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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]
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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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BackgroundUsing minor variant genomes and machine learning to study the genome biology of SARS-CoV-2 over time
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The course of the UK COVID 19 pandemic; no measurable impact of new variantsPreprint
Ellis, D., Papadopoulos, D., Mukherjee, S. K., Ukwu, U., Chari, N., Charitopoulos, K., Donkov, I., & Bishara, S. (2021) · medRxiv · doi:10.1101/2021.03.16.21253534 · Cited by 2
“It has also been demonstrated that mutations that helped avoid the immune system may lead to a defect in infectivity that is counterbalanced by the emergence of further mutations.[31] New variants may only become more infective due a relatively increased immunity to an older variant.”
BackgroundCourjon, J., Contenti, J., Demonchy, É., Levraut, J., Barbry, P., Rios, G., Dellamonica, J., Chirio, D., Bonnefoy, C., Giordanengo, V., et al. (2021) · Research Square · doi:10.21203/rs.3.rs-343317/v1 · Cited by 2
Unlocking capacities of viral genomics for the COVID-19 pandemic responsePreprint
Knyazev, S., Chhugani, K., Sarwal, V., Ayyala, R., Singh, H., Karthikeyan, S., Deshpande, D., Comarova, Z., Lu, A., Porozov, Y. B., et al. (2021) · PubMed · doi:10.48550/arxiv.2104.14005 · Cited by 2
Chauhan, V., & Thakur, S. (2021) · Journal of Global Infectious Diseases · doi:10.4103/jgid.jgid_114_21 · Cited by 2
“[9] Use of convalescent plasma is feared to be the cause of emergence of double mutant strains of SARS‑CoV‑2.”
BackgroundSequencing SARS-CoV-2 in Slovakia: An Unofficial Genomic Surveillance ReportPreprint
Brejová, B., Hodorová, V., Boršová, K., Čabanová, V., Szemes, T., Mišík, M., Klempa, B., Nosek, J., & Vinař, T. (2021) · medRxiv · doi:10.1101/2021.07.13.21260431 · Cited by 2
Niemeyer, D., Schroeder, S., Friedmann, K., Weege, F., Trimpert, J., Richter, A. M., Stenzel, S., Jansen, J., Emanuel, J., Kazmierski, J., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.10.20.465121 · Cited by 1
Self-citationWithin-host virus evolution during the extended treatment of RSV infection with mutagenic drugsPreprint
Illingworth, C. J. R., Kreins, A. Y., Margarit, A., Best, T., Dyal, P. L., Lucchini, G., Rao, K., Williams, R. J., Worth, A. J. J., & Breuer, J. (2022) · medRxiv · doi:10.1101/2022.09.02.22279474 · Cited by 2
Self-citationSnell, L. B., Bakrania, P., Williams, T. G. S., Tam, J. C. H., Fontoura, D. D. S., Shaw, E., Daunt, A., Edgeworth, J. D., Hemsley, C. J., Fields, P. A., et al. (2022) · Research Square · doi:10.21203/rs.3.rs-2227591/v1 · Cited by 2
Self-citationStructural prediction of chimeric immunogens to elicit targeted antibodies against betacoronavirusesPreprint
Simpson, J., & Kasson, P. M. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.01.31.526494 · Cited by 2
Karim, F., Bernstein, M. P., Jule, Z., Lustig, G., Upton, J., Ganga, Y., Khan, K., Reedoy, K., Mazibuko, M., Govender, K., et al. (2023) · medRxiv · doi:10.1101/2023.08.18.23293746 · Cited by 2
A Review Article on Vaccine Development and Therapeutics Approach Against SARS-CoV-2
Yadav, A., Singh, S., Srivastava, V. P., Bardhan, N., Gupta, S., Sarkar, P., & Kaur, H. (2021) · The Open COVID Journal · doi:10.2174/2666958702101010117 · Cited by 1
Alterations of SARS-CoV-2 Evolutionary Dynamics by Pharmaceutical Factors
Halma, M. T. J. (2024) · Infectious Diseases & Immunity · doi:10.1097/id9.0000000000000103 · Cited by 1
