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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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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
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Brandolini, M., Dirani, G., Taddei, F., Zannoli, S., Denicolò, A., Arfilli, V., Battisti, A., Manera, M., Mancini, A., Grumiro, L., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-16533-4 · Cited by 5
Pohler, A., Abdelfatah, S., Riedl, M., Meesters, C., Hildebrandt, A., & Efferth, T. (2022) · Pharmaceuticals · doi:10.3390/ph15091046 · Cited by 5
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BackgroundCueno, M. E., Wada, K., Tsuji, A., Ishikawa, K., & Imai, K. (2022) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2022.111376 · Cited by 5
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BackgroundCueno, M. E., & Imai, K. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.773726 · Cited by 5
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Lodi, L., Moriondo, M., Pucci, A., Pisano, L., Ricci, S., Indolfi, G., & Azzari, C. (2021) · Clinical Infectious Diseases · doi:10.1093/cid/ciab538 · Cited by 5
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BackgroundRamanathan, M., Murugesan, K., Yang, L. M., Costales, C., Bulterys, P. L., Schroers‐Martin, J. G., Alizadeh, A. A., Boyd, S. D., Brown, J. W., Nadeau, K. C., et al. (2021) · medRxiv · doi:10.1101/2021.07.21.21260921 · Cited by 5
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Mushegian, A. A., Long, S. W., Olsen, R. J., Christensen, P. A., Subedi, S., Chung, M. C., Davis, J. J., Musser, J. M., & Ghedin, E. (2022) · medRxiv · doi:10.1101/2022.08.17.22278898 · Cited by 5
Översti, S., Gaul, E., Jensen, B. O., & Kühnert, D. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.11.01.565087 · Cited by 5
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Bayarri‐Olmos, R., Sutta, A., Rosbjerg, A., Mortensen, M. M., Helgstrand, C., Nielsen, P. F., Pérez‐Alós, L., González‐García, B., Johnsen, L. B., Matthiesen, F., et al. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1412873 · Cited by 4
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Ferrareze, P. A. G., Zimerman, R. A., Franceschi, V. B., Caldana, G. D., Netz, P. A., & Thompson, C. E. (2022) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2022.2076154 · Cited by 4
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BackgroundVeličković, J., Adžić‐Vukičević, T., Spurnić, A. R., Lazić, I., Popovic, B. M., Bogdanović, I., Raičević, S., Marić, D., & Berisavac, I. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2022.973817 · Cited by 4
Verkhivker, G. M., Alshahrani, M., & Gupta, G. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24076642 · Cited by 4
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BackgroundUse of Monoclonal Antibodies in Pregnant Women Infected by COVID-19: A Case Series
Crispino, P., Marocco, R., Trento, D. D., Guarisco, G., Kertusha, B., Carraro, A., Corazza, S., Pane, C., Troia, L. D., del Borgo, C., et al. (2023) · Microorganisms · doi:10.3390/microorganisms11081953 · Cited by 4
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BackgroundSayed, A. A., & Nozha, O. M. A. (2023) · Biomedicines · doi:10.3390/biomedicines11102649 · Cited by 4
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BackgroundManuelpillai, B., Zendt, M., Chang-Rabley, E., & Ricotta, E. (2024) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2024.03.027 · Cited by 4
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BackgroundMisasi, J., Wei, R. R., Wang, L., Pegu, A., Wei, C., Oloniniyi, O. K., Zhou, T., Moliva, J. I., Zhao, B., Choe, M., et al. (2024) · Science Translational Medicine · doi:10.1126/scitranslmed.ado9026 · Cited by 9
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Durrant, R., Cobbold, C. A., Brunker, K., Campbell, K., Dushoff, J. G., Ferguson, E. A., Jaswant, G., Lugelo, A., Lushasi, K. S., Sikana, L., et al. (2024) · PLoS Pathogens · doi:10.1371/journal.ppat.1012740 · Cited by 3
Gong, T., Zhang, X., Lin, H., Li, J., Tao, J., Zeng, T., Ren, X., Xie, Z., Xiao, L., Zhang, S., et al. (2025) · Virus Research · doi:10.1016/j.virusres.2025.199626 · Cited by 4
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BackgroundYamasaki, L., & Moi, M. L. (2021) · Pathogens · doi:10.3390/pathogens10101262 · Cited by 4
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BackgroundCOVID-19 variants that escape vaccine immunity: Global and Indian context—are more vaccines needed?
