The DOI matches its Crossref record; 34 of the 34 references it cites were found in a registry or an index.
Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data
Open accessPreprint — published as 10.1038/s41586-021-03470-x · Paper page
Abstract
The SARS-CoV-2 lineage B.1.1.7, now designated Variant of Concern 202012/01 (VOC) by Public Health England, originated in the UK in late Summer to early Autumn 2020. We examine epidemiological evidence for this VOC having a transmission advantage from several perspectives. First, whole genome sequence data collected from community-based diagnostic testing provides an indication of changing prevalence of different genetic variants through time. Phylodynamic modelling additionally indicates that genetic diversity of this lineage has changed in a manner consistent with exponential growth. Second, we find 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. Third, we examine growth trends in SGTF and non-SGTF case numbers at local area level across England, and show that the VOC has higher transmissibility than non-VOC lineages, even if the VOC has a different latent period or generation time. Available SGTF data indicate a shift in the age composition of reported cases, with a larger share of under 20 year olds among reported VOC than non-VOC cases. Fourth, we assess the association of VOC frequency with independent estimates of the overall SARS-CoV-2 reproduction number through time. Finally, we fit a semi-mechanistic model directly to local VOC and non-VOC case incidence to estimate the reproduction numbers over time for each. There is a consensus among all analyses that the VOC has a substantial transmission advantage, with the estimated difference in reproduction numbers between VOC and non-VOC ranging between 0.4 and 0.7, and the ratio of reproduction numbers varying between 1.4 and 1.8. We note that these estimates of transmission advantage apply to a period where high levels of social distancing were in place in England; extrapolation to other transmission contexts therefore requires caution.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“In particular, the mild restrictions that kept around 0.9 with the original virus strain would keep it around 1.3 (at least) if the new variants increase transmissibility of at least 40–50%, as reported in the literature49–51.”
From Modeling vaccination rollouts, SARS-CoV-2 variants and the requirement for non-pharmaceutical interventions in Italy (2021) · cites this paper as [49]
Experimental — accuracy not yet measuredIn the citing paper
“Recently, viral variants of concern have emerged in the UK (B.1.1.7), South Africa (B.1.351), and Brazil (P.1) that harbor specific mutations in their S proteins that may be associated with increased transmissibility (50–55).”
From mRNA vaccination boosts cross-variant neutralizing antibodies elicited by SARS-CoV-2 infection (2021) · cites this paper as [51]
In the citing paper
“SARS-CoV-2 and SARS-CoV enter host cells through binding of the S glycoprotein to angiotensin converting enzyme 2 (ACE2)1,28.”
From Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies (2021) · cites this paper as [1]
In the citing paper
“and has been reported to increase transmissibility of the B.1.17 variant circulating in the UK.16”
From Efficacy of NVX-CoV2373 Covid-19 Vaccine against the B.1.351 Variant (2021) · cites this paper as [16]
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
The Elements of Statistical Learning
Hastie, T., Friedman, J., & Tibshirani, R. (2001) · Springer Series in Statistics · doi:10.1007/978-0-387-21606-5 · Cited by 24,162
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-citationbrms : An R Package for Bayesian Multilevel Models Using Stan
Bürkner, P.-C. (2017) · Journal of Statistical Software · doi:10.18637/jss.v080.i01 · Cited by 9,476
Bayesian 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-citationHastie, T. J., & Tibshirani, R. J. (2014) · Wiley StatsRef: Statistics Reference Online · doi:10.1002/9781118445112.stat03141 · Cited by 3,156
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
Self-citation
Cited by
Sorted by citations
SARS-CoV-2 variants, spike mutations and immune escape
Harvey, W. T., Carabelli, A. M., Jackson, B., Gupta, R. K., Thomson, E. C., Harrison, E. M., Ludden, C., Reeve, R., Rambaut, A., COVID-19 Genomics UK (COG-UK) Consortium, et al. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00573-0 · Cited by 3,528
Self-citationDetection 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
Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant
Madhi, S. A., Baillie, V., Cutland, C. L., Voysey, M., Koen, A. L., Fairlie, L., Padayachee, S. D., Dheda, K., Barnabas, S. L., Bhorat, Q. E., et al. (2021) · New England Journal of Medicine · doi:10.1056/nejmoa2102214 · Cited by 1,257
SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma
Wibmer, C. K., Ayres, F., Hermanus, T., Madzivhandila, M., Kgagudi, P., Oosthuysen, B., Lambson, B. E., de Oliveira, T., Vermeulen, M., van der Berg, K., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01285-x · Cited by 1,147
“Lastly, variants in the UK and USA, albeit with fewer potential antibody escape mutations have also been described, suggesting the global emergence of new SARS-CoV-2 variants 26 .”
