Variants of SARS-CoV-2
From Wikipedia the free encyclopedia
|Part of a series on the|
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), has many variants; some are or have been believed to be of particular importance. This article discusses such notable variants of SARS-CoV-2, and also discusses notable mutations found in some, or all, of these variants.
The sequence WIV04/2019, belonging to the GISAID S clade / PANGOLIN A lineage / Nextstrain 19B clade, is thought likely to most closely reflect the sequence of the original virus infecting humans known as "sequence zero", and is widely referred to as such and used as a reference sequence.
|Pango lineages (by Rambaut et al.)||Notes to pango lineages (see Alm et al.)||Nextstrain clades, 2021||GISAID clades||Notable variants|
|A.1–A.6||19B||S||contains "reference sequence" WIV04/2019|
|B.3–B.7, B.9, B.10, B.13–B.16||19A||L|
|B.1||B.1.5–B.1.72||20A||G||Lineage B.1 in the Rambaut et al. system|
|B.1.9, B.1.13, B.1.22, B.1.26, B.1.37||GH|
|20G||Predominant in US generally, Jan '21|
|20H||Includes B.1.351 aka 20H/501Y.V2 or 501.V2 lineage|
|20D||Includes P.1 and P.2|
|20I||Includes lineage B.1.1.7 aka VOC-202012/01 or 20I/501Y.V1|
|B.1.177||20E (EU1)||GV[a]||Derived from 20A|
No consistent nomenclature has been established for SARS-CoV-2. Colloquially, including by governments and news organizations, concerning variants are often referred to by the country in which they were first identified, but as of January 2021[update], the World Health Organization (WHO) is working on "standard nomenclature for SARS-CoV-2 variants that does not reference a geographical location".
While there are many thousands of variants of SARS-CoV-2, subtypes of the virus can be put into larger groupings such as lineages or clades.[b] Three main, generally used nomenclatures have been proposed:
- As of January 2021[update], GISAID—referring to SARS-CoV-2 as hCoV-19—had identified eight global clades (S, O, L, V, G, GH, GR, and GV).
- In 2017, Hadfield et al. announced Nextstrain, intended "for real-time tracking of pathogen evolution". Nextstrain has later been used for tracking SARS-CoV-2, identifying 11 major clades[c] (19A, 19B, and 20A–20I) as of January 2021[update].
- In 2020, Rambaut et al. of the Phylogenetic Assignment of Named Global Outbreak Lineages (PANGOLIN) software team proposed in an article "a dynamic nomenclature for SARS-CoV-2 lineages that focuses on actively circulating virus lineages and those that spread to new locations"; as of February 2021[update], six major lineages (A, B, B.1, B.1.1, B.1.177, B.1.1.7) had been identified.
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 labeled as an "emerging variant".
- 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 neutralizing 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-haul 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 labeled "variants of interest" pending verification and validation of these properties. Once validated, "variants of interest" may be renamed "variants of concern" by monitoring organizations, such as the CDC.
In early November 2020, Cluster 5, also referred to as ΔFVI-spike by the Danish State Serum Institute (SSI), was discovered in Northern Jutland, Denmark, 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.
The World Health Organization (WHO) has stated that cluster 5 has a "moderately decreased sensitivity to neutralizing antibodies". SSI warned that the mutation could reduce the effect of COVID-19 vaccines under development, although it was unlikely to render them useless. Following the lockdown and mass-testing, SSI announced on 19 November 2020 that cluster 5 in all probability had become extinct. As of 1 February 2021, authors to a peer-reviewed paper, all of whom were from the SSI, assessed that cluster 5 was not in circulation in the human population.
First sequenced in August 2020 in Nigeria, the implications for transmission and virulence are unclear but it has been listed as an emerging variant by the US Centers for Disease Control. Sequenced by the African Centre of Excellence for Genomics of Infectious Diseases in Nigeria, this variant has a P681H mutation, shared in common with UK's VOC-202012/01. It shares no other mutations with VOC-202012/01 and as of late December 2020 this variant accounts for around 1% of viral genomes sequenced in Nigeria, though this may rise.
