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SARS-CoV-2 evolution during treatment of chronic infection
Open accessPublished version of a preprint
Abstract
The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for virus infection through the engagement of the human ACE2 protein 1 and is a major antibody target. Here we show that chronic infection with SARS-CoV-2 leads to viral evolution and reduced sensitivity to neutralizing antibodies in an immunosuppressed individual treated with convalescent plasma, by generating whole-genome ultra-deep sequences for 23 time points that span 101 days and using in vitro techniques to characterize the mutations revealed by sequencing. There was little change in the overall structure of the viral population after two courses of remdesivir during the first 57 days. However, after convalescent plasma therapy, we observed large, dynamic shifts in the viral population, with the emergence of a dominant viral strain that contained a substitution (D796H) in the S2 subunit and a deletion (ΔH69/ΔV70) in the S1 N-terminal domain of the spike protein. As passively transferred serum antibodies diminished, viruses with the escape genotype were reduced in frequency, before returning during a final, unsuccessful course of convalescent plasma treatment. In vitro, the spike double mutant bearing both ΔH69/ΔV70 and D796H conferred modestly decreased sensitivity to convalescent plasma, while maintaining infectivity levels that were similar to the wild-type virus.The spike substitution mutant D796H appeared to be the main contributor to the decreased susceptibility to neutralizing antibodies, but this mutation resulted in an infectivity defect. The spike deletion mutant ΔH69/ΔV70 had a twofold higher level of infectivity than wild-type SARS-CoV-2, possibly compensating for the reduced infectivity of the D796H mutation. These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy, which is associated with the emergence of viral variants that show evidence of reduced susceptibility to neutralizing antibodies in immunosuppressed individuals.
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“The possible theories about the origin of novel variants are the evolution of circulating intermediate mutants in the chronically infected immunocompromised patients supporting high viral replication while on treatment with immune plasma or monoclonal antibodies [88, 89].”
From Waves and variants of SARS-CoV-2: understanding the causes and effect of the COVID-19 catastrophe (2022) · cites this paper as [89]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“Previous studies showed that the binding affinity of SARS-CoV for human ACE2 correlated with the rate of viral replication in distinct species, transmissibility and disease severity 29–31.”
From Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies (2021) · cites this paper as [31]
Experimental — accuracy not yet measuredIn the citing paper
“The recent emergence of B.1.1.7,B.1.351and P.1 marks the beginning of SARS-CoV-2 antigenic drift.”
From Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7 (2021) · cites this paper as [44]
In the citing paper
“Interestingly, repeated use of plasma therapy in an immunocompromised individual led to the transient emergence of the N501Y mutation as well as the 69–70 deletion in the NTD, which is characteristic of B.1.1.7 (Kemp et al., 2021).”
From Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera (2021) · cites this paper as Kemp et al., 2021
In the citing paper
“The B.1.1.7 variant emerged in the United Kingdom, the B.1.351variant (also termed 501Y.V2) in South Africa and the P.1 and P.2 lineages in Brazil 2,3,5,9-12 .”
From Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies (2021) · cites this paper as [3]
In the citing paper
“Although distinct, the variants share common characteristics, including known escape mutations that were previously identified under antibody pressure selection in vitro 2,3,[13][14][15][16][17] .”
From Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies (2021) · cites this paper as [3]
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Ramanathan, S., Veramendi-Espinoza, L. E., Shillitoe, B. M. J., Flinn, A. M., Owens, S., Williams, E., Emonts, M., Hambleton, S., Burton-Fanning, S., Waugh, S., et al. (2022) · Journal of Allergy and Clinical Immunology Global · doi:10.1016/j.jacig.2022.08.006 · Cited by 7
“8 Available treatments include antiviral drugs, convalescent plasma, and synthetic mAbs.”
Self-citationBez, P., D’Ippolito, G., Deiana, C. M., Gambier, R. F., Pica, A., Costanzo, G. A. M. L., Garzi, G., Scarpa, R., Landini, N., Cinetto, F., et al. (2023) · Life · doi:10.3390/life13071530 · Cited by 7
Elko, E. A., Mead, H., Nelson, G. A., Zaia, J. A., Ladner, J. T., & Altin, J. A. (2024) · Microbiology Spectrum · doi:10.1128/spectrum.03291-23 · Cited by 8
“Intriguingly, D796Y occurs at the same residue as a mutation (D796H) that emerged independently in 2020 in a chronically infected patient treated with remdesivir and convalescent plasma, which was shown to confer reduced sensitivity to neutralization by convalescent plasma (11).”
BackgroundOzowe, C., Sofoluwe, O. O., Ukato, A., & Jambol, D. D. (2024) · World Journal of Advanced Research and Reviews · doi:10.30574/wjarr.2024.22.2.1468 · Cited by 7
“Emerging technologies, such as artificial intelligence and robotics, have the potential to revolutionize environmental management and operational efficiency in the industry (Kemp et al., 2021).”
Ruiz-Rodríguez, P., Francés-Gómez, C., Chiner‐Oms, Á., López, M. G., Jiménez-Serrano, S., Cancino‐Muñoz, I., Ruiz-Hueso, P., Torres‐Puente, M., Bracho, M. A., D’Auria, G., et al. (2021) · mBio · doi:10.1128/mbio.02315-21 · Cited by 8
Machado, D. J., White, R. A., III, Kofsky, J., & Janies, D. A. (2021) · Antimicrobial Stewardship & Healthcare Epidemiology · doi:10.1017/ash.2021.222 · Cited by 8
Zhang, X., Zheng, M., Liang, T., Zhou, H., Wang, H., Zhang, J., Ren, J. F., Peng, H., Li, S., Bian, H., et al. (2022) · Theranostics · doi:10.7150/thno.67038 · Cited by 7
“Unfortunately, SARS-CoV-2 is mutating, with new variants emerging nearly every week that could impede drug development and reduce the efficacy of COVID-19 vaccines [3, 4].”