Fiolet, T., Kherabi, Y., MacDonald, C.-J., Ghosn, J., & Peiffer-Smadja, N. (2022) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2021.10.005 · Cited by 911
Challen, R., Brooks-Pollock, E., Read, J. M., Dyson, L., Tsaneva-Atanasova, K., & Danon, L. (2021) · BMJ · doi:10.1136/bmj.n579 · Cited by 776
Hall, V. J., Foulkes, S., Charlett, A., Atti, A., Monk, E. J. M., Simmons, R., Wellington, E., Cole, M. J., Saei, A., Oguti, B., et al. (2021) · The Lancet · doi:10.1016/s0140-6736(21)00675-9 · Cited by 638
Self-citationSARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies
Collier, D. A., De Marco, A., Ferreira, I. A. T. M., Meng, B., Datir, R., Walls, A. C., Kemp S, S. A., Bassi, J., Pinto, D., Fregni, C. S., et al. (2021) · doi:10.1101/2021.01.19.21249840 · Cited by 729
Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies
Collier, D. A., De Marco, A., Ferreira, I. A. T. M., Meng, B., Datir, R. P., Walls, A. C., Kemp, S. A., Bassi, J., Pinto, D., Silacci-Fregni, C., et al. (2021) · Nature · doi:10.1038/s41586-021-03412-7 · Cited by 728
Thomson, E. C., Rosen, L. E., Shepherd, J. G., Spreafico, R., da Silva Filipe, A., Wojcechowskyj, J. A., Davis, C., Piccoli, L., Pascall, D. J., Dillen, J., et al. (2021) · Cell · doi:10.1016/j.cell.2021.01.037 · Cited by 606
Self-citationEmary, K. R. W., Golubchik, T., Aley, P. K., Ariani, C. V., Angus, B., Bibi, S., Blane, B., Bonsall, D., Cicconi, P., Charlton, S., et al. (2021) · The Lancet · doi:10.1016/s0140-6736(21)00628-0 · Cited by 603
“…measures in place to control the virus failed to control spread of SGTF-containing lineages but were effective for those lineages without SGTF. 14 Several unpublished, independent analyses suggest that infections associated with SGTF on PCR from upper respiratory samples might be associated…”
InfluentialSelf-citationEfficacy of NVX-CoV2373 Covid-19 Vaccine against the B.1.351 Variant
Shinde, V., Bhikha, S., Hoosain, Z., Archary, M., Bhorat, Q., Fairlie, L., Lalloo, U., Masilela, M. S. L., Moodley, D., Hanley, S., et al. (2021) · New England Journal of Medicine · doi:10.1056/nejmoa2103055 · Cited by 625
Emergence of SARS-CoV-2 B.1.1.7 Lineage — United States, December 29, 2020–January 12, 2021
Galloway, S. E., Paul, P., MacCannell, D., Johansson, M. A., Brooks, J. T., MacNeil, A., Slayton, R. B., Tong, S., Silk, B. J., Armstrong, G. L., et al. (2021) · MMWR Morbidity and Mortality Weekly Report · doi:10.15585/mmwr.mm7003e2 · Cited by 609
“5 times the Rt of current variants, based on initial estimates from the United Kingdom (1,3).”
BackgroundInfluentialmRNA vaccination boosts cross-variant neutralizing antibodies elicited by SARS-CoV-2 infection
Stamatatos, L., Czartoski, J., Wan, Y.-H., Homad, L. J., Rubin, V., Glantz, H., Neradilek, M., Seydoux, E., Jennewein, M. F., MacCamy, A. J., et al. (2021) · Science · doi:10.1126/science.abg9175 · Cited by 557
Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant
Deng, X., Garcia-Knight, M. A., Khalid, M. M., Servellita, V., Wang, C., Morris, M. K., Sotomayor-González, A., Glasner, D. R., Reyes, K. R., Gliwa, A. S., et al. (2021) · Cell · doi:10.1016/j.cell.2021.04.025 · Cited by 651
Neutralization of SARS-CoV-2 lineage B.1.1.7 pseudovirus by BNT162b2 vaccine–elicited human sera
Muik, A., Wallisch, A.-K., Sänger, B., Swanson, K. A., Mühl, J., Chen, W., Cai, H., Maurus, D., Sarkar, R., Türeci, Ö., et al. (2021) · Science · doi:10.1126/science.abg6105 · Cited by 515
“7 was detected in the United Kingdom (2), and it subsequently increased in prevalence, showed enhanced transmissibility, and spread to other countries and continents (3).”
BackgroundWu, K., Werner, A. P., Moliva, J. I., Koch, M., Choi, A., Stewart-Jones, G. B. E., Bennett, H., Boyoglu-Barnum, S., Shi, W., Graham, B. S., et al. (2021) · doi:10.1101/2021.01.25.427948 · Cited by 419
“351 lineage) has raised concerns due to their increased rates of transmission as well as their potential to circumvent immunity elicited by natural infection or vaccination (Volz et al., 2021; Tegally et al., 2020; Wibmer et al., 2021; Wang et al., 2021; Collier et al., 2021).”
