The DOI matches its Crossref record; 38 of the 38 references it cites were found in a registry or an index.
Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England
Open accessPublished version of a preprint
Abstract
The SARS-CoV-2 lineage B.1.1.7, designated variant of concern (VOC) 202012/01 by Public Health England 1, was first identified in the UK in late summer to early autumn 2020 2. Whole-genome SARS-CoV-2 sequence data collected from community-based diagnostic testing for COVID-19 show an extremely rapid expansion of the B.1.1.7 lineage during autumn 2020, suggesting that it has a selective advantage. Here we show that changes in VOC frequency inferred from genetic data correspond closely to changes inferred by S gene target failures (SGTF) in community-based diagnostic PCR testing. Analysis of trends in SGTF and non-SGTF case numbers in local areas across England shows that B.1.1.7 has higher transmissibility than non-VOC lineages, even if it has a different latent period or generation time. The SGTF data indicate a transient shift in the age composition of reported cases, with cases of B.1.1.7 including a larger share of under 20-year-olds than non-VOC cases. We estimated time-varying reproduction numbers for B.1.1.7 and co-circulating lineages using SGTF and genomic data. The best-supported models did not indicate a substantial difference in VOC transmissibility among different age groups, but all analyses agreed that B.1.1.7 has a substantial transmission advantage over other lineages, with a 50% to 100% higher reproduction number.
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?
In the citing paper
“Epidemiological studies suggest that it was approximately 50% more transmissible than previously circulating UK variants 191,197,198 .”
From The biological and clinical significance of emerging SARS-CoV-2 variants (2021) · cites this paper as [191]
In the citing paper
“Volz and colleagues have shown that the B.1.1.7 variant increases the effective reproduction number, Rt, by a factor of 1·5–2·0.5”
From Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study (2021) · cites this paper as [5]
In the citing paper
“Preliminary evidence from epidemiological studies suggests that the B.1.1.7 variant is more transmissible than pre-existing variants.”
From Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study (2021) · cites this paper as [5]
In the citing paper
“In addition, the emergence of new variants with increased transmissibility 8 and reduced sensitivity to vaccine-elicited antibodies 9 , and for which vaccines are less able to prevent infection 10 , has raised fears for vulnerable groups in whom the magnitude and quality of immune responses may be suboptimal.”
From Age-related immune response heterogeneity to SARS-CoV-2 vaccine BNT162b2 (2021) · cites this paper as [8]
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
The Elements of Statistical Learning
Hastie, T., Tibshirani, R., & Friedman, J. (2009) · Springer Series in Statistics · doi:10.1007/978-0-387-84858-7 · Cited by 25,970
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
Hastie, T., & Tibshirani, R. (1986) · Statistical Science · doi:10.1214/ss/1177013604 · Cited by 12,575
Posterior summarization in Bayesian phylogenetics using tracer 1.7
Rambaut, A., Drummond, A. J., Xie, D., Baele, G., & Suchard, M. A. (2018) · Systematic Biology · doi:10.1093/sysbio/syy032 · Cited by 11,159
Self-citationBayesian phylogenetic and phylodynamic data integration using BEAST 1.10
Suchard, M. A., Lemey, P., Baele, G., Ayres, D. L., Drummond, A. J., & Rambaut, A. (2018) · Virus Evolution · doi:10.1093/ve/vey016 · Cited by 3,749
