The DOI matches its Crossref record; 65 of the 65 references it cites were found in a registry or an index.
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
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?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209
Cutadapt removes adapter sequences from high-throughput sequencing reads
Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889
Hoffmann, M., Kleine-Weber, H., Schroeder, S., Krüger, N., Herrler, T., Erichsen, S., Schiergens, T. S., Herrler, G., Wu, N.-H., Nitsche, A., et al. (2020) · Cell · doi:10.1016/j.cell.2020.02.052 · Cited by 20,286
ModelFinder: fast model selection for accurate phylogenetic estimates
Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A., & Jermiin, L. S. (2017) · Nature Methods · doi:10.1038/nmeth.4285 · Cited by 18,449
IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era
(2019) · doi:10.1101/849372 · Cited by 16,873
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
Minh, B. Q., Schmidt, H. A., Chernomor, O., Schrempf, D., Woodhams, M. D., von Haeseler, A., & Lanfear, R. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa015 · Cited by 16,873
Minimap2: Pairwise alignment for nucleotide sequences
Li, H. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty191 · Cited by 14,807
BEAST 2: a software platform for Bayesian evolutionary analysis
Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C.-H., Xie, D., Suchard, M. A., Rambaut, A., & Drummond, A. J. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003537 · Cited by 6,527
Ultrafast Approximation for Phylogenetic Bootstrap
Minh, B. Q., Nguyen, M. A. T., & von Haeseler, A. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst024 · Cited by 4,844
Korber, B., Fischer, W. M., Gnanakaran, S., Yoon, H., Theiler, J., Abfalterer, W., Hengartner, N., Giorgi, E. E., Bhattacharya, T., Foley, B., et al. (2020) · Cell · doi:10.1016/j.cell.2020.06.043 · Cited by 4,281
Research works printed but not linked: 2
- 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. Preprint at https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 (2020).
- Meredith, L. W. et al. Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study. Lancet Infect. Dis. 20, 1263–1271 (2020). · DOI
Cited by
Sorted by citations
Items 201–300 of 1,006
Cheng, M. H., Krieger, J., Kaynak, B., Arditi, M., & Bahar, İ. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.10.426143 · Cited by 57
Could live attenuated vaccines better control COVID-19?
Okamura, S., & Ebina, H. (2021) · Vaccine · doi:10.1016/j.vaccine.2021.08.018 · Cited by 61
SARS-CoV-2 spike N-terminal domain modulates TMPRSS2-dependent viral entry and fusogenicity
Meng, B., Datir, R. P., Choi, J., Baker, S. G., Dougan, G., Hess, C., Kingston, N., Lehner, P. J., Lyons, P., Matheson, N. J., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111220 · Cited by 58
“We included a deletion mutant in the NTD (delH69/V70) as a control due to its known efficient spike cleavage (Kemp et al., 2021; Meng et al., 2021).”
InfluentialSelf-citationThe evolutionary dynamics of endemic human coronaviruses
Jo, W. K., Drosten, C., & Drexler, J. F. (2021) · Virus Evolution · doi:10.1093/ve/veab020 · Cited by 60
Emergence and outcomes of the SARS-CoV-2 ‘Marseille-4’ variant
Fournier, P., Colson, P., Levasseur, A., Devaux, C. A., Gautret, P., Bedotto, M., Delerce, J., Bréchard, L., Pinault, L., Lagier, J., et al. (2021) · International Journal of Infectious Diseases · doi:10.1016/j.ijid.2021.03.068 · Cited by 57
Structural and functional insights into the spike protein mutations of emerging SARS-CoV-2 variants
Gupta, D., Sharma, P., Singh, M., Kumar, M., Ethayathulla, A. S., & Kaur, P. (2021) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-04008-0 · Cited by 56
“2 Δ69 /70 S1 -NTD Role in immune escape and diagnostic failure [159]”
BackgroundUnderstanding the Secret of SARS-CoV-2 Variants of Concern/Interest and Immune Escape
Lou, F., Li, M., Pang, Z., Jiang, L., Guan, L., Tian, L., Hu, J., Fan, J., & Fan, H. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.744242 · Cited by 54
“617 variants, and were proximal to the furin cleavage site (33), which could accelerate virus spread by increasing the membrane fusion rate (53).”
BackgroundInfluentialKarim, Q. A., & Baxter, C. (2022) · Current HIV/AIDS Reports · doi:10.1007/s11904-021-00588-5 · Cited by 57
Interfering with Interferons: A Critical Mechanism for Critical COVID-19 Pneumonia
Su, H. C., Jing, H., Zhang, Y., & Casanova, J. (2023) · Annual Review of Immunology · doi:10.1146/annurev-immunol-101921-050835 · Cited by 68
Nooruzzaman, M., Johnson, K., Rani, R., Finkelsztein, E. J., Caserta, L. C., Kodiyanplakkal, R. P., Wang, W., Hsu, J., Salpietro, M. T., Banakis, S., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-51924-3 · Cited by 57
Self-citationMoore, J. P. (2021) · JAMA · doi:10.1001/jama.2021.3465 · Cited by 60
Self-citationIbrahim, M. A. A., Abdelrahman, A. H. M., Mohamed, T. A., Atia, M. A. M., Alhammady, M. A., Abdeljawaad, K. A. A., Elkady, E. M., Moustafa, M., Alrumaihi, F., Allemailem, K. S., et al. (2021) · Molecules · doi:10.3390/molecules26072082 · Cited by 53
“Recently, an increasing number of escape mutations in the spike protein threaten the effectiveness of vaccines [6].”
BackgroundImproving the Outcomes of Immunocompromised Patients With Coronavirus Disease 2019
Haidar, G., & Mellors, J. W. (2021) · Clinical Infectious Diseases · doi:10.1093/cid/ciab397 · Cited by 53
“Several studies have shown the emergence of deletions in the N-terminal domain (NTD) of the spike glycoprotein gene (S gene) and mutations in the receptor binding domain (RBD) of the S gene and in other regions of the SARS-CoV-2 genome, all within the same host in the absence of reinfection [8, 9, 11, 13, 14].”
