The DOI matches its Crossref record; 281 of the 281 references it cites were found in a registry or an index; 16 of the 147 sources its claims cite were checked for support.
The biological and clinical significance of emerging SARS-CoV-2 variants
Open accessAbstract
The past several months have witnessed the emergence of SARS-CoV-2 variants with novel spike protein mutations that are influencing the epidemiological and clinical aspects of the COVID-19 pandemic. These variants can increase rates of virus transmission and/or increase the risk of reinfection and reduce the protection afforded by neutralizing monoclonal antibodies and vaccination. These variants can therefore enable SARS-CoV-2 to continue its spread in the face of rising population immunity while maintaining or increasing its replication fitness. The identification of four rapidly expanding virus lineages since December 2020, designated variants of concern, has ushered in a new stage of the pandemic. The four variants of concern, the Alpha variant (originally identified in the UK), the Beta variant (originally identified in South Africa), the Gamma variant (originally identified in Brazil) and the Delta variant (originally identified in India), share several mutations with one another as well as with an increasing number of other recently identified SARS-CoV-2 variants. Collectively, these SARS-CoV-2 variants complicate the COVID-19 research agenda and necessitate additional avenues of laboratory, epidemiological and clinical research. In this Review, the authors describe our latest understanding of the emergence and properties of SARS-CoV-2 genetic variants, particularly those designated as WHO (World Health Organization) ‘variants of concern’. They focus on the consequences of these variants for antibody-mediated virus neutralization, with important implications for reinfection risk and for vaccine effectiveness.
Overview
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Written from the paper’s full text.
TL;DR
This review synthesizes SARS-CoV-2 evolution, spike structure and the biological/clinical significance of the four WHO variants of concern as of June 2021: Alpha, Beta, Gamma and Delta. It shows that recurrent spike mutations increase transmissibility and immune evasion, reducing neutralization by monoclonal antibodies and vaccinee plasma, and calls for integrated genomic, neutralization and vaccine-efficacy surveillance.
Key findings
- Four VOCs emerged independently: Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1) and Delta (B.1.617.2). Alpha was estimated to be ~50% more transmissible than prior UK variants and associated with an estimated 50% increased mortality; Beta was estimated to be 50% more transmissible than preceding lineages; Gamma was estimated to cause 3–4 times higher virus levels and 1.1-fold to 1.8-fold higher mortality; Delta spread to 54 countries and replaced Alpha in the UK and USA.
- Neutralization escape varied by variant. Beta showed 3-fold to 10-fold reduced susceptibility to 46% and >10-fold reduced susceptibility to 22% of convalescent plasma samples; mRNA vaccinee plasma showed 45% with 3-fold to 10-fold and 30% with >10-fold reduced Beta neutralization. Delta showed 3-fold to 10-fold reduced susceptibility to 45% and >10-fold to 5% of convalescent plasma samples, while ~15% of BNT162b vaccinee plasma had 3-fold to 10-fold reduced Delta neutralization. Alpha was rarely associated with reduced convalescent plasma susceptibility but showed 3-fold to 10-fold reduced susceptibility to ~15% of mRNA vaccinee plasma samples.
- Vaccine efficacy against VOCs was reduced in several studies: BNT162b retained >90% efficacy against Alpha in Israel and Qatar; Beta efficacy was 72% in a Qatar cohort and 75% in a test-negative case-control study; Delta efficacy was ~85% for BNT162b and ~60% for AZD1222 in UK case-control studies. In trials, AZD1222 efficacy against Beta was 10% in South Africa, and NVX-CoV2373 efficacy was 49% against Beta and 86.3% against Alpha versus 96.4% against non-Alpha variants.
- Key mutations include D614G, which rose to near 100% global prevalence by June 2020; N501Y, which increases ACE2 affinity; E484K, which reduces susceptibility to several monoclonal antibodies and plasma; and non-spike mutations that antagonize innate immunity, with Alpha and Beta showing mean 112-fold and 8-fold reduced susceptibility to type I interferons, respectively, compared with an early pandemic virus.
Methods
- Narrative review creating a framework for SARS-CoV-2 variants by describing evolution, spike protein structure/function, laboratory characterization methods, biological and epidemiological properties of VOCs/VOIs, and required research responses; data summarized as of June 2021.
- Synthesizes genomic surveillance data from more than two million partially or fully sequenced virus isolates, in vitro selection and neutralization experiments using pseudotyped viruses, VSV-based chimeric viruses, full-length recombinant SARS-CoV-2 and cultured isolates, deep mutational scanning, and vaccine efficacy trials, test-negative case-control studies and cohort studies.
- Neutralization results were pooled in the Stanford University Coronavirus Antiviral & Resistance Database and summarized as <3-fold, 3–10-fold and >10-fold reductions compared with control viruses.
Limitations
- The paper states that as of June 2021 it is uncertain whether current lineage-based variant classification will be sustainable, and that classifying variants by component mutations may become challenging if recurrent mutations increase.
- The paper notes unresolved questions, including whether neutralizing antibodies are the most important protective mechanism versus memory B cells, Fc-effector functions and T cell immunity, and whether updated immunogens can broaden responses in animal models more predictive of humans.
- Evident from the text: this is a synthesis as of June 2021, so later variants and data are not included; neutralization estimates pool results across pseudotyped, chimeric and infectious virus assays, and some distributions are approximate because they include results reported only as aggregate mean fold reductions.
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Claims the paper makes
70 Not checked yet · 10 Own interpretation · 7 Partly supported · 3 No basis given · accuracy not yet measured
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“However, in three other studies, the median reduction in neutralizing activity was between onefold and threefold 102,214,215 .”
What the sources say
- Partly supportedcites [102] Supasa, P. et al. Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera. Cell 184, 2201–2211 (2021). sourceExperimental — accuracy not yet measured
The Results section ('Neutralization activity of convalescent plasma and vaccine sera'; page not provided) reports a 2.9-fold reduction for convalescent plasma and 2.1- and 2.5-fold reductions for AstraZeneca vaccine sera, all within the claimed range. These are geometric means, not medians, and the reported Pfizer vaccine-serum reduction is 3.3-fold, outside that range. This source cannot establish the results of the other two cited studies. (LLM, conf=0.85)
- Supportedcites [214] Planas, D. et al. Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization. Nature 596, 276–280 (2021). source
In “Sensitivity of Delta to convalescent sera” (page unavailable), the paper reports median neutralization titres and says Delta titres were fourfold lower than Alpha titres and sixfold lower than D614G titres. Those comparisons imply an approximately 1.5-fold reduction for Alpha relative to D614G, within the claimed onefold-to-threefold range. This paper is one of the three studies cited; it need not itself report the other two. (LLM, conf=0.84)
- Not checked yetcites [215] Mlcochova, P. et al. SARS-CoV-2 B.1.617.2 Delta variant emergence and vaccine breakthrough. Preprint at Research Square https://www.researchsquare.com/article/rs-637724/v1 (2021).
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Partly supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Of plasma samples obtained from persons receiving one of the mRNA vaccines, 45% had 3-fold to 10-fold and 30% had >10-fold reduced Beta variant neutralizing activity 97,104,117,121,151,204,208,209,222,223 (fIg.5).”
What the sources say
- Not checked yetcites [97] Chen, X. et al. Neutralizing antibodies against SARS-CoV-2 variants induced by natural infection or vaccination: a systematic review and pooled meta-analysis. Clin. Infect. Dis. https://doi.org/10.1093/cid/ciab646 (2021). This paper presents a systematic review and meta-analysis of in vitro neutralization studies of SARS-CoV-2 variants by convalescent and vaccinee plasma. source
- Partly supportedcites [104] Zhou, D. et al. Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine induced sera. Cell 184, 2348–2361 (2021). sourceExperimental — accuracy not yet measured
The Results section, “Neutralization of B.1.351 by vaccinee serum” (page unavailable), reports that serum from Pfizer-BioNTech vaccine recipients had a 7.6-fold lower geometric mean neutralization titer against B.1.351 than against Victoria. It does not report that 45% of mRNA-vaccine samples had a 3- to 10-fold reduction or that 30% had a greater-than-10-fold reduction. (LLM, conf=0.88)
- Partly supportedcites [117] Chen, R. E. et al. Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Nat. Med. 27, 717–726 (2021). sourceExperimental — accuracy not yet measured
The Results report reduced neutralization of the Beta (B.1.351) variant by sera from BNT162b2 mRNA-vaccine recipients: a 10-fold reduction in geometric mean activity in one assay and a 6- to 9-fold reduction in another. They do not report the claimed distribution of samples—45% with 3- to 10-fold reductions and 30% with reductions greater than 10-fold—or results from more than one mRNA vaccine. (LLM, conf=0.88)
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“By contrast, among plasma samples obtained from recipients of the AZD1222 vaccine, higher proportions displayed reduced neutralizing activity against this variant 100,209,214 .”