Lineage B.1.1.7 / Variant of Concern 202012/01
First detected in October 2020 during the COVID-19 pandemic in the United Kingdom from a sample taken the previous month, Variant of Concern 202012/01 (VOC-202012/01), was previously known as the first Variant Under Investigation in December 2020 (VUI – 202012/01) and also as lineage B.1.1.7 or 20I/501Y.V1 (formerly 20B/501Y.V1). Since then, its prevalence odds have doubled every 6.5 days, the presumed generational interval. It is correlated with a significant increase in the rate of COVID-19 infection in United Kingdom, associated partly with the N501Y mutation. There is some evidence that this variant has 30–70% increased transmissibility, and early analyses suggest an increase in lethality. Variant of Concern 202102/02 (VOC-202102/02), described by Public Health England (PHE) as "B.1.1.7 with E484K" is of the same lineage in the Rambaut classification system but has an additional E484K mutation. There are 26 confirmed cases of VOC-202102/02 in the UK.
On 18 December 2020, the 501.V2 variant, also known as 501.V2, 20H/501Y.V2 (formerly 20C/501Y.V2), VOC-202012/02 (PHE), or lineage B.1.351, was first detected in South Africa and reported by the country's health department. Researchers and officials reported that the prevalence of the variant was higher among young people with no underlying health conditions, and by comparison with other variants it is more frequently resulting in serious illness in those cases. The South African health department also indicated that the variant may be driving the second wave of the COVID-19 epidemic in the country due to the variant spreading at a more rapid pace than other earlier variants of the virus.
Scientists noted that the variant contains several mutations that allow it to attach more easily to human cells because of the following three mutations in the receptor-binding domain (RBD) in the spike glycoprotein of the virus: N501Y, K417N, and E484K. The N501Y mutation has also been detected in the United Kingdom.
Lineage B.1.429 / CAL.20C
CAL.20C, also known as lineage B.1.429, is defined by five distinct mutations, including L452R (which had previously been detected in unrelated lineages). CAL.20C is possibly more transmissible, but further study is necessary to confirm this. It was first observed in July 2020 by researchers at the Cedars-Sinai Medical Center, California, in one of 1,230 virus samples collected in Los Angeles County since the start of the COVID-19 epidemic. It was not detected again until September when it reappeared among samples in California, but numbers remained very low until November. In November 2020, the CAL.20C variant accounted for 36 percent of samples collected at Cedars-Sinai Medical Center, and by January 2021, the CAL.20C variant accounted for 50 percent of samples. In a joint press release by University of California, San Francisco, California Department of Public Health, and Santa Clara County Public Health Department, the variant was also detected in multiple counties in Northern California. From November to December 2020, the frequency of the variant in sequenced cases from Northern California rose from 3% to 25%. In a preprint, CAL.20C is described as belonging to clade 20C and contributing approximately 36% of samples, while an emerging variant from the 20G clade accounts for some 24% of the samples in a study focused on Southern California. Note however that in the US as a whole, the 20G clade predominates, as of January 2021. Following the increasing numbers of CAL.20C in California, the variant has been detected at varying frequencies in most US states and small numbers have been detected in other countries in North America, Europe, Asia and Australia.
