B, Gudimella R, Bukur T, Roesler T, Loewer M, Sahin U (4 February 2021). "Large-scale analysis of SARS-CoV-2 spike-glycoprotein mutants demonstrates the need for continuous screening of virus isolates". bioRxiv 10.1101/2021.02.04.429765.
  199. ^ "People Are Talking About A 'Double Mutant' Variant In India. What Does That Mean?". NPR.org. Retrieved 27 April 2021. ...scientifically, the term "double mutant" makes no sense, Andersen says. "SARS-CoV-2 mutates all the time. So there are many double mutants all over the place. The variant in India really shouldn't be called that."
  200. ^ Jump up to: a b c Mandavilli A, Mueller B (2 March 2021). "Why Virus Variants Have Such Weird Names". The New York Times. ISSN 0362-4331. Retrieved 2 March 2021.
  201. ^ "escape mutation". HIV i-Base. 11 October 2012. Retrieved 19 February 2021.
  202. ^ Wise J (February 2021). "Covid-19: The E484K mutation and the risks it poses". BMJ. 372: n359. doi:10.1136/bmj.n359. PMID 33547053. S2CID 231821685.
  203. ^ Jump up to: a b c "Brief report: New Variant Strain of SARS-CoV-2 Identified in Travelers from Brazil" (PDF) (Press release). Japan: NIID (National Institute of Infectious Diseases). 12 January 2021. Retrieved 14 January 2021.
  204. ^ Greaney AJ, Loes AN, Crawford KH, Starr TN, Malone KD, Chu HY, Bloom JD (March 2021). "Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies". Cell Host & Microbe. 29 (3): 463–476.e6. doi:10.1016/j.chom.2021.02.003. PMC 7869748. PMID 33592168.
  205. ^ Kupferschmidt K (January 2021). "New mutations raise specter of 'immune escape'". Science. 371 (6527): 329–330. Bibcode:2021Sci...371..329K. doi:10.1126/science.371.6527.329. PMID 33479129.
  206. ^ Rettner R (2 February 2021). "UK coronavirus variant develops vaccine-evading mutation – In a handful of instances, the U.K. coronavirus variant has developed a mutation called E484K, which may impact vaccine effectiveness". Live Science. Retrieved 2 February 2021.
  207. ^ Achenbach J, Booth W (2 February 2021). "Worrisome coronavirus mutation seen in U.K. variant and in some U.S. samples". The Washington Post. Retrieved 2 February 2021.
  208. ^ Jump up to: a b COG-UK update on SARS-CoV-2 Spike mutations of special interest: Report 1 (PDF) (Report). COVID-19 Genomics UK Consortium (COG-UK). 20 December 2020. p. 7. Archived from the original (PDF) on 25 December 2020. Retrieved 31 December 2020.
  209. ^ "Researchers Discover New Variant of COVID-19 Virus in Columbus, Ohio". wexnermedical.osu.edu. 13 January 2021. Retrieved 16 January 2021.
  210. ^ Tu H, Avenarius MR, Kubatko L, Hunt M, Pan X, Ru P, et al. (26 January 2021). "Distinct Patterns of Emergence of SARS-CoV-2 Spike Variants including N501Y in Clinical Samples in Columbus Ohio". bioRxiv 10.1101/2021.01.12.426407.
  211. ^ Jump up to: a b c d Maison DP, Ching LL, Shikuma CM, Nerurkar VR (January 2021). "Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation". bioRxiv 10.1101/2021.01.06.425497. CC-BY icon.svg Available under CC BY 4.0.
  212. ^ Corum J, Zimmer C (4 June 2021). "Coronavirus Variants and Mutations". The New York Times.
  213. ^ Schraer R (18 July 2020). "Coronavirus: Are mutations making it more infectious?". BBC News. Retrieved 3 January 2021.
  214. ^ "New, more infectious strain of COVID-19 now dominates global cases of virus: study". medicalxpress.com. Archived from the original on 17 November 2020. Retrieved 16 August 2020.
  215. ^ Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, et al. (August 2020). "Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus". Cell. 182 (4): 812–827.e19. doi:10.1016/j.cell.2020.06.043. PMC 7332439. PMID 32697968.