Self-citationEstimating the effects of non-pharmaceutical interventions on COVID-19 in Europe
Flaxman, S. R., Mishra, S., Gandy, A., Unwin, H. J. T., Mellan, T. A., Coupland, H., Whittaker, C., Zhu, H., Berah, T., Eaton, J. W., et al. (2020) · Nature · doi:10.1038/s41586-020-2405-7 · Cited by 3,398
Self-citationEstimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England
Davies, N. G., Abbott, S., Barnard, R. C., Jarvis, C. I., Kucharski, A. J., Munday, J. D., Pearson, C. A. B., Russell, T. W., Tully, D. C., Washburne, A. D., et al. (2021) · Science · doi:10.1126/science.abg3055 · Cited by 2,581
Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England
Davies, N. G., Abbott, S., Barnard, R. C., Jarvis, C. I., Kucharski, A. J., Munday, J. D., Pearson, C. A. B., Russell, T. W., Tully, D. C., Washburne, A. D., et al. (2020) · doi:10.1101/2020.12.24.20248822 · Cited by 2,557
Detection of a SARS-CoV-2 variant of concern in South Africa
Tegally, H., Wilkinson, E., Giovanetti, M., Iranzadeh, A., Fonseca, V., Giandhari, J., Doolabh, D., Pillay, S., San, E. J., Msomi, N., et al. (2021) · Nature · doi:10.1038/s41586-021-03402-9 · Cited by 2,510
Bi, Q., Wu, Y., Mei, S., Ye, C., Zou, X., Zhang, Z., Liu, X., Wei, L., Truelove, S., Zhang, T., et al. (2020) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(20)30287-5 · Cited by 1,960
Cited by
Sorted by citations
Items 301–400 of 1,003
Epidemiological drivers of transmissibility and severity of SARS-CoV-2 in England
Perez-Guzman, P. N., Knock, E., Imai, N., Rawson, T., Santoni, C. N., Alcada, J., Whittles, L. K., Thekke Kanapram, D., Sonabend, R., Gaythorpe, K. A. M., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-39661-5 · Cited by 42
Self-citationDorigatti, I., Lavezzo, E., Manuto, L., Ciavarella, C., Pacenti, M., Boldrin, C., Cattai, M., Saluzzo, F., Franchin, E., Vecchio, C. D., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24622-7 · Cited by 44
Self-citationA highly potent antibody effective against SARS-CoV-2 variants of concern
Fenwick, C. W., Turelli, P., Perez, L. H., Pellaton, C., Esteves-Leuenberger, L., Farina, A., Campos, J., Lana, E., Fiscalini, F., Raclot, C., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109814 · 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
Mazzoni, A., Vanni, A., Spinicci, M., Capone, M., Lamacchia, G., Salvati, L., Coppi, M., Antonelli, A., Carnasciali, A., Farahvachi, P., et al. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.801431 · Cited by 44
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
Biological Properties of SARS-CoV-2 Variants: Epidemiological Impact and Clinical Consequences
Hoteit, R., & Yassine, H. M. (2022) · Vaccines · doi:10.3390/vaccines10060919 · Cited by 47
Miersch, S., Li, Z., Saberianfar, R., Ustav, M., Case, J. B., Blazer, L. L., Chen, C., Ye, W., Pavlenco, A., Gorelik, M., et al. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167177 · Cited by 45
Weiss, A., Touret, F., Baronti, C., Gilles, M., Hoen, B., Nougaırède, A., de Lamballerie, X. N., & Sommer, M. O. A. (2021) · PLoS ONE · doi:10.1371/journal.pone.0260958 · Cited by 45
Multiple expansions of globally uncommon SARS-CoV-2 lineages in Nigeria
Ozer, E. A., Simons, L. M., Adewumi, M. O., Fowotade, A., Omoruyi, E. C., Adeniji, J. A., Olayinka, O. A., Dean, T. J., Zayas, J. P., Bhimalli, P. P., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28317-5 · Cited by 48
Stefanelli, P., Trentini, F., Petrone, D., Mammone, A., Ambrosio, L., Manica, M., Guzzetta, G., d’Andrea, V., Marziano, V., Zardini, A., et al. (2022) · Eurosurveillance · doi:10.2807/1560-7917.es.2022.27.45.2200125 · Cited by 46
Emergence of a recurrent insertion in the N-terminal domain of the SARS-CoV-2 spike glycoprotein