BackgroundInfluentialSARS-CoV-2 variants and ending the COVID-19 pandemic
Fontanet, A. L., Autran, B., Lina, B., Kiény, M. P., Karim, S. S. A., & Sridhar, D. (2021) · The Lancet · doi:10.1016/s0140-6736(21)00370-6 · Cited by 535
A guideline to limit indoor airborne transmission of COVID-19
Bazant, M. Z., & Bush, J. W. M. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2018995118 · Cited by 493
The RECOVERY Collaborative Group, Horby, P., Estcourt, L. J., Peto, L., Emberson, J., Staplin, N., Spata, E., Pessoa-Amorim, G., Campbell, M. R., Roddick, A., et al. (2021) · medRxiv · doi:10.1101/2021.03.09.21252736 · Cited by 69
Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7
Meng, B., Kemp, S. A., Papa, G., Datir, R. P., Ferreira, I. A. T. M., Marelli, S., Harvey, W. T., Lytras, S., Mohamed, A., Gallo, G., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109292 · Cited by 407
“Sequences belonging to this lineage were subsequently called B.1.1.7 and classified as a variant of concern (VOC) due to a higher rate of transmission (Volz et al., 2021b).”
InfluentialShen, X., Tang, H., McDanal, C., Wagh, K., Fischer, W., Theiler, J., Yoon, H., Li, D., Haynes, B. F., Sanders, K. O., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.03.002 · Cited by 378
SARS-CoV-2 within-host diversity and transmission
Lythgoe, K., Hall, M. D., Luca Ferretti, A., de Cesare, M., MacIntyre-Cockett, G., Trebes, A., Andersson, M. I., Otecko, N. O., Wise, E. L., Moore, N. A., et al. (2021) · Science · doi:10.1126/science.abg0821 · Cited by 389
“lineage (7, 8), with an estimated transmission advantage of ~50% (9), and the B.”
BackgroundSARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution
Zahradník, J., Marciano, S., Shemesh, M., Zoler, E., Harari, D., Chiaravalli, J., Meyer, B., Rudich, Y., Li, C., Marton, I., et al. (2021) · Nature Microbiology · doi:10.1038/s41564-021-00954-4 · Cited by 454
Age groups that sustain resurging COVID-19 epidemics in the United States
Monod, M., Blenkinsop, A., Xi, X., Hebert, D. J., Bershan, S., Tietze, S., Baguelin, M., Bradley, V. C., Chen, Y., Coupland, H., et al. (2021) · Science · doi:10.1126/science.abe8372 · Cited by 335
“More-transmissible SARS-CoV-2 variants could increase reproduction numbers to above one from all age groups, which implies substantial spread from all age groups, and require generally stricter control measures across all ages to prevent COVID-19–attributable deaths (31).”
BackgroundSelf-citationPrendecki, M., Clarke, C., Brown, J., Cox, A., Gleeson, S., Guckian, M., Randell, P., Pria, A. D., Lightstone, L., Xu, X.-N., et al. (2021) · The Lancet · doi:10.1016/s0140-6736(21)00502-x · Cited by 271
The variant gambit: COVID-19’s next move
Plante, J. A., Mitchell, B. M., Plante, K. S., Debbink, K., Weaver, S. C., & Menachery, V. D. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.02.020 · Cited by 328
SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma
Wibmer, C. K., Ayres, F., Hermanus, T., Madzivhandila, M., Kgagudi, P., Oosthuysen, B., Lambson, B. E., de Oliveira, T., Vermeulen, M., van der Berg, K., et al. (2021) · doi:10.1101/2021.01.18.427166
The epidemiological impact of the NHS COVID-19 app
Wymant, C., Ferretti, L., Tsallis, D., Charalambides, M., Abeler-Dörner, L., Bonsall, D., Hinch, R., Kendall, M., Milsom, L., Ayres, M., et al. (2021) · Nature · doi:10.1038/s41586-021-03606-z · Cited by 271
COVID-19: breaking down a global health crisis
Mallah, S. I., Ghorab, O. K. H. A., Al-Salmi, S., Abdellatif, O. S., Tharmaratnam, T., Iskandar, M. M. A., Sefen, J. A. N., Sidhu, P., Atallah, B., El-Lababidi, R. M., et al. (2021) · Annals of Clinical Microbiology and Antimicrobials · doi:10.1186/s12941-021-00438-7 · Cited by 401
“Epidemiological studies have shown that despite the increased transmissibility, the VOC cases are expected to decline faster than non-VOC cases [110].”