  216. ^ Hou YJ, Chiba S, Halfmann P, Ehre C, Kuroda M, Dinnon KH, et al. (December 2020). "SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo". Science. 370 (6523): 1464–1468. Bibcode:2020Sci...370.1464H. doi:10.1126/science.abe8499. PMC 7775736. PMID 33184236. an emergent Asp614→Gly (D614G) substitution in the spike glycoprotein of SARS-CoV-2 strains that is now the most prevalent form globally
  217. ^ Volz EM, Hill V, McCrone JT, Price A, Jorgensen D, O'Toole A, et al. (4 August 2020). "Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity". Cell. 184 (1): 64–75.e11. doi:10.1101/2020.07.31.20166082. hdl:10044/1/84079. PMC 7674007. PMID 33275900.
  218. ^ Butowt R, Bilinska K, Von Bartheld CS (October 2020). "Chemosensory Dysfunction in COVID-19: Integration of Genetic and Epidemiological Data Points to D614G Spike Protein Variant as a Contributing Factor". ACS Chemical Neuroscience. 11 (20): 3180–3184. doi:10.1021/acschemneuro.0c00596. PMC 7581292. PMID 32997488.
  219. ^ "Study shows P681H mutation is becoming globally prevalent among SARS-CoV-2 sequences". News-Medical.net. 10 January 2021. Retrieved 11 February 2021.
  220. ^ "Malaysia identifies new Covid-19 strain, similar to one found in 3 other countries". The Straits Times. 23 December 2020. Retrieved 10 January 2021. Tan Sri Dr Noor Hisham Abdullah, said it is still unknown whether the strain - dubbed the "A701B" mutation - is more infectious than usual
  221. ^ "Duterte says Sulu seeking help after new COVID-19 variant detected in nearby Sabah, Malaysia". GMA News. 27 December 2020. Retrieved 10 January 2021.
  222. ^ Jump up to: a b c d "The current situation and Information on the Spike protein mutation of Covid-19 in Malaysia". Kementerian Kesihatan Malaysia - Covid-19 Malaysia. 25 December 2020.
  223. ^ Jump up to: a b c "COVID-19 A701V mutation spreads to third wave clusters". focusmalaysia.my. 25 December 2020. Retrieved 13 May 2021.
  224. ^ "Variants of Concerns (VOC), B.1.524, B.1.525, South African B.1.351, STRAIN D614G, A701V, B1.1.7". covid-19.moh.gov.my. 14 April 2021. Retrieved 15 May 2021.
  225. ^ Burioni R, Topol EJ (June 2021). "Has SARS-CoV-2 reached peak fitness?". Nature Medicine. 27 (8): 1323–1324. doi:10.1038/s41591-021-01421-7. PMID 34155413.
  226. ^ Jump up to: a b Office of the Commissioner (23 February 2021). "Coronavirus (COVID-19) Update: FDA Issues Policies to Guide Medical Product Developers Addressing Virus Variants". U.S. Food and Drug Administration (FDA). Retrieved 7 March 2021.
  227. ^ Rella, Simon A.; Kulikova, Yuliya A.; Dermitzakis, Emmanouil T.; Kondrashov, Fyodor A. (30 July 2021). "Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains". Scientific Reports. 11 (1): 15729. doi:10.1038/s41598-021-95025-3. ISSN 2045-2322. PMC 8324827. PMID 34330988.
  228. ^ Mahase E (March 2021). "Covid-19: Where are we on vaccines and variants?". BMJ. 372: n597. doi:10.1136/bmj.n597. PMID 33653708. S2CID 232093175.
  229. ^ Jump up to: a b c d Weekly epidemiological update on COVID-19 – 8 June 2021 (Situation report). World Health Organization. 8 June 2021. Table 3. Retrieved 14 June 2021.
  230. ^ Muik A, Wallisch AK, Sänger B, Swanson KA, Mühl J, Chen W, et al. (March 2021). "Neutralization of SARS-CoV-2 lineage B.1.1.7 pseudovirus by BNT162b2 vaccine-elicited human sera". Science. 371 (6534): 1152–53. Bibcode:2021Sci...371.1152M. doi:10.1126/science.abg6105. PMC 7971771. PMID 33514629.
  231. ^ Jump up to: a b Wang P, Nair MS, Liu L, Iketani S, Luo Y, Guo Y, et al. (March 2021). "Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7". Nature. 593 (7857): 130–35. Bibcode:2021Natur.593..130W. doi:10.1038/s41586-021-03398-2. PMID 33684923.