Gerdol, M., Dishnica, K., & Giorgetti, A. (2022) · Virus Research · doi:10.1016/j.virusres.2022.198674 · Cited by 47
SARS-CoV-2 journey: from alpha variant to omicron and its sub-variants
Hattab, D., Amer, M. F. A., Al‐Alami, Z. M., & Bakhtiar, A. (2024) · Infection · doi:10.1007/s15010-024-02223-y · Cited by 48
Akache, B., Renner, T. M., Tran, A., Deschatelets, L., Dudani, R., Harrison, B. A., Duque, D., Haukenfrers, J., Rossotti, M. A., Gaudreault, F., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-01363-7 · Cited by 43
International consensus on lung function testing during the COVID-19 pandemic and beyond
McGowan, A., Laveneziana, P., Bayat, S., Beydon, N., Boros, P. W., Burgos, F., Fležar, M., Franczuk, M., Galarza-Jimenez, M.-A., Kendrick, A. H., et al. (2021) · ERJ Open Research · doi:10.1183/23120541.00602-2021 · Cited by 44
Pople, D., Monk, E. J. M., Evans, S., Foulkes, S., Islam, J., Wellington, E., Atti, A., Hope, R., Robotham, J. V., Hopkins, S., et al. (2022) · BMJ · doi:10.1136/bmj-2022-070379 · Cited by 41
Self-citationOptimizing social and economic activity while containing SARS-CoV-2 transmission using DAEDALUS
Haw, D., Forchini, G., Doohan, P., Christen, P., Pianella, M., Johnson, R. C., Bajaj, S., Hogan, A. B., Winskill, P., Miraldo, M., et al. (2022) · Nature Computational Science · doi:10.1038/s43588-022-00233-0 · Cited by 41
Self-citationAlhamlan, F. S., & Al-Qahtani, A. A. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26031263 · Cited by 46
Contact tracing efficiency, transmission heterogeneity, and accelerating COVID-19 epidemics
Gardner, B. J., & Kilpatrick, A. M. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009122 · Cited by 44
Ponsford, M., Jefferies, R., Davies, C. R., Farewell, D. M., Humphreys, I. R., Jolles, S. R. A., Fairbairn, S., Lewis, K. E., Menzies, D., Benjamin, A., et al. (2020) · Thorax · doi:10.1136/thoraxjnl-2021-216964 · Cited by 41
Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland
Chen, C., Nadeau, S., Topolsky, I., Manceau, M., Huisman, J. S., Jablonski, K. P., Fuhrmann, L., Dreifuss, D., Jahn, K., Beckmann, C., et al. (2021) · Epidemics · doi:10.1016/j.epidem.2021.100480 · Cited by 39
Detection of SARS-CoV-2 variants by Abbott molecular, antigen, and serological tests
Rodgers, M. A., Olivo, A., Harris, B. J., Lark, C., Luo, X., Berg, M. G., Meyer, T. V., Mohaimani, A., Orf, G. S., Goldstein, D. Y., et al. (2022) · Journal of Clinical Virology · doi:10.1016/j.jcv.2022.105080 · Cited by 41
Park, S. W., Bolker, B. M., Funk, S., Metcalf, C. J. E., Weitz, J. S., Grenfell, B. T., & Dushoff, J. G. (2022) · Journal of The Royal Society Interface · doi:10.1098/rsif.2022.0173 · Cited by 44
Epidemic spreading under mutually independent intra- and inter-host pathogen evolution
Zhang, X., Ruan, Z., Zheng, M., Zhou, J., Boccaletti, S., & Barzel, B. (2022) · Nature Communications · doi:10.1038/s41467-022-34027-9 · Cited by 44
Westheim, A. J. F., Bitorina, A. V., Theys, J., & Shiri‐Sverdlov, R. (2021) · Obesity Reviews · doi:10.1111/obr.13313 · Cited by 44
Superspreading in the emergence of COVID-19 variants
Gómez‐Carballa, A., Pardo‐Seco, J., Bello, X., Martinón‐Torres, F., & Salas, A. (2021) · Trends in Genetics · doi:10.1016/j.tig.2021.09.003 · Cited by 42
Will vaccine-derived protective immunity curtail COVID-19 variants in the US?
Mancuso, M., Eikenberry, S. E., & Gumel, A. B. (2021) · Infectious Disease Modelling · doi:10.1016/j.idm.2021.08.008 · Cited by 42
Schrörs, B., Riesgo-Ferreiro, P., Sorn, P., Gudimella, R., Bukur, T., Rösler, T., Löwer, M., & Şahin, U. (2021) · PLoS ONE · doi:10.1371/journal.pone.0249254 · Cited by 41