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BackgroundMurugadoss, K., Niesen, M. J. M., Raghunathan, B., Lenehan, P. J., Ghosh, P., Feener, T., Anand, P., Simsek, S., Suratekar, R., Hughes, T. K., et al. (2022) · PNAS Nexus · doi:10.1093/pnasnexus/pgac018 · Cited by 4
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Acharjee, A., Kingsly, J. S., Kamat, M., Kurlawala, V., Chakraborty, A., Vyas, P., Vaishnav, R., & Srivastava, S. (2022) · Expert Review of Proteomics · doi:10.1080/14789450.2022.2085564 · Cited by 4
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Aliabadi, N., Jamalidoust, M., Pouladfar, G., Marandi, N. H., & Ziyaeyan, M. (2023) · Health Science Reports · doi:10.1002/hsr2.1052 · Cited by 4
Ose, N. J., Campitelli, P., Modi, T., Kazan, I. C., Kumar, S., & Ozkan, S. B. (2023) · eLife · doi:10.7554/elife.92063 · Cited by 9
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Self-citationAzzeri, A. B., Mohamed, N. A., Rosli, S. H. W., Samat, M. N. A., Rashid, Z. Z., Jamali, M. A. M., Zoqratt, M. Z. H. M., Nasir, M., Singh, H., & Azmi, L. (2024) · PLoS ONE · doi:10.1371/journal.pone.0291892 · Cited by 4
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BackgroundSong, N., Cui, G., & Zeng, Q. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.673855 · Cited by 4
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Ropa, J. P., Trinh, T. L. P., Aljoufi, A., & Broxmeyer, H. E. (2021) · Current Opinion in Hematology · doi:10.1097/moh.0000000000000645 · Cited by 4
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Akther, S., Bezrucenkovas, E., Li, L., Sulkow, B., Di, L., Pante, D., Martin, C., Luft, B. J., & Qiu, W. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.07.443114 · Cited by 3
FXR inhibition reduces ACE2 expression, SARS-CoV-2 infection and may improve COVID-19 outcomePreprint
Brevini, T., Maes, M., Webb, G. J., Gelson, W., Forrest, S., Mlčochová, P., Dillon, S., Varankar, S., Darvish-Damavandi, M., Mulcahy, V., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.06.06.446781 · Cited by 7
Self-citationCheng, M. H., Krieger, J., Xiang, Y., Kaynak, B., Shi, Y., Arditi, M., & Bahar, İ. (2021) · SSRN Electronic Journal · doi:10.2139/ssrn.3907841 · Cited by 4
Consulting the Oracle of SARS-CoV-2 Infection
Lemieux, J. E., & Luban, J. (2021) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiab623 · Cited by 4
“The Alpha variant was notable for a sudden leap in the rate of accumulation of SARS-CoV-2 mutations, and for the eerie familiarity of its constituent mutations such as spike (S) N501Y and S:del69-70, which had been observed in people chronically infected with SARS-CoV-2 [2, 3].”