  232. ^ Emary KR, Golubchik T, Aley PK, Ariani CV, Angus BJ, Bibi S, et al. (February 2021). "Efficacy of ChAdOx1 nCoV-19 (AZD1222) Vaccine Against SARS-CoV-2 VOC 202012/01 (B.1.1.7)". SSRN 3779160.
  233. ^ Mahase E (February 2021). "Covid-19: Novavax vaccine efficacy is 86% against UK variant and 60% against South African variant". BMJ. 372: n296. doi:10.1136/bmj.n296. PMID 33526412. S2CID 231730012.
  234. ^ Kuchler H (25 January 2021). "Moderna develops new vaccine to tackle mutant Covid strain". Financial Times. Retrieved 30 January 2021.
  235. ^ Liu Y, Liu J, Xia H, Zhang X, Fontes-Garfias CR, Swanson KA, et al. (February 2021). "Neutralizing Activity of BNT162b2-Elicited Serum – Preliminary Report". The New England Journal of Medicine. doi:10.1056/nejmc2102017. PMID 33596352.
  236. ^ Jump up to: a b Hoffmann M, Arora P, Gross R, Seidel A, Hoernich BF, Hahn AS, et al. (March 2021). "1 SARS-CoV-2 variants B.1.351 and P.1 escape from neutralizing antibodies". Cell. 184 (9): 2384–2393.e12. doi:10.1016/j.cell.2021.03.036. PMC 7980144. PMID 33794143.
  237. ^ "Pfizer and BioNTech Confirm High Efficacy and No Serious Safety Concerns Through Up to Six Months Following Second Dose in Updated Topline Analysis of Landmark COVID-19 Vaccine Study". Pfizer (Press release). 1 April 2021. Retrieved 2 April 2021.
  238. ^ Cite error: The named reference COVID-19 vaccine clinical research auto was invoked but never defined (see the help page).
  239. ^ Francis D, Andy B (6 February 2021). "Oxford/AstraZeneca COVID shot less effective against South African variant: study". Reuters. Retrieved 8 February 2021.
  240. ^ Jump up to: a b "Covid: South Africa halts AstraZeneca vaccine rollout over new variant". BBC News Online. 8 February 2021. Retrieved 8 February 2021.
  241. ^ Booth W, Johnson CY (7 February 2021). "South Africa suspends Oxford-AstraZeneca vaccine rollout after researchers report 'minimal' protection against coronavirus variant". The Washington Post. London. Retrieved 8 February 2021. South Africa will suspend use of the coronavirus vaccine being developed by Oxford University and AstraZeneca after researchers found it provided 'minimal protection' against mild to moderate coronavirus infections caused by the new variant first detected in that country.
  242. ^ "A Phase 2A/B, Randomized, Observer-blinded, Placebo-controlled Study to Evaluate the Efficacy, Immunogenicity, and Safety of a SARS-CoV-2 Recombinant Spike Protein Nanoparticle Vaccine (SARS-CoV-2 rS) With Matrix-M1 Adjuvant in South African Adult Subjects Living Without HIV; and Safety and Immunogenicity in Adults Living With HIV". ClinicalTrials.gov. 30 October 2020.
  243. ^ Edara, Venkata-Viswanadh; Pinsky, Benjamin A.; Suthar, Mehul S.; Lai, Lilin; Davis-Gardner, Meredith E.; Floyd, Katharine; Flowers, Maria W.; Wrammert, Jens; Hussaini, Laila; Ciric, Caroline Rose; Bechnak, Sarah; Stephens, Kathy; Graham, Barney S.; Bayat Mokhtari, Elham; Mudvari, Prakriti; Boritz, Eli; Creanga, Adrian; Pegu, Amarendra; Derrien-Colemyn, Alexandrine; Henry, Amy R.; Gagne, Matthew; Douek, Daniel C.; Sahoo, Malaya K.; Sibai, Mamdouh; Solis, Daniel; Webby, Richard J.; Jeevan, Trushar; Fabrizio, Thomas P. (August 2021). "Infection and Vaccine-Induced Neutralizing-Antibody Responses to the SARS-CoV-2 B.1.617 Variants". New England Journal of Medicine. 385 (7): 664–666. doi:10.1056/NEJMc2107799. PMC 8279090. PMID 34233096.