BackgroundThe Infectivity and Antigenicity of Epidemic SARS-CoV-2 Variants in the United KingdomPreprint
Wang, Y., Wu, J., Zhang, L., Zhang, Y., Wang, H., Ding, R., Nie, J., Li, Q., Liu, S., Yu, Y., et al. (2021) · Research Square · doi:10.21203/rs.3.rs-153108/v1 · Cited by 7
A missense variant effect prediction and annotation resource for SARS-CoV-2Preprint
Dunham, A. S., Jang, G. Μ., Muralidharan, M., Swaney, D. L., & Beltrão, P. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.02.24.432721 · Cited by 7
“We also examined the predictions made against variants that emerged in a case study with a patient treated with convalescent antibodies (Kemp et al., 2021).”
BackgroundGarushyants, S. K., Rogozin, I. B., & Koonin, E. V. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.23.441209 · Cited by 8
Lustig, G., Ganga, Y., Rodel, H. E., Tegally, H., Jackson, L., Cele, S., Khan, K., Jule, Z., Reedoy, K., Karim, F., et al. (2022) · medRxiv · doi:10.1101/2022.11.23.22282673 · Cited by 9
Moussaoui, M. E., Bontems, S., Meex, C., Hayette, M., Lejeune, M., Hong, S. L., Dellicour, S., Moutschen, M. P., Cambisano, N., Renotte, N., et al. (2024) · Virus Evolution · doi:10.1093/ve/veae073 · Cited by 7
“…long-term replication has been documented in chronically infected immunocompromised individuals, accelerating intrahost viral evolution and leading to the acquisition of amino acid changes that often overlap with those identified in VOCs (Avanzato et al. 2020, Choi et al. 2020, Kemp et al. 2021).”
BackgroundChiang, K. C., Chiu, C. E. N., Altaf, M., Cheng, M. T. K., & Gupta, R. K. (2025) · Viruses · doi:10.3390/v17111405 · Cited by 8
“Mutations including N429K and Y453F at the receptor-binding motif improved ACE2 receptor binding and conferred antibody escape but at the cost of an infectivity defect [33,51].”
Self-citationFrom viral democratic genomes to viral wild bunch of quasispecies
Colson, P., Bader, W., Fantini, J., Dudouet, P., Levasseur, A., Pontarotti, P., Devaux, C. A., & Raoult, D. (2023) · Journal of Medical Virology · doi:10.1002/jmv.29209 · Cited by 9
Kinsella, P. M., Moso, M. A., Morrissey, C. O., Dendle, C., Guy, S., Bond, K. A., Sasadeusz, J., & Slavin, M. A. (2024) · Transplant Infectious Disease · doi:10.1111/tid.14301 · Cited by 6
Singh, K., Rocco, J. M., & Nussenblatt, V. R. (2024) · Seminars in Hematology · doi:10.1053/j.seminhematol.2024.08.002 · Cited by 6
Gentile, I., Viceconte, G., Cuccurullo, F. M., Pietroluongo, D., D’Agostino, A., Silvitelli, M., Mercinelli, S., Scotto, R., Grimaldi, F., Palmieri, S., et al. (2024) · Annals of Medicine · doi:10.1080/07853890.2024.2439541 · Cited by 6
Eco-evolutionary dynamics of pathogen immune-escape: deriving a population-level phylodynamic curve
Nielsen, B. F., Saad-Roy, C. M., Metcalf, C. J. E., Viboud, C. G., & Grenfell, B. T. (2025) · Journal of The Royal Society Interface · doi:10.1098/rsif.2024.0675 · Cited by 4
Viral syncytia evolve to resist interferon
Li, T., Kang, I., Ye, J., Hu, Z., Gibbs, J. S., Ye, C., Takeda, K., Košík, I., Shi, G., Hollý, J., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-74676-8 · Cited by 6
Self-citationXu, S.-Y., Fomenkov, A. I., Chen, T.-H., & Yigit, E. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.660149 · Cited by 7
Innovative vaccine approaches—a Keystone Symposia report
Cable, J., Rappuoli, R., Klemm, E. J., Kang, G., Mutreja, A., Wright, G. J., Pizza, M., Castro, S. A., Hoffmann, J. P., Alter, G., et al. (2022) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.14739 · Cited by 6
Self-citationImmunotherapy and CRISPR Cas Systems: Potential Cure of COVID-19?
He, X., & Zeng, X. X. (2022) · Drug Design Development and Therapy · doi:10.2147/dddt.s347297 · Cited by 7
“Moreover, in Kemp et al an immunocompromised patient who had B cell lymphoma underwent convalescent plasma therapy for COVID-19 and the results indicated evolution of the culprit virus producing spike double mutation with both ΔH69/ΔV70 and D796H which enabled SARS-CoV-2 to evade neutralizing antibodies with increased…”
Yadav, D., Agarwal, S., Pancham, P., Jindal, D., Agarwal, V., Dubey, P. K., Jha, S. K., Mani, S., Rachana, R., Dey, A., et al. (2022) · Immuno · doi:10.3390/immuno2020022 · Cited by 7
“β-variant Spike protein K417N, E484K and N501Y [28] Epsilon variant Spike protein S13I, W152C and L452R [29] γ-variant Spike protein K417T, E484K, N501Y [30] Eta-variant Spike protein E484K ∆H69/∆V70 deletion [31] Cluster 5 Spike protein ∆H69/∆V70 deletion [32]”
BackgroundCords, L., Knapp, M., Woost, R., Schulte, S., Kummer, S., Ackermann, C., Beisel, C., Peine, S., Johansson, A. M., Kwok, W. W., et al. (2022) · Viruses · doi:10.3390/v14061265 · Cited by 6
Khamadi, S. A., Opanda, S. M., Symekher, S. L., Konongoi, S. L., Langat, S. K., Cirindi, J., Mwangi, M., Mwikwabe, N. M., Okeyo, S., Koskei, E., et al. (2022) · Virology Journal · doi:10.1186/s12985-022-01895-y · Cited by 6
Evaluating the effect of SARS-CoV-2 spike mutations with a linear doubly robust learner
Wang, X., Hu, M., Liu, B., Xu, H., Jin, Y., Wang, B., Zhao, Y., Wu, J., Yue, J., & Ren, H. (2023) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2023.1161445 · Cited by 7
Guilbaud, R., Yusti, A.-M. F., Leducq, V., Zafilaza, K., Bridier‐Nahmias, A., Todesco, È., Soulié, C., Fauchois, A., Hingrat, Q. L., Kramer, L. D., et al. (2023) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiad499 · Cited by 7
Lim, T., Rajoriya, S., Kim, B., Natasha, A., Im, H., Shim, H. S., Yoo, J.-S., Kim, J. W., Lee, E., Shin, H. J., et al. (2024) · Virus Research · doi:10.1016/j.virusres.2024.199325 · Cited by 6
“Emerging SARS-CoV-2 variants and concurrent outbreaks, such as the monkeypox virus, highlight the urgent need for broad-spectrum antiviral therapies (Kemp SA et al., 2021; Minhaj et al., 2022).”