What the sources say
- Partly supportedcites [100] Liu, C. et al. Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum. Cell 184, 4220–4336 (2021). sourceExperimental — accuracy not yet measured
The Results section, “Protection from B.1.617.1 and B.1.617.2 by vaccine serum” (page unavailable), reports that neutralization titers in serum from Oxford-AstraZeneca (AZD1222) recipients were 4.3-fold lower against B.1.617.2 (Delta) than against the Victoria strain. That supports reduced neutralizing activity, but the passage reports a reduction in the group's geometric mean titer, not a higher proportion of individual samples showing reduced activity. (LLM, conf=0.83)
- Partly supportedcites [209] Wall, E. C. et al. Neutralising antibody activity against SARS-CoV-2 VOCs B.1.617.2 and B.1.351 by BNT162b2 vaccination. Lancet 397, 2331–2333 (2021). sourceExperimental — accuracy not yet measured
The main text (page not given; appendix p. 2 cited) reports that a higher proportion of samples from BNT162b2 recipients had low neutralising titres against B.1.617.2 (Delta) than against wild-type virus. It does not report this result for AZD1222 recipients; searches for AZD1222 and ChAdOx1 found no such analysis in our copy. (LLM, conf=0.86)
- Partly supportedcites [214] Planas, D. et al. Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization. Nature 596, 276–280 (2021). sourceExperimental — accuracy not yet measured
In “Sensitivity of Delta to sera from vaccinated individuals,” the paper reports that after one AstraZeneca (AZD1222) dose, only 9% of recipients’ sera neutralized Delta, compared with 74% for D614G and 61% for Alpha. The claim omits the dose qualification: four weeks after a second dose, sera from 95–100% of AstraZeneca recipients neutralized all four strains. The paper tested sera, rather than describing the samples as plasma. (LLM, conf=0.86)
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Partly supported
None of the sources cited for this claim have been checked yet.
In the paper
“The past several months have witnessed the emergence of four SArS-cov-2 variants of concern (Alpha, beta, Gamma and Delta)”
- Also stated in: § SARS-CoV-2 evolution · plain
“The four variants of concern, the Alpha variant (originally identified in the UK), the Beta variant (originally identified in South Africa), the Gamma variant (originally identified in Brazil) and the Delta variant (originally identified in India)”
What the sources say
- Not checked yetcites [27] Rambaut, A. et al. Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations. Virological https://virological.org/t/563 (2020).
- Not checked yetcites [16] Tegally, H. et al. Detection of a SARS-CoV-2 variant of concern in South Africa. Nature 592, 438–443 (2021). This molecular epidemiological study charts the spread of the beta variant in South Africa and shows that it resulted from selective evolutionary forces. source
- Not checked yetcites [19] Faria, N. R. et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science 372, 815–821 (2021). This paper presents an analysis showing that the Gamma variant is about twofold more transmissible than previous variants in Manaus, Brazil, and that it poses an increased risk of reinfection compared with previous variants. source
plain- Asserted: passes — The authors put it forward as true.
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- Based: passes — The paper gives a reason why it holds.
- Also stated in: § SARS-CoV-2 evolution · plain
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The increasing number of SArS-cov-2 variants share a repertoire of mutations that is enabling the virus to spread despite rising population immunity while maintaining or increasing its replication fitness.”
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: unclear — It is unclear why the paper says it holds.
In the paper
“In a post-hoc analysis of a NVX-CoV2373 clinical trial, vaccine efficacy was 86.3% against Alpha variants compared with 96.4% against non-Alpha variants 212 (TABLe 2).”
What the sources say
- Not checked yetcites [212] Heath, P. T. et al. Safety and efficacy of NVX-CoV2373 Covid-19 vaccine. N. Engl. J. Med. https://doi.org/10.1056/NEJMoa2107659 (2021). source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
None of the sources cited for this claim have been checked yet.
In the paper
“By the second quarter of 2021, the Alpha variant accounted for the majority of infections in the USA and many European countries 23,196 .”
What the sources say
- Not checked yetcites [23] Hodcroft, E. CoVariants: SARS-CoV-2 mutations and variants of interest (NextStrain). CoVariants https://covariants.org/ (2021).
- Not checked yetcites [196] Mullen, J. L. et al. Outbreak.info https://outbreak.info/citation (2020).
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
None of the sources cited for this claim have been checked yet.
In the paper
“It was also associated with threefold to eightfold higher upper-airway levels [199][200][201]”
What the sources say
- Not checked yetcites [199] Golubchik, T. et al. Early analysis of a potential link between viral load and the N501Y mutation in the SARS-COV-2 spike protein. Preprint at bioRxiv https://doi.org/10.1101/2021.01.12.20249080 (2021). source
- Not checked yetcites [200] Kidd, M. et al. S-variant SARS-CoV-2 lineage B1.1.7 is associated with significantly higher viral loads in samples tested by ThermoFisher TaqPath RT-qPCR. J. Infect. Dis. 223, 1666–1670 (2021). source
- Not checked yetcites [201] Borges, V. et al. Tracking SARS-CoV-2 lineage B.1.1.7 dissemination: insights from nationwide spike gene target failure (SGTF) and spike gene late detection (SGTL) data, Portugal, week 49 2020 to week 3 2021. Eur. Surveill. 26, 2100131 (2021). source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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None of the sources cited for this claim have been checked yet.
In the paper
“and an estimated 50% increased mortality 194,195,202 .”
What the sources say
- Not checked yetcites [194] Davies, N. G. et al. Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7. Nature 593, 270–274 (2021). source
- Not checked yetcites [195] Challen, R. et al. Risk of mortality in patients infected with SARS-CoV-2 variant of concern 202012/1: matched cohort study. BMJ 372, n579 (2021). source
- Not checked yetcites [202] Grint, D. J. et al. Case fatality risk of the SARS-CoV-2 variant of concern B.1.1.7 in England, 16 November to 5 February. Eur. Surveill. 26, 2100256 (2021). source
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“The Beta variant was estimated to be 50% more transmissible than the lineages that preceded it 16 .”
What the sources say
- Not checked yetcites [16] Tegally, H. et al. Detection of a SARS-CoV-2 variant of concern in South Africa. Nature 592, 438–443 (2021). This molecular epidemiological study charts the spread of the beta variant in South Africa and shows that it resulted from selective evolutionary forces. source
hedgeddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- It may state two separate claims as one. 33
- Probably not a substantial claim. 8
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Of 34 convalescent plasma samples from persons infected with the Alpha variant, 59% had 3-fold to 10-fold reduced neutralizing activity and 18% had >10-fold reduced neutralizing activity to the Beta variant 99,104,221 .”
What the sources say
- Partly supportedcites [99] Faulkner, N. et al. Reduced antibody cross-reactivity following infection with B.1.1.7 than with parental SARS-CoV-2 strains. Elife 10, e69317 (2021). sourceExperimental — accuracy not yet measured
The Results and Discussion report reduced neutralisation of B.1.351 (Beta) by B.1.1.7 (Alpha) sera, with a 7.7-fold change and a range of 3.4- to 17.9-fold. They do not report the claimed breakdown of 59% and 18%; the Materials and methods describe 29 patients with B.1.1.7 infection, not 34. (LLM, conf=0.88)
- Partly supportedcites [104] Zhou, D. et al. Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine induced sera. Cell 184, 2348–2361 (2021). sourceExperimental — accuracy not yet measured
The Results section reports reduced neutralization of Beta (B.1.351), but the 34 convalescent samples were collected before Alpha (B.1.1.7) emerged. The paper reports a separate Alpha-infected group of 13 patients, not 34, and does not report the claimed 59% and 18% breakdown for that group. Page numbers are unavailable in our copy. (LLM, conf=0.86)
- Partly supportedcites [221] McCallum, M. et al. SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern. Science 373, 648–654 (2021). sourceExperimental — accuracy not yet measured
The Results section (page unavailable) reports reduced neutralization of the Beta variant (B.1.351) by convalescent plasma. But its nine donors were likely infected with Wuhan-1 or a related virus, not Alpha, and it does not report the claimed 34 samples or the 59% and 18% breakdowns. (LLM, conf=0.84)
plaindirectn = 34- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
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It may state two separate claims as one.
- Partly supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“By June 2021, the Gamma variant accounted for a high proportion of infections in several South American and Caribbean countries 196 and 10% of US infections 33 .”
What the sources say
- Not checked yetcites [196] Mullen, J. L. et al. Outbreak.info https://outbreak.info/citation (2020).