Lineage P.1, termed Variant of Concern 202101/02 by Public Health England and 20J/501Y.V3 by Nextstrain, was detected in Tokyo on 6 January 2021 by the National Institute of Infectious Diseases (NIID). The new lineage was first identified in four people who arrived in Tokyo having travelled from the Brazilian Amazonas state on 2 January 2021. On 12 January 2021, the Brazil-UK CADDE Centre confirmed 13 local cases of the P.1 new lineage in the Amazon rain forest. This variant of SARS-CoV-2 has been named P.1 lineage (although it is a descendant of B.1.1.28, the name B.220.127.116.11 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 N501Y and E484K. The new lineage was absent in samples from March to November from Manaus, Amazonas state, but it was identified in 42% of the samples from December 2020 collected in the same city, suggesting a recent increase in frequency. A separate preprint by Voloch et al. identified another sub-lineage of the B.1.1.28 lineage circulating in the state of Rio de Janeiro, Brazil, now named P.2 lineage, that harbours the E484K mutation. The P.2 lineage is not directly related with the P.1 lineage identified in Manaus. Although both lineages harbour the E484K mutation, the mutation was acquired independently through convergent evolution.[better source needed]
Notable missense mutations
D614G is a missense mutation that affects the spike protein of SARS-CoV-2. The frequency of this mutation in the viral population has increased during the pandemic. G (glycine) has replaced D (aspartic acid) 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 titers and infectivity in vitro. In July 2020, it was reported that the more infectious D614G SARS-CoV-2 variant had become the dominant form in the pandemic. PHE confirmed that the D614G mutation had a "moderate effect on transmissibility" and was being tracked internationally.
The global prevalence of D614G correlates with the prevalence of loss of smell (anosmia) as a symptom of COVID-19, possibly mediated by higher binding of the RBD to the ACE2 receptor or higher protein stability and hence higher infectivity of the olfactory epithelium.
E484K has been reported to be an escape mutation (i.e., a mutation that improves a virus's ability to evade the host's immune system) from at least one form of monoclonal antibody against SARS-CoV-2, indicating there may be a "possible change in antigenicity". The P.1. lineage described in Japan and Manaus, the P.2 lineage (also known as B.1.1.248 lineage, Brazil) and 501.V2 (South Africa) exhibit this mutation. A limited number of B.1.1.7 genomes with E484K mutation have also been detected. The name of the mutation, E484K, refers to an exchange whereby the glutamic acid (E) is replaced by lysine (K) at position 484. Monoclonal and serum-derived antibodies are reported to be from 10 to 60 times less effective in neutralizing virus bearing the E484K mutation. On 2 February 2021, medical scientists in the United Kingdom reported the detection of E484K in 11 samples (out of 214,000 samples), a mutation that may compromise current vaccine effectiveness.
N501Y denotes a change from asparagine (N) to tyrosine (Y) in amino-acid position 501. 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. Variants with N501Y include P.1 (Brazil/Japan), Variant of Concern 202012/01 (UK), 501.V2 (South Africa), and COH.20G/501Y (Columbus, Ohio). This last became the dominant form of the virus in Columbus in late December 2020 and January and appears to have evolved independently of other variants.
A highly flexible region in the receptor binding domain (RBD) of SARS-CoV-2, starting from residue 475 up to residue 485 was identified using bioinformatics and statistical methods in several studies. The University of Graz and the Biotech Company Innophore have shown in a recent publication, that structurally, the position S477 shows the highest flexibility among them. At the same time, S477 is hitherto the most frequently exchanged amino acid residue in the RBDs of SARS-CoV-2 mutants. By using molecular dynamics simulations of RBD during the binding process to hACE2 it has been shown, that both S477G and S477N strengthen the binding of the SARS-COV-2 spike with the hACE2 receptor. The vaccine developer BioNTech referenced this amino acid exchange as relevant regarding future vaccine design in a preprint published in February 2021.
New variant detection and assessment
On 26 January 2021, the British government said it would share its genomic sequencing capabilities with other countries in order to increase the genomic sequencing rate and trace new variants, and announced a "New Variant Assessment Platform". As of January 2021[update], more than half of all genomic sequencing of COVID-19 was carried out in the UK.
Differential vaccine effectiveness
A preliminary study by Pfizer, Inc. has indicated that there is, at most, only minor reduction of the company's mRNA vaccine effectiveness against different SARS-CoV-2 variants. Another study of the effectiveness of the same Comirnaty vaccine against the Variant of Concern 202012/01 confirmed this. According to the US CDC, most experts believe that, due to the nature of the virus, the emergence of variants that completely escape the immune response (both natural and vaccine induced) is considered unlikely.
T-cell immunity is under investigation as a potential solution to the problem of reduced effectiveness of vaccines against the relevant variants. Biotechnology firm Gritstone is experimenting to develop a vaccine aimed specifically at creating T-cell immunity.