BackgroundFocosi, D., Maggi, F., Franchini, M., Aguzzi, A., Lanza, M., Mazzoni, A., & Menichetti, F. (2021) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2021.04.003 · Cited by 6
Passive Immunity Should and Will Work for COVID-19 for Some Patients
Cimolai, N. (2021) · Clinical Hematology International · doi:10.2991/chi.k.210328.001 · Cited by 7
Laubscher, F., Cordey, S., Friedlaender, A., Schweblin, C., Noetzlin, S., Simand, P.-F., Bordry, N., Sousa, F. D., Pigny, F., Baggio, S., et al. (2021) · Microorganisms · doi:10.3390/microorganisms9102145 · Cited by 5
“Several case reports identified SARS-CoV-2 RNA persistence lasting up to 5 months, associated with virus genetic evolution in specifically highly immunocompromised patients [2,3].”
BackgroundKhalaf, R. A., Bernasconi, A., Pinoli, P., & Ceri, S. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.07.051 · Cited by 5
“Both Spike_H69-/V70- and Spike_Y144- are deletions that lie in the NTD region of Spike and may modulate antigenicity [25,29,30].”
Walter, K. S., Kim, E., Verma, R., Altamirano, J., Leary, S., Carrington, Y. J., Jagannathan, P., Singh, U., Holubar, M. K., Subramanian, A. K., et al. (2023) · Open Forum Infectious Diseases · doi:10.1093/ofid/ofad001 · Cited by 7
“○ Within-host viral diversity can be structured temporally [33, 40, 43] or”
BackgroundB.1.1.7 became the dominant variant in LebanonPreprint
Younes, M., Hamze, K., Carter, D. P., Osman, K. L., Vipond, R., Carroll, M. W., Pullan, S. T., Nassar, H., Mohamad, N., Makki, M., et al. (2021) · medRxiv · doi:10.1101/2021.03.17.21253782 · Cited by 6
SARS-CoV-2 convergent evolution as a guide to explore adaptive advantagePreprint
Zahradník, J., Nunvář, J., & Schreiber, G. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.24.445534 · Cited by 6
Convergent evolution in SARS-CoV-2 Spike creates a variant soup that causes new COVID-19 wavesPreprint
Focosi, D., Quiroga, R., McConnell, S. A., Johnson, M. C., & Casadevall, A. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.12.05.518843 · Cited by 6
Complex vaccination strategies prevent the emergence of vaccine resistance
Rella, S. A., Kulikova, Y. A., Minnegalieva, A. R., & Kondrashov, F. A. (2024) · Evolution · doi:10.1093/evolut/qpae106 · Cited by 6
“An interesting aspect of SARS-CoV-2 is its propensity for rapid evolution driven by the host immune response in immunocompromised individuals in the course of very long infection periods (Choi et al. 2020; Kemp et al. 2021; Sonnleitner et al. 2022).”
BackgroundA Systematic Review of Prolonged SARS‐CoV‐2 Shedding in Immunocompromised Persons
Christofferson, R. C., Giovanni, J., Koumans, E. H., Ategbole, M., Clark, S., Godfred‐Cato, S., Menon, M. P., Sastalla, I., Schweitzer, B. K., & Uyeki, T. M. (2025) · Influenza and Other Respiratory Viruses · doi:10.1111/irv.70121 · Cited by 5
SARS-CoV-2 Omicron infection reveals imprinted antibody responses in the absence of vaccination
Abdullahi, A., Morse, R. B., Cheng, M. T. K., Ige, F. A., Onyemata, J., Edun, M., Kramná, A., Sievers, B. L., Turner, S., Wisso, H., et al. (2026) · iScience · doi:10.1016/j.isci.2026.115910 · Cited by 6
Self-citationFeng, S., Reid, G., Clark, N. M., Harrington, A., Uprichard, S. L., & Baker, S. C. (2024) · Virology Journal · doi:10.1186/s12985-024-02378-y · Cited by 5
Self-citationAdvancements in the Development of Anti-SARS-CoV-2 Therapeutics
Huang, J., Ma, Q., Su, Z., & Cheng, X. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms251910820 · Cited by 5
“It can also act as a compensatory mutation, countering mutations that enable immune evasion while diminishing its own infectivity [34].”