Evolution 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
Wertheim, J. O., Wang, J. C., Leelawong, M., Martin, D. P., Havens, J. L., Chowdhury, M. A., Pekar, J. E., Amin, H., Arroyo, A., Awandare, G. A., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31247-x · Cited by 46
COVID-19: From emerging variants to vaccination
Senevirathne, T. H., Wekking, D., Swain, J. W. R., Solinas, C., & Silva, P. D. (2023) · Cytokine & Growth Factor Reviews · doi:10.1016/j.cytogfr.2023.11.005 · Cited by 45
Projecting the impact of a two-dose COVID-19 vaccination campaign in Ontario, Canada
VILCHES, T. N., Zhang, K., Exan, R. V., Langley, J. M., & Moghadas, S. M. (2021) · Vaccine · doi:10.1016/j.vaccine.2021.03.058 · Cited by 39
COVID-19 Vaccines and SARS-CoV-2 Transmission in the Era of New Variants: A Review and Perspective
Marcelin, J. R., Pettifor, A. E., Janes, H., Brown, E. R., Kublin, J. G., & Stephenson, K. E. (2022) · Open Forum Infectious Diseases · doi:10.1093/ofid/ofac124 · Cited by 41
SARS-CoV-2 Delta variant induces enhanced pathology and inflammatory responses in K18-hACE2 mice
Lee, K. S., Wong, T. Y., Russ, B. P., Horspool, A. M., Miller, O. A., Rader, N. A., Givi, J. P., Winters, M. T., Wong, Z. Y., Cyphert, H. A., et al. (2022) · PLoS ONE · doi:10.1371/journal.pone.0273430 · Cited by 42
Peng, J., Liu, J., Mann, S. A., Mitchell, A. M., Laurie, M. T., Sunshine, S., Pilarowski, G., Ayscue, P., Kistler, A., Vanaerschot, M., et al. (2022) · Clinical Infectious Diseases · doi:10.1093/cid/ciab283 · Cited by 41
Circulating SARS-CoV-2 variants in Italy, October 2020–March 2021
Lai, A., Bergna, A., Menzo, S., Zehender, G., Caucci, S., Ghisetti, V., Rizzo, F. M., Maggi, F., Cerutti, F., Giurato, G., et al. (2021) · Virology Journal · doi:10.1186/s12985-021-01638-5 · Cited by 41
Fidan, Ö., Mujwar, S., & Kciuk, M. (2022) · Molecular Diversity · doi:10.1007/s11030-022-10440-6 · Cited by 42
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
Domenico, L. D., Sabbatini, C. E., Boëlle, P., Poletto, C., Crépey, P., Paireau, J., Cauchemez, S., Beck, F., Noël, H., Lévy-Bruhl, D., et al. (2021) · Communications Medicine · doi:10.1038/s43856-021-00057-5 · Cited by 46
Communicate hope to motivate the public during the COVID-19 pandemic
Petersen, M. B., Christiansen, L. E., Bor, A., Lindholt, M. F., Jørgensen, F. J., Adler‐Nissen, R., Roepstorff, A., & Lehmann, S. (2022) · Scientific Reports · doi:10.1038/s41598-022-06316-2 · Cited by 41
Genomic 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
Ward, H., Cooke, G., Whitaker, M. D., Redd, R., Eales, O. D., Brown, J. C., Collet, K., Cooper, E., Daunt, A., Jones, K., et al. (2021) · medRxiv · doi:10.1101/2021.02.26.21252512 · Cited by 44
Tauzin, A., Nayrac, M., Benlarbi, M., Gong, S. Y., Gasser, R., Beaudoin-Bussières, G., Brassard, N., Laumaea, A., Vézina, D., Prévost, J., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.18.435972 · Cited by 41
Hanke, L., Sheward, D. J., Pankow, A., Vidakovics, L. P., Karl, V., Kim, C., Urgard, E., Smith, N. L., Astorga-Wells, J., Ekström, S., et al. (2022) · Science Advances · doi:10.1126/sciadv.abm0220 · Cited by 38
Hirotsu, Y., & Omata, M. (2021) · PLoS Pathogens · doi:10.1371/journal.ppat.1009619 · Cited by 40
Pathogen evolution during vaccination campaigns
Day, T., Kennedy, D. A., Read, A. F., & Gandon, S. (2022) · PLoS Biology · doi:10.1371/journal.pbio.3001804 · Cited by 42
COVID‐19 and the liver: A 2021 update
Spearman, C. W., Aghemo, A., Valenti, L. V. C., & Sonderup, M. W. (2021) · Liver International · doi:10.1111/liv.14984 · Cited by 40
Delayed reaction towards emerging COVID-19 variants of concern: Does history repeat itself?