On January 29, 2021, a deputy of the Moscow City Duma, Darya Besedina, turned to the Russian Minister of Health with a request to fund the study of new strains and conduct research on the effectiveness of Russian vaccines against these strains. On February 10, 2021, the European Medicines Agency made a similar appeal to vaccine manufacturers. On February 15, Russian President Vladimir Putin instructed the government to deploy the sequencing of the genomes of Russian SARS-CoV-2 strains within a month, allocate funds for these studies, and also check whether Russian vaccines are effective against new strains.
On 19 February 2021, Pfizer announced its vaccine produced around 66% fewer antibodies than normal when combating the 501.V2 variant, but was still successful in neutralizing the virus.
|First detection||Pango ||Other names||Notable mutations||Evidence of clinical changes[note 1]||Spread||Ref.|
|United Kingdom||Sep 2020||B.1.1.7||VOC-202012/01, 20I/501Y.V1||N501Y, 69–70del, P681H||Increased ~50% (NERVTAG)||Potentially 30% more lethal (NERVTAG)||Indications of ostensible reduced antigenic activity (ECDC)||Global|||
|Denmark||Oct 2020||—||Cluster 5, ΔFVI-spike (SSI)||Y453F, 69–70deltaHV||—||—||Moderately decreased sensitivity to neutralising antibodies (WHO)||Likely extinct|||
|South Africa||Dec 2020||B.1.351||501.V2, 20H/501Y.V2, |
|N501Y, K417N, E484K||Increased 50% (ECDC)||—||21% reduction in antigenicity, but effective neutralisation (ECDC)||Global|||
| Japan |
|Jan 2021||P.1||Descendant of B.1.1.28, VOC-202101/02||N501Y, E484K||Likely increased (CDC)||—||Overall reduction in effective neutralisation (ECDC)||Global|||
- "—" denotes that no reliable sources could be found to cite.
- Explanatory notes
- In another source, GISAID name a set of 7 clades without the O clade but including a GV clade.
- According to the WHO, "[l]ineages or clades can be defined based on viruses that share a phylogenetically determined common ancestor".
- As of January 2021[update], at least one of the following criteria must be met in order to count as a clade in the Nextstrain system (quote from source):
- A clade reaches >20% global frequency for 2 or more months
- A clade reaches >30% regional frequency for 2 or more months
- A VOC (‘variant of concern’) is recognized (applies currently [6 January 2021] to 501Y.V1 and 501Y.V2)
- Zhukova, Anna; Blassel, Luc; Lemoine, Frédéric; Morel, Marie; Voznica, Jakub; Gascuel, Olivier (24 November 2020). "Origin, evolution and global spread of SARS-CoV-2". Comptes Rendus Biologies: 1–20. doi:10.5802/crbiol.29. PMID 33274614.
- This table is an adaptation and expansion of Alm et al., figure 1.
- Bedford, Trevor; Hodcroft, Emma B; Neher, Richard A (6 January 2021). "Updated Nextstrain SARS-CoV-2 clade naming strategy". nextstrain.org/blog. Retrieved 19 January 2021.
- Zhang, Wenjuan; Davis, Brian D.; Chen, Stephanie S.; Martinez, Jorge M Sincuir; Plummer, Jasmine T.; Vail, Eric (2021). "Emergence of a novel SARS-CoV-2 strain in Southern California, USA". doi:10.1101/2021.01.18.21249786. S2CID 231646931. Cite journal requires
- PANGO lineages-Lineage B.1.1.28 cov-lineages.org, accessed 4 February 2021
- "clade tree (from 'Clade and lineage nomenclature')". www.gisaid.org. 4 July 2020. Retrieved 7 January 2021.
- 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.
- "Don't call it the 'British variant.' Use the correct name: B.1.1.7". STAT. 9 February 2021. Retrieved 12 February 2021.
- Flanagan, Ryan (2 February 2021). "Why the WHO won't call it the 'U.K. variant', and you shouldn't either". Coronavirus. Retrieved 12 February 2021.