Rapid emergence of transmissible SARS-CoV-2 variants in mild community cases
Crone, M. A., Hakki, S., Zhou, J., de Oliveira, C. R., Madon, K. J., Koycheva, A., Badhan, A., Jonnerby, J., Fenn, J. R., Kundu, R., et al. (2024) · Microbiology Spectrum · doi:10.1128/spectrum.03634-23 · Cited by 1
Self-citationBlenkinsop, A., Sofocleous, L., Lauro, F. D., Kostaki, E. G., van Sighem, A., Bezemer, D., van de Laar, T. J. W., Reiss, P., de Bree, G. J., Pantazis, N., et al. (2025) · Statistical Methods in Medical Research · doi:10.1177/09622802241309750 · Cited by 1
“We address this, using HIV as an example, by leveraging additional data that can be used to estimate the time since infection and approximate the time elapsed as the interval between the infection event and the sampling time of two observed sequences, which assumes that the two lineages diverged at…”
Chai, Y., Zhou, L., Yang, Y. L., Tan, L., Ma, K., & Huang, Z. (2025) · Journal of Pharmaceutical and Biomedical Analysis · doi:10.1016/j.jpba.2025.116770 · Cited by 1
Coats, A., Wang, Y. R., & Koelle, K. (2025) · Virus Evolution · doi:10.1093/ve/veaf054 · Cited by 2
Deo, R., Choudhary, M. C., Glover, O. T., Ignacio, R. B., Boucau, J., Chew, K. W., Moser, C., Currier, J. S., Eron, J. J., Javan, A. C., et al. (2025) · Open Forum Infectious Diseases · doi:10.1093/ofid/ofaf542 · Cited by 1
“However, resistance has been report-ed in both immunocompromised and immunocompetent individuals following treatment [8–14].”
Self-citationIntra-Host Evolution of SARS-CoV-2 During Persistent Infection of Pediatric COVID-19 Patients
Boyle, C., Doan, T., Rios-Guzman, E., Maciuch, J., Simons, L. M., Garcia, D., Williams, D. B., Alisoltani, A., Ozer, E. A., Lorenzo-Redondo, R., et al. (2025) · Journal of the Pediatric Infectious Diseases Society · doi:10.1093/jpids/piag070/piag070.015 · Cited by 1
Self-citationImpact of prolonged infection on SARS-CoV-2 evolution
Yan, F., Jin, Q., Li, Y., Wang, X., Dong, C., Xia, X., Gao, Y., Zhang, J., & Hou, Z. (2025) · Microbiology Spectrum · doi:10.1128/spectrum.02432-25 · Cited by 1
“Longitudinal sequencing analyses of chronic infection cases have revealed a greater number of mutations and distinctive mutational patterns compared to those observed in transmission chains among acutely infected individuals (6, 13, 14).”
Snell, L. B., Pickering, S., Alcolea-Medina, A., Winstone, H., Seow, J., Graham, C., O’Connell, L., Batra, R., Malim, M. H., Doores, K. J., et al. (2026) · Cell Reports Medicine · doi:10.1016/j.xcrm.2026.102587 · Cited by 2
Self-citationKawashima, A., Tsuchiya, K., Kuroki, K., Nagashima, M., Koizumi, Y., Nakamoto, T., Mizushima, D., Aoki, T., Sadamasu, K., Teruya, K., et al. (2026) · International Journal of Infectious Diseases · doi:10.1016/j.ijid.2026.108453 · Cited by 1
Herzig, J. C., Magwira, M. L., & Lovell, S. C. (2026) · Genome Biology and Evolution · doi:10.1093/gbe/evag049 · Cited by 1
Linkage-aware inference of fitness from short-read time-series genomic data
Abdullah, S. M., Sohail, M. S., Louie, R. H. Y., Sun, Y., Barton, J. P., & McKay, M. R. (2026) · Virus Evolution · doi:10.1093/ve/veag027 · Cited by 1
HLA class I escape drives the evolution of SARS-CoV-2 in human populations
Riumina, E. D., Alekseeva, E. I., Klink, G. V., Feigin, S. E., Vinogradova, I., Ivanova, N., Dianov, D., Zornikova, K. V., Davydova, V. D., Васильевна, Б. А., et al. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2619192123 · Cited by 1
Extracorporal hemocorrection methods for COVID-19: are there outlooks?