Sun, X., Wandelt, S., & Zhang, A. (2021) · Transportation Research Part A Policy and Practice · doi:10.1016/j.tra.2021.08.007 · Cited by 40
Halle, C., Robertson, A. H., Hungnes, O., Tunheim, G., Bekkevold, T., Laake, I., Aune, I. F., Killengreen, M. F., Strand, T. R., Rykkvin, R., et al. (2021) · Microorganisms · doi:10.3390/microorganisms9112371 · Cited by 40
Trimpert, J., Adler, J. M., Eschke, K., Abdelgawad, A., Firsching, T. C., Ebert, N., Thao, T. T. N., Gruber, A. D., Thiel, V., Osterrieder, N., et al. (2021) · Science Advances · doi:10.1126/sciadv.abk0172 · Cited by 41
Dynamics of competing SARS-CoV-2 variants during the Omicron epidemic in England
Eales, O. D., Martins, L. D. O., Page, A. J., Wang, H., Bodinier, B., Tang, D. G., Haw, D., Jonnerby, J., Atchison, C. J., Ashby, D., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-32096-4 · Cited by 38
Vaccines platforms and COVID-19: what you need to know
Acosta-Coley, I., Cervantes-Ceballos, L., Benítez, L. P. T., Sierra-Marquez, L., Cabarcas-Montalvo, M., Espiñeira, M. C. G., Coronell-Rodríguez, W., & Arroyo-Salgado, B. (2022) · Tropical Diseases Travel Medicine and Vaccines · doi:10.1186/s40794-022-00176-4 · Cited by 40
COVID-19 rise in Bangladesh correlates with increasing detection of B.1.351 variant
Saha, S., Tanmoy, A. M., Hooda, Y., Tanni, A. A., Goswami, S., Sium, S. M. A., Sajib, M. S. I., Malaker, R., Islam, S., Rahman, H., et al. (2021) · BMJ Global Health · doi:10.1136/bmjgh-2021-006012 · Cited by 39
Cabecinhas, A. R. G., Roloff, T. C., Stange, M., Bertelli, C., Huber, M., Ramette, A., Chen, C., Nadeau, S., Gerth, Y., Yerly, S., et al. (2021) · Microorganisms · doi:10.3390/microorganisms9040677 · Cited by 37
Douglas, J., Geoghegan, J. L., Hadfield, J., Bouckaert, R., Storey, M., Ren, X., de Ligt, J., French, N. P., & Welch, D. (2021) · Emerging infectious diseases · doi:10.3201/eid2709.211097 · Cited by 37
Butera, Y., Mukantwari, E., Artesi, M., Umuringa, J. D., O’Toole, Á., Hill, V., Rooke, S., Hong, S. L., Dellicour, S., Majyambere, O., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25985-7 · Cited by 36
Self-citationModeling waning and boosting of COVID-19 in Canada with vaccination
Childs, L. M., Dick, D. W., Feng, Z., Heffernan, J. M., Li, J., & Röst, G. (2022) · Epidemics · doi:10.1016/j.epidem.2022.100583 · Cited by 41
Flores-Alanis, A., Cruz‐Rangel, A., Rodríguez‐Gómez, F., González, J., Torres-Guerrero, C. A., Delgado, G., Cravioto, A., & Morales-Espinosa, R. (2021) · Pathogens · doi:10.3390/pathogens10020184 · Cited by 40
Brejová, 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
Inflight transmission of COVID-19 based on experimental aerosol dispersion data
Wang, Z., Galea, E. R., Grandison, A., Ewer, J., & Jia, F. (2021) · Journal of Travel Medicine · doi:10.1093/jtm/taab023 · Cited by 39
Nandakumar, V., Profaizer, T., Lozier, B. K., Elgort, M., Larragoite, E. T., Williams, E. S. C. P., Solis‐Leal, A., Lopez, J., Berges, B. K., Planelles, V., et al. (2021) · Archives of Pathology & Laboratory Medicine · doi:10.5858/arpa.2021-0213-sa · Cited by 38
Changrob, S., Fu, Y., Guthmiller, J. J., Halfmann, P., Li, L., Stamper, C. T., Dugan, H. L., Accola, M., Rehrauer, W., Zheng, N.-Y., et al. (2021) · mBio · doi:10.1128/mbio.02975-21 · Cited by 40
A second functional furin site in the SARS-CoV-2 spike protein
Zhang, Y., Zhang, L., Wu, J., Yu, Y., Liu, S., Li, T., Li, Q., Ding, R., Wang, H., Nie, J., et al. (2021) · Emerging Microbes & Infections · doi:10.1080/22221751.2021.2014284 · Cited by 42
Muecksch, F., Weisblum, Y., Barnes, C. O., Schmidt, F., Schaefer-Babajew, D., Lorenzi, J. C. C., Flyak, A. I., DeLaitsch, A. T., Huey-Tubman, K. E., Hou, S., et al. (2021) · doi:10.1101/2021.03.07.434227 · Cited by 39
matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2
Ye, C., Thornlow, B. P., Hinrichs, A. S., Krämer, A., Mirchandani, C., Torvi, D., Lanfear, R., Corbett-Detig, R. B., & Turakhia, Y. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac401 · Cited by 36