BackgroundVariable rates of SARS-CoV-2 evolution in chronic infections
Smith, E. W., Hamilton, W. L., Warne, B., Walker, E. R., Jahun, A. S., Hosmillo, M. D. T., Gupta, R. K., Goodfellow, I., Gkrania‐Klotsas, E., Török, M. E., et al. (2025) · PLoS Pathogens · doi:10.1371/journal.ppat.1013109 · Cited by 5
Self-citationAntimicrobial immunotherapeutics: past, present and future
Mercer, D. K., Francis, M.-L. R., & Fraser-Pitt, D. J. (2021) · Emerging Topics in Life Sciences · doi:10.1042/etls20200348 · Cited by 5
Self-citationBonnet, C., Masse, S., Benamar, H., Vilcu, A., Swital, M., Hanslik, T., van der Werf, S., Duval, X., Carrat, F., Falchi, A., et al. (2022) · Life · doi:10.3390/life12020163 · Cited by 4
“It also presents a deletion at positions 69 and 70 of the spike protein (∆69–70) that is linked to immune escape in immunocompromised patients [3] and has”
Background
Metadata
- Authors
- Kemp, S. A., Collier, D. A., Datir, R. P., Ferreira, I. A. T. M., Gayed, S., Jahun, A., Hosmillo, M., Rees-Spear, C., Mlcochova, P., Lumb, I. U., Roberts, D. J., Chandra, A., Temperton, N., The CITIID-NIHR BioResource COVID-19 Collaboration, Principal investigators, Baker, S., Dougan, G., Hess, C., Kingston, N., Lehner, P. J., Lyons, P. A., Matheson, N. J., Owehand, W. H., Saunders, C., Summers, C., Thaventhiran, J. E. D., Toshner, M., Weekes, M. P., nurses, C. &. V. R., Bucke, A., Calder, J., Canna, L., Domingo, J., Elmer, A., Fuller, S., Harris, J., Hewitt, S., Kennet, J., Jose, S., Kourampa, J., Meadows, A., O’Brien, C., Price, J., Publico, C., Rastall, R., Ribeiro, C., Rowlands, J., Ruffolo, V., Tordesillas, H., logistics, S., Bullman, B., Dunmore, B. J., Fawke, S., Gräf, S., Hodgson, J., Huang, C., Hunter, K., Jones, E., Legchenko, E., Matara, C., Martin, J., Mescia, F., O’Donnell, C., Pointon, L., Pond, N., Shih, J., Sutcliffe, R., Tilly, T., Treacy, C., Tong, Z., Wood, J., Wylot, M., acquisition, S. P. &. D., Bergamaschi, L., Betancourt, A., Bower, G., Cossetti, C., De Sa, A., Epping, M., Fawke, S., Gleadall, N., Grenfell, R., Hinch, A., Huhn, O., Jackson, S., Jarvis, I., Lewis, D., Marsden, J., Nice, F., Okecha, G., Omarjee, O., Perera, M., Richoz, N., Romashova, V., Yarkoni, N. S., Sharma, R., Stefanucci, L., Stephens, J., Strezlecki, M., Turner, L., collection, C. D., De Bie, E. M. D. D., Bunclark, K., Josipovic, M., Mackay, M., Rossi, S., Selvan, M., Spencer, S., Yong, C., Royal Papworth Hospital, I. C. U., Ansaripour, A., Michael, A., Mwaura, L., Patterson, C., Polwarth, G., Addenbrooke’s Hospital, I. C. U., Polgarova, P., di Stefano, G., Cambridge & Peterborough Foundation Trust, Fahey, C., Michel, R., ANPC & Centre for Molecular Medicine & Innovative Therapeutics, Bong, S.-H., Coudert, J. D., Holmes, E., BioResource, N., Allison, J., Butcher, H., Caputo, D., Clapham-Riley, D., Dewhurst, E., Furlong, A., Graves, B., Gray, J., Ivers, T., Kasanicki, M., Le Gresley, E., Linger, R., Meloy, S., Muldoon, F., Ovington, N., Papadia, S., Phelan, I., Stark, H., Stirrups, K. E., Townsend, P., Walker, N., Webster, J., The COVID-19 Genomics UK (COG-UK) Consortium, Funding acquisition, L. &. S., Robson, S. C., Funding acquisition, L. &. S., Loman, N. J., Connor, T. R., Leadership & supervision, M. C., Golubchik, T., Funding acquisition, M. C., Martinez Nunez, R. T., Funding acquisition, L. &. S., Ludden, C., Funding acquisition, L. &. S., Corden, S., Funding acquisition, L. &. S., Johnston, I., Bonsall, D., Funding acquisition, L. &. S., Smith, C. P., Awan, A. R., Funding acquisition, S. &. L., Bucca, G., Leadership & supervision, M. C., Estee Torok, M., Leadership & supervision, M. C., Saeed, K., Prieto, J. A., Leadership & supervision, M. C., Jackson, D. K., Metadata curation, P. A., Hamilton, W. L., Metadata curation, P. A., Snell, L. B., Funding acquisition, L. &. S., Moore, C., Funding acquisition, L. &. S., Harrison, E. M., Leadership & supervision, M. C., Goncalves, S., Leadership & supervision, M. C., Fairley, D. J., Loose, M. W., Watkins, J., Leadership & supervision, M. C., Livett, R., Leadership & supervision, M. C., Moses, S., Leadership & supervision, M. C., Amato, R., Nicholls, S., Bull, M., Leadership & supervision, P. A., Smith, D. L., Leadership & supervision, S. &. A., Barrett, J., Aanensen, D. M., Metadata curation, P. A., Curran, M. D., Parmar, S., Aggarwal, D., Shepherd, J. G., Metadata curation, P. A., Parker, M. D., Metadata curation, S. &. L., Glaysher, S., Metadata curation, S. &. A., Bashton, M., Underwood, A. P., Pacchiarini, N., Loveson, K. F., Project administration, S. &. A., Carabelli, A. M., Funding acquisition, L. &. S. A. M. C., Templeton, K. E., Funding acquisition, L. &. S. A. P. A., Langford, C. F., Sillitoe, J., de Silva, T. I., Wang, D., Funding acquisition, L. &. S. A. S. &. A., Kwiatkowski, D., Rambaut, A., O’Grady, J., Cottrell, S., Leadership & supervision, M. C. A. S. &. A., Holden, M. T. G., Thomson, E. C., Leadership & supervision, P. A. A. S. &. L., Osman, H., Andersson, M., Chauhan, A. J., Hassan-Ibrahim, M. O., Leadership & supervision, P. A. A. S. &. A., Lawniczak, M., Leadership & supervision, S. &. L. A. S. &. A., Alderton, A., Chand, M., Constantinidou, C., Unnikrishnan, M., Darby, A. C., Hiscox, J. A., Paterson, S., Leadership & supervision, S. &. A. A. S. &. A. T., Martincorena, I., Robertson, D. L., Volz, E. M., Page, A. J., Pybus, O. G., Leadership & supervision, S. &. A. A. V., Bassett, A. R., Metadata curation, P. A. A. S. &. L., Ariani, C. V., Spencer Chapman, M. H., Li, K. K., Shah, R. N., Jesudason, N. G., Taha, Y., Metadata curation, P. A. A. S. &. A., McHugh, M. P., Dewar, R., Metadata curation, S. &. L. A. S. &. A., Jahun, A. S., McMurray, C., Pandey, S., McKenna, J. P., Nelson, A., Young, G. R., McCann, C. M., Elliott, S., Metadata curation, S. &. L. A. V., Lowe, H., Metadata curation, S. &. A. A. S. &. A. T., Temperton, B., Roy, S., Price, A., Rey, S., Wyles, M., Metadata curation, S. &. A. A. V., Rooke, S., Shaaban, S., Project administration, S. &. L. A. S. &. A., de Cesare, M., Project administration, S. &. L. A. S. &. A. T., Letchford, L., Project administration, S. &. L. A. V., Silveira, S., Pelosi, E., Wilson-Davies, E., Samples & logistics, S. &. A. A. S. &. A. T., Hosmillo, M., Sequencing & analysis, S. &. A. T. A. V., O’Toole, Á., Hesketh, A. R., Stark, R., du Plessis, L., Ruis, C., Adams, H., Bourgeois, Y., supervision, F. A. A. L. &., Michell, S. L., Grammatopoulos, D., Edgeworth, J., Breuer, J., Todd, J. A., Fraser, C., Funding acquisition and project administration, Buck, D., John, M., curation, L. &. S. A. M., Kay, G. L., Leadership & supervision and project administration, Palmer, S., Peacock, S. J., Heyburn, D., logistics, L. &. S. A. S. &., Weldon, D., Robinson, E., McNally, A., Muir, P., Vipond, I. B., Boyes, J., Sivaprakasam, V., Salluja, T., Dervisevic, S., Meader, E. J., analysis, L. &. S. A. S. &., Park, N. R., Oliver, K., Jeffries, A. R., Ott, S., da Silva Filipe, A., Simpson, D. A., Williams, C., visualization, L. &. S. A., Masoli, J. A. H., logistics, M. C. A. S. &., Knight, B. A., Jones, C. R., Koshy, C., Ash, A., Casey, A., Bosworth, A., Ratcliffe, L., Xu-McCrae, L., Pymont, H. M., Hutchings, S., Berry, L., Jones, K., Halstead, F., Davis, T., Holmes, C., Iturriza-Gomara, M., Lucaci, A. O., Randell, P. A., Cox, A., Madona, P., Harris, K. A., Brown, J. R., Mahungu, T. W., Irish-Tavares, D., Haque, T., Hart, J., Witele, E., Fenton, M. L., Liggett, S., Graham, C., Swindells, E., Collins, J., Eltringham, G., Campbell, S., McClure, P. C., Clark, G., Sloan, T. J., Jones, C., Lynch, J., analysis, M. C. A. S. &., Warne, B., Leonard, S., Durham, J., Williams, T., Haldenby, S. T., Storey, N., Alikhan, N.-F., Holmes, N., Moore, C., Carlile, M., Perry, M., Craine, N., Lyons, R. A., Beckett, A. H., Goudarzi, S., Fearn, C., Cook, K., Dent, H., Paul, H., tools, M. C. A. S. &. A., Davies, R., Project administration and samples & logistics, Blane, B., Girgis, S. T., Beale, M. A., Bellis, K. L., Dorman, M. J., Drury, E., Kane, L., Kay, S., McGuigan, S., Nelson, R., Prestwood, L., Rajatileka, S., Batra, R., Williams, R. J., Kristiansen, M., Green, A., Justice, A., Mahanama, A. I. K., Samaraweera, B., Project administration and sequencing & analysis, Hadjirin, N. F., Quick, J., Project administration and software & analysis tools, Poplawski, R., analysis, S. &. L. A. S. &., Kermack, L. M., Reynolds, N., Hall, G., Chaudhry, Y., Pinckert, M. L., Georgana, I., Moll, R. J., Thornton, A., Myers, R., Stockton, J., Williams, C. A., Yew, W. C., Trotter, A. J., Trebes, A., MacIntyre-Cockett, G., Birchley, A., Adams, A., Plimmer, A., Gatica-Wilcox, B., McKerr, C., Hilvers, E., Jones, H., Asad, H., Coombes, J., Evans, J. M., Fina, L., Gilbert, L., Graham, L., Cronin, M., Kumziene-Summerhayes, S., Taylor, S., Jones, S., Groves, D. C., Zhang, P., Gallis, M., Louka, S. F., tools, S. &. L. A. S. &. A., Starinskij, I., tools, S. &. A. A. S. &. A., Jackson, C., Gourtovaia, M., Tonkin-Hill, G., Lewis, K., Tovar-Corona, J. M., James, K., Baxter, L., Alam, M. T., Orton, R. J., Hughes, J., Vattipally, S., Ragonnet-Cronin, M., Nascimento, F. F., Jorgensen, D., Boyd, O., Geidelberg, L., Zarebski, A. E., Raghwani, J., Kraemer, M. U. G., Southgate, J., Lindsey, B. B., Freeman, T. M., visualization, S. &. A. T. A., Keatley, J.-P., Singer, J. B., de Oliveira Martins, L., Yeats, C. 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- Affiliations
- University College London (GB)
- University of Cambridge (GB)
- Cambridge University Hospitals NHS Foundation Trust (GB)
- NHS Blood and Transplant (GB)
- Medway School of Pharmacy (GB)
- University of Basel (CH)
- Addenbrooke's Hospital (GB)
- Papworth Hospital NHS Foundation Trust (GB)
- Fulbourn Hospital (GB)
- Murdoch University (AU)