Rumyantsev, A. S., Khasun, M. H., Panina, I. Y., Коростелева, Н. Ю., Shurakova, V. A., & Zemchenkov, G. A. (2021) · Nephrology (Saint-Petersburg) · doi:10.36485/1561-6274-2021-25-4-95-106 · Cited by 1
Fatores de virulência microbianos e terapias emergentes
Barbosa, A. V., da Silva, S. M., da Silva, F. H. S., de Assunção, M. A. S., & dos Anjos, F. B. R. (2022) · Latin American Publicações eBooks · doi:10.47174/lap2020.ed.0000093 · Cited by 2
Yuan, Q., Lv, B., & Zhang, H. (2022) · Current Chinese Science · doi:10.2174/2210298102666220615160026 · Cited by 1
Hisamatsu, D., Ikeda, A., Ito, L., Matsushita, Y., Hiki, M., Mori, H., Tabe, Y., Naito, T., & Akazawa, C. (2022) · Vaccines · doi:10.3390/vaccines10111815 · Cited by 1
“Immunocompromised hosts receiving convalescent plasma therapy, immunoglobulin replacement therapy, or antiviral drugs exhibit aberrant mutations in the SARS-CoV-2 genome that could trigger viral evolution [32].”
BackgroundJeong, B.-S., Jeon, J. Y., Lai, C., Yun, H.-Y., Jung, J. U., & Oh, B. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.1049867 · Cited by 1
Bedoya‐Joaqui, V., Lopez, M., Caicedo, P. A., Villegas-Torres, M. F., Albornóz, L. L., Vélez, J. D., Hidalgo-Cardona, A., Tobón, G. J., & Cañas, C. A. (2023) · Journal of Medical Case Reports · doi:10.1186/s13256-023-03917-x · Cited by 1
“The literature reported that the changes in the population dynamics of patients with persistent SARS CoV-2 infection are evident after Days 29 [9], 49 [10], and 65 [11].”
BackgroundJacobs, J. L., Haidar, G., Naqvi, A., McCormick, K. D., Sobolewski, M. D., Treat, B. R., Heaps, A., Simpson, J., Kramer, K. H., McCreary, E. K., et al. (2023) · Open Forum Infectious Diseases · doi:10.1093/ofid/ofad278 · Cited by 1
“some variants of concern emerged in immunocompromised patients with prolonged infection [2] and that selection by monoclonal antibodies (mAbs) could accelerate the emergence of immune escape variants [3].”
BackgroundDevelopment and validation of a novel CD4+ T cell‐related gene signature to detect severe COVID‐19
Zhang, D., Li, F., Wei, Y., Hu, L., Chen, S., Yang, M., Zhang, W., & Fei, G. (2023) · Clinical and Translational Medicine · doi:10.1002/ctm2.1294 · Cited by 1
Yamamoto, S., Yamayoshi, S., Ito, M., Sakai‐Tagawa, Y., Nakachi, I., Baba, R., Kamimoto, S., Ogura, T., Hagiwara, S., Kato, H., et al. (2023) · iScience · doi:10.1016/j.isci.2023.107208 · Cited by 1
“The deletion of both H69 and V70 at the N2 loop of the NTD is associated indirectly with a reduction of neutralization titers.(23,45) The A67V substitution, which is located near the N2 loop of the NTD, was found in BA.”