BackgroundPandemic-Induced Wealth and Health Inequality and Risk ExposurePreprint
Angelopoulos, K., Lazarakis, S., Mancy, R., & Schroeder, M. (2021) · SSRN Electronic Journal · doi:10.2139/ssrn.3985772 · Cited by 4
SARS-CoV-2 Antibody Responses to AZD1222 Vaccination in West AfricaPreprint
Abdullahi, A., Oladele, D. A., Owusu, M., Kemp, S. A., James, A. B., Salako, A. O., Fink, D., Sylverken, A. A., Ige, F. A., Onwuamah, C. K., et al. (2022) · Research Square · doi:10.21203/rs.3.rs-1834968/v1 · Cited by 4
Self-citationA highly divergent SARS-CoV-2 lineage B.1.1 sample in a patient with long-term COVID-19Preprint
Nabieva, E., Komissarov, A. B., Klink, G. V., Zaitsev, S. V., Sergeeva, M. V., Fadeev, A. V., Сергеевна, К. К., Ivanova, A. A., Pisareva, M., Kudrya, K., et al. (2023) · medRxiv · doi:10.1101/2023.09.14.23295379 · Cited by 4
Schmidt, H., Schick, L., Podlech, J., Renzaho, A., Lieb, B., Diederich, S., Hankeln, T., Plachter, B., & Kriege, O. (2025) · npj Genomic Medicine · doi:10.1038/s41525-025-00463-x · Cited by 3
Mycophenolic acid treatment drives the emergence of novel SARS-CoV-2 variants
Meister, T. L., Nocke, M. K., Heinen, N., Burkard, T. L., Brüggemann, Y., Westhoven, S., Trüeb, B. S., Ebert, N., Thomann, L., Lubieniecki, K. P., et al. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2500276122 · Cited by 7
Self-citationKumar, S., Delipan, R., Sharma, C., Jadoun, J., Kanjo, K., Singh, R., Rajmani, R., Deshpande, S., Pandey, R., Thakur, K. G., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-65099-y · Cited by 3
Persistent attenuation of lymphocyte subsets after mass SARS-CoV-2 infection
Jiang, Z., Shan, T., Li, Y., Han, F., Feng, B., Zhen, X., Ma, J., Ni, H., Peng, J., & Xu, M. (2025) · International Journal of Infectious Diseases · doi:10.1016/j.ijid.2025.108287 · Cited by 3
Hyperedge size-driven multiscale epidemic dynamics on hypergraphs
Yan, S.-L., Wang, Y.-F., Li, Y., Luo, X., Yang, J., & Sun, G.-Q. (2026) · Chaos An Interdisciplinary Journal of Nonlinear Science · doi:10.1063/5.0307432 · Cited by 3
Arıkan, A., & Sayan, M. (2022) · Diagnostics · doi:10.3390/diagnostics12112869 · Cited by 3
Kaya, H., Tani, H., Inasaki, N., Yazawa, S., Itamochi, M., Higashi, D., Tsuji, N., Nakamura, M., & Oishi, K. (2023) · International Journal of Infectious Diseases · doi:10.1016/j.ijid.2023.09.010 · Cited by 3
Zeng, H.-L., Yang, C.-L., Jing, B., Barton, J. P., & Aurell, E. (2024) · Physical Biology · doi:10.1088/1478-3975/ad9213 · Cited by 3
Machine learning based predictive modeling and risk factors for prolonged SARS-CoV-2 shedding
Zhang, Y., Li, Q., Duan, H., Tan, L., Cao, Y., & Chen, J. (2024) · Journal of Translational Medicine · doi:10.1186/s12967-024-05872-7 · Cited by 3
“More seriously, SARS-CoV-2 viruses may evolve to produce immune evasion mutations during prolonged infection, potentially increasing the probability of virus transmission and disease severity to enhance the pressure of combating the epidemic [9].”
Becker, W., Rebbani, K., Duan, Z., Valkov, E., Bryant, S., Ho, M., Berzofsky, J. A., & Olkhanud, P. B. (2024) · Scientific Reports · doi:10.1038/s41598-024-80636-3 · Cited by 3
Unninayar, D., Falcone, E. L., Chapdelaine, H., Vinh, D. C., Top, K. A., Dérfalvi, B., Issekutz, T. B., Decaluwe, H., Pham‐Huy, A., Upton, J. E. M., et al. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1501908 · Cited by 3
Kashour, T. S., & Tleyjeh, I. M. (2021) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2021.02.024 · Cited by 3
“What potentially poses more risk of SARS-CoV-2 evolution is the ongoing spread of the virus among the chronically immunocompromised population, the indiscriminate use of convalescent plasma therapy [17] and the delay in vaccination worldwide.”