- For a list of sources using names referring to the country in which the variants were first identified, see, for example, Talk:South African COVID variant and Talk:U.K. Coronavirus variant.
- 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.
- Koyama, Takahiko; Platt, Daniel; Parida, Laxmi (June 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.
- Alm, E.; Broberg, E. K.; Connor, T.; Hodcroft, E. B.; Komissarov, A. B.; Maurer-Stroh, S.; Melidou, A.; Neher, R. A.; O’Toole, Áine; Pereyaslov, D.; The WHO European Region sequencing laboratories and GISAID EpiCoV group; et al. (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.
- "Global phylogeny, updated by Nextstrain". GISAID. 18 January 2021. Retrieved 19 January 2021.
- Hadfield, J.; Megill, C; Bell, S.M.; Huddleston, J.; Potter, B.; Callender, C. (May 2018). "Nextstrain: real-time tracking of pathogen evolution". Bioinformatics. 34 (23): 4121–4123. doi:10.1093/bioinformatics/bty407. PMC 6247931. PMID 29790939.CS1 maint: multiple names: authors list (link)
Preprint: ——— (November 2017). "Nextstrain: real-time tracking of pathogen evolution". doi:10.1101/224048. S2CID 196637131 – via bioRxiv. Cite journal requires
|journal=(help)CS1 maint: numeric names: authors list (link)
- "Nextclade" (What are the clades?). clades.nextstrain.org. Archived from the original on 19 January 2021. Retrieved 19 January 2021.
- "cov-lineages/pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages". Github. Retrieved 2 January 2021.
- Rambaut, A.; Holmes, E.C.; O’Toole, Á.; et al. (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. PMID 32669681. S2CID 220544096. Cited in Alm et al.
- "Lineages". cov-lineages.org. Retrieved 24 December 2020.
- CDC. "Emerging SARS-CoV-2 Variants". Centers for Disease Control and Prevention. Retrieved 4 January 2021. This article incorporates text from this source, which is in the public domain.
- Contributor, IDSA (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.
- "Variants: distribution of cases data". GOV.UK. 28 January 2021. At "Differences between a Variant of Concern and Variant Under Investigation". Retrieved 19 February 2021.
SARS-CoV-2 variants, if considered to have concerning epidemiological, immunological, or pathogenic properties, are raised for formal investigation. At this point they are designated Variant Under Investigation (VUI) with a year, month, and number. Following a risk assessment with the relevant expert committee, they may be designated Variant of Concern (VOC)
- Lassaunière, Ria (11 November 2020). "SARS-CoV-2 spike mutations arising in Danish mink and their spread to humans". Statens Serum Institut. Archived from the original on 10 November 2020. Retrieved 11 November 2020.
- "Detection of new SARS-CoV-2 variants related to mink" (PDF). European Centre for Disease Prevention and Control. 12 November 2020. Retrieved 12 November 2020.
- "SARS-CoV-2 mink-associated variant strain – Denmark". World Health Organization. 6 November 2020. Retrieved 16 January 2021.
- "De fleste restriktioner lempes i Nordjylland" [most restrictions eased in North Jutland]. Sundheds- og Ældreministeriet. 19 November 2020. Retrieved 16 January 2021.
Sekventeringen af de positive prøver viser samtidig, at der ikke er påvist yderligere tilfælde af minkvariant med cluster 5 siden den 15. september, hvorfor Statens Serums Institut vurderer, at denne variant med stor sandsynlighed er døet ud. ("With high probability [...] died out")
- Larsen, Helle Daugaard; Fonager, Jannik; Lomholt, Frederikke Kristensen; Dalby, Tine; Benedetti, Guido; Kristensen, Brian; Urth, Tinna Ravnholt; Rasmussen, Morten; Lassaunière, Ria; Rasmussen, Thomas Bruun; Strandbygaard, Bertel (4 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". Eurosurveillance. 26 (5). doi:10.2807/1560-7917.ES.2021.26.5.210009. ISSN 1025-496X. PMC 7863232. PMID 33541485.