- Partly supportedcites [33] Bolze, A. et al. Rapid displacement of SARS-CoV-2 variant B.1.1.7 by B.1.617.2 and P.1 in the United States. Preprint at medRxiv https://doi.org/10.1101/2021.06.20.21259195 (2021). sourceExperimental — accuracy not yet measured
The Results (page not available) report that Gamma reached 15% of sequenced US samples by May 28–June 3, 2021. This supports a substantial US presence around June, but not the cited figure of 10% of infections. The South American and Caribbean statement carries a different citation and is not assessed here. (LLM, conf=0.85)
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“In addition, the mRNA vaccines appear to often elicit memory B cells that undergo somatic hypermutation, which should broaden the response to viruses with variant spike proteins 239,240 .”
What the sources say
- Partly supportedcites [239] Wang, Z. et al. Naturally enhanced neutralizing breadth against SARS-CoV-2 one year after infection. Nature 595, 426–431 (2021). sourceExperimental — accuracy not yet measured
The Memory B cells section reports continued somatic hypermutation after infection, and the Discussion says mRNA vaccination enhances memory B-cell responses and likely protects vaccinated convalescent individuals against variants (page not specified). But the paper says vaccine-driven expansion of persistent memory clones does not accumulate large numbers of additional mutations. It does not establish that mRNA vaccines often elicit this mutation-driven broadening in people without prior infection. (LLM, conf=0.88)
- Partly supportedcites [240] Turner, J. S. et al. SARS-CoV-2 mRNA vaccines induce persistent human germinal centre responses. Nature https://doi.org/10.1038/s41586-021-03738-2 (2021). sourceExperimental — accuracy not yet measured
The paper reports persistent germinal-centre responses after mRNA vaccination and finds that a small fraction of cross-reactive B-cell clones had higher somatic hypermutation, suggesting a pre-existing memory B-cell origin (Abstract; page not provided). It does not show that vaccination often elicits memory B cells that undergo new somatic hypermutation, or establish that this process broadens responses to variant SARS-CoV-2 spike proteins. (LLM, conf=0.85)
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Partly supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Of convalescent plasma samples, about 40% had 3-fold to 10-fold and 15% had >10-fold reduced neutralizing activity 100,122,234 .”
What the sources say
- Partly supportedcites [100] Liu, C. et al. Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum. Cell 184, 4220–4336 (2021). sourceExperimental — accuracy not yet measured
The Results section, ‘Neutralization of B.1.617.1 by convalescent serum’ (page unavailable), reports reduced neutralization of the Kappa variant in convalescent samples, including a 3.9-fold reduction in geometric mean titer for B.1.617.1-B. It does not report that about 40% of samples had 3- to 10-fold reductions or that 15% had reductions greater than 10-fold; a group mean cannot establish those sample-level proportions. (LLM, conf=0.84)
- Partly supportedcites [122] Edara, V. V. et al. Infection and Vaccine-Induced Neutralizing-Antibody Responses to the SARS-CoV-2 B.1.617 Variants. N. Engl. J. Med. 385, 664–666 (2021) sourceExperimental — accuracy not yet measured
The paper’s main text (page unavailable) reports reduced neutralizing activity against B.1.617.1 (Kappa) in convalescent serum, including a lower geometric mean titer than against WA1/2020. It does not report that about 40% of samples had a 3- to 10-fold reduction or that 15% had a greater-than-10-fold reduction. (LLM, conf=0.86)
- Partly supportedcites [234] Hoffmann, M. et al. SARS-CoV-2 variant B.1.617 is resistant to bamlanivimab and evades antibodies induced by infection and vaccination. Cell Rep. 36, 109415 (2021). sourceExperimental — accuracy not yet measured
The Results section ('Diminished neutralization by plasma from COVID-19 convalescent patients'; page unavailable) reports reduced neutralization of B.1.617 by plasma from 15 patients, averaging about 2-fold. It does not report that about 40% of samples had 3- to 10-fold reductions or that 15% had reductions greater than 10-fold. (LLM, conf=0.88)
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Partly supported
None of the sources cited for this claim have been checked yet.
In the paper
“The Alpha variant is susceptible to neutralization by most neutralizing mAbs as well as by most plasma samples from previously infected persons 97,102,121,149,159,[203][204][205][206] (fIg.5).”
What the sources say
- Not checked yetcites [97] Chen, X. et al. Neutralizing antibodies against SARS-CoV-2 variants induced by natural infection or vaccination: a systematic review and pooled meta-analysis. Clin. Infect. Dis. https://doi.org/10.1093/cid/ciab646 (2021). This paper presents a systematic review and meta-analysis of in vitro neutralization studies of SARS-CoV-2 variants by convalescent and vaccinee plasma. source
- Not checked yetcites [102] Supasa, P. et al. Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera. Cell 184, 2201–2211 (2021). source
- Not checked yetcites [121] Wang, P. et al. Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7. Nature 593, 130–135 (2021). This paper presents a comprehensive analysis of the effects of Alpha and Beta variant mutations on antibody neutralization. source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“The fact that the Alpha variant is rarely associated with reduced susceptibility to convalescent plasma is consistent with it not being associated with an increased risk of reinfection 207 .”
What the sources say
- Not checked yetcites [207] Graham, M. S. et al. Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study. Lancet Public Health 6, e335–e345 (2021). source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“associated with increased transmissibility, increased risk of reinfection and/or reduced vaccine efficacy”
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: unclear — It is unclear why the paper says it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“The Beta variant is associated with reduced susceptibility to many mAbs because E484K interferes with binding of several RBM class 1 and 2 mAbs and K417N interferes with the binding of several RBM class 1 mAbs 104,117,121,163,217 .”
What the sources say
- Not checked yetcites [104] Zhou, D. et al. Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine induced sera. Cell 184, 2348–2361 (2021). source
- Not checked yetcites [117] Chen, R. E. et al. Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Nat. Med. 27, 717–726 (2021). source
- Not checked yetcites [121] Wang, P. et al. Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7. Nature 593, 130–135 (2021). This paper presents a comprehensive analysis of the effects of Alpha and Beta variant mutations on antibody neutralization. source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“E484K has resulted in 3-fold to 10-fold reduced susceptibility to about 30% and >10-fold reduced susceptibility to about 10% of convalescent plasma samples”
What the sources say
- Not checked yetcites [121] Wang, P. et al. Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7. Nature 593, 130–135 (2021). This paper presents a comprehensive analysis of the effects of Alpha and Beta variant mutations on antibody neutralization. source
- Not checked yetcites [130] Greaney, A. J. et al. Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition. Cell Host Microbe 29, 44–57.e9 (2021). source
- Not checked yetcites [160] Liu, Z. et al. Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Cell Host Microbe 29, 477–488.e4 (2021). source
plaindirect- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“The Alpha variant also contains several non-spike mutations including nsp6:Δ106-108 and the nucleocapsid mutations D3L, R203K and G204R, which may increase transmission by antagonizing innate immunity 25,[185][186][187] .”
What the sources say
- Not checked yetcites [25] Martin, D. P. et al. The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. Preprint at medRxiv https://doi.org/10.1101/2021.02.23.21252268 (2021). source
- Not checked yetcites [185] Thorne, L. G. et al. Evolution of enhanced innate immune evasion by the SARS-CoV-2 B.1.1.7 UK variant. Preprint at bioRxiv https://doi.org/10.1101/2021.06.06.446826 (2021). This systems biology study shows that in contrast to earlier SARS-CoV-2 variants, the alpha variant may owe its increased transmissibility and virulence to its antagonism of cellular innate immunity. source
- Not checked yetcites [186] Jiang, H. et al. SARS-CoV-2 Orf9b suppresses type I interferon responses by targeting TOM70. Cell Mol. Immunol. 17, 998–1000 (2020). source
hedgedconditional- Asserted: passes — The authors put it forward as true.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“N501Y increases ACE2 affinity 128,146,147 and increases virus replication in human upper-airway cells and in the upper respiratory tracts of hamsters 127”
What the sources say
- Not checked yetcites [128] Starr, T. N. et al. Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding. Cell 182, 1295–1310.e20 (2020). source
- Not checked yetcites [146] Zhu, X. et al. Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. PLoS Biol. 19, e3001237 (2021).
- Not checked yetcites [127] Liu, Y. et al. The N501Y spike substitution enhances SARS-CoV-2 transmission. Preprint at bioRxiv https://doi.org/10.1101/2021.03.08.434499 (2021). source
plaindirect- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
In the paper
“In the previously cited Qatar cohort study, the efficacy of BNT162b against the Beta variant was estimated to be 72%, which was 15% lower than that for the Alpha variant 211 .”