BackgroundDiversity due to mutations in circulating virus strains of SARS-CoV-2 may delay control of COVID-19
Patil Sharanagouda, S., Shivamallu, C., Dharmashekara, C., Sushma, P., Puttahonnappa, S. K., Ashwini, P., Prasad, K. S., Yadav Mahendra, P., Chandrashekar, S., & Bramhadev, P. (2022) · Journal of Applied Biology & Biotechnology · doi:10.7324/jabb.2022.100223 · Cited by 3
Sabino, J. S., Amorim, M. R., de Souza, W. M., Marega, L. F., Mofatto, L. S., de Toledo-Teixeira, D. A., Forato, J., Stábeli, R. G., Costa, M. L., Spilki, F. R., et al. (2022) · Viruses · doi:10.3390/v14051042 · Cited by 3
Wang, C., Li, Y., Pan, Y., Zhou, L., Zhang, X., Yan, W., Guo, F., Shu, Y., & Gao, J. (2022) · Journal of Zhejiang University SCIENCE B · doi:10.1631/jzus.b2200054 · Cited by 3
Assessment of the Prevalence and Incidence of COVID-19 in Saudi Arabia
Alyahyawi, H. E., Alharbi, R., Alatawi, S. K., Ahmed, W. A. M., & Almalki, S. S. R. (2023) · Journal of Multidisciplinary Healthcare · doi:10.2147/jmdh.s394038 · Cited by 3
“variant is a deletion in the spike protein at amino acid positions 69–70 (deletion ∆H69/∆V70), which is linked to immune escape in immunocompromised patients, and enhances viral infectivity in vitro.(25,26) This deletion variant is noted to affect”
BackgroundFittall, M. W., Liu, J., Platt, J. R., Ionescu, M. C., Sheehan, R., Johal, S., Mew, R., Clark, J., Watts, I., Tripathy, A. R., et al. (2023) · British Journal of Cancer · doi:10.1038/s41416-023-02251-9 · Cited by 3
“These novel approaches encompassed clinical testing, risk stratification and the development of therapeutics: the RECOVERY programme rapidly established a coordinated national clinical trial assessing repurposed therapeutics in hospitalised patients [1], the FALCON Moonshot C-19 studies provided the validation for lat…”
BackgroundSelf-citationLong-range linkage effects in adapting sexual populations
Rouzine, I. M. (2023) · Scientific Reports · doi:10.1038/s41598-023-39392-z · Cited by 3
Third COVID-19 vaccine dose boosts antibody function in Rwandans with high HIV viral load
Swan, C. L., Dushimiyimana, V., Ndishimye, P., Buchanan, R. M., Yourkowski, A., Semafara, S., Nsanzimana, S., Francis, M. E., Thivierge, B. M., Lew, J. M., et al. (2023) · iScience · doi:10.1016/j.isci.2023.107959 · Cited by 3
“39 It has been postulated that new variants such as Omicron may have emerged from those who are immuno-compromized due to the continued viral replication leading to mutations within the virus which can occur when the immune response is not robust.”
BackgroundSelf-citationSeth-Smith, H. M. B., Vesenbeckh, S. M., Egli, A., & Ott, S. R. (2023) · BMJ Case Reports · doi:10.1136/bcr-2023-255255 · Cited by 3
“15 22 It has been suggested that such patients increase the risk of the development of immune escape mutants, particularly affecting the S gene encoding the surface spike protein.”
BackgroundSelf-citationCompetitive fitness and homologous recombination of SARS‐CoV‐2 variants of concern
Chen, Q., Qin, S., Zhou, H., Deng, Y., Shi, P., Zhao, H. J., Li, X., Huang, X., Wu, Y., Guo, Y., et al. (2023) · Journal of Medical Virology · doi:10.1002/jmv.29278 · Cited by 3
“19 However, whether immune selection pressure contributes to the emergence and displacement of SARS ‐ CoV ‐ 2 epidemic variants lacks direct evidence.”
BackgroundVaccination Shapes Within-Host SARS-CoV-2 Diversity of Omicron BA.2.2 Breakthrough Infection
Zhang, Y., Zhou, Y., Chen, J., Wu, J., Wang, X., Zhang, Y., Wang, S., Cui, P., Xu, Y., Li, Y., et al. (2023) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiad572 · Cited by 3
Importance of Timely Sequencing, Tracking, and Surveillance of Emergent Variants
Lin, J., Greenleaf, M. N., Lu, Y., Bassit, L., Wesselman, C., & Piantadosi, A. L. (2024) · Cambridge University Press eBooks · doi:10.1017/9781009396998.012 · Cited by 3
Role of the Neanderthal Genome in Genetic Susceptibility to COVID-19: 3p21.31 Locus in the Spotlight
Yaghmouri, M., & Izadi, P. (2024) · Biochemical Genetics · doi:10.1007/s10528-024-10669-w · Cited by 3
Manuto, L., Bado, M., Cola, M., Vanzo, E., Antonello, M., Mazzotti, G., Pacenti, M., Cordioli, G., Sasset, L., Cattelan, A. M., et al. (2024) · Viruses · doi:10.3390/v16030447 · Cited by 2
“In addition to the compromised immune system, typical treatments, such as convalescent plasma, monoclonal antibodies or antivirals, have also been reported to induce selective pressure on SARS-CoV-2 intra-host evolution [5,8–11].”