- "Detection of SARS-CoV-2 P681H Spike Protein Variant in Nigeria". Virological. 23 December 2020. Retrieved 1 January 2021.
- "Covid: Ireland, Italy, Belgium and Netherlands ban flights from UK". BBC News. 20 December 2020.
- Chand, Meera; Hopkins, Susan; Dabrera, Gavin; Achison, Christina; Barclay, Wendy; Ferguson, Neil; Volz, Erik; Loman, Nick; Rambaut, Andrew; Barrett, Jeff (21 December 2020). Investigation of novel SARS-COV-2 variant: Variant of Concern 202012/01 (PDF) (Report). Public Health England. Retrieved 23 December 2020.
- "PHE investigating a novel strain of COVID-19". Public Health England (PHE). 14 December 2020.
- Rambaut, Andrew; Loman, Nick; Pybus, Oliver; Barclay, Wendy; Barrett, Jeff; Carabelli, Alesandro; Connor, Tom; Peacock, Tom; L. Robertson, David; Vol, Erik (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.CS1 maint: multiple names: authors list (link)
- Kupferschmidt, Kai (20 December 2020). "Mutant coronavirus in the United Kingdom sets off alarms but its importance remains unclear". Science Mag. Retrieved 21 December 2020.
- "New evidence on VUI-202012/01 and review of the public health risk assessment". khub.net. 15 December 2020.
- "COG-UK Showcase Event - YouTube". YouTube. Retrieved 25 December 2020.
- Gallagher, James (22 January 2021). "Coronavirus: UK variant 'may be more deadly'". BBC News. Retrieved 22 January 2021.
- Public Health England (18 February 2021). "Variants: distribution of cases data". GOV.UK. Retrieved 18 February 2021.
- "South Africa announces a new coronavirus variant". The New York Times. 18 December 2020. Retrieved 20 December 2020.
- Wroughton, Lesley; Bearak, Max (18 December 2020). "South Africa coronavirus: Second wave fueled by new strain, teen 'rage festivals'". The Washington Post. Retrieved 20 December 2020.
- Mkhize, Dr Zwelini (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.
- 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.
- "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.
- Lowe, Derek (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.
- "Novel mutation combination in spike receptor binding site" (Press release). GISAID. 21 December 2020. Retrieved 23 December 2020.
- "New California Variant May Be Driving Virus Surge There, Study Suggests". New York Times. 19 January 2021.
- "Local COVID-19 Strain Found in Over One-Third of Los Angeles Patients" (Press release). California: Cedars Sinai Medical Center. 18 January 2021. Retrieved 19 January 2021.
- "B.1.429". Rambaut Group, University of Edinburgh. PANGO Lineages. 15 February 2021. Retrieved 16 February 2021.
- "B.1.429 Lineage Report". Scripps Research. outbreak.info. 15 February 2021. Retrieved 16 February 2021.
- "COVID-19 Variant First Found in Other Countries and States Now Seen More Frequently in California". www.cdph.ca.gov. Retrieved 30 January 2021.
- Weise, Karen Weintraub and Elizabeth. "New strains of COVID swiftly moving through the US need careful watch, scientists say". USA TODAY. Retrieved 30 January 2021.
- "Cases, Data, and Surveillance". Centers for Disease Control and Prevention. 11 February 2020. Retrieved 19 February 2021.
- "SARS-CoV-2 Variants". Centers for Disease Control and Prevention. 31 January 2020. Retrieved 20 February 2021.
- "Japan finds new coronavirus variant in travelers from Brazil". Japan Today. Japan. 11 January 2021. Retrieved 14 January 2021.
- "Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings". Virological. 12 January 2021. Retrieved 23 January 2021.
- PANGO lineages Lineage P.2 cov-lineages.org, accessed 28 January 2021 "P.2...Alias of B.18.104.22.168, Brazilian lineage"
- Voloch, Carolina M.; et al. (26 December 2020). "Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil". doi:10.1101/2020.12.23.20248598 – via medRxiv.