BackgroundNanoplasmonic biosensor for rapid detection of multiple viral variants in human serum
Bhalla, N., Payam, A. F., Morelli, A., Sharma, P. K., Johnson, R., Thomson, A., Jolly, P., & Canfarotta, F. (2022) · Sensors and Actuators B Chemical · doi:10.1016/j.snb.2022.131906 · Cited by 53
“Whilst antibodies remain the molecular recognition workhorse of choice for bio-sensing devices, their use can impose limitations on widespread technology adoption due to rapidly mutating viral proteins [21].”
Self-citationCovid-19: virology, variants, and vaccines
Young, M., Crook, H., Scott, J. T., & Edison, P. (2022) · BMJ Medicine · doi:10.1136/bmjmed-2021-000040 · Cited by 55
Inter-domain communication in SARS-CoV-2 spike proteins controls protease-triggered cell entry
Qing, E., Li, P., Cooper, L. M., Schulz, S. R., Jäck, H., Rong, L., Perlman, S. M., & Gallagher, T. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110786 · Cited by 45
“Also evaluated were D796H/Y changes that disrupt an interdomain D796-Y707 bridge (Figure 5C) and were reported to operate allosterically in conferring virus resistance to neutralization by convalescent patient sera (Kemp et al., 2021).”
Clinical course and management of COVID-19 in the era of widespread population immunity
Meyerowitz, E. A., Scott, J. A., Richterman, A. G., Male, V. H., & Çevik, M. (2023) · Nature Reviews Microbiology · doi:10.1038/s41579-023-01001-1 · Cited by 53
“It is important to note that viral evolution may occur during persistent infections, with mutations accumulating over time in immunocompromised hosts, which may contribute to the development of new SARS-CoV-2 variants 69,70 .”
Coronavirus 2019 Infectious Disease Epidemic: Where We Are, What Can Be Done and Hope For
Carbone, M., Lednicky, J. A., Xiao, S., Venditti, M., & Bucci, E. M. (2021) · Journal of Thoracic Oncology · doi:10.1016/j.jtho.2020.12.014 · Cited by 62
SARS-CoV-2 variants and convalescent plasma: reality, fallacies, and opportunities
Casadevall, A., Henderson, J. P., Joyner, M. J., & Pirofski, L. (2021) · Journal of Clinical Investigation · doi:10.1172/jci148832 · Cited by 49
Hettle, D., Hutchings, S., Muir, P., & Moran, E. (2022) · Clinical Infection in Practice · doi:10.1016/j.clinpr.2022.100210 · Cited by 54
Self-citationAndi, B., Kumaran, D., Kreitler, D. F., Soares, A. S., Keereetaweep, J., Jakoncic, J., Lazo, E., Shi, W., Fuchs, M. R., Sweet, R. M., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-15930-z · Cited by 51
Host–Pathogen Interactions Influencing Zoonotic Spillover Potential and Transmission in Humans
Escudero-Pérez, B., Lalande, A., Mathieu, C., & Lawrence, P. (2023) · Viruses · doi:10.3390/v15030599 · Cited by 56
Huang, S., & Wang, S. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22063060 · Cited by 50
“• Enhance the infectivity and compensate the decrease of infectivity due to emerge of RBD immune escape mutations, such as D796H.”
BackgroundInfluentialMeir, J., Abid, M. A., & Abid, M. B. (2021) · Transplantation and Cellular Therapy · doi:10.1016/j.jtct.2021.09.016 · Cited by 51
Hamilton, F., Lee, T. C., Arnold, D., Lilford, R. J., & Hemming, K. (2021) · International Journal of Infectious Diseases · doi:10.1016/j.ijid.2021.06.034 · Cited by 44
Genomic epidemiology of SARS-CoV-2 under an elimination strategy in Hong Kong
Gu, H., Xie, R., Adam, D. C., Tsui, J. L.-H., Chu, D. K. W., Chang, L. D. J., Cheuk, S. S. Y., Gurung, S., Krishnan, P., Ng, D. Y. M., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28420-7 · Cited by 46
Ameratunga, R., Longhurst, H. J., Steele, R. H., Lehnert, K., Leung, E. Y., Brooks, A. E. S., & Woon, S. (2021) · The Journal of Allergy and Clinical Immunology In Practice · doi:10.1016/j.jaip.2021.06.019 · Cited by 49
COVID-19, the first pandemic in the post-genomic era
van Dorp, L., Houldcroft, C. J., Richard, D., & Balloux, F. (2021) · Current Opinion in Virology · doi:10.1016/j.coviro.2021.07.002 · Cited by 49
“Deletions in the NTD may contribute to altered antibody recognition [61,62] with genetic variation in this region also suggested as supporting conformational changes in the spike protein [63,64], either permitting or compensating for other changes in the RBD, with which they are often associated.”
BackgroundChanchlani, N., Lin, S., Chee, D., Hamilton, B., Nice, R., Arkir, Z., Bewshea, C., Cipriano, B., Derikx, L. A. A. P., Dunlop, A., et al. (2021) · Journal of Crohn s and Colitis · doi:10.1093/ecco-jcc/jjab153 · Cited by 48
Self-citationAhmad, L. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.742167 · Cited by 46
Cheng, M. H., Krieger, J., Banerjee, A., Xiang, Y., Kaynak, B., Shi, Y., Arditi, M., & Bahar, İ. (2022) · iScience · doi:10.1016/j.isci.2022.103939 · Cited by 50
“Countries of origin are listed, but these variants have now been observed in multiple countries (Kemp et al., 2021; Plante et al., 2021; Tegally et al., 2020; Zhang et al., 2021c).”
Evolutionary implications of SARS-CoV-2 vaccination for the future design of vaccination strategies
Rouzine, I. M., & Rozhnova, G. (2023) · Communications Medicine · doi:10.1038/s43856-023-00320-x · Cited by 49
“Alternative theories of the emergence of VOCs 19 include reverse zoonosis, evolution within immunocompromised patients with chronic infection 136 – 138 , and evolution in subpopulations not covered by genetic surveillance.”