  244. ^ Planas, Delphine; Veyer, David; Baidaliuk, Artem; Staropoli, Isabelle; Guivel-Benhassine, Florence; Rajah, Maaran Michael; Planchais, Cyril; Porrot, Françoise; Robillard, Nicolas; Puech, Julien; Prot, Matthieu; Gallais, Floriane; Gantner, Pierre; Velay, Aurélie; Le Guen, Julien; Kassis-Chikhani, Najiby; Edriss, Dhiaeddine; Belec, Laurent; Seve, Aymeric; Courtellemont, Laura; Péré, Hélène; Hocqueloux, Laurent; Fafi-Kremer, Samira; Prazuck, Thierry; Mouquet, Hugo; Bruel, Timothée; Simon-Lorière, Etienne; Rey, Felix A.; Schwartz, Olivier (August 2021). "Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization". Nature. 596 (7871): 276–280. doi:10.1038/s41586-021-03777-9. PMID 34237773. S2CID 235775860.
  245. ^ Yurkovetskiy L, Wang X, Pascal KE, Tomkins-Tinch C, Nyalile TP, Wang Y, et al. (October 2020). "Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant". Cell. 183 (3): 739–751.e8. doi:10.1016/j.cell.2020.09.032. PMC 7492024. PMID 32991842.
  246. ^ Thomson EC, Rosen LE, Shepherd JG, Spreafico R, da Silva Filipe A, Wojcechowskyj JA, et al. (March 2021). "Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity". Cell. 184 (5): 1171–1187.e20. doi:10.1016/j.cell.2021.01.037. PMC 7843029. PMID 33621484.
  247. ^ Smout A (26 January 2021). "Britain to help other countries track down coronavirus variants". Reuters. Retrieved 27 January 2021.
  248. ^ Donnelly L (26 January 2021). "UK to help sequence mutations of Covid around world to find dangerous new variants". The Telegraph. Retrieved 28 January 2021.
  249. ^ Latif AA, Mullen JL, Alkuzweny M, Tsueng G, Cano M, Haag E, et al. "Lineage Comparison". outbreak.info. Retrieved 24 June 2021.
  250. ^ SARS-CoV-2 variants of concern and variants under investigation in England, technical briefing 15 (PDF) (Briefing). Public Health England. 11 June 2021. GOV-8576. Retrieved 15 June 2021.
  251. ^ Kupferschmidt K (23 December 2020). "U.K. variant puts spotlight on immunocompromised patients' role in the COVID-19 pandemic". Science. doi:10.1126/science.abg2911.
  252. ^ Sutherland S (23 February 2021). "COVID Variants May Arise in People with Compromised Immune Systems". Scientific American.
  253. ^ McCarthy KR, Rennick LJ, Nambulli S, Robinson-McCarthy LR, Bain WG, Haidar G, Duprex WP (March 2021). "Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape". Science. 371 (6534): 1139–1142. Bibcode:2021Sci...371.1139M. doi:10.1126/science.abf6950. PMC 7971772. PMID 33536258.
  254. ^ Lassaunière R, Fonager J, Rasmussen M, Frische A, Strandh C, Rasmussen T, et al. (10 November 2020). SARS-CoV-2 spike mutations arising in Danish mink, their spread to humans and neutralization data (Preprint). Statens Serum Institut. Archived from the original on 10 November 2020. Retrieved 11 November 2020.
  255. ^ "Detection of new SARS-CoV-2 variants related to mink" (PDF). ECDC.eu. European Centre for Disease Prevention and Control. 12 November 2020. Retrieved 12 November 2020.
  256. ^ "SARS-CoV-2 mink-associated variant strain – Denmark". WHO Disease Outbreak News. 6 November 2020. Retrieved 19 March 2021.
  257. ^ Kevany S, Carstensen T (19 November 2020). "Danish Covid mink variant 'very likely extinct', but controversial cull continues". The Guardian.
  258. ^ Larsen HD, Fonager J, Lomholt FK, Dalby T, Benedetti G, Kristensen B, et al. (February 2021). "Preliminary report of an outbreak of SARS-CoV-2 in mink and mink farmers associated with community spread, Denmark, June to November 2020". Euro Surveillance. 26 (5). doi:10.2807/1560-7917.ES.2021.26.5.210009. PMC 7863232. PMID 33541485.
  259. ^ Green ST, Cladi L (26 January 2021). "Covid-19 and evolutionary pressure - can we predict which genetic dangers lurk beyond the horizon?". BMJ: n230.

Further reading

External links

Retrieved from ""