- Schraer, Rachel (18 July 2020). "Coronavirus: Are mutations making it more infectious?". BBC News. Retrieved 3 January 2021.
- "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.
- Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, et al. (2 July 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. ISSN 0092-8674. PMC 7332439. PMID 32697968.
- SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo "an emergent Asp614→Gly (D614G) substitution in the spike glycoprotein of SARS-CoV-2 strains that is now the most prevalent form globally" 18 December 2020 science.sciencemag.org, accessed 14 January 2021 DOI: 10.1126/science.abe8499
- 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.
- Butowt, R; Bilinska, K; Von Bartheld, CS (21 October 2020). "Chemosensory Dysfunction in COVID-19: Integration of Genetic and Epidemiological Data Points to D614G Spike Protein Variant as a Contributing Factor". ACS Chem Neurosci. 11 (20): 3180–3184. doi:10.1021/acschemneuro.0c00596. PMC 7581292. PMID 32997488.
- "escape mutation". HIV i-Base. 11 October 2012. Retrieved 19 February 2021.
- Wise, Jacqui (5 February 2021). "Covid-19: The E484K mutation and the risks it poses". The BMJ. 372: n359. doi:10.1136/bmj.n359. ISSN 1756-1833. PMID 33547053. S2CID 231821685.
- "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.
- Voloch, Carolina M.; F, Ronaldo da Silva; Almeida, Luiz G. P. de; Cardoso, Cynthia C.; Brustolini, Otavio J.; Gerber, Alexandra L.; Guimarães, Ana Paula de C.; Mariani, Diana; Costa, Raissa Mirella da; Ferreira, Orlando C.; Workgroup, Covid19-UFRJ (26 December 2020). "Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil". Le Phare de l'Esperanto: 2020.12.23.20248598. doi:10.1101/2020.12.23.20248598. ISSN 2024-8598. S2CID 229379623 – via MedRxiv.
- "Technical briefing 5" (PDF). Gov.uk. Public Health England. p. 17. Retrieved 2 February 2021.
- Michael Greenwood (15 January 2021). "What Mutations of SARS-CoV-2 are Causing Concern?". News Medical Lifesciences. Retrieved 16 January 2021.
- Greaney, Allison (4 January 2021). "Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies". doi:10.1101/2020.12.31.425021. S2CID 231615359. Retrieved 25 January 2021 – via bioRxiv. Cite journal requires
- Kupferschmidt, Kai (22 January 2021). "New mutations raise specter of 'immune escape'". Science. 371 (6527): 329–330. doi:10.1126/science.371.6527.329. PMID 33479129. Retrieved 25 January 2021.
- Rettner, Rachael (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.
- Achenbach, Joel; Booth, William (2 February 2021). "Worrisome coronavirus mutation seen in U.K. variant and in some U.S. samples". The Washington Post. Retrieved 2 February 2021.
- Chand et al., "Potential impact of spike variant N501Y" (p. 6).
- Researchers Discover New Variant of COVID-19 Virus in Columbus, Ohio 13 January 2021, wexnermedical.osu.edu, accessed 16 January 2021
- Tu, Huolin; Avenarius, Matthew R.; Kubatko, Laura; Hunt, Matthew; Pan, Xiaokang; Ru, Peng; Garee, Jason; Thomas, Keelie; Mohler, Peter; Pancholi, Preeti; Jones, Dan (26 January 2021). "Distinct Patterns of Emergence of SARS-CoV-2 Spike Variants including N501Y in Clinical Samples in Columbus Ohio". bioRxiv: 2021.01.12.426407. doi:10.1101/2021.01.12.426407.
- "University of Graz". www.uni-graz.at. Retrieved 22 February 2021.
- "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.
- Singh, Amit; Steinkellner, Georg; Köchl, Katharina; Gruber, Karl; Gruber, Christian C. (22 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. doi:10.1038/s41598-021-83761-5. ISSN 2045-2322.
- "BioNTech: We aspire to individualize cancer medicine". BioNTech. Retrieved 22 February 2021.