The Genetic Variant of SARS-CoV-2: Would it matter for Controlling the Devastating Pandemic?
Guo, S., Liu, K., & Zheng, J. (2021) · International Journal of Biological Sciences · doi:10.7150/ijbs.59137 · Cited by 46
“It was shown that ΔH69/ΔV70 either has a similar susceptibility as wild type to the neutralization by convalescent plasma [58, 63], or an enhanced sensitivity to the neutralization by the sera from the participants vaccinated by mRNA-1273 vaccine (Moderna) [64].”
BackgroundIntranasal gene therapy to prevent infection by SARS-CoV-2 variants
Sims, J. J., Greig, J. A., Michalson, K. T., Lian, S., Martino, R. A., Meggersee, R., Turner, K. B., Nambiar, K., Dyer, C., Hinderer, C. J., et al. (2021) · PLoS Pathogens · doi:10.1371/journal.ppat.1009544 · Cited by 42
“An immediate application could be in immune-suppressed individuals who do not respond to traditional vaccines, develop chronic infection with SARS-CoV-2, and may be reservoirs for new variants[1].”
BackgroundInfluentialSARS-CoV-2 resistance to monoclonal antibodies and small-molecule drugs
Iketani, S., & Ho, D. D. (2024) · Cell chemical biology · doi:10.1016/j.chembiol.2024.03.008 · Cited by 49
SARS-CoV-2 Spike Protein Stabilized in the Closed State Induces Potent Neutralizing Responses
Carnell, G., Ciazynska, K. A., Wells, D. A., Xiong, X., Aguinam, E. T., McLaughlin, S. H., Mallery, D. L., Ebrahimi, S., Ceron‐Gutierrez, L., Asbach, B., et al. (2021) · Journal of Virology · doi:10.1128/jvi.00203-21 · Cited by 46
Self-citationLassaunière, R., Fonager, J., Rasmussen, M., Frische, A., Polacek, C., Rasmussen, T. B., Lohse, L., Belsham, G. J., Underwood, A. P., Winckelmann, A. A., et al. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.698944 · Cited by 44
Self-citationStructure and Mutations of SARS-CoV-2 Spike Protein: A Focused Overview
Mehra, R., & Kepp, K. P. (2021) · ACS Infectious Diseases · doi:10.1021/acsinfecdis.1c00433 · Cited by 45
Spike protein of SARS-CoV-2 variants: a brief review and practical implications
Candido, K. L., Eich, C. R., de Fariña, L. O., Kadowaki, M. K., Silva, J. L. D. C., Maller, A., & Simão, R. D. C. G. (2022) · Brazilian Journal of Microbiology · doi:10.1007/s42770-022-00743-z · Cited by 46
Severe impairment of T-cell responses to BNT162b2 immunization in patients with multiple myeloma
Enssle, J. C., Campe, J., Schwenger, A., Wiercinska, E., Hellstern, H., Dürrwald, R., Rieger, M. A., Wolf, S., Balló, O., Steffen, B., et al. (2021) · Blood · doi:10.1182/blood.2021013429 · Cited by 46
Garushyants, S. K., Rogozin, I. B., & Koonin, E. V. (2021) · Communications Biology · doi:10.1038/s42003-021-02858-9 · Cited by 46
The Development of SARS-CoV-2 Variants: The Gene Makes the Disease
Pérez-Gómez, R. (2021) · Journal of Developmental Biology · doi:10.3390/jdb9040058 · Cited by 47
Yang, Z. L., Zhang, S., Tang, Y., Zhang, S., Xu, D.-Q., Yue, S., & Liu, Q. (2022) · Aging and Disease · doi:10.14336/ad.2021.1210 · Cited by 46
“that immune plasma or monoclonal antibody (mAbs) therapy may prompt selection variants which show mutations that evade the antibody response [11].”
BackgroundThe impact of Spike mutations on SARS-CoV-2 neutralizationPreprint
Rees-Spear, C., Muir, L., Griffith, S. A., Heaney, J., Aldon, Y., Snitselaar, J. L., Pataillot-Meakin, T., Graham, C., Seow, J., Lee, N., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.15.426849 · Cited by 45
Self-citationResende, P. C., Naveca, F. G., Lins, R. D., Dezordi, F. Z., Ferraz, M. V. F., Moreira, E. G., Coêlho, D. F., Motta, F. C., Paixão, A. C. D., Appolinario, L., et al. (2021) · Virus Evolution · doi:10.1093/ve/veab069 · Cited by 47
Self-citationImmunocompromised patients have been neglected in COVID-19 trials: a call for action
Trøseid, M., Hentzien, M., Ader, F., Cardoso, S. W., Arribas, J. R., Molina, J., Mueller, N. J., Hites, M., Bonnet, F., Manuel, O., et al. (2022) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2022.05.005 · Cited by 43
“Persistence of SARS-CoV2 replication in immunosuppressed patients despite the use of antiviral treatments can lead to virus evolution and accumulation of resistance mutations [2], as well as the possibility of generation of new variants of concern [3].”
BackgroundKo, S. H., Mokhtari, E. B., Mudvari, P., Stein, S. R., Stringham, C. D., Wagner, D. A., Ramelli, S. C., Ramos-Benítez, M. J., Strich, J. R., Davey, R. T., et al. (2021) · PLoS Pathogens · doi:10.1371/journal.ppat.1009431 · Cited by 41
Emergence of multiple SARS-CoV-2 mutations in an immunocompromised hostPreprint
Khatamzas, E., Rehn, A., Muenchhoff, M., Hellmuth, J. C., Gaitzsch, E., Weiglein, T., Georgi, E., Scherer, C., Stecher, S. S., Weigert, O., et al. (2021) · medRxiv · doi:10.1101/2021.01.10.20248871 · Cited by 44
Verhagen, J., van der Meijden, E. D., Lang, V., Kremer, A. E., Völkl, S., Mackensen, A., Aigner, M., & Kremer, A. N. (2021) · Clinical & Experimental Immunology · doi:10.1111/cei.13627 · Cited by 40
“Moreover, a recent report warned that convalescent plasma treatment of severe disease may promote the evolution of the virus to avoid interaction with neutralising antibodies [3].”