- King's College London (GB)
- Public Health Wales (GB)
- Wellcome Sanger Institute (GB)
- University of Oxford (GB)
- University of Brighton (GB)
- Guy's Hospital (GB)
- University Hospital Southampton NHS Foundation Trust (GB)
- St Thomas' Hospital (GB)
- Belfast Health and Social Care Trust (GB)
- East Kent Hospitals University NHS Foundation Trust (GB)
- University of Birmingham (GB)
- Public Health England (GB)
- University of Sheffield (GB)
- University of Nottingham (GB)
- Northumbria University (GB)
- Queen's University Belfast (GB)
- University of Kent (GB)
- Quadram Institute (GB)
- Public Health Scotland (GB)
- Portsmouth Hospitals NHS Trust (GB)
- University of Liverpool (GB)
- Imperial College London (GB)
- MRC University of Glasgow Centre for Virus Research (GB)
- NHS Lothian (GB)
- University Hospitals Coventry and Warwickshire NHS Trust (GB)
- University of East Anglia (GB)
- University of Exeter (GB)
- Brighton and Sussex University Hospitals NHS Trust (GB)
- Betsi Cadwaladr University Health Board (GB)
- Centre for Human Genetics (GB)
- Cardiff and Vale University Health Board (GB)
- Gloucestershire Hospitals NHS Foundation Trust (GB)
- Sandwell & West Birmingham Hospitals NHS Trust (GB)
- Norfolk and Norwich University Hospital (GB)
- University of Warwick (GB)
- Barking, Havering And Redbridge University Hospitals NHS Trust (GB)
- Queen Elizabeth Hospital Birmingham (GB)
- Wye Valley NHS Trust (GB)
- University Hospitals of Leicester NHS Trust (GB)
- Great Ormond Street Hospital (GB)
- Royal Free London NHS Foundation Trust (GB)
- South Tees Hospitals NHS Foundation Trust (GB)
- North Cumbria Integrated Care NHS Foundation Trust (GB)
- North Tees and Hartlepool NHS Foundation Trust (GB)
- County Durham and Darlington NHS Foundation Trust (GB)
- Basingstoke and North Hampshire Hospital (GB)
- University of Portsmouth (GB)
- Kettering General Hospital (GB)
- North West London Pathology (GB)
- University of Surrey (GB)
- Swansea University (GB)
- Royal Hampshire County Hospital (GB)
- Wellcome/MRC Cambridge Stem Cell Institute (GB)
- Royal Devon & Exeter NHS Foundation Trust (GB)
- National Institute for Health and Care Research (GB)
- NHS Greater Glasgow and Clyde (GB)
- Leeds Teaching Hospitals NHS Trust (GB)
- London School of Hygiene & Tropical Medicine (GB)
- Maidstone and Tunbridge Wells NHS Trust (GB)
- University of Edinburgh (GB)
- Norfolk County Council (GB)
- East Suffolk and North Essex NHS Foundation Trust (GB)
- Queen's Medical Centre (GB)
- Manchester University NHS Foundation Trust (GB)
- Princess Alexandra Hospital NHS Trust (GB)
- Guy's and St Thomas' NHS Foundation Trust (GB)
- MRC Laboratory of Molecular Biology (GB)
- Amsterdam UMC Location University of Amsterdam (NL)
- Facultad de Estudios Superiores Cuautitlán (MX)
- Newcastle University (GB)
- Cardiff University (GB)
- University of Colorado Anschutz (US)
- Corresponding author
- Gupta, Ravindra K.
- ORCID
- Kemp, Steven A.
- Collier, Dami A.
- Datir, Rawlings P.
- Ferreira, Isabella A. T. M.
- Jahun, Aminu
- Rees-Spear, Chloe
- Roberts, David J.
- Chandra, Anita
- Temperton, Nigel
- Baker, Stephen
- Hess, Christoph
- Kingston, Nathalie
- Lehner, Paul J.
- Lyons, Paul A.
- Matheson, Nicholas J.
- Summers, Charlotte
- Thaventhiran, James E. D.
- Toshner, Mark
- Weekes, Michael P.
- Domingo, Jason
- Kennet, Jane
- Price, Jane
- Rowlands, Jane
- Dunmore, Benjamin J.
- Gräf, Stefan
- Legchenko, Ekaterina
- Martin, Jennifer
- Mescia, Federica
- Pointon, Linda
- Tilly, Tobias
- Wood, Jennifer
- Cossetti, Chiara
- Epping, Madeline
- Grenfell, Richard
- Jackson, Sarah
- Nice, Francesca
- Omarjee, Ommar
- Perera, Marianne
- Richoz, Nathan
- Yarkoni, Natalia Savinykh
- Sharma, Rahul
- Stefanucci, Luca
- Stephens, Jonathan
- Bunclark, Katherine
- Rossi, Sabrina
- Yong, Cissy
- Ansaripour, Ali
- Mwaura, Lucy
- Polwarth, Gary
- Polgarova, Petra
- Bong, Sze-How
- Holmes, Elaine
- Papadia, Sofia
- Stark, Hannah
- Stirrups, Kathleen E.
- Walker, Neil
- Webster, Jennifer
- Robson, Samuel C.
- Loman, Nicholas J.
- Connor, Thomas R.
- Golubchik, Tanya
- Bonsall, David
- Smith, Colin P.
- Bucca, Giselda
- Saeed, Kordo
- Prieto, Jacqui A.
- Snell, Luke B.
- Moore, Catherine
- Fairley, Derek J.
- Loose, Matthew W.
- Moses, Samuel
- Bull, Matthew
- Aanensen, David M.
- Curran, Martin D.
- Parmar, Surendra
- Aggarwal, Dinesh
- Shepherd, James G.
- Glaysher, Sharon
- Bashton, Matthew
- Pacchiarini, Nicole
- Carabelli, Alessandro M.
- Templeton, Kate E.
- Wang, Dennis
- Rambaut, Andrew
- O’Grady, Justin
- Cottrell, Simon
- Holden, Matthew T. G.
- Thomson, Emma C.
- Andersson, Monique
- Chauhan, Anoop J.
- Chand, Meera
- Constantinidou, Chrystala
- Unnikrishnan, Meera
- Darby, Alistair C.
- Hiscox, Julian A.
- Paterson, Steve
- Robertson, David L.
- Volz, Erik M.
- Page, Andrew J.
- Pybus, Oliver G.
- Li, Kathy K.
- Shah, Rajiv N.