What the sources say
- Not checked yetcites [211] Abu-Raddad, L. J., Chemaitelly, H. & Butt, A. A. Effectiveness of the BNT162b2 Covid-19 Vaccine against the B.1.1.7 and B.1.351 Variants. N. Engl. J. Med. 385, 187-189 (2021). source
hedged- Asserted: passes — The authors put it forward as true.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Even though E484Q is more likely than T478K to evade antibody neutralization 48,100,165 , only the Delta variant has demonstrated increased transmissibility, spreading to 54 countries and rapidly replacing the Alpha variant in the UK 32,35 and the USA 33 .”
What the sources say
- Not checked yetcites [48] Weisblum, Y. et al. Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants. eLife 9, e61312 (2020). source
- Not checked yetcites [100] Liu, C. et al. Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum. Cell 184, 4220–4336 (2021). source
- Not checked yetcites [165] Ferreira, I. et al. SARS-CoV-2 B.1.617 mutations L452 and E484Q are not synergistic for antibody evasion. J. Infect. Dis. https://doi.org/10.1093/infdis/jiab368 (2021). source
boosteddirect- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
In the paper
“It also contains five NTD mutations, of which L18F has been shown to interfere with the binding of NTD-targeting neutralizing antibodies 51 .”
What the sources say
- Not checked yetcites [51] McCallum, M. et al. N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2. Cell 184, 2332–2347.e16 (2021). source
plaindirect- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
In the paper
“It was estimated to result in virus levels 3-4 times higher than earlier variants and to be responsible for an estimated 1.1-fold to 1.8-fold higher mortality 19 .”
What the sources say
- Not checked yetcites [19] Faria, N. R. et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science 372, 815–821 (2021). This paper presents an analysis showing that the Gamma variant is about twofold more transmissible than previous variants in Manaus, Brazil, and that it poses an increased risk of reinfection compared with previous variants. source
hedgeddirect- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Of the five FDA EUA-approved mAbs, bamlanivimab, etesevimab and casirivimab are largely inactive against B.1.351whereas imdevimab and sotrovimab, which bind to the RBD core, retain neutralizing activity 104,109,117,175,204 (TABLe 1).”
What the sources say
- Not checked yetcites [104] Zhou, D. et al. Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine induced sera. Cell 184, 2348–2361 (2021). source
- Not checked yetcites [109] Copin, R. et al. The monoclonal antibody combination REGEN-COV protects against SARS-CoV-2 mutational escape in preclinical and human studies. Cell 184, 3949–3961 (2021). source
- Not checked yetcites [117] Chen, R. E. et al. Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Nat. Med. 27, 717–726 (2021). source
plain- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“As the Gamma variant was associated with a surge of infections in a region of Brazil estimated to have achieved a high infection rate, it is suspected of being able to infect and cause illness in persons previously infected with other variants 19,29,30 .”
What the sources say
- Not checked yetcites [19] Faria, N. R. et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science 372, 815–821 (2021). This paper presents an analysis showing that the Gamma variant is about twofold more transmissible than previous variants in Manaus, Brazil, and that it poses an increased risk of reinfection compared with previous variants. source
- Not checked yetcites [29] Buss, L. F. et al. Three-quarters attack rate of SARS-CoV-2 in the Brazilian Amazon during a largely unmitigated epidemic. Science 371, 288–292 (2021). source
- Not checked yetcites [30] Sabino, E. C. et al. Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence. Lancet 397, 452–455 (2021). source
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Of convalescent plasma samples, about 40% display 3-fold to 10-fold and 10% display >10-fold reduced Iota variant neutralizing activity 166,235 .”
What the sources say
- Not checked yetcites [166] Zhang, L. et al. Comparison of 10 emerging SARS-CoV-2 variants: infectivity, animal tropism, and antibody neutralization. Preprint at Research Square https://doi.org/10.21203/rs.3.rs-492659/v1 (2021). source
- Not checked yetcites [235] Zhou, H. et al. B.1.526 SARS-CoV-2 variants identified in new york city are neutralized by vaccine-elicited and therapeutic monoclonal antibodies. mBio https://doi.org/10.1128/mBio.01386-21 (2021). source
plain- Asserted: passes — The authors put it forward as true.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Although SARS-CoV-2 variants differ in their transmission rates, disease severity and risk of reinfection, there is no evidence that they are differentially affected by non-pharmaceutical public health measures such as social distancing and the use of personal protective equipment, or that they will respond differently to most antiviral therapies.”
plain- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
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It may state two separate claims as one.
In the paper
“The Zeta variant was common in Brazil in late 2020 and early 2021 (ref. 157 ), but appears to be decreasing in prevalence.”
What the sources say
- Not checked yetcites [157] Ferrareze, P. A. G. et al. E484K as an innovative phylogenetic event for viral evolution: genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. Infect. Genet. Evol. 93, 104941 (2021). source
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The two most recently approved mAb preparations, casirivimab/imdevimab and sotrovimab, retain activity against all VOCs and VOIs, in part because imdevimab and sotrovimab target the RBD core whereas the most prevalent immune escape mutations are in the RBD RBM.”
plaindirect- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
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It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“The Theta variant was first reported in March 2021 in the Philippines.It contains 13 lineage-defining mutations including N501Y, E484K, P681H and the NTD deletion at positions 141-143 (refs 155,156 ).”
What the sources say
- Not checked yetcites [155] Bascos, N. A. D., Mirano-Bascos, D. & Saloma, C. P. Structural analysis of spike protein mutations in an emergent SARS-CoV-2 variant from the Philippines. Preprint at bioRxiv https://doi.org/10.1101/2021.03.06.434059 (2021). source
- Not checked yetcites [156] Tablizo, F. A. et al. Genome sequencing and analysis of an emergent SARS-CoV-2 variant characterized by multiple spike protein mutations detected from the Central Visayas Region of the Philippines. Preprint at bioRxiv https://doi.org/10.1101/2021.03.03.21252812 (2021). source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Of plasma samples from recipients of an mRNA vaccine, approximately 55% had 3-fold to 10-fold and 5% had >10-fold reduced neutralizing activity 100,118,122,234 .”
What the sources say
- Not checked yetcites [100] Liu, C. et al. Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum. Cell 184, 4220–4336 (2021). source
- Not checked yetcites [118] Liu, J. et al. BNT162b2-elicited neutralization of B.1.617 and other SARS-CoV-2 variants. Nature 596, 273–275 (2021). source
- Not checked yetcites [122] Edara, V. V. et al. Infection and Vaccine-Induced Neutralizing-Antibody Responses to the SARS-CoV-2 B.1.617 Variants. N. Engl. J. Med. 385, 664–666 (2021) source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“The Iota variant was first identified in New York state.In June 2021, it had a prevalence of 5-10% in the USA but remained rare outside the USA 154 .”
What the sources say
- Not checked yetcites [154] Annavajhala, M. K. et al. A novel SARS-CoV-2 variant of concern, B.1.526, identified in New York. Preprint at bioRxiv https://doi.org/10.1101/2021.02.23.21252259 (2021). source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The Beta and Gamma variants are each associated with increased transmissibility because of their ability to evade humoral immunity and cause reinfections.”
plaincorrelational- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
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It may state two separate claims as one.
In the paper
“AY.1 and AY.2 are recently reported sub-lineages of the Delta variant that have developed additional mutations including the RBD mutation K417N (ref. 196 ).”
What the sources say
- Not checked yetcites [196] Mullen, J. L. et al. Outbreak.info https://outbreak.info/citation (2020).
plain- Asserted: passes — The authors put it forward as true.
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- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“It is highly prevalent in several South American countries and is associated with reduced susceptibility to the locally used CoronaVac vaccine 238 .”
What the sources say
- Not checked yetcites [238] Acevedo, M. L. et al. Infectivity and immune escape of the new SARS-CoV-2 variant of interest Lambda. Preprint at medRxiv https://doi.org/10.1101/2021.06.28.21259673 (2021). source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“In case-control studies from the UK, the BNT162b vaccine was approximately 85% effective for the Delta variant whereas the AZD1222 vaccine was approximately 60% effective 232,233 .”
What the sources say
- Not checked yetcites [232] Bernal, J. L. et al. Effectiveness of COVID-19 vaccines against the B.1.617.2 variant. N. Engl. J. Med. 385, 585–594 (2021). source
- Not checked yetcites [233] Sheikh, A., McMenamin, J., Taylor, B. & Robertson, C. SARS-CoV-2 Delta VOC in Scotland: demographics, risk of hospital admission, and vaccine effectiveness. Lancet 397, 2461–2462 (2021). source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“It was estimated to be about 20% more transmissible than co-circulating lineages and to be associated with twofold higher upper-airway virus levels 123,192 .”