BackgroundNikolaidis, M., Markoulatos, P., de Peer, Y. V., Oliver, S. G., & Amoutzias, G. D. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab292 · Cited by 42
“However, given the observed genomic diversity and inherent genomic instability of CoVs, in this new era of urbanization, global transport, intensive farming, and habitat destruction (Beyer et al. 2021), intratypic and intertypic recombination events may lead to new epidemic strains that may prove…”
BackgroundEvolution of the SARS-CoV-2 genome and emergence of variants of concern
Safari, I., & Elahi, E. (2021) · Archives of Virology · doi:10.1007/s00705-021-05295-5 · Cited by 41
Omicron subvariant BA.5 efficiently infects lung cells
Hoffmann, M., Wong, L.-Y. R., Arora, P., Zhang, L., Rocha, C., Odle, A. E., Nehlmeier, I., Kempf, A. M., Richter, A. M., Halwe, N. J., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-39147-4 · Cited by 38
Self-citationPérez‐Lago, L., Aldámiz‐Echevarría, T., García‐Martínez, R., Latorre, L. P., Herránz, M., Sola‐Campoy, P. J., Suárez‐González, J., Martínez‐Laperche, C., Comas, I., Gónzález‐Candelas, F., et al. (2021) · Biomedicines · doi:10.3390/biomedicines9070808 · Cited by 40
The past, current and future epidemiological dynamic of SARS-CoV-2
Balloux, F., Tan, C. C. S., Swadling, L., Richard, D., Jenner, C., Maini, M. K., & van Dorp, L. (2022) · Oxford Open Immunology · doi:10.1093/oxfimm/iqac003 · Cited by 41
“has been observed in chronic infections [170] and persistent infection in immunocompromised hosts may provide the virus with a possibility to explore a wider range of the fitness landscape.”
BackgroundGenomic surveillance at scale is required to detect newly emerging strains at an early timepointPreprint
Vavrek, D. A., Speroni, L., Curnow, K. J., Oberholzer, M., Moeder, V., & Febbo, P. G. (2021) · medRxiv · doi:10.1101/2021.01.12.21249613 · Cited by 38
Agrati, C., Bartolini, B., Bordoni, V., Locatelli, F., Capobianchi, M. R., Di, A., Castilletti, C., & Ippolito, G. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1147871 · Cited by 48
“Nonetheless, several key questions remain about immunocompromised individuals with protracted COVID-19 not only to improve the well-being of the patient, but also to better understand intra-host viral evolution leading to the emergence of novel variants and to immune escape mechanisms (63).”
BackgroundLu, L., Chu, A. W., Zhang, R., Chan, W.-M., Ip, J. D., Tsoi, H., Chen, L., Cai, J., Lung, D. C., Tam, A. R., et al. (2021) · EBioMedicine · doi:10.1016/j.ebiom.2021.103544 · Cited by 39
“D796H mutation in the S2 region has been proposed to reduce neutralization susceptibility by convalescent plasma and is found in the B.1.1.318 [37,38].”
InfluentialBhola, S., Trisal, J., Thakur, V., Kaur, P., Kulshrestha, S., Bhatia, S. K., & Kumar, P. (2022) · Neurological Sciences · doi:10.1007/s10072-022-05875-6 · Cited by 42
“Despite that, the new variants seem to have found the way to escape from the monoclonal antibodies, it seems that the evolution of intermediate mutants which are flowing and targeting the immunocompromised patients where the possibilities of viral replication is higher while on going treatment with immune plasma or mo…”
BackgroundBrejová, B., Boršová, K., Hodorová, V., Čabanová, V., Reizigová, L., Paul, E. D., Čekan, P., Klempa, B., Nosek, J., & Vinař, T. (2021) · Virus Genes · doi:10.1007/s11262-021-01866-5 · Cited by 47
Impact of mutations in SARS-COV-2 spike on viral infectivity and antigenicity
Zhou, W., Xu, C., Wang, P., Anashkina, A. A., & Jiang, Q. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab375 · Cited by 42
Taha, Y., Wardle, H., Evans, A. B., Hunter, E., Marr, H. J., Osborne, W., Bashton, M., Smith, D., Burton-Fanning, S., Schmid, M. L., et al. (2021) · Annals of Clinical Microbiology and Antimicrobials · doi:10.1186/s12941-021-00491-2 · Cited by 37
Self-citationMartin, D. P., Lytras, S., Lucaci, A. G., Maier, W., Grüning, B. A., Shank, S. D., Weaver, S., MacLean, O. A., Orton, R. J., Lemey, P., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.01.14.476382 · Cited by 40
Self-citationThe rise in cases of mucormycosis, candidiasis and aspergillosis amidst COVID19
Ghosh, A., Sarkar, A., Paul, P., & Patel, P. K. (2021) · Fungal Biology Reviews · doi:10.1016/j.fbr.2021.09.003 · Cited by 38
Strohl, W. R., Ku, Z., An, Z., Carroll, S. F., Keyt, B. A., & Strohl, L. M. (2022) · BioDrugs · doi:10.1007/s40259-022-00529-7 · Cited by 35
In Vitro Selection of Remdesivir-Resistant SARS-CoV-2 Demonstrates High Barrier to Resistance
Checkmahomed, L., Carbonneau, J., Pont, V. D., Riola, N. C., Perry, J. K., Li, J., Paré, B., Simpson, S. M., Smith, M. A., Porter, D., et al. (2022) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00198-22 · Cited by 38
“shedding, the V166L substitution in nsp12 was observed after treatment with two 10-day 114 courses of RDV and two units of convalescent plasma (unknown phenotype) (13).”