Pashameah, R. A., Soltane, R., & Sayed, A. M. (2023) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2023.125818 · Cited by 2
Molecular evolution and targeted recombination of SARS-CoV-2 in South Korea
Demirev, A. V., Lee, K., Bae, J., Park, H., Park, S., Kim, H., Lee, J., Cho, J., Yang, J., Kim, K.-C., et al. (2023) · iScience · doi:10.1016/j.isci.2023.107689 · Cited by 1
Self-citationAvdeev, S. N., Chulanov, V., Alexeeva, E. I., Aleshina, O. A., Bereznikov, A. V., Kotenko, O. N. K., Lila, A. M., Mutovina, Z. Y., Parovichnikova, E. N., Fomina, D. S., et al. (2023) · Terapevticheskii arkhiv · doi:10.26442/00403660.2023.08.202391 · Cited by 1
“Следует помнить, что продол-жительная инфекция у пациента с иммунодефицитом мо-жет стимулировать эволюцию коронавируса с появлением более вирулентных и трансмиссивных вариантов, приводя к новым вспышкам заболеваемости [5].”
Capoluongo, N., Mascolo, A., Bernardi, F. F., Sarno, M., Iacono, V. M., Flumeri, G. D., Pustorino, B., Spaterella, M., Trama, U., Capuano, A., et al. (2023) · Pharmaceuticals · doi:10.3390/ph16101493 · Cited by 1
“Specifically, patients with an impaired immune system are at higher risk of prolonged or unresolved SARS-CoV-2 infection, which might also facilitate the development of new variants [18].”
BackgroundMing, S. W. Y., Smith, M., & Zhou, Y. (2023) · doi:10.33590/microbiolinfectdisamj/10304488 · Cited by 1
Self-citationSam, S., Ofoghi, H., & Farahmand, B. (2024) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2024.2302941 · Cited by 1
“However, the mutations in the RBD of these variants have raised concerns about the potential impact on diagnostic accuracy (Garcia-Beltran et al., 2021; Kemp et al., 2021).”
Ju, C., Wang, M., Yuan, J., Xu, Y., Xue, W., Lu, H., Li, Y., & Li, S. (2024) · International Journal of Rheumatic Diseases · doi:10.1111/1756-185x.14998 · Cited by 1
Together Apart: Decoding Support Dynamics in Online COVID-19 Communities
Jangra, H., Pandey, T., Singhal, S., Kandhari, P., Tomar, A., & Kumaraguru, P. (2023) · IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM) · doi:10.1145/3625007.3627297 · Cited by 1
Perevaryukha, A. Y. (2023) · Биофизика · doi:10.31857/s0006302923050277 · Cited by 1
Silva, H. M. (2024) · Ciência & Educação (Bauru) · doi:10.1590/1516-731320240009 · Cited by 1
Wouters, C., Sachithanandham, J., Akin, E., Pieterse, L., Fall, A., Truong, T., Bard, J. D., Yee, R., Sullivan, D. J., Mostafa, H. H., et al. (2024) · Viruses · doi:10.3390/v16091436 · Cited by 2
“…of this observation, monoclonal antibody or convalescent plasma therapy in ICPs has corresponded to increased frequencies of mutations in the Spike protein [1,3,6,7,9,20], and SARS-CoV-2 evolving in an immunocompromised HIV patient was only weakly neutralized by the patient’s own plasma [21].”
BackgroundBaek, K., Kim, D., Kang, B. M., Kim, J.-S., Demirev, A. V., Lee, S., Kim, M., Kim, S., Park, S., Kim, J. I., et al. (2024) · Journal of Medical Virology · doi:10.1002/jmv.70072 · Cited by 1
“For example, natural prolonged infection, known as chronic or persistent infection, typically occurs in immunocompromised rather than immunodeficient individuals [15 – 17, 46, 47].”
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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