BackgroundInfluentialBarton, M. I., MacGowan, S. A., Kutuzov, M. A., Dushek, O., Barton, G. J., & van der Merwe, P. A. (2021) · eLife · doi:10.7554/elife.70658 · Cited by 346
Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States
Washington, N. L., Gangavarapu, K., Zeller, M., Bolze, A., Cirulli, E. T., Barrett, K. M. S., Larsen, B. B., Anderson, C., White, S., Cassens, T., et al. (2021) · Cell · doi:10.1016/j.cell.2021.03.052 · Cited by 324
Kidd, M., Richter, A., Best, A., Cumley, N., Mirza, J., Percival, B., Mayhew, M., Megram, O., Ashford, F., White, T., et al. (2021) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiab082 · Cited by 237
Muecksch, F., Weisblum, Y., Barnes, C. O., Schmidt, F., Schaefer-Babajew, D. J., Wang, Z., Lorenzi, J. C. C., Flyak, A. I., DeLaitsch, A. T., Huey‐Tubman, K. E., et al. (2021) · Immunity · doi:10.1016/j.immuni.2021.07.008 · Cited by 279
Deng, X., Garcia-Knight, M. A., Khalid, M. M., Servellita, V., Wang, C., Morris, M. K., Sotomayor-González, A., Glasner, D. R., Reyes, K. R., Gliwa, A. S., et al. (2021) · doi:10.1101/2021.03.07.21252647 · Cited by 651
Bovornkitti, S. (2021) · SpringerBriefs in Microbiology · doi:10.1007/978-3-030-87324-0_6 · Cited by 244
“7 variant increased relative to other variants during a lockdown period, which should have limited opportunities for transmission [16].”
BackgroundInfluentialBal, A., Destras, G., Gaymard, A., Stefic, K., Marlet, J., Eymieux, S., Regue, H., Semanas, Q., d’Aubarede, C., Billaud, G., et al. (2021) · Eurosurveillance · doi:10.2807/1560-7917.es.2021.26.3.2100008 · Cited by 212
“In the meantime, a similar approach has been adopted in the United Kingdom where the frequency of SGTF is used as a proxy for estimating and monitoring the spread of the VOC 202012/01 [14,20].”
BackgroundMethodRecurrent emergence and transmission of a SARS-CoV-2 spike deletion H69/V70
Kemp, S. A., Meng, B., Ferriera, I. A., Datir, R., Harvey, W. T., Papa, G., Lytras, S., Collier, D. A., Mohamed, A., Gallo, G., et al. (2020) · doi:10.1101/2020.12.14.422555 · Cited by 252
Giordano, G., Colaneri, M., Di Filippo, A., Blanchini, F., Bolzern, P., De Nicolao, G., Sacchi, P., Colaneri, P., & Bruno, R. (2021) · Nature Medicine · doi:10.1038/s41591-021-01334-5 · Cited by 192
Emerging SARS-CoV-2 variants of concern and potential intervention approaches
Khateeb, J., Li, Y., & Zhang, H. (2021) · Critical Care · doi:10.1186/s13054-021-03662-x · Cited by 231
Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2
O'Toole, Á., Hill, V., Pybus, O. G., Watts, A., Bogoch, I. I., Khan, K., Messina, J. P., The COVID-19 Genomics UK (COG-UK) consortium, Network for Genomic Surveillance in South Africa (NGS-SA), Brazil-UK CADDE Genomic Network, et al. (2021) · Wellcome Open Research · doi:10.12688/wellcomeopenres.16661.1 · Cited by 192
Self-citationGenomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, BrazilPreprint
Faria, N., Mellan, T., Whittaker, C., et al. (2021) · medRxiv · doi:10.1101/2021.02.26.21252554 · Cited by 207
“𝑅𝑅𝑅𝑅 We note that other work has shown that the degree of transmission advantage exhibited by the B.1.1.7 can vary over time as a function of control interventions and behavior ( 68 ).”
InfluentialSelf-citationMultiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2
Vogels, C. B. F., Breban, M. I., Ott, I. M., Alpert, T., Petrone, M. E., Watkins, A. E., Kalinich, C. C., Earnest, R., Rothman, J. E., de Jesus, J. G., et al. (2021) · PLoS Biology · doi:10.1371/journal.pbio.3001236 · Cited by 225
Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants
Laffeber, C., de Koning, K., Kanaar, R., & Lebbink, J. H. G. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167058 · Cited by 194
“7 increased transmission has been established [10], increased prevalence of the other lineages may (also) be due to immune escape [5, 11].”