- Jesudason, Natasha G.
- Dewar, Rebecca
- McMurray, Claire
- McKenna, James P.
- Nelson, Andrew
- Young, Gregory R.
- McCann, Clare M.
- Temperton, Ben
- Roy, Sunando
- Price, Anna
- Rey, Sara
- Rooke, Stefan
- Shaaban, Sharif
- Silveira, Siona
- Pelosi, Emanuela
- Wilson-Davies, Eleri
- Stark, Richard
- Bourgeois, Yann
- Grammatopoulos, Dimitris
- Edgeworth, Jonathan
- Breuer, Judith
- Todd, John A.
- Fraser, Christophe
- Buck, David
- Kay, Gemma L.
- McNally, Alan
- Muir, Peter
- Sivaprakasam, Venkat
- Dervisevic, Samir
- Jeffries, Aaron R.
- Ott, Sascha
- Simpson, David A.
- Masoli, Jane A. H.
- Knight, Bridget A.
- Jones, Christopher R.
- Bosworth, Andrew
- Pymont, Hannah M.
- Hutchings, Stephanie
- Jones, Katie
- Halstead, Fenella
- Holmes, Christopher
- Randell, Paul Anthony
- Cox, Alison
- Harris, Kathryn Ann
- Brown, Julianne Rose
- Haque, Tanzina
- Liggett, Steven
- Graham, Clive
- Collins, Jennifer
- Clark, Gemma
- Sloan, Tim J.
- Lynch, Jessica
- Warne, Ben
- Williams, Thomas
- Haldenby, Sam T.
- Storey, Nathaniel
- Alikhan, Nabil-Fareed
- Holmes, Nadine
- Perry, Malorie
- Lyons, Ronan A.
- Beckett, Angela H.
- Fearn, Christopher
- Cook, Kate
- Blane, Beth
- Batra, Rahul
- Williams, Rachel J.
- Green, Angie
- Samaraweera, Buddhini
- Quick, Joshua
- Poplawski, Radoslaw
- Reynolds, Nicola
- Hall, Grant
- Chaudhry, Yasmin
- Pinckert, Malte L.
- Georgana, Iliana
- Myers, Richard
- Stockton, Joanne
- Williams, Charlotte A.
- Yew, Wen C.
- Trotter, Alexander J.
- Trebes, Amy
- Plimmer, Amy
- McKerr, Caoimhe
- Asad, Hibo
- Graham, Lee
- Taylor, Sarah
- Gallis, Marta
- Louka, Stavroula F.
- Starinskij, Igor
- Jackson, Chris
- Baxter, Laura
- Alam, Mohammad T.
- Orton, Richard J.
- Hughes, Joseph
- Jorgensen, David
- Geidelberg, Lily
- Zarebski, Alex E.
- Raghwani, Jayna
- Kraemer, Moritz U. G.
- Southgate, Joel
- Lindsey, Benjamin B.
- Singer, Joshua B.
- Yeats, Corin A.
- Taylor, Ben E. W.
- Danesh, John
- Eldirdiri, Sahar
- Holmes, Alison
- Price, James
- Hartley, John A.
- Mather, Alison E.
- Chapman, Michael R.
- Mookerjee, Siddharth
- Stanley, Rachael
- Eyre, David
- Crook, Derrick
- Vernet, Gabrielle
- Merrick, Ian
- Bradley, Declan T.
- Bolt, Frances
- Coll, Francesc
- Attwood, Stephen W.
- Davies, Alisha
- Scarlett, Garry P.
- Leek, Danielle
- Sridhar, Sushmita
- Cormie, Claire
- Higginson, Ellen E.
- Maes, Mailis
- Young, Jamie
- Wantoch, Michelle
- Hill, Verity
- Bewshea, Claire M.
- Ellard, Sian
- Auckland, Cressida
- Harrison, Ian
- Richter, Alex
- Beggs, Andrew
- Best, Angus
- Percival, Benita
- Mirza, Jeremy
- Megram, Oliver
- Mayhew, Megan
- Crawford, Liam
- Cumley, Nicola
- Asamaphan, Patawee
- Niebel, Marc O.
- Gunson, Rory N.
- Mollett, Guy
- Blacow, Rachel
- Bird, Paul
- Tang, Julian
- Carden, Holli
- Jackson, Kathryn A.
- Ahmad, Shazaad S. Y.
- Turtle, Lance
- Alcolea-Medina, Adela
- Charalampous, Themoula
- Patel, Amita
- Rowan, Aileen
- Taylor, Graham P.
- Shah, Divya
- Atkinson, Laura
- Lee, Jack C. D.
- Westhorpe, Adam P.
- Lowe, Helen L.
- Ensell, Leah
- Baker, Paul
- Bonner, Stephen
- Essex, Sarah
- Payne, Brendan A. I.
- Raviprakash, Veena
- Smith, Louise
- Davidson, Rose K.
- Bedford, Luke
- Coupland, Lindsay
- Wright, Victoria
- Chappell, Joseph G.
- Tsoleridis, Theocharis
- Ball, Jonathan
- Lister, Michelle M.
- Joseph, Amelia
- Willingham, Iona
- Walsh, Sarah
- Wise, Emma
- Moore, Nathan
- Mori, Matilde
- Kidd, Stephen
- Williams, Rebecca
- Bicknell, Kelly
- Wyllie, Sarah
- Keeley, Alexander J.
- Partridge, David G.
- Raza, Mohammad
- Evans, Cariad
- Johnson, Kate
- Abnizova, Irina
- Barrett, Jeffrey
- Bellis, Katie
- Berger, Duncan
- Blackburn, Kirsty
- Buddenborg, Sarah Kay
- Cagan, Alex
- Clark, Richard
- Cook, Elizabeth
- Coppola, Maria
- Corton, Craig
- Crawford, Mark
- Dogga, Sunil
- Gray, Emma
- Harrott, Alexandria
- Harry, Edward
- Heath, Paul
- Holmes, Sarah
- Iqbal, Sameena
- Jones, Matthew
- Keatley, Jon
- Langford, Cordelia
- Liddle, Jennifer
- Lin, Quan
- Lindsay, Sarah
- Mayho, Matthew
- Murie, Kathryn
- Naydenova, Plamena
- Noell, Guillaume G.