BackgroundResultIp, J. D., Chu, W.-M., Chan, W.-M., Chu, A. W., Leung, R. C.-Y., Peng, Q., Tam, A. R., Chan, B. P.-C., Cai, J., Yuen, K., et al. (2024) · EBioMedicine · doi:10.1016/j.ebiom.2024.105273 · Cited by 3
Sivasubramanian, B. P., Joshi, S., Ravikumar, D. B., Jagannathan, M., Babu, S., Sripathi, S. R., Javvaji, A., Jain, P., Shanmugam, D. K., Kannan, B. D. S., et al. (2024) · Frontiers in Oncology · doi:10.3389/fonc.2024.1446482 · Cited by 3
“These mutations have led to viral evolution, a protracted period (4 months) for neutralizing antibodies to appear, and reduced sensitivity to neutralizing antibodies (16 – 19).”
BackgroundIntra-host variability of SARS-CoV-2: Patterns, causes and impact on COVID-19
Jones, L. R. (2024) · Virology · doi:10.1016/j.virol.2024.110366 · Cited by 3
Diverse patterns of intra-host genetic diversity in chronically infected SARS-CoV-2 patients
Zvi, A. B., Rutsinsky, N., Jacobi, B., Fabian, I., Segev, S., Harari, S., Meijer, S. E., Paran, Y., & Stern, A. (2025) · Virus Evolution · doi:10.1093/ve/veaf047 · Cited by 4
“Chronic infections are defined as cases where actively replicating virus persists for more than 21 days, and de facto such infections often last months to over a year (Avanzato et al. 2020, Baang et al. 2021, Kemp et al.2021,Harari et al.2022).”
de Oliveira, V. M., Marinho, M. M., Magalhães, E. P., de Menezes, R. R. P. P. B., Sampaio, T. L., Martins, A. M. C., dos Santos, H. S., & Marinho, E. S. (2021) · Journal of the Indian Chemical Society · doi:10.1016/j.jics.2021.100157 · Cited by 3
SAS: A Platform of Spike Antigenicity for SARS-CoV-2
Zhang, L., Cao, R., Mao, T., Wang, Y., Lv, D., Yang, L., Tang, Y., Zhou, M., Ling, Y., Zhang, G., et al. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.713188 · Cited by 3
“Besides that, recent studies demonstrated that the neutralization ability of mAbs and convalescent or vaccinated sera is decreased against new circulating mutants such as B.1.1.7 and P.1 (Choi et al., 2020; Kemp et al., 2021; McCarthy et al., 2021).”
ResultInfluentialFreise, N. F., Gliga, S., Fischer, J., Lübke, N., Lutterbeck, M., Schöler, M., Bölke, E., Orth, H. M., Feldt, T., Römmele, C., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-23200-1 · Cited by 3
Hosaka, Y., Yan, Y., Naito, T., Oyama, R., Tsuchiya, K., Yamamoto, N., Nojiri, S., Hori, S., Takahashi, K., & Tabe, Y. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.944369 · Cited by 3
“Meanwhile, patients with immunosuppression were reported to be at risk for prolonged infection with SARS-CoV-2, along with a number of identified substitutions and deletions in genome sequences (Choi et al., 2020; Corey et al., 2021; Kemp et al., 2021).”
BackgroundMoisan, A., Soares, A., Oliveira, F. D., Alessandri-Gradt, É., Lecoquierre, F., Fourneaux, S., Plantier, J., & Gueudin, M. (2023) · Viruses · doi:10.3390/v15051115 · Cited by 3
Agass, R., Wilson, A. M., Weller, R., & Pfau, T. (2014) · Equine Veterinary Journal · doi:10.1111/evj.12323_44 · Cited by 3
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 ›
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