Public health actions to control new SARS-CoV-2 variants
Grubaugh, N. D., Hodcroft, E. B., Fauver, J. R., Phelan, A. L., & Cevik, M. (2021) · Cell · doi:10.1016/j.cell.2021.01.044 · Cited by 147
“…estimated that B.1.1.7 is approximately 50% more transmissible (Davies et al., 2020), which could increase the average number of people that one infected person will pass the virus to (effective reproductive rate) by between 0.4 and 0.7 people (Volz et al., 2021).”
BackgroundInfluentialMacLean, O. A., Lytras, S., Weaver, S., Singer, J. B., Boni, M. F., Lemey, P., Pond, S. L. K., & Robertson, D. L. (2021) · PLoS Biology · doi:10.1371/journal.pbio.3001115 · Cited by 227
Timing the SARS-CoV-2 index case in Hubei Province
Pekar, J., Worobey, M., Moshiri, N., Scheffler, K., & Wertheim, J. O. (2021) · Science · doi:10.1126/science.abf8003 · Cited by 156
The SARS-CoV-2 mutations versus vaccine effectiveness: New opportunities to new challenges
Malik, J. A., Ahmed, S., Aroosa, M., Shinde, M., Bender, O., Alshammari, F., Ansari, M., & Anwar, S. (2022) · Journal of Infection and Public Health · doi:10.1016/j.jiph.2021.12.014 · Cited by 206
“The transmission rate was 40–70% more than the original virus [15].”
van Oosterhout, C., Hall, N., Ly, H., & Tyler, K. M. (2021) · Virulence · doi:10.1080/21505594.2021.1877066 · Cited by 192
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) · Cell Host & Microbe · doi:10.1016/j.chom.2021.06.001 · Cited by 193
Effects of SARS-CoV-2 variants on vaccine efficacy and response strategies
Bian, L., Gao, F., Zhang, J., He, Q., Mao, Q., Xu, M., & Liang, Z. (2021) · Expert Review of Vaccines · doi:10.1080/14760584.2021.1903879 · Cited by 183
SARS-CoV-2 one year on: evidence for ongoing viral adaptation
Peacock, T. P., Penrice-Randal, R., Hiscox, J. A., & Barclay, W. (2021) · Journal of General Virology · doi:10.1099/jgv.0.001584 · Cited by 155
Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York
Annavajhala, M. K., Mohri, H., Wang, P., Nair, M., Zucker, J. E., Sheng, Z., Gomez-Simmonds, A., Kelley, A. L., Tagliavia, M., Huang, Y., et al. (2021) · doi:10.1101/2021.02.23.21252259
(2021) · doi:10.1101/2021.02.27.433180 · Cited by 706
“The emergence of several SARS-CoV-2 variants of concern (VOC) with multiple amino acid replacements has implications for the future control of the COVID-19 pandemic (Davies et al., 2020; Kirby, 2021; Tegally et al., 2020; Volz et al., 2021).”
An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants
Chan, K. K., Tan, T. J. C., Narayanan, K. K., & Procko, E. (2021) · Science Advances · doi:10.1126/sciadv.abf1738 · Cited by 152
Just 2% of SARS-CoV-2−positive individuals carry 90% of the virus circulating in communities
Yang, Q., Saldi, T. K., Gonzales, P. K., Lasda, E. L., Decker, C. J., Tat, K. L., Fink, M. R., Hager, C. R., Davis, J. C., Ozeroff, C. D., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2104547118 · Cited by 155
“”) SARS-CoV-2 variant, and subsequent major variants of concern, were first documented in the United States during the final weeks of 2020 and the beginning of 2021 [21].”
BackgroundEvaluation of COVID-19 vaccination strategies with a delayed second dose
Moghadas, S., Vilches, T., Zhang, K., et al. (2021) · medRxiv · doi:10.1101/2021.01.27.21250619 · Cited by 146
“Challenges with vaccine supply and rollout, coupled with a deadly wave of outbreaks that overwhelmed hospitals [48–50], and the emergence of highly transmissible SARS-CoV-2 variants [12,51,52], sparked a debate as to whether available vaccines should be used to rapidly increase the coverage with the first dose [14–17]…”
Triggle, C. R., Bansal, D., Ding, H., Islam, M. M., Farag, E., Hadi, H. A., & Sultan, A. A. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.631139 · Cited by 187
Fix, O. K., Blumberg, E. A., Chang, K., Chu, J., Chung, R. T., Goacher, E. K., Hameed, B., Kaul, D. R., Kulik, L., Kwok, R. M., et al. (2021) · Hepatology · doi:10.1002/hep.31751 · Cited by 157
Immune response to SARS-CoV-2 variants of concern in vaccinated individuals
Becker, M., Dulovic, A., Junker, D., Ruétalo, N., Kaiser, P. D., Pinilla, Y. T., Heinzel, C., Häring, J., Traenkle, B., Wagner, T. R., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23473-6 · Cited by 137
Abani, O., Abbas, A. H., Abbas, F., Abbas, M. A., Abbasi, S., Abbass, H., Abbott, A., Abdallah, N., Abdelaziz, A., Abdelfattah, M., et al. (2021) · The Lancet · doi:10.1016/s0140-6736(21)00897-7 · Cited by 493
“Of the patients who were not receiving invasive mechanical ventilation at baseline, the number of patients progressing to the prespecified composite secondary outcome of invasive mechanical ventilation or death was similar in the two groups (1568 [29”
InfluentialSonabend, R., Whittles, L. K., Imai, N., Perez-Guzman, P. N., Knock, E. S., Rawson, T., Gaythorpe, K. A. M., Djaafara, B. A., Hinsley, W. R., FitzJohn, R. G., et al. (2021) · The Lancet · doi:10.1016/s0140-6736(21)02276-5 · Cited by 160
Self-citationHodcroft, E. B., Domman, D., Snyder, D. J., Oguntuyo, K. Y., Diest, M. V., Densmore, K. H., Schwalm, K. C., Femling, J., Carroll, J. L., Scott, R. S., et al. (2021) · medRxiv · doi:10.1101/2021.02.12.21251658 · Cited by 110
“Therefore, SARS-CoV-2 variants can emerge and increase greatly in number over time in the absence of any clear or sustained selective advantage.”