What the sources say
- Not checked yetcites [123] Deng, X. et al. Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant. Cell 184, 3426–3437.e8 (2021). source
- Not checked yetcites [192] Peng, J. et al. Estimation of secondary household attack rates for emergent spike L452R SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco. Clin. Infect. Dis. https://doi.org/10.1093/cid/ciab283 (2021). source
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“The levels of neutralizing mAbs elicited by the mRNA vaccines has been high and in most persons are likely to be maintained for many months above the levels required for protection against even the most resistant circulating variants 164,239,240 .”
What the sources say
- Not checked yetcites [164] Greaney, A. J. et al. Antibodies elicited by mRNA-1273 vaccination bind more broadly to the receptor binding domain than do those from SARS-CoV-2 infection. Sci. Transl Med. 13, eabi9915 (2021). source
- Not checked yetcites [239] Wang, Z. et al. Naturally enhanced neutralizing breadth against SARS-CoV-2 one year after infection. Nature 595, 426–431 (2021). source
- Not checked yetcites [240] Turner, J. S. et al. SARS-CoV-2 mRNA vaccines induce persistent human germinal centre responses. Nature https://doi.org/10.1038/s41586-021-03738-2 (2021). source
hedgeddirect- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
In the paper
“The Eta variant is present at low levels in many countries, with Nigeria having the highest proportion of infections 236 .”
What the sources say
- Not checked yetcites [236] Ozer, E. A. et al. High prevalence of SARS-CoV-2 B.1.1.7 (UK variant) and the novel B.1.525 lineage in Oyo State, Nigeria. Preprint at medRxiv https://doi.org/10.1101/2021.04.09.21255206 (2021). source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“It results in approximately 3-fold to 10-fold reduced susceptibility to 45% and >10-fold reduced susceptibility to 5% of convalescent plasma samples 100,118,214,215,231 (fIg.5).”
What the sources say
- Not checked yetcites [100] Liu, C. et al. Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum. Cell 184, 4220–4336 (2021). source
- Not checked yetcites [118] Liu, J. et al. BNT162b2-elicited neutralization of B.1.617 and other SARS-CoV-2 variants. Nature 596, 273–275 (2021). source
- Not checked yetcites [214] Planas, D. et al. Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization. Nature 596, 276–280 (2021). source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
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It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The Alpha and Delta variants are each associated with increased transmissibility and greater disease severity because of immune evasion, and potentially because of higher virus levels resulting from the antagonism of innate immunity.”
hedgeddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: unclear — It is unclear why the paper says it holds.
It may state two separate claims as one.
In the paper
“This paper presents a meta-analysis showing that the level of neutralizing antibodies elicited by a vaccine is strongly correlated with its efficacy.”
What the sources say
- Not checked yetcites Khoury, D. S. et al.
boostedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“This post-hoc analysis of a clinical trial shows that the beta variant was frequently responsible for reinfections in South Africa.”
What the sources say
- Not checked yetcites Shinde, V. et al.
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“This study demonstrates the likely importance of SARS-CoV-2 neutralizing mAb Fc-effector functions in an animal model.”
What the sources say
- Not checked yetcites Schäfer, A. et al.
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“This post-hoc analysis of a clinical trial shows that AZD1222 appeared ineffective at preventing infection with the beta variant.”
What the sources say
- Not checked yetcites Madhi, S. A. et al.
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“This experimental study shows that the plasma from persons infected with the beta variant can usually neutralize pre-variant viruses.”
What the sources say
- Not checked yetcites Moyo-Gwete, T. et al.
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“This systems biology study shows that in contrast to earlier SARS-CoV-2 variants, the alpha variant may owe its increased transmissibility and virulence to its antagonism of cellular innate immunity.”
What the sources say
- Not checked yetcites Thorne, L. G. et al.
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“This paper demonstrates that a high proportion of neutralizing antibodies elicited by SARS-CoV-2 infection will bind poorly to epitopes containing the spike RBD mutation E484K.”
What the sources say
- Not checked yetcites Greaney, A. J. et al.
boostedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“These VOCs exhibit increased transmissibility and/or immune evasion, traits that have been linked to mutations in the viral spike (S) protein”
From The Omicron variant is highly resistant against antibody-mediated neutralization: Implications for control of the COVID-19 pandemic (2022) · cites this paper as Tao et al., 2021
Citations
Cites
Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine
Polack, F. P., Thomas, S. J., Kitchin, N., Absalon, J., Gurtman, A., Lockhart, S., Perez, J. L., Pérez Marc, G., Moreira, E. D., Zerbini, C., et al. (2020) · New England Journal of Medicine · doi:10.1056/nejmoa2034577 · Cited by 14,592
Efficacy and Safety of the mRNA-1273 SARS-CoV-2 Vaccine
Baden, L. R., El Sahly, H. M., Essink, B., Kotloff, K., Frey, S., Novak, R., Diemert, D., Spector, S. A., Rouphael, N., Creech, C. B., et al. (2021) · New England Journal of Medicine · doi:10.1056/nejmoa2035389 · Cited by 10,119
Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation
Wrapp, D., Wang, N., Corbett, K. S., Goldsmith, J. A., Hsieh, C.-L., Abiona, O., Graham, B. S., & McLellan, J. S. (2020) · Science · doi:10.1126/science.abb2507 · Cited by 8,897
Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein
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Masuda, Y., Nasser, H., Zahradník, J., Mitoma, S., Shimizu, R., Nagata, K., Takaori‐Kondo, A., Schreiber, G., Shirakawa, K., Saito, A., et al. (2023) · Frontiers in Virology · doi:10.3389/fviro.2023.1328229 · Cited by 6
Reis, A. C., Pinto, D., Monteiro, S., Santos, R., Martins, J. V., Sousa, A., Páscoa, R., Lourinho, R., & Cunha, M. V. (2023) · medRxiv · doi:10.1101/2023.10.30.23297774 · Cited by 5
Identification of conserved immunogenic peptides of SARS-CoV-2 nucleocapsid protein
Verma, J., Kaushal, N., Manish, M., Subbarao, N., Shakirova, V., Martynova, E., Liu, R.-Z., Hamza, S., Rizvanov, A., Khaiboullina, S., et al. (2023) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2023.2260484 · Cited by 5
“These mutation could facilitate virus entry as was shown with N501Y mutation in alpha, beta and gamma strains which increased binding affinity of S protein with ACE2 receptor (Tao et al., 2021).”
Naim, M. L., Fu, Y., Shagan, M., Bar-Or, I., Marks, R. S., Sun, Q., Granek, R., & Kushmaro, A. (2023) · Viruses · doi:10.3390/v15091862 · Cited by 5
Asashima, H., Kim, D., Wang, K., Lele, N., Buitrago-Pocasangre, N., Lutz, R., Cruz, I., Raddassi, K., Ruff, W. E., Racke, M. K., et al. (2023) · JCI Insight · doi:10.1172/jci.insight.168102 · Cited by 5
“Patients on B cell depletion therapy often fail to effectively clear SARS-CoV-2 after infection, which can lead to prolonged periods of viral replication, viral mutation, and new variant emergence within the same host (27–29).”
BackgroundAbduljaleel, Z., Melebari, S., Athar, M., Dehlawi, S., Kumar, S., Aziz, S. A. A., Dannoun, A., Malik, S. M., Thasleem, J., & Doss, C. (2023) · Cellular Signalling · doi:10.1016/j.cellsig.2023.110798 · Cited by 5
Chrysostomou, A. C., Vrancken, B., Haralambous, C., Alexandrou, M., Aristokleous, A., Christodoulou, C., Gregoriou, I., Ioannides, M., Kalakouta, O., Karagiannis, C., et al. (2022) · Viruses · doi:10.3390/v15010108 · Cited by 14
“Although these four referenced VOCs exhibited increased transmissibility, the Beta and Gamma variants were initially associated with a higher degree of concern due to mutations in the spike gene, which were reported to confer reduced susceptibility to antibodies and to decrease vaccine efficacy [11,22].”
BackgroundIqbal, R., Khan, S., Ali, H. M., Khan, M., Wahab, S., & Khan, T. (2022) · Frontiers in Nanotechnology · doi:10.3389/fnano.2022.1060756 · Cited by 11
ViralVar: A Web Tool for Multilevel Visualization of SARS-CoV-2 Genomes
Alisoltani, A., Jaroszewski, L., Godzik, A., Iranzadeh, A., Simons, L. M., Dean, T. J., Lorenzo-Redondo, R., Hultquist, J., & Ozer, E. A. (2022) · Viruses · doi:10.3390/v14122714 · Cited by 5
“The majority of studies using phylogenetic trees to study SARS-CoV-2 variants of concern (VOCs), therefore, must rely on subsampling approaches [52,53].”