Evolution and implications of SARS-CoV-2 variants in the post-pandemic era
Manirambona, E., Okesanya, O. J., Olaleke, N. O., Oso, T. A., & Lucero‐Prisno, D. E. (2024) · Discover Public Health · doi:10.1186/s12982-024-00140-x · Cited by 41
Dispersal dynamics of SARS-CoV-2 lineages during the first epidemic wave in New York City
Dellicour, S., Hong, S. L., Vrancken, B., Chaillon, A., Gill, M. S., Maurano, M. T., Ramaswami, S., Zappile, P., Marier, C., Harkins, G. W., et al. (2021) · PLoS Pathogens · doi:10.1371/journal.ppat.1009571 · Cited by 38
Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data
Stirrup, O., Hughes, J., Parker, M. D., Partridge, D. G., Shepherd, J. G., Blackstone, J., Coll, F., Keeley, A. J., Lindsey, B. B., Marek, A., et al. (2021) · eLife · doi:10.7554/elife.65828 · Cited by 38
Brandherm, L., Kobaš, A. M., Klöhn, M., Brüggemann, Y., Pfaender, S., Rassow, J., & Kreimendahl, S. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22179233 · Cited by 39
Anderson, R. M., Vegvari, C., Hollingsworth, T. D., Pi, L., Maddren, R., Ng, C. W., & Baggaley, R. F. (2021) · Interface Focus · doi:10.1098/rsfs.2021.0008 · Cited by 38
de Hoffer, A., Vatani, S., Cot, C., Cacciapaglia, G., Chiusano, M. L., Cimarelli, A., Conventi, F., Giannini, A., Hohenegger, S., & Francesco Sannino, A. (2022) · Scientific Reports · doi:10.1038/s41598-022-12442-8 · Cited by 39
Xiao, 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
The localized rise of a B.1.526 SARS-CoV-2 variant containing an E484K mutation in New York StatePreprint
Lasek‐Nesselquist, E., Lapierre, P., Schneider, E., George, K. S., & Pata, J. D. (2021) · medRxiv · doi:10.1101/2021.02.26.21251868 · Cited by 38
Rando, H. M., MacLean, A. L., Lee, A. J., Lordan, R., Ray, S., Bansal, V., Skelly, A. N., Sell, E., Dziak, J. J., Shinholster, L., et al. (2021) · mSystems · doi:10.1128/msystems.00095-21 · Cited by 42
Pereira, F. (2021) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2021.02.080 · Cited by 39
The Evolutionary Landscape of SARS-CoV-2 Variant B.1.1.519 and Its Clinical Impact in Mexico City
Cedro‐Tanda, A., Gómez-Romero, L., Alcaraz, N., de Anda‐Jáuregui, G., Peñaloza, F., Moreno, B., Escobar-Arrazola, M. A., Ramirez-Vega, O. A., Munguía-Garza, P., Garcia-Cardenas, F., et al. (2021) · Viruses · doi:10.3390/v13112182 · Cited by 32
The variants of SARS‐CoV‐2 and the challenges of vaccines
Han, X., & Ye, Q. (2021) · Journal of Medical Virology · doi:10.1002/jmv.27513 · Cited by 37
Xia, Q., Yang, Y., Wang, F., Huang, Z., Qiu, W., & Mao, A. (2024) · International Journal of Infectious Diseases · doi:10.1016/j.ijid.2024.01.017 · Cited by 38
Nagy‐Szakal, D., Couto-Rodriguez, M., Wells, H., Barrows, J., Debieu, M., Butcher, K. D., Chen, S., Berki, A., Hager, C., Boorstein, R. J., et al. (2021) · Microbiology Spectrum · doi:10.1128/spectrum.00197-21 · Cited by 36
Trick, A. Y., Chen, F., Chen, L., Lee, P., Hasnain, A. C., Mostafa, H. H., Carroll, K. C., & Wang, T. (2022) · Advanced Materials Technologies · doi:10.1002/admt.202101013 · Cited by 37
Coincident rapid expansion of two SARS-CoV-2 lineages with enhanced infectivity in Nigeria
Ozer, E. A., Simons, L. M., Adewumi, O. M., Fowotade, A. A., Omoruyi, E. C., Adeniji, J. A., Dean, T. J., Zayas, J., Bhimalli, P. P., Ash, M. K., et al. (2021) · doi:10.1101/2021.04.09.21255206 · Cited by 34
Increased Transmissibility of the SARS-CoV-2 Alpha Variant in a Japanese Population
Tanaka, H., Hirayama, A., Nagai, H., Shirai, C., Takahashi, Y., Shinomiya, H., Taniguchi, C., & Ogata, T. (2021) · International Journal of Environmental Research and Public Health · doi:10.3390/ijerph18157752 · Cited by 36
van Beek, J., Iglὁi, Z., Boelsums, T., Fanoy, E., Gotz, H., Molenkamp, R., van Kampen, J., GeurtsvanKessel, C. H., van der Eijk, A., van de Vijver, D. A. M. C., et al. (2022) · Eurosurveillance · doi:10.2807/1560-7917.es.2022.27.8.2100702 · Cited by 34