Evolutionary trajectory of SARS-CoV-2 and emerging variants
Singh, J., Pandit, P., McArthur, A. G., Banerjee, A., & Mossman, K. L. (2021) · Virology Journal · doi:10.1186/s12985-021-01633-w · Cited by 150
Effect of SARS-CoV-2 B.1.1.7 mutations on spike protein structure and function
Yang, T., Yu, P., Chang, Y., Liang, K.-H., Tso, H.-C., Ho, M., Wy, C., Lin, H.-T., Wu, H., & Hsu, S. D. (2021) · Nature Structural & Molecular Biology · doi:10.1038/s41594-021-00652-z · Cited by 167
The emerging SARS-CoV-2 variants of concern
Sanyaolu, A. O., Okorie, C., Marinkovic, A., Haider, N., Abbasi, A. F., Jaferi, U., Prakash, S., & Balendra, V. (2021) · Therapeutic Advances in Infectious Disease · doi:10.1177/20499361211024372 · Cited by 122
Isolation and characterization of cross-neutralizing coronavirus antibodies from COVID-19+ subjects
Jennewein, M. F., MacCamy, A. J., Akins, N. R., Feng, J., Homad, L. J., Hurlburt, N. K., Seydoux, E., Wan, Y.-H., Stuart, A. B., Edara, V. V., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109353 · Cited by 108
“harbor specific mutations in their S proteins that may be associated with increased transmissibility (Davies et al., 2020; Faria et al., 2021; Rambaut et al., 2020; Sabino et al., 2021; Tegally et al., 2020; Volz et al., 2021).”
Madhi, S. A., Baillie, V., Cutland, C. L., Voysey, M., Koen, A. L., Fairlie, L., Padayachee, S. D., Dheda, K., Barnabas, S. L., Bhorat, Q. E., et al. (2021) · doi:10.1101/2021.02.10.21251247 · Cited by 1,257
“7 lineage, first identified in the United Kingdom (UK), includes the N501Y mutation which has been associated with 53% increased transmissibly.(18) Neutralizing antibody activity elicited by infection or mRNA vaccines against the B.”
BackgroundEarly introductions and transmission of SARS-CoV-2 variant B.1.1.7 in the United States
Alpert, T., Brito, A. F., Lasek‐Nesselquist, E., Rothman, J. E., Valesano, A. L., MacKay, M. J., Petrone, M. E., Breban, M. I., Watkins, A. E., Vogels, C. B. F., et al. (2021) · Cell · doi:10.1016/j.cell.2021.03.061 · Cited by 122
Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness
Obermeyer, F., Jankowiak, M., Barkas, N., et al. (2021) · medRxiv · doi:10.1101/2021.09.07.21263228 · Cited by 119
Zahradník, J., Marciano, S., Shemesh, M., Zoler, E., Chiaravalli, J., Meyer, B., Rudich, Y., Dym, O., Elad, N., & Schreiber, G. (2021) · doi:10.1101/2021.01.06.425392 · Cited by 458
(2021) · doi:10.1016/j.vaccine.2021.04.002 · Cited by 101
“For a more transmissible strain (such as the recently iden-tified UK variant [46,47]) with an R 0 of 4 the coverage required for herd immunity increases to 75%.”