BackgroundChest CT Findings in Hospitalized Patients with SARSCoV-2: Delta versus Omicron Variants.
Yoon, S., Lee, J. H., & Kim, B.-N. (2022) · Radiology · doi:10.1148/radiol.229022 · Cited by 5
“S the COVID-19 pandemic began, SARS-CoV-2 has evolved through genetic mutations during viral replication (1,2).”
Olmstead, A. D., Nikiforuk, A. M., Schwartz, S., Márquez, A. C., Valadbeigy, T., Flores, E., Saran, M., Goldfarb, D. A., Hayden, A. S., Masud, S., et al. (2022) · Viruses · doi:10.3390/v14112416 · Cited by 8
A Simplified Sanger Sequencing Method for Detection of Relevant SARS-CoV-2 Variants
Deminco, F., Vaz, S. N., de Santana, D. S., Pedroso, C., Tadeu, J., Stöcker, A., Vieira, S. M., Netto, E. M., & Brites, C. R. (2022) · Diagnostics · doi:10.3390/diagnostics12112609 · Cited by 5
“SARS-CoV-2, a new coronavirus that causes a severe acute respiratory syndrome (COVID-19), was first reported in December 2019 [1] and soon after became a pandemic due to its high transmission rate, which favored the formation of new genomic mutations and contributed to the emergence of new variants [2].”
BackgroundInfluentialBiological characterization of cold-adapted SARS-CoV-2 variants
Faĭzuloev, E., Korchevaya, E., Gracheva, A., Samoilikov, R., Smirnova, D., Sokolova, O., Glukhov, G., Moiseenko, A. V., Leneva, I., Nagieva, F. G., et al. (2022) · Journal of microbiology, epidemiology and immunobiology · doi:10.36233/0372-9311-280 · Cited by 5
Prospects of animal models and their application in studies on adaptive immunity to SARS-CoV-2
Wei, X., Rong, N., & Liu, J. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.993754 · Cited by 6
“html), which has had an impact on global public security and the global economy (1, 2).”
BackgroundIn silico design of refined ferritin-SARS-CoV-2 glyco-RBD nanoparticle vaccine
Nomandan, S. Z. M., Irani, M. A., & Hosseini, S. M. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.976490 · Cited by 5
Cortés-Sarabia, K., Luna-Pineda, V., Rodríguez-Ruíz, H., Leyva-Vázquez, M., Hernández-Sotelo, D., Beltrán-Anaya, F., Vences-Velázquez, A., del Moral-Hernández, O., & Illades-Aguiar, B. (2022) · Scientific Reports · doi:10.1038/s41598-022-18517-w · Cited by 5
Veleanu, A., Kelch, M. A., Ye, C.-J., Flohr, M., Wilhelm, A., Widera, M., Martínez-Sobrido, L., Ciesek, S., & Toptan, T. (2022) · Viruses · doi:10.3390/v14092017 · Cited by 5
RETRACTED: The pathogenicity of COVID-19 and the role of pentraxin-3: An updated review study
Margiana, R., Sharma, S. K., Khan, B. I., Alameri, A. A., Opulencia, M. J. C., Hammid, A. T., Hamza, T. A., Хамракулович, Б. Ш., Abdelbasset, W. K., & Jawhar, Z. H. (2022) · Pathology - Research and Practice · doi:10.1016/j.prp.2022.154128 · Cited by 5
RetractedWhy do some coronaviruses become pandemic threats when others do not?
Rice, B. L., Lessler, J., McKee, C., & Metcalf, C. J. E. (2022) · PLoS Biology · doi:10.1371/journal.pbio.3001652 · Cited by 4
“Comparisons of the genetic characteristics of SARS-CoV-2 variants [81] and MERS-CoV strains [82], alongside sequence analyses [79], competition-based assays and structural biophysics [83–85], and cell line [78,86] and experimental infections [78] are beginning to yield insights into the functionality of a range of cor…”
BackgroundGenomic Epidemiology of SARS-CoV-2 in Seychelles, 2020–2021
Morobe, J., Pool, B., Marie, L., Didon, D., Lambisia, A., Makori, T., Mohammed, K., de Laurent, Z. R., Ndwiga, L., Mburu, M., et al. (2022) · medRxiv · doi:10.3390/v14061318 · Cited by 5
“Further, in the last quarter of 2021, Omicron SARS-CoV-2 variants of concern (VOCs) were detected globally [4,5].”
BackgroundCong, M., Yang, Y., Tong, H., Shimu, A. S., Wang, B.-L., Li, Q., Li, F.-Y., Yang, Y., Jin, T.-C., & Li, B.-F. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-00937-9 · Cited by 5
Booster doses for inactivated COVID-19 vaccines: if, when, and for whom
Croda, J., & Ranzani, O. (2021) · Lancet. Infectious Diseases (Print) · doi:10.1016/s1473-3099(21)00696-4 · Cited by 5
Development of a potent monoclonal antibody for treatment of human metapneumovirus infections
Harris, E. D., McGovern, M., Pernikoff, S., Ikeda, R., Kipnis, L., Hannon, W. W., Sobolik, E. B., Gray, M. D., Greninger, A. L., He, S., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-69328-w · Cited by 8
Xie, M.-X., Qiu, Y.-N., Zhao, X.-Y., Shi, J.-L., Liu, Y., Zhang, Q., He, J., Li, J.-Y., Liu, L., Sun, S., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-65596-0 · Cited by 4
Compromised efferocytosis during aging is related to COVID-19 severity in mice
Ke, X., Lin, X., Wang, J., Chen, M., Jian, X., Ye, C., & Chen, Q.-J. (2025) · Virologica Sinica · doi:10.1016/j.virs.2025.05.008 · Cited by 4
Collins, C. P., Herzog, C., Vick, L. V., Nielsen, R. N., Harville, Y. I., Longo, D. L., Arthur, J. M., & Murphy, W. J. (2025) · Vaccines · doi:10.3390/vaccines13030224 · Cited by 5
“The continuous emergence of CoV2 variants also necessitates the generation of newer vaccine constructs that adapt the immunogen to the spike protein of the subtype currently causing disease in the community and seasonal boosts [6].”
Aggravating mechanisms from COVID-19
Lee, J., Sergi, C. M., Kast, R. E., Kanwar, B. A., Altschuler, E. L., Bourbeau, J., Sohn, M.-G., Sohn, M.-G., Lee, K. H., & Coleman, M. D. (2024) · Virology Journal · doi:10.1186/s12985-024-02506-8 · Cited by 6
Mi, Y., Xu, K., Wang, W., Kong, W., Xu, X., Rong, X., & Tan, J. (2024) · Vaccines · doi:10.3390/vaccines12080927 · Cited by 4
Structural impact of synonymous mutations in six SARS-CoV-2 Variants of Concern
Ziesel, A., & Jabbari, H. (2025) · PLoS ONE · doi:10.1371/journal.pone.0325858 · Cited by 3
“An excellent review of the major VoCs prior to the summer of 2021 is available [8].”
Motlagh, F. G., Irani, M. A., Nomandan, S. Z. M., & Assadizadeh, M. (2024) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2024.1403635 · Cited by 4
Jeong, G. U., Hwang, I., Lee, W., Choi, J. H., Yoon, G. Y., Kim, H. S., Yang, J., Kim, K.-C., Lee, J.-Y., Kim, S., et al. (2024) · Experimental & Molecular Medicine · doi:10.1038/s12276-024-01197-z · Cited by 4
A program for real-time surveillance of SARS-CoV-2 genetics
Brochu, H., Song, K., Zhang, Q., Zeng, Q.-D., Shafi, A., Robinson, M., Humphrey, J., Croy, B., Peavy, L., Perera, M., et al. (2024) · Scientific Reports · doi:10.1038/s41598-024-70697-9 · Cited by 4
Comparative epidemiology of outbreaks caused by SARS-CoV-2 Delta and Omicron variants in China
Peng, L., Huang, X.-T., Wang, C., Xin, H.-L., Cowling, B., Wu, P., & Tsang, T. (2024) · Epidemiology and Infection · doi:10.1017/s0950268824000360 · Cited by 4
“SARS-CoV-2 has evolved and emerged into multiple variants, including Alpha, Beta, Delta [2], and Omicron [3].”
BackgroundFan, J., Li, S., Zhang, Y., Zheng, J., Wang, D., Liao, Y., Cui, Z., Zhao, D., Barouch, D. H., & Yu, J. (2023) · Viruses · doi:10.3390/v15122401 · Cited by 4
Xia, W., Jiang, T., Tan, Y., Li, C.-B., Wu, S., & Mei, B. (2023) · BMC Infectious Diseases · doi:10.1186/s12879-023-08771-2 · Cited by 4
“Subsequently, the WHO has identified several novel variants of concern (VOC) of the SARS-CoV-2 virus, including Alpha, Beta, Gamma, and Delta, which have consecutively been detected in numerous countries [3].”