Self-citationXiao, H., Hu, J., Huang, C., Feng, W., Liu, Y., Kumblathan, T., Tao, J., Xu, J., Le, X. C., & Zhang, H. (2023) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2023.117000 · Cited by 39
Self-citationKasparian, N. A., Bränström, R., Chang, Y., Affleck, P., Aspinwall, L. G., Tibben, A., Azizi, E., Baron‐Epel, O., Battistuzzi, L., Bruno, W., et al. (2012) · Archives of Dermatology · doi:10.1001/archdermatol.2012.1817 · Cited by 39
Rapid inactivation of SARS-CoV-2 by titanium dioxide surface coating
Micochova, P., Chadha, A., Hesseloj, T., Fraternali, F., Ramsden, J. J., & Gupta, R. K. (2021) · Wellcome Open Research · doi:10.12688/wellcomeopenres.16577.1 · Cited by 37
Self-citationAntigenic evolution of SARS coronavirus 2
Mykytyn, A. Z., Fouchier, R. A. M., & Haagmans, B. L. (2023) · Current Opinion in Virology · doi:10.1016/j.coviro.2023.101349 · Cited by 36
Using big sequencing data to identify chronic SARS-Coronavirus-2 infections
Harari, S., Miller, D., Fleishon, S., Burstein, D., & Stern, A. (2024) · Nature Communications · doi:10.1038/s41467-024-44803-4 · Cited by 37
SARS-CoV-2 B.1.617 emergence and sensitivity to vaccine-elicited antibodies
Mlčochová, P., Kemp, S. A., Dhar, M. S., Papa, G., Meng, B., Mishra, S., Whittaker, C., Mellan, T. A., Ferreira, I., Datir, R. P., et al. (2021) · Greater South Information System · doi:10.60692/dy28a-h7650 · Cited by 44
Self-citationAiello, A., Fard, S. N., & Goletti, D. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1244556 · Cited by 38
Intra- vs. Interhost Evolution of SARS-CoV-2 Driven by Uncorrelated Selection—The Evolution Thwarted
Hou, M., Shi, J., Gong, Z., Wen, H., Lan, Y., Deng, X., Fan, Q., Li, J. J., Jiang, M., Tang, X., et al. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad204 · Cited by 35
“Interestingly, hitchhiking and compensation have been detected in persistent SARS-CoV-2 infection in immuno-suppressed individuals (Kemp et al. 2021).”
BackgroundInfluentialCase Series: Convalescent Plasma Therapy for Patients with COVID-19 and Primary Antibody Deficiency
Lang‐Meli, J., Fuchs, J., Mathé, P., Ho, H.-E., Kern, L., Jaki, L., Rusignuolo, G., Mertins, S., Somogyi, V., Neumann‐Haefelin, C., et al. (2021) · Journal of Clinical Immunology · doi:10.1007/s10875-021-01193-2 · Cited by 35
Emergence of SARS-CoV-2 Spike Mutations during Prolonged Infection in Immunocompromised Hosts
Ko, K. K. K., Yingtaweesittikul, H., Tan, T. T., Wijaya, L., Cao, D. Y., Goh, S. S., Rahman, N. B. A., Chan, K. X. L., Tay, H. M., Sim, J. H. C., et al. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.00791-22 · Cited by 37
Evolutionary remodelling of N‐terminal domain loops fine‐tunes SARS‐CoV‐2 spike
Cantoni, D. M., Murray, M. J., Kalemera, M. D., Dicken, S. J., Stejskal, L., Brown, G., Lytras, S., Coey, J. D., McKenna, J. P., Bridgett, S., et al. (2022) · EMBO Reports · doi:10.15252/embr.202154322 · Cited by 37
“However, the development of NTD deletions has been linked to persistent infection of immunodeficient patients with impaired nAb responses (Kemp et al , 2021; Truong et al , 2021).”
Self-citationMartin, D. P., Weaver, S., Tegally, H., San, E. J., Shank, S. D., Wilkinson, E., Lucaci, A. G., Giandhari, J., Naidoo, S., Pillay, Y., et al. (2021) · PubMed · doi:10.34944/dspace/7022 · Cited by 49
Self-citationWhole genome sequencing of SARS-CoV2 strains circulating in Iran during five waves of pandemic
Yavarian, J., Nejati, A., Salimi, V., Shafiei-Jandaghi, N.-Z., Sadeghi, K., Abedi, A., Sharifi‐Zarchi, A., Gouya, M. M., & Mokhtari‐Azad, T. (2022) · PLoS ONE · doi:10.1371/journal.pone.0267847 · Cited by 35
SARS-CoV-2 evolution during prolonged infection in immunocompromised patients
Marques, A. D., Graham-Wooten, J., Fitzgerald, A. S., Leonard, A. S., Cook, E. J., Everett, J. K., Rodino, K. G., Moncla, L. H., Kelly, B. J., Collman, R. G., et al. (2024) · mBio · doi:10.1128/mbio.00110-24 · Cited by 35
“Spike V987F emerged in patient 637, which was reported previously in a B cell lymphoma patient with prolonged infection but is rarely observed in surveillance samples ( 0.01% of uploaded sequences, (15).”
BackgroundResultInfluentialSelf-citationda Silva, S. J. R., de Lima, S. C., da Silva, R. C., Kohl, A., & Pena, L. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2021.836826 · Cited by 35
Long and persistent COVID-19 in patients with hematologic malignancies: from bench to bedside
Laracy, J. C., Kamboj, M., & Vardhana, S. A. (2022) · Current Opinion in Infectious Diseases · doi:10.1097/qco.0000000000000841 · Cited by 34
Dicken, S. J., Murray, M. J., Thorne, L., Reuschl, A., Forrest, C., Ganeshalingham, M., Muir, L., Kalemera, M. D., Palor, M., McCoy, L. E., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.22.436468 · Cited by 30
“This is consistent with recent reports on viruses containing the 69/70 mutation (38, 39).”
BackgroundResultSelf-citationMolecular Determinants of SARS-CoV-2 Variants
Banerjee, A., Mossman, K. L., & Grandvaux, N. (2021) · Trends in Microbiology · doi:10.1016/j.tim.2021.07.002 · Cited by 34
“A clinical study also reported the rapid evolution of SARSCoV-2 variants in the presence of antibodies from convalescent plasma therapy [11].”