Self-citationTada, T., Dcosta, B. M., Samanovic-Golden, M., Herati, R. S., Cornelius, A., Mulligan, M. J., & Landau, N. R. (2021) · doi:10.1101/2021.02.05.430003 · Cited by 153
SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes
Jungreis, I., Sealfon, R. S. G., & Kellis, M. (2021) · Nature Communications · doi:10.1038/s41467-021-22905-7 · Cited by 193
Accelerated vaccine rollout is imperative to mitigate highly transmissible COVID-19 variants
Sah, P., VILCHES, T. N., Moghadas, S. M., Fitzpatrick, M. C., Singer, B. H., Hotez, P. J., & Galvani, A. P. (2021) · EClinicalMedicine · doi:10.1016/j.eclinm.2021.100865 · Cited by 108
“These new variants exhibit a multiplicative transmissibility up to 74% higher than the original strain, [5 (cid:1) 7] and higher case fatality rates [8,9].”
de Vries, M., Mohamed, A., Prescott, R. A., Valero-Jimenez, A. M., Desvignes, L., O’Connor, R., Steppan, C. M., Devlin, J. C., Ivanova, E. N., Herrera, A. M., et al. (2021) · Journal of Virology · doi:10.1128/jvi.01819-20 · Cited by 137
A look into the future of the COVID-19 pandemic in Europe: an expert consultation
Iftekhar, E. N., Priesemann, V., Balling, R., Bauer, S., Beutels, P., Valdez, A. C., Cuschieri, S., Czypionka, T., Dumpis, U., Glaab, E., et al. (2021) · The Lancet Regional Health - Europe · doi:10.1016/j.lanepe.2021.100185 · Cited by 132
“7) variant, which was first detected in the United Kingdom, demonstrated enhanced transmissibility [51,52], a longer duration of acute infection [53], a higher hospitalization rate [54], and probably a higher infection fatality rate than previously circulating variants [51,55-57].”
Tauzin, A., Gong, S. Y., Beaudoin-Bussières, G., Vézina, D., Gasser, R., Nault, L., Marchitto, L., Benlarbi, M., Chatterjee, D., Nayrac, M., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.12.004 · Cited by 106
“Some harbor specific mutations in S that are associated with increased transmissibility and/or immune evasion (Davies et al., 2021; Sabino et al., 2021; Tegally et al., 2020; Volz et al., 2021).”
Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York
Annavajhala, M. K., Mohri, H., Wang, P., Nair, M. S., Zucker, J. E., Sheng, Z., Gomez‐Simmonds, A., Kelley, A. L., Tagliavia, M., Huang, Y., et al. (2021) · Nature · doi:10.1038/s41586-021-03908-2 · Cited by 227
Gushchin, V. А., Dolzhikova, I. V., Shchetinin, A. M., Odintsova, A. S., Siniavin, A. E., Nikiforova, M. A., Pochtovyi, A. A., Shidlovskaya, E. V., Kuznetsova, N. A., Burgasova, O., et al. (2021) · Vaccines · doi:10.3390/vaccines9070779 · Cited by 110
The European Health Data Space
Marcus, J., Martens, B., Carugati, C., et al. (2025) · Social Science Research Network · doi:10.2139/ssrn.4300393 · Cited by 104
Dyson, L., Hill, E. M., Moore, S., Curran-Sebastian, J. L., Tildesley, M. J., Lythgoe, K., House, T., Pellis, L., & Keeling, M. J. (2021) · Nature Communications · doi:10.1038/s41467-021-25915-7 · Cited by 104
“7 variant had a positive growth rate [7, 8].”
BackgroundPascarella, S., Ciccozzi, M., Zella, D., Bianchi, M., Benedetti, F., Benvenuto, D., Broccolo, F., Cauda, R., Caruso, A., Angeletti, S., et al. (2021) · Journal of Medical Virology · doi:10.1002/jmv.27210 · Cited by 100
“Others VOCs have been isolated in South Africa and Brazil and have been studied for their enhanced contagiousness and resistance to neutralization by antibodies from convalescent and vaccine-recipient subjects (6-8) (Table 1).”
BackgroundDroplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater
Heijnen, L., Elsinga, G., de Graaf, M., Molenkamp, R., Koopmans, M., & Medema, G. J. (2021) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2021.149456 · Cited by 109
An action plan for pan-European defence against new SARS-CoV-2 variants
Priesemann, V., Balling, R., Brinkmann, M. M., Ciesek, S., Czypionka, T., Eckerle, I., Giordano, G., Hanson, C., Hel, Z., Hotulainen, P., et al. (2021) · The Lancet · doi:10.1016/s0140-6736(21)00150-1 · Cited by 107
Stamatatos, L., Czartoski, J., Wan, Y.-H., Homad, L. J., Rubin, V., Glantz, H., Neradilek, M., Seydoux, E., Jennewein, M. F., MacCamy, A. J., et al. (2021) · doi:10.1101/2021.02.05.21251182 · Cited by 559
“1) that harbor specific mutations in their S proteins that may be associated with increased transmissibility (50-55).”