BackgroundKim, T.-H., Bae, S., Goo, S., & Myoung, J. (2023) · Journal of Microbiology and Biotechnology · doi:10.4014/jmb.2308.08020 · Cited by 6
“As a result, coronaviruses generally exhibit a lower mutation rate during replication compared to other RNA viruses such as influenza viruses, roughly by 10-fold [15].”
BackgroundSpecific immune responses after BNT162b2 mRNA vaccination and COVID-19 infection
Arientová, S., Matúšková, K., Bartoš, O., Holub, M., & Beran, O. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1271353 · Cited by 5
Negi, V., Gavlock, D. C., Miedel, M. T., Lee, J. K., Shun, T., Gough, A., Vernetti, L. A., Stern, A. M., Taylor, D. L., & Yechoor, V. K. (2023) · Lab on a Chip · doi:10.1039/d3lc00285c · Cited by 6
Genomic analysis of SARS-CoV-2 variants: diagnosis and vaccination challenges
Abbasi, H., Behrouzikhah, M., Divbandi, M., Tabaraei, A., Khosravi, A., & Nikoo, H. R. (2023) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2023.2252069 · Cited by 4
“During the seventh wave of this pandemic, some variants harboring different mutations are associated with changes in the virus behavior, including increased transmissibility, increased virulence, and evasion of neutralizing antibodies (Weisblum et al., 2020, Tao et al., 2021).”
BackgroundLi, J., Li, X., Mao, H., Huang, C., Sun, Y., Miao, L., Li, J., Song, W., Zhang, Y., Huang, J., et al. (2023) · Virus Research · doi:10.1016/j.virusres.2023.199131 · Cited by 4
“, 2021), and D614G, which enhances viral replication and transmission (Tao et al., 2021; Zhou et al., 2021).”
SARS-CoV-2 Omicron subvariant spike N405 unlikely to rapidly deamidate
Beaudoin, C. A., Petsolari, E., Hamaia, S., Hala, S., Alofi, F., Pandurangan, A., Blundell, T., Vedithi, S. C., Huang, C. L.-H., & Jackson, A. (2023) · Biochemical and Biophysical Research Communications - BBRC · doi:10.1016/j.bbrc.2023.04.088 · Cited by 4
“1)) have arisen since the initial outbreak[1].”
Mechanism of an RBM-targeted rabbit monoclonal antibody 9H1 neutralizing SARS-CoV-2
Chu, X., Ding, X., Yang, Y., Lu, Y., Li, T., Gao, Y., Zheng, L., Xiao, H., Yang, T., Cheng, H., et al. (2023) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2023.04.002 · Cited by 4
King, E. R., Garrett, H., Abernathy, H. A., Cassidy, C., Cabell, C., Shook-Sa, B., Juliano, J., Boyce, R. M., Aiello, A. E., & Ciccone, E. (2023) · medRxiv · doi:10.1101/2023.03.13.23286935 · Cited by 4
“However, household phlebotomy visits pose a risk of COVID-19 transmission between participants and staff, especially as new variants that are more transmissible become more prevalent (1).”
BackgroundEvaluating COVID-19 vaccine allocation policies using Bayesian m-top exploration
Cimpean, A., Verstraeten, T., Willem, L., Hens, N., Now'e, A., & Libin, P. J. K. (2023) · Scientific Reports · doi:10.1038/s41598-026-40787-x · Cited by 4
“We consider the Alpha VoC variant of SARS-CoV-2, which is 50% more infectious compared to previously circulating variants [58].”
Hsu, C.-Y., Chang, J., Chen, S. L.-S., Chang, H., Lin, T.-Y., Yen, A. M.-F., & Chen, H.-H. (2022) · Journal of Infection and Public Health · doi:10.1016/j.jiph.2022.11.028 · Cited by 4
“However, the waning in the protective effect of vaccination and the emergence of VOCs with the characteristic of immune escape render the booster vaccination required for maintaining the immunity at population level [1-5, 40-42].”
BackgroundZhang, Y., Zhang, X., Zheng, H., & Liu, L. (2022) · Biomolecules · doi:10.3390/biom12111680 · Cited by 5
“Mutant strains can increase the viral transmission rate and risk of reinfection, reduce the protection provided by monoclonal neutralizing antibodies and vaccines [65], and enable SARS-CoV-2 to maintain or improve replication fitness [6], allowing it to continue to spread under the conditions of continuously growing h…”
BackgroundA Robust, Highly Multiplexed Mass Spectrometry Assay to Identify SARS-CoV-2 Variants
Hernandez, M., Banu, R., Shrestha, P., Gonzalez-Reiche, A., van de Guchte, A., Farrugia, K., Sebra, R., Gitman, M., Nowak, M., Cordon-Cardo, C., et al. (2022) · Microbiology spectrum · doi:10.1128/spectrum.01736-22 · Cited by 4
de la Torre, E. P., Obando, I., Vidal, M., de Felipe, B., Aguilar, R., Izquierdo, L., Carolis, C., Olbrich, P., Capilla-Miranda, A., Serra, P., et al. (2022) · Viruses · doi:10.3390/v14092039 · Cited by 4
Hussey, H., Davies, M., Heekes, A., Williamson, C., Valley-Omar, Z., Hardie, D., Korsman, S., Doolabh, D., Preiser, W., Maponga, T. G., et al. (2022) · Gates Open Research · doi:10.12688/gatesopenres.13654.1 · Cited by 4
Velu, P., Cong, L., Rand, S., Qiu, Y., Zhang, Z., Zhang, J., Guo, J., Ruggiero, P., Sukhu, A. C., Fauntleroy, K. A., et al. (2022) · Diagnostic Microbiology and Infectious Disease · doi:10.1016/j.diagmicrobio.2022.115789 · Cited by 11
“While variants of SARS-CoV-2 are not new, there has been a drastic change in the number of mutations the virus has accumulated in short periods of time, causing concern around the world [2,3].”
BackgroundInfluentialMa, J., Luo, J., & Xu, M. (2022) · Annals of Translational Medicine · doi:10.21037/atm-22-3064 · Cited by 4
“The newly emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have presented even further challenges to the global anti-epidemic efforts (6-8).”
BackgroundMartínez, F., Muñoz, S., Guerrero-Nancuante, C., & Taramasco, C. (2022) · Biology · doi:10.3390/biology11081136 · Cited by 4
Humer, E. C., Keil, T. O. P., Stupp, C., Schlee, W., Wildner, M., Heuschmann, P. U., Winter, M. R., Probst, T., & Pryss, R. C. (2022) · JMIR Public Health and Surveillance · doi:10.2196/40958 · Cited by 6
“Since most reports were collected in 2020 and the first variants of concern emerged around the turn of 2020/2021 [26], we defined 2 categories (2020 and 2021/2022) for the calendar year variable.”
Genomic surveillance of SARS-CoV-2 in patients presenting neurological manifestations
Vicco, A., Caccuri, F., Messali, S., Vitiello, A., Emmi, A., Vecchio, C. D., Reale, A., Caruso, A., Ottaviano, G., Mucignat‐Caretta, C., et al. (2022) · PLoS ONE · doi:10.1371/journal.pone.0270024 · Cited by 5
Immunosuppression as a Hub for SARS-CoV-2 Mutational Drift
Shapira, G., Patalon, T., Gazit, S., & Shomron, N. (2022) · medRxiv · doi:10.3390/v15040855 · Cited by 4
“concern (VOCs) [13] are the product of a drastically different evolutionary process, one that is approximately four times faster [14], strongly adaptive [15], and has the capacity to accumulate multiple epistatic mutations that are individually deleterious [16].”