Open questions in the social lives of viruses
Leeks, A., Bono, L. M., Ampolini, E. A., Souza, L. S., Höfler, T., Mattson, C. L., Dye, A. E., & Díaz‐Muñoz, S. L. (2023) · Journal of Evolutionary Biology · doi:10.1111/jeb.14203 · Cited by 38
Pandemic monitoring with global aircraft-based wastewater surveillance networks
St-Onge, G., Davis, J. T., Hébert‐Dufresne, L., Allard, A., Urbinati, A., Scarpino, S. V., Chinazzi, M., & Vespignani, A. (2025) · Nature Medicine · doi:10.1038/s41591-025-03501-4 · Cited by 37
In War Times: Fictionalizing Iraq
Luckhurst, R. (2012) · Contemporary Literature · doi:10.1353/cli.2012.0040 · Cited by 38
ACE2‐based decoy receptors for SARS coronavirus 2
Jing, W., & Procko, E. (2021) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.26140 · Cited by 32
Tran, T. N.-A., Wikle, N. B., Albert, E., Inam, H., Strong, E. R., Břinda, K., Leighow, S. M., Yang, F., Hossain, S., Pritchard, J. R., et al. (2021) · BMC Medicine · doi:10.1186/s12916-021-02038-w · Cited by 35
Lusvarghi, S., Wang, W., Herrup, R., Neerukonda, S. N., Vassell, R. A., Bentley, L., Eakin, A. E., Erlandson, K. J., & Weiss, C. D. (2021) · Journal of Virology · doi:10.1128/jvi.01110-21 · Cited by 33
Investigating vaccine-induced immunity and its effect in mitigating SARS-CoV-2 epidemics in China
Liu, H., Zhang, J., Cai, J., Deng, X., Peng, C., Chen, X., Yang, J., Wu, Q., Chen, X., Chen, Z., et al. (2022) · BMC Medicine · doi:10.1186/s12916-022-02243-1 · 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
Martin, 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
Detecting Rapid Spread of SARS-CoV-2 Variants, France, January 26–February 16, 2021
Haïm‐Boukobza, S., Roquebert, B., Trombert‐Paolantoni, S., Lecorché, E., Verdurme, L., Foulongne, V., Selinger, C., Michalakis, Y., Sofonea, M. T., & Alizon, S. (2021) · Emerging infectious diseases · doi:10.3201/eid2705.210397 · Cited by 35
SARS-CoV-2 Tests: Bridging the Gap between Laboratory Sensors and Clinical Applications
Toropov, N. A., Osborne, E. L., Joshi, L. T., Davidson, J., Morgan, C., Page, J. W., Pepperell, J., & Vollmer, F. (2021) · ACS Sensors · doi:10.1021/acssensors.1c00612 · Cited by 35
Epidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil
Moreira, F. R. R., D’arc, M., Mariani, D., Herlinger, A. L., Schiffler, F. B., Rossi, Á. D., Leitão, I. D. C., Miranda, T. D. S., Cosentino, M. A. C., Tôrres, M. C. D. P., et al. (2021) · Virus Evolution · doi:10.1093/ve/veab087 · Cited by 34
da 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
Reinfection by the SARS-CoV-2 Gamma variant in blood donors in Manaus, Brazil
Junior, C. A. P., Buss, L., Buccheri, R., Abrahim, C. M. M., Salomon, T., Crispim, M. A. E., Oikawa, M. K., Grebe, E., Costa, A. G., Fraiji, N. A., et al. (2022) · BMC Infectious Diseases · doi:10.1186/s12879-022-07094-y · Cited by 35
Kim, Y., Gaudreault, N. N., Meekins, D. A., Perera, K. D., Bold, D., Trujillo, J. D., Morozov, I., McDowell, C. D., Chang, K., & Richt, J. A. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.01789-21 · Cited by 35
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
Webster, H. H., Nyberg, T., Sinnathamby, M., Aziz, N. I. B. A., Ferguson, N. M., Seghezzo, G., Blomquist, P. B., Bridgen, J. R. E., Chand, M. A., Groves, N., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-33740-9 · Cited by 34
Self-citation
Metadata
- Authors
- The COVID-19 Genomics UK (COG-UK) consortium, Volz, E., Mishra, S., Chand, M., Barrett, J. C., Johnson, R., Geidelberg, L., Hinsley, W. R., Laydon, D. J., Dabrera, G., O’Toole, Á., Amato, R., Ragonnet-Cronin, M., Harrison, I., Jackson, B., Ariani, C. V., Boyd, O., Loman, N. J., McCrone, J. T., Gonçalves, S., Jorgensen, D., Myers, R., Hill, V., Jackson, D. K., Gaythorpe, K., Groves, N., Sillitoe, J., Kwiatkowski, D. P., Flaxman, S., Ratmann, O., Bhatt, S., Hopkins, S., Gandy, A., Rambaut, A., & Ferguson, N. M.