BackgroundBrown, K. A., Gubbay, J. B., Hopkins, J. P., Patel, S. N., Buchan, S. A., Daneman, N., & Goneau, L. W. (2021) · JAMA · doi:10.1001/jama.2021.5607 · Cited by 116
Brown, J. C., Goldhill, D. H., Zhou, J., Peacock, T. P., Frise, R., Goonawardane, N., Baillon, L., Kugathasan, R., Pinto, A., McKay, P. F., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.02.24.432576 · Cited by 70
SARS-CoV-2 genomics: An Indian perspective on sequencing viral variants
Srivastava, S., Banu, S., Singh, P., Sowpati, D. T., & Mishra, R. K. (2021) · Journal of Biosciences · doi:10.1007/s12038-021-00145-7 · Cited by 96
Borges, V., Sousa, C., Menezes, L., Gonçalves, A. M., Picão, M., Almeida, J. P., Vieita, M., Santos, R., Silva, A. R., Costa, M., et al. (2021) · Eurosurveillance · doi:10.2807/1560-7917.es.2021.26.10.2100130 · Cited by 73
HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens
Fischer, W., Giorgi, E. E., Chakraborty, S., Nguyen, K., Tanmoy Bhattacharya, A., Theiler, J. P., Goloboff, P. A., Yoon, H., Abfalterer, W., Foley, B. T., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.05.012 · Cited by 109
Liu, J., Bodnar, B. H., Meng, F., Khan, A. I., Wang, X., Luo, G. G., Saribas, S., Wang, T., Lohani, S. C., Wang, P., et al. (2021) · Cell & Bioscience · doi:10.1186/s13578-021-00680-8 · Cited by 97
“Worst of all, as the COVID-19 pandemic rages on, there have emerged variants of SARS-CoV-2 in the different regions of the world, including the United Kingdom (UK), South Africa (SA), Brazil, and the United States[1-3].”
BackgroundSARS-CoV-2 vaccines in advanced clinical trials: Where do we stand?
Chakraborty, S., Mallajosyula, V. V. A., Tato, C. M., Tan, G. S., & Wang, T. T. (2021) · Advanced Drug Delivery Reviews · doi:10.1016/j.addr.2021.01.014 · Cited by 90
Wang, H., Miller, J. A., Verghese, M., Sibai, M., Solis, D., Mfuh, K. O., Jiang, B., Iwai, N., Mar, M., Huang, C., et al. (2021) · Journal of Clinical Microbiology · doi:10.1128/jcm.00859-21 · Cited by 93
Wang, W. B., Liang, Y., Jin, Y. Q., Zhang, J., Su, J. G., & Li, Q. M. (2021) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2021.108035 · Cited by 83
The emergence of new strains of SARS-CoV-2. What does it mean for COVID-19 vaccines?
Hossain, M. K., Hassanzadeganroudsari, M., & Apostolopoulos, V. (2021) · Expert Review of Vaccines · doi:10.1080/14760584.2021.1915140 · Cited by 92
“92 for the original non-mutated SARS-CoV-2 virus [11].”
BackgroundWere pregnant women more affected by COVID-19 in the second wave of the pandemic?
Kadiwar, S., Smith, J. J., Ledot, S., Johnson, M., Bianchi, P. A., Singh, N., Montanaro, C., Gatzoulis, M., Shah, N. M., & Ukor, E.-F. (2021) · The Lancet · doi:10.1016/s0140-6736(21)00716-9 · Cited by 92
Predicting the zoonotic capacity of mammals to transmit SARS-CoV-2
Fischhoff, I. R., Castellanos, A. A., Rodrigues, J., Varsani, A., & Han, B. A. (2021) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2021.1651 · Cited by 90
“…the transmission chain (Garry, 2021; Oude Munnink et al., 2020) affects host range (Rodrigues et al., 2020) or leads to distinct epidemiology in humans (e.g., via increased transmissibility among humans (Davies et al., 2020; Volz et al., 2021), but see (Rambaut et al., 2020; Tegally et al., 2020)).”
The global transmission of new coronavirus variants
Zhao, Y., Huang, J., Zhang, L., Chen, S., Gao, J., & Jiao, H. (2021) · Environmental Research · doi:10.1016/j.envres.2021.112240 · Cited by 73
“Compared to the original lineage, the new coronavirus variants show a higher transmissibility and resistance to antibody (Greaney et al., 2021; Volz et al., 2021a, b), for instance, the percentage of people that infected with alpha lineage in the UK had raised from 0.1% in early October to 49.7% in…”
Influential
Metadata
- Authors
- 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., The COVID-19 Genomics UK (COG-UK) consortium, 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
- Publisher
- openRxiv
- Published
- 2021-01-04
- Volume
- 593
- Issue
- 7858
- Pages
- 