BackgroundTasakis, R. N., Samaras, G., Jamison, A., Lee, M., Paulus, A., Whitehouse, G., Verkoczy, L., Papavasiliou, F. N., & Diaz, M. (2021) · PLOS ONE · doi:10.1371/journal.pone.0255169 · Cited by 26
“Further supporting this, are reports of problematic variants arising within individual immunocompromised patients treated with convalescent sera [50] as these escape mutants can clearly arise when subjected to low levels of anti-Spike protein antibody.”
BackgroundWang, X., Haeussler, K., Spellman, A., Phillips, L. E., Ramiller, A., Bausch-Jurken, M. T., Sharma, P., Krivelyova, A., Vats, S., & de Velde, N. V. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1204831 · Cited by 32
“SARS-CoV-2 infection (19-26) and viral evolution (19-22; 24; 27; 28) due to poor humoral All rights reserved.”
BackgroundCorrelates of Neutralization against SARS-CoV-2 Variants of Concern by Early Pandemic Sera
Vidal, S. J., Collier, A.-R. Y., Yu, J., McMahan, K., Tostanoski, L. H., Ventura, J. D., Aïd, M., Peter, L. E., Jacob-Dolan, C., Anioke, T., et al. (2021) · Journal of Virology · doi:10.1128/jvi.00404-21 · Cited by 34
Łaźniewski, M., Dermawan, D., Hidayat, S., Muchtaridi, M., Dawson, W., & Plewczyński, D. (2022) · Methods · doi:10.1016/j.ymeth.2022.02.004 · Cited by 37
Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern
Ghafari, M., Liu, Q., Dhillon, A., Katzourakis, A., & Weissman, D. B. (2022) · Frontiers in Virology · doi:10.3389/fviro.2022.942555 · Cited by 35
“Several studies have now shown evidence of recurrent SARS-CoV-2 mutations in 351 immunocompromised patients [15-17], with some suggesting the detection of a variant-like 352”
BackgroundHalfmann, P., Minor, N. R., Haddock, L. A., Maddox, R., Moreno, G. K., Braun, K. M., Baker, D. A., Riemersa, K. K., Prasad, A., Alman, K. J., et al. (2022) · Virus Evolution · doi:10.1093/ve/veac104 · Cited by 36
Self-citationSARS-CoV-2 variants: Impact on biological and clinical outcome
Mahilkar, S., Agrawal, S. R., Chaudhary, S., Parikh, S., Sonkar, S. C., Verma, D. K., Chitalia, V., Mehta, D., Koner, B. C., Vijay, N., et al. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2022.995960 · Cited by 36
Upasani, V., Townsend, K., Wu, M., Carr, E. J., Hobbs, A., Dowgier, G., Ragno, M., Herman, L. S., Sharma, S., Shah, D., et al. (2023) · Clinical Infectious Diseases · doi:10.1093/cid/ciad368 · Cited by 35
“There is a risk of intrahost evolution during prolonged infection [22], and partially effective treatments may contribute to this [23–25].”
BackgroundSelf-citationSpreading of a new SARS-CoV-2 N501Y spike variant in a new lineage
Colson, P., Levasseur, A., Delerce, J., Pinault, L., Dudouet, P., Devaux, C. A., Fournier, P., Scola, B. L., Lagier, J., & Raoult, D. (2021) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2021.05.006 · Cited by 32
“Overlooked genome evolution following transmission to minks and back to humans [3], or promotion and selection of mutations during administration of remdesivir or convalescent plasma [14] have been suspected.”
Update on COVID-19 Therapeutics for Solid Organ Transplant Recipients, Including the Omicron Surge
Avery, R. K. (2022) · Transplantation · doi:10.1097/tp.0000000000004200 · Cited by 33
“The public health implications for society are that they are potential transmitters of a virus that may have undergone mutations during its long tenure in that individual, under the influence of associated therapeutics that may have been received.(100) To stem the spread of new variants arising in such circumstances,…”
BackgroundImmune correlates of protection for SARS-CoV-2, Ebola and Nipah virus infection
Escudero-Pérez, B., Lawrence, P., & Castillo‐Olivares, J. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1156758 · Cited by 37
“Likewise, as alluded to earlier, ADCC and ADCP can also be considered as hybrid effector mechanisms of immunity involving the synergistic action of antibodies and innate immune effector cells.”
BackgroundInfluentialMaeda, D. L. N. F., Tian, D., Yu, H., Dar, N., Rajasekaran, V., Meng, S., Mahsoub, H. M., Sooryanarain, H., Wang, B., Heffron, C. L., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2025622118 · Cited by 33
SARS-CoV-2 and pathological matrix remodeling mediators
Guizani, I., Fourti, N., Zidi, W., Feki, M., & Elasmi, M. (2021) · Inflammation Research · doi:10.1007/s00011-021-01487-6 · Cited by 35
Stirrup, O., Boshier, F. A. T., Venturini, C., Guerra‐Assunção, J. A., Alcolea-Medina, A., Beckett, A. H., Charalampous, T., Filipe, A. D. S., Glaysher, S., Khan, T., et al. (2021) · BMJ Open Respiratory Research · doi:10.1136/bmjresp-2021-001029 · Cited by 32
Self-citationThe Immune Response to SARS-CoV-2 and Variants of Concern
Torbati, E., Krause, K. L., & Ussher, J. E. (2021) · Viruses · doi:10.3390/v13101911 · Cited by 36
Lamarca, A. P., de Almeida, L. G. P., Francisco, R. D. S., Agnez‐Lima, L. F., Scortecci, K. C., Perez, V. P., Brustolini, O. J. B., Sousa, E. S. S., Secco, D., Santos, Â., et al. (2021) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0009835 · Cited by 35
“Previous studies have shown that both N501Y and E484K have independently emerged in patients with persistent infection [54,59].”