- Ohan, Valeriu
- Patel, Gaurang
- Plowman, Deborah
- Robinson, Katrina
- Robinson, David
- Rogers, Hazel
- Schwach, Frank
- Skeldon, Kenneth
- Smith, James
- Smith, Michelle
- Smith, Sean
- Strickland, Michelle
- Thomson, Nicholas
- Thurston, Scott
- Vancollie, Valerie
- Walker, Matthew
- Waller, Matt
- Wells, Eloise
- Whitton, Georgia
- Widaa, Sara
- Williams, Mia
- Makunin, Alex
- Williamson, Kathleen A.
- Warwick-Dugdale, Joanna
- Farbos, Audrey
- Harrison, James W.
- Sambles, Christine M.
- Studholme, David J.
- Lackenby, Angie
- Miah, Shahjahan
- Bibby, David
- Hubb, Jonathan
- Dabrera, Gavin
- Ramsay, Mary
- Bradshaw, Daniel
- Groves, Natalie
- Gallagher, Eileen
- Lee, David
- Ellaby, Nicholas
- Hartman, Hassan
- Ledesma, Juan
- Twohig, Katherine A.
- Allara, Elias
- Cheng, Jeffrey K. J.
- Bridgewater, Hannah E.
- Frost, Lucy R.
- Brown, Paul E.
- Tong, Lily
- Broos, Alice
- Mair, Daniel
- Nichols, Jenna
- Carmichael, Stephen N.
- Smollett, Katherine L.
- Nomikou, Kyriaki
- Eccles, Richard
- Whitehead, Mark
- Gemmell, Matthew
- Wierzbicki, Claudia
- Webster, Hermione J.
- Signell, Adrian W.
- Betancor, Gilberto
- Wilson, Harry D.
- Nebbia, Gaia
- Flaviani, Flavia
- Cotic, Marius
- Bayzid, Nadua
- Thompson, Thomas
- O’Brien, Sarah
- Baker, David J.
- Rudder, Steven
- Aydin, Alp
- Sang, Fei
- Debebe, Johnny
- Vasylyeva, Tetyana I.
- Marchbank, Angela
- Morgan, Mari
- Workman, Trudy
- Fuller, William
- Bresner, Catherine
- Angyal, Adrienn
- Green, Luke R.
- Parsons, Paul J.
- Tucker, Rachel M.
- Brown, Rebecca
- Whiteley, Max
- Siveroni, Igor
- Le-Viet, Thanh
- Sharrocks, Katherine
- Modis, Yorgo
- Leigh, Kendra E.
- Briggs, John A. G.
- Smith, Kenneth G. C.
- Bradley, John R.
- Pollock, David D.
- Goldstein, Richard A.
- Smielewska, Anna
- Skittrall, Jordan P.
- Gouliouris, Theodore
- Goodfellow, Ian G.
- Gkrania-Klotsas, Effrossyni
- Illingworth, Christopher J. R.
- McCoy, Laura E.
- Gupta, Ravindra K.
- Venue
- Nature
- Published
- 2021-02-05
- Volume
- 592
- Issue
- 7853
- Pages
- 277-282
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC7610568
- OpenAlex
- W3128154910
- Cited by
- 1,097
- References
- 54
- Citations by year
- 2026: 36 · 2025: 72 · 2024: 121 · 2023: 157 · 2022: 283 · 2021: 411
- FWCI
- 77.05
- Type
- journal article
- Language
- en
- Update notices
- correction (2022-07-21)
- Open access
- bronze
- doi.org
- Locations
- Nature (publishedVersion)
- medRxiv (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Pure Amsterdam UMC (publishedVersion, cc-by)
- PubMed Central (acceptedVersion)
- Kent Academic Repository (University of Kent) (acceptedVersion)
- LSHTM Research Online (London School of Hygiene and Tropical Medicine) (acceptedVersion)
- UEA Digital Repository (University of East Anglia) (submittedVersion)
- Europe PMC (PubMed Central) (submittedVersion, cc-by-nc-nd)
- PubMed Central (submittedVersion, cc-by-nc-nd)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam) (submittedVersion, cc-by-sa)
- ePrints Soton (University of Southampton) (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- White Rose Research Online (University of Leeds, The University of Sheffield, University of York) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Institutional Research Information System (Università degli Studi di Brescia) (submittedVersion)
- Pure Amsterdam UMC (submittedVersion, other-oa)
- University of Birmingham Research Portal (University of Birmingham) (submittedVersion, other-oa)
- Funders
- Bill and Melinda Gates Foundation (OPP 1175094)
- Wellcome Trust (108082/A/15/Z, 108082, 204911/Z/16/Z, Z/17/Z, WT108082AIA, 217191, 206618/Z/17/Z, 207498, 207498/Z/17/Z)
- UK Research and Innovation (MC_UU_00002/11)
- Cancer Research UK (23923)
- National Institute for Health and Care Research (NF-SI-0514-10109, 207498, RP-PG-0514-20018, ACF-2017-15-004, ACF-2018-04-014, COVID-19-RECPLAS)
- Academy of Medical Sciences (AMS-CSF4-Torok)
- National Institutes of Health (COVID-19)
- NIHR BioResource
- Medical Research Council (MC_UU_00002/11, MR/R015600/1, MR/R008698/1, COVID-19, MC_UP_1201/16)
- Biotechnology and Biological Sciences Research Council (BBS/E/F/000PR10348, BB/P007562/1)
- NIHR Cambridge Biomedical Research Centre
- National Institute of General Medical Sciences (R01GM083127)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Health Sciences › Medicine › Infectious Diseases › COVID-19 Clinical Research Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- SARS-CoV-2, chronic infection, viral evolution, spike protein, convalescent plasma therapy, neutralizing antibodies, antibody escape, remdesivir, immunosuppression, viral selection, viral infectivity, ultra-deep sequencing
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.
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.
What counts as a claim ›How we measure confidence ›How we check this ›
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