- Affiliations
- Imperial College London (GB)
- Public Health England (GB)
- Wellcome Sanger Institute (GB)
- University of Edinburgh (GB)
- University of Copenhagen (DK)
- Corresponding author
- Volz, Erik
- Ferguson, Neil M.
- ORCID
- Volz, Erik
- Mishra, Swapnil
- Chand, Meera
- Barrett, Jeffrey C.
- Geidelberg, Lily
- Hinsley, Wes R.
- Laydon, Daniel J.
- Dabrera, Gavin
- Harrison, Ian
- Jackson, Ben
- Ariani, Cristina V.
- Boyd, Olivia
- Loman, Nicholas J.
- McCrone, John T.
- Gonçalves, Sónia
- Jorgensen, David
- Myers, Richard
- Hill, Verity
- Jackson, David K.
- Gaythorpe, Katy
- Groves, Natalie
- Kwiatkowski, Dominic P.
- Flaxman, Seth
- Ratmann, Oliver
- Bhatt, Samir
- Hopkins, Susan
- Gandy, Axel
- Rambaut, Andrew
- Ferguson, Neil M.
- Venue
- Nature
- Published
- 2021-03-25
- Volume
- 593
- Issue
- 7858
- Pages
- 266-269
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W3136588845
- Cited by
- 1,611
- References
- 32
- Citations by year
- 2026: 38 · 2025: 86 · 2024: 116 · 2023: 216 · 2022: 464 · 2021: 685
- FWCI
- 116.92
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nature (publishedVersion)
- medRxiv (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, other-oa)
- White Rose Research Online (University of Leeds, The University of Sheffield, University of York) (acceptedVersion)
- UEA Digital Repository (University of East Anglia) (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- ePrints Soton (University of Southampton) (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Figshare (submittedVersion)
- Research Portal (King's College London) (submittedVersion, other-oa)
- Northumbria Research Link (Northumbria University) (submittedVersion)
- University of Birmingham Research Portal (University of Birmingham) (submittedVersion, other-oa)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, other-oa)
- Spiral (Imperial College London) (submittedVersion, cc-by)
- Spiral (Imperial College London) (submittedVersion)
- Apollo (University of Cambridge) (submittedVersion)
- Apollo
- Funders
- Bill and Melinda Gates Foundation (OPP 1175094, 206194, OPP1197730, MR/R015600/1, OPP1084362)
- Wellcome Trust (MR/R015600/1, 204911/Z/16/Z, Z/17/Z, 206298/Z/17/Z, RDA02, 206298, 206194)
- UK Research and Innovation (MR/V038109/1, MR/R015600/1, MC_PC_19027)
- National Institute for Health Research Health Protection Research Unit
- Cancer Research UK (23923)
- National Institute for Health and Care Research (PR-OD-1017–20002, MR/R015600/1, RDA02, NIHR301445, OPP1175094, ACF-2018-04-014)
- Academy of Medical Sciences (AMS-CSF4-Torok, SBF004\1080)
- Imperial College London (MR/R015600/1)
- European Commission (725422, MR/R015600/1, 101003653, COVID-19, 206298/Z/17/Z)
- Rural Development Administration
- Novo Nordisk (NNF20OC0059309)
- Novo Nordisk Fonden (NNF20OC0059309)
- Medical Research Council (MR/R015600/1, MR/M006212/1, MC_PC_19026, MR/V038109/1, MR/S00291X/1, MC_PC_19012, COVID-19)
- Engineering and Physical Sciences Research Council (EP/V002910/1, EP/V002910/2)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Physical Sciences › Mathematics › Modeling and Simulation › COVID-19 epidemiological studies
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 detection and testing
- Keywords
- SARS-CoV-2, B.1.1.7 lineage, variants of concern, transmissibility, S-gene target failure, time-varying reproduction number, viral genomic surveillance, COVID-19 pandemic, England
- MeSH terms
- COVID-19, SARS-CoV-2, Adolescent, Adult, Aged, Aged, 80 and over, Child, Child, Preschool, England, Humans, Infant, Infant, Newborn, Middle Aged, Phylogeny, Time Factors, Genome, Viral, Age Distribution, Evolution, Molecular, Basic Reproduction Number, Young Adult, Spike Glycoprotein, Coronavirus
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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