ResultResearch progress of biosensors for detection of SARS-CoV-2 variants based on ACE2
Wei, H., Zhang, C., Du, X., & Zhang, Z. (2022) · Talanta · doi:10.1016/j.talanta.2022.123813 · Cited by 34
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. A., Abudahab, K., Taylor, B. E. W., Menegazzo, M., supervision, L. &., Danesh, J., Hogsden, W., Eldirdiri, S., Kenyon, A., Mason, J., Robinson, T. I., Holmes, A., Price, J., Hartley, J. A., Curran, T., Mather, A. E., Shankar, G., Jones, R., Howe, R., Morgan, S., curation, M., Wastenge, E., Chapman, M. R., Mookerjee, S., Stanley, R., Smith, W., Peto, T., Eyre, D., Crook, D., Vernet, G., Kitchen, C., Gulliver, H., Merrick, I., Guest, M., Munn, R., Bradley, D. T., Wyatt, T., Project administration, Beaver, C., Foulser, L., Palmer, S., Churcher, C. M., Brooks, E., Smith, K. S., Galai, K., McManus, G. M., Bolt, F., Coll, F., Meadows, L., Attwood, S. W., Davies, A., De Lacy, E., Downing, F., Edwards, S., Scarlett, G. P., Jeremiah, S., Smith, N., logistics, S. &., Leek, D., Sridhar, S., Forrest, S., Cormie, C., Gill, H. K., Dias, J., Higginson, E. E., Maes, M., Young, J., Wantoch, M., Jamrozy, D., Lo, S., Patel, M., Hill, V., Bewshea, C. M., Ellard, S., Auckland, C., Harrison, I., Bishop, C., Chalker, V., Richter, A., Beggs, A., Best, A., Percival, B., Mirza, J., Megram, O., Mayhew, M., Crawford, L., Ashcroft, F., Moles-Garcia, E., Cumley, N., Hopes, R., Asamaphan, P., Niebel, M. O., Gunson, R. N., Bradley, A., Maclean, A., Mollett, G., Blacow, R., Bird, P., Helmer, T., Fallon, K., Tang, J., Hale, A. D., Macfarlane-Smith, L. R., Harper, K. L., Carden, H., Machin, N. W., Jackson, K. A., Ahmad, S. S. Y., George, R. P., Turtle, L., O’Toole, E., Watts, J., Breen, C., Cowell, A., Alcolea-Medina, A., Charalampous, T., Patel, A., Levett, L. J., Heaney, J., Rowan, A., Taylor, G. P., Shah, D., Atkinson, L., Lee, J. C. D., Westhorpe, A. P., Jannoo, R., Lowe, H. L., Karamani, A., Ensell, L., Chatterton, W., Pusok, M., Dadrah, A., Symmonds, A., Sluga, G., Molnar, Z., Baker, P., Bonner, S., Essex, S., Barton, E., Padgett, D., Scott, G., Greenaway, J., Payne, B. A. I., Burton-Fanning, S., Waugh, S., Raviprakash, V., Sheriff, N., Blakey, V., Williams, L.-A., Moore, J., Stonehouse, S., Smith, L., Davidson, R. K., Bedford, L., Coupland, L., Wright, V., Chappell, J. G., Tsoleridis, T., Ball, J., Khakh, M., Fleming, V. M., Lister, M. M., Howson-Wells, H. C., Berry, L., Boswell, T., Joseph, A., Willingham, I., Duckworth, N., Walsh, S., Wise, E., Moore, N., Mori, M., Cortes, N., Kidd, S., Williams, R., Gifford, L., Bicknell, K., Wyllie, S., Lloyd, A., Impey, R., Malone, C. S., Cogger, B. J., Levene, N., Monaghan, L., Keeley, A. J., Partridge, D. G., Raza, M., Evans, C., Johnson, K., Abnizova, I., Aigrain, L., Alderton, A., Ali, M., Allen, L., Amato, R., Anderson, R., Ariani, C., Austin-Guest, S., Bala, S., Barrett, J., Bassett, A., Battleday, K., Beal, J., Beale, M., Beaver, C., Bellany, S., Bellerby, T., Bellis, K., Berger, D., Berriman, M., Betteridge, E., Bevan, P., Binley, S., Bishop, J., Blackburn, K., Bonfield, J., Boughton, N., Bowker, S., Brendler-Spaeth, T., Bronner, I., Brooklyn, T., Buddenborg, S. K., Bush, R., Caetano, C., Cagan, A., Carter, N., Cartwright, J., Monteiro, T. C., Chapman, L., Chillingworth, T.-J., Clapham, P., Clark, R., Clarke, A., Clarke, C., Cole, D., Cook, E., Coppola, M., Cornell, L., Cornwell, C., Corton, C., Crackett, A., Cranage, A., Craven, H., Craw, S., Crawford, M., Cutts, T., Dabrowska, M., Davies, M., Davies, R., Dawson, J., Day, C., Densem, A., Dibling, T., Dockree, C., Dodd, D., Dogga, S., Dorman, M., Dougan, G., Dougherty, M., Dove, A., Drummond, L., Drury, E., Dudek, M., Durham, J., Durrant, L., Easthope, E., Eckert, S., Ellis, P., Farr, B., Fenton, M., Ferrero, M., Flack, N., Fordham, H., Forsythe, G., Foulser, L., Francis, M., Fraser, A., Freeman, A., Galvin, A., Garcia-Casado, M., Gedny, A., Girgis, S., Glover, J., Goncalves, S., Goodwin, S., Gould, O., Gourtovaia, M., Gray, A., Gray, E., Griffiths, C., Gu, Y., Guerin, F., Hamilton, W., Hanks, H., Harrison, E., Harrott, A., Harry, E., Harvison, J., Heath, P., Hernandez-Koutoucheva, A., Hobbs, R., Holland, D., Holmes, S., Hornett, G., Hough, N., Huckle, L., Hughes-Hallet, L., Hunter, A., Inglis, S., Iqbal, S., Jackson, A., Jackson, D., James, K., Jamrozy, D., Verdejo, C. J., Johnston, I., Jones, M., Kallepally, K., Kane, L., Kay, K., Kay, S., Keatley, J., Keith, A., King, A., Kitchin, L., Kleanthous, M., Klimekova, M., Korlevic, P., Krasheninnkova, K., Kwiatkowski, D., Lane, G., Langford, C., Laverack, A., Law, K., Lawniczak, M., Lensing, S., Leonard, S., Letchford, L., Lewis, K., Lewis-Wade, A., Liddle, J., Lin, Q., Lindsay, S., Linsdell, S., Livett, R., Lo, S., Long, R., Lovell, J., Lovell, J., Ludden, C., Mack, J., Maddison, M., Makunin, A., Mamun, I., Mansfield, J., Marriott, N., Martin, M., Martincorena, I., Mayho, M., McCarthy, S., McClintock, J., McGuigan, S., McHugh, S., McMinn, L., Meadows, C., Mobley, E., Moll, R., Morra, M., Morrow, L., Murie, K., Nash, S., Nathwani, C., Naydenova, P., Neaverson, A., Nelson, R., Nerou, E., Nicholson, J., Nimz, T., Noell, G. G., O’Meara, S., Ohan, V., Oliver, K., Olney, C., Ormond, D., Oszlanczi, A., Palmer, S., Pang, Y. F., Pardubska, B., Park, N., Parmar, A., Patel, G., Patel, M., Payne, M., Peacock, S., Petersen, A., Plowman, D., Preston, T., Prestwood, L., Puethe, C., Quail, M., Rajan, D., Rajatileka, S., Rance, R., Rawlings, S., Redshaw, N., Reynolds, J., Reynolds, M., Rice, S., Richardson, M., Roberts, C., Robinson, K., Robinson, M., Robinson, D., Rogers, H., Rojo, E. M., Roopra, D., Rose, M., Rudd, L., Sadri, R., Salmon, N., Saul, D., Schwach, F., Scott, C., Seekings, P., Shirley, L., Sillitoe, J., Simms, A., Sinnott, M., Sivadasan, S., Siwek, B., Sizer, D., Skeldon, K., Skelton, J., Slater-Tunstill, J., Sloper, L., Smerdon, N., Smith, C., Smith, C., Smith, J., Smith, K., Smith, M., Smith, S., Smith, T., Sneade, L., Soria, C. D., Sousa, C., Souster, E., Sparkes, A., Spencer-Chapman, M., Squares, J., Stanley, R., Steed, C., Stickland, T., Still, I., Stratton, M., Strickland, M., Swann, A., Swiatkowska, A., Sycamore, N., Swift, E., Symons, E., Szluha, S., Taluy, E., Tao, N., Taylor, K., Taylor, S., Thompson, S., Thompson, M., Thomson, M., Thomson, N., Thurston, S., Tonkin-Hill, G., Toombs, D., Topping, B., Tovar-Corona, J., Ungureanu, D., Uphill, J., Urbanova, J., Jansen Van, P., Vancollie, V., Voak, P., Walker, D., Walker, M., Waller, M., Ward, G., Weatherhogg, C., Webb, N., Weldon, D., Wells, A., Wells, E., Westwood, L., Whipp, T., Whiteley, T., Whitton, G., Whitwham, A., Widaa, S., Williams, M., Wilson, M., Wright, S., analysis, S. &., Betteridge, E., Farr, B. W., Goodwin, S., Quail, M. A., Scott, C., Shirley, L., Thurston, S. A. J., Rajan, D., Bronner, I. F., Aigrain, L., Redshaw, N. M., Lensing, S. V., McCarthy, S., Makunin, A., Balcazar, C. E., Gallagher, M. D., Williamson, K. A., Stanton, T. D., Michelsen, M. L., Warwick-Dugdale, J., Manley, R., Farbos, A., Harrison, J. W., Sambles, C. M., Studholme, D. J., Lackenby, A., Mbisa, T., Platt, S., Miah, S., Bibby, D., Manso, C., Hubb, J., Dabrera, G., Ramsay, M., Bradshaw, D., Schaefer, U., Groves, N., Gallagher, E., Lee, D., Williams, D., Ellaby, N., Hartman, H., Manesis, N., Patel, V., Ledesma, J., Twohig, K. A., Allara, E., Pearson, C., Cheng, J. K. J., Bridgewater, H. E., Frost, L. R., Taylor-Joyce, G., Brown, P. E., Tong, L., Broos, A., Mair, D., Nichols, J., Carmichael, S. N., Smollett, K. L., Nomikou, K., Aranday-Cortes, E., Johnson, N., Nickbakhsh, S., Vamos, E. E., Hughes, M., Rainbow, L., Eccles, R., Nelson, C., Whitehead, M., Gregory, R., Gemmell, M., Wierzbicki, C., Webster, H. J., Fisher, C. L., Signell, A. W., Betancor, G., Wilson, H. D., Nebbia, G., Flaviani, F., Cerda, A. C., Merrill, T. V., Wilson, R. E., Cotic, M., Bayzid, N., Thompson, T., Acheson, E., Rushton, S., O’Brien, S., Baker, D. J., Rudder, S., Aydin, A., Sang, F., Debebe, J., Francois, S., Vasylyeva, T. I., Zamudio, M. E., Gutierrez, B., Marchbank, A., Maksimovic, J., Spellman, K., McCluggage, K., Morgan, M., Beer, R., Afifi, S., Workman, T., Fuller, W., Bresner, C., Angyal, A., Green, L. R., Parsons, P. J., Tucker, R. M., Brown, R., Whiteley, M., tools, S. &. A., Bonfield, J., Puethe, C., Whitwham, A., Liddle, J., Rowe, W., Siveroni, I., Le-Viet, T., Gaskin, A., Visualization, Johnson, R., Sharrocks, K., Blane, E., Modis, Y., Leigh, K. E., Briggs, J. A. G., van Gils, M. J., Smith, K. G. C., Bradley, J. R., Smith, C., Doffinger, R., Ceron-Gutierrez, L., Barcenas-Morales, G., Pollock, D. D., Goldstein, R. A., Smielewska, A., Skittrall, J. P., Gouliouris, T., Goodfellow, I. G., Gkrania-Klotsas, E., Illingworth, C. J. R., McCoy, L. E., & Gupta, R. K.
- 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 ›
Are you an author, or do you see a problem with this page? Request a review