- Schrörs, Barbara; Gudimella, Ranganath; Bukur, Thomas; Rösler, Thomas; Löwer, Martin; Sahin, Ugur (4 February 2021). "Large-scale analysis of SARS-CoV-2 spike-glycoprotein mutants demonstrates the need for continuous screening of virus isolates". bioRxiv: 2021.02.04.429765. doi:10.1101/2021.02.04.429765.
- Smout, Alistair (26 January 2021). "Britain to help other countries track down coronavirus variants". www.reuters.com. Retrieved 27 January 2021.
- Donnelly, Laura (26 January 2021). "UK to help sequence mutations of Covid around world to find dangerous new variants". www.telegraph.co.uk. Retrieved 28 January 2021.
- Collier DA, Meng B, Ferreira, Gupta RK (2021). "Neutralization of spike 69/70 deletion, E484K, and N501Y SARS-CoV-2 by BNT162b2 vaccine-elicited sera" (PDF). bioRxiv : The Preprint Server for Biology. doi:10.1101/2021.01.27.427998. PMC 7852264. PMID 33532771 – via medRxiv.
- Muik, Alexander; Wallisch, Ann-Kathrin; Sänger, Bianca; Swanson, Kena A.; Mühl, Julia; Chen, Wei; Cai, Hui; Maurus, Daniel; Sarkar, Ritu; Türeci, Özlem; Dormitzer, Philip R. (29 January 2021). "Neutralization of SARS-CoV-2 lineage B.1.1.7 pseudovirus by BNT162b2 vaccine–elicited human sera". Science: eabg6105. doi:10.1126/science.abg6105. ISSN 0036-8075. PMID 33514629.
- "Covid: South Africa halts AstraZeneca vaccine rollout over new variant". BBC News. 8 February 2021. Retrieved 12 February 2021.
- Ledford, Heidi (12 February 2021). "How 'killer' T cells could boost COVID immunity in face of new variants". www.nature.com. Retrieved 15 February 2021.
- "Эффективна ли российская вакцина против южноафриканского штамма ковида?" [Is the Russian vaccine effective against the South African strain of covid?]. besedina.moscow. 26 January 2021. Retrieved 22 February 2021.
- "EMA preparing guidance to tackle COVID-19 variants". www.ema.europa.eu. 10 February 2021. Retrieved 22 February 2021.
- "Перечень поручений по итогам совещания с членами Правительства" [List of instructions following a meeting with members of the Government]. kremlin.ru. 12 February 2021. Retrieved 22 February 2021.
- Polack FP, Kadire SR., et al. Neutralizing Activity of BNT162b2-Elicited Serum - Preliminary Report: New England Journal of Medicine. 2021 [cited 2021 Feb 22]; doi:10.1056/NEJMc2102017
- ECDC (21 January 2021). "Risk related to the spread of new SARS-CoV-2 variants of concern in the EU/EEA - first update" (PDF). European Centre for Disease Prevention and Control. Retrieved 2 February 2021.
- Kupferschmidt, Kai (15 January 2021). "New coronavirus variants could cause more reinfections, require updated vaccines". Science. American Association for the Advancement of Science. doi:10.1126/science.abg6028. Retrieved 2 February 2021.
- "Coronavirus variants and mutations: The science explained". BBC News. 6 January 2021. Retrieved 2 February 2021.
- Voloch, Carolina M.; et al. (2020). "Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil" full text (see figure 5). Retrieved 15 January 2021. doi:10.1101/2020.12.23.20248598 – via medRxiv.
- Lovett, Samuel (14 January 2021). "What we know about the new Brazilian coronavirus variant". The Independent. London. Retrieved 14 January 2021.
|Scholia has a profile for variant of SARS-CoV-2 (Q104450895).|
|Look up COVID in Wiktionary, the free dictionary.|
- "CoVariants". CoVariants.org. Retrieved 10 February 2021.
- "Coronavirus Variants and Mutations". The New York Times.
- Corum, Jonathan; Zimmer, Carl (18 January 2021). "Inside the B.1.1.7 Coronavirus Variant". The New York Times.