BackgroundThe Cross-Protective Immunity Landscape Among Different SARS-CoV-2 Variant RBDs
Sun, W., He, L., Lou, H., Fan, W., Yang, L., Cheng, G., Liu, W., & Sun, L. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.898520 · Cited by 4
A Repeat Pattern of Founder Events for SARS-CoV-2 Variants in Alaska
Haan, T. J., Smith, L., DeRonde, S., House, E., Zidek, J., Puhak, D., Mullen, L. J., Redlinger, M., Parker, J., Barnes, B. M., et al. (2023) · Viruses · doi:10.3390/v15010222 · Cited by 4
Association of Results of Four Lateral Flow Antibody Tests with Subsequent SARS-CoV-2 Infection
Findlater, L., Trickey, A., Jones, H. E., Trindall, A., Taylor‐Phillips, S., Mulchandani, R., EDSAB-HOME investigators, Oliver, I., & Wyllie, D. H. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.02468-22 · Cited by 4
“An ongoing program of field study would be required to show whether the LFIA-associated protection seen in this study extends to self-read and health care worker-read tests, to currently prevalent SARS-CoV-2 strains which may differ from the strains circulating during this study (32, 33), and (if surveillance of vacci…”
BackgroundSong, X.-C., Zhou, X.-L., Cheng, J., Zhang, W.-H., Shen, X., Xu, H., Nie, S., Xiao, J.-L., Sun, F., Shu, C., et al. (2022) · Aging · doi:10.18632/aging.204085 · Cited by 4
Alkhamis, M., Fountain-Jones, N. M., Khajah, M., Alghounaim, M., & Al-Sabah, S. (2022) · Virus Evolution · doi:10.1093/ve/veac040 · Cited by 4
Antibody escape and cryptic cross-domain stabilization in the SARS-CoV-2 Omicron spike protein
Javanmardi, K., Segall-Shapiro, T. H., Chou, C.-W., Boutz, D., Olsen, R. J., Xie, X.-P., Xia, H.-J., Shi, P.-Y., Johnson, C. D., Annapareddy, A., et al. (2022) · bioRxiv · doi:10.1101/2022.04.18.488614 · Cited by 4
“two interesting cases emerge: (1) mutations that are sufficient for escape in the WHU1 spike but not 218”
BackgroundYe, C., Lv, Y., Kuang, W., Yang, L., Lu, Y., Gu, J., Ding, F., Shen, H., & Yang, Y. (2022) · Journal of Medical Virology · doi:10.1002/jmv.27759 · Cited by 4
Neuromuscular complications of severe COVID-19 in paediatric patients: Medium-term follow-up
Avila-Smirnow, D., Céspedes, P., Reyes, F., Angulo, J., Cavagnaro, A., & Wegner, A. (2022) · Neuromuscular Disorders · doi:10.1016/j.nmd.2022.04.001 · Cited by 4
Ziakas, P., Kourbeti, I., & Mylonakis, E. (2022) · Open Forum Infectious Diseases · doi:10.1093/ofid/ofac006 · Cited by 4
“2) [4], which exhibits an elevated transmissibility compared to the Alpha variant [5–7].”
BackgroundOuissa, R., Guillou, C. L., Broudic, M., Markowicz, S., Curlier, E., & Roger, P.-M. (2022) · Infectious Diseases Now · doi:10.1016/j.idnow.2022.02.006 · Cited by 4
Collection of Monoclonal Antibodies Targeting SARS-CoV-2 Proteins
Matešić, M. P., Brlić, P. K., Roviš, T. L., Šafranko, Ž. M., Chaouat, A., Miklić, K., Malić, S., Ivanković, N., Schubert, M., Bertoglio, F., et al. (2022) · Viruses · doi:10.3390/v14020443 · Cited by 4
“SARS-CoV-2, like other RNA viruses, is prone to the development of mutations while adapting to the human host, and multiple variants have already emerged [6].”
BackgroundLai, E., Becker, D., Brzoska, P., Cassens, T., Davis-Turak, J., Diamond, E., Furtado, M., Gandhi, M., Gort, D., Greninger, A. L., et al. (2022) · medRxiv · doi:10.1101/2022.01.08.22268865 · Cited by 4
Interpretable and Predictive Deep Modeling of the SARS-CoV-2 Spike Protein Sequence
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“[2 ] One drawback for tree-based approaches to classification is that particular variants may occur independently in different lineages, as has been observed, for example, in the N501Y substitution which has arisen in multiple clades (without any evidence for recombination).”
BackgroundMethodInfluentialEffects of COVID-19 pandemic on education and society
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Discovery of a broad-spectrum affibody ligand for COVID-19 vaccine purification.
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“As SARS-CoV-2 spread globally, it accumulated mutations, leading to the emergence of variants of concern (VOCs) such as Alpha, Beta, Gamma, Delta, and Omicron [1, 5, 6].”
Nanomaterial‐Based Optical Biosensors for SARS‐CoV‐2 Detection: A Retrospective of the Pandemic
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“Chronologically, the emergence of the beta, delta, and omicron VOCs was associated with new waves of worldwide infection, the most serious of which seemed to occur in unvaccinated individuals; individuals vaccinated against previous strains also experienced immune evasion and infection [19,20].”
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“Furthermore, differ - ent variants of the virus occurred over time (69 ).”
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Genomic and Epidemiological Surveillance of SARS-CoV-2 Epidemic in Northwestern Greece
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“Many variants of SARS-CoV-2 with novel spike protein mutations have emerged over the past few months, affecting the clinical as well as epidemiological aspects of the COVID-19 pandemic [3,4].”
In-silico evaluation of the T-cell based immune response against SARS-CoV-2 omicron variants
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“Since its identification, SARS-CoV-2 has spread rapidly and acquired new mutations, resulting in the identification of many variants with increased transmissibility, severity, and immune evasion 6 .”
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“Continued surveillance and monitoring of the virus’s genetic changes will be crucial in controlling the ongoing pandemic and developing effective treatments and vaccines [16].”
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“However, a concerning aspect is that SARS-CoV-2 continues to evolve, with mutations accumulating and recombina-52 tion processes contributing to increased diversity [10, 11].”
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“However, as a result of genetic variations in SARS-CoV-2 during viral replication to evade the human immune system and achieve self-protection, several SARS-CoV-2 variants have been reported worldwide (5, 6), with the Omicron variant notably becoming predominant (7, 8).”
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“Further comparisons of the infection rate (Tao et al. 2021) and viral loads (Pan et al. 2020) among different variants aim to provide scientific reference for control measures of new SARS-CoV-2 variants.”
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“The efficacy of these neutralizing antibodies against S glycoprotein in decreasing disease incidence suggests that antivirals that target the early events in SARS-CoV-2 viral attachment and fusion would be a successful strategy to eliminate and/or reduce the disease [13,14].”
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“There is evidence to support the theory that SARS-CoV-2 has a high potential for acquiring advantageous mutations (6, 18).”
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Single-Molecule Investigation of the Binding Interface Stability of SARS-CoV-2 Variants with ACE2
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“SARS-CoV-2 is now a stable viral infection in humans with a broad range of clinical manifestations [2,46].”
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“Furthermore, the emergence of variants with significantly altered pathogenesis has been detected.(7) New variants of SARS‐CoV‐2(8,9) with specific amino acid changes affecting mortality are also being actively investigated.”
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“Symptomatology has changed over time from the first phase, which was dominated by fever in the mildest cases to dyspnea in the most severe cases, similar to the first studies conducted during the first pandemic in hemodialysis patients [16–18] in which the symptoms evolved over time to more flu-like symptoms, possibly…”
Result
Metadata
- Authors
- Tao, K., Tzou, P. L., Nouhin, J., Gupta, R. K., de Oliveira, T., Kosakovsky Pond, S. L., Fera, D., & Shafer, R. W.
- Affiliations
- Stanford Medicine (US)
- University of Cambridge (GB)
- Swarthmore College (US)
- Corresponding author
- Shafer, Robert W.
- Venue
- Nature Reviews Genetics
- Published
- 2021-09-17
- Volume
- 22
- Issue
- 12
- Pages
- 757-773
- ISSN
- 1471-0056 (ISSN-L)
- 1471-0064
- PMC
- PMC8447121
- OpenAlex
- W3199849883
- Cited by
- 1,009
- References
- 281
- Citations by year
- 2026: 43 · 2025: 90 · 2024: 170 · 2023: 251 · 2022: 415 · 2021: 38
- FWCI
- 25.63
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Nature Reviews Genetics (publishedVersion, cc-by)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Works - Scholarship, Research, & Creative Expression (Swarthmore College) (submittedVersion)
- Funders
- University of Washington
- National Institute of Allergy and Infectious Diseases (R24AI136618)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Health Sciences › Medicine › Infectious Diseases › COVID-19 Clinical Research Studies
- Physical Sciences › Mathematics › Modeling and Simulation › COVID-19 epidemiological studies
- Keywords
- SARS-CoV-2, COVID-19 variants of concern, spike protein mutations, Alpha variant, Beta variant, Gamma variant, Delta variant, virus transmission, reinfection risk, neutralizing antibodies, vaccine effectiveness, herd immunity, viral replication fitness
- MeSH terms
- COVID-19, SARS-CoV-2, Epitopes, Biological Evolution, Humans, Mutation, Spike Glycoprotein, Coronavirus
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
A language model drew the claims from the paper on 2026-10-06, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-06 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
Cited sources are checked with a language model’s help (gpt-6-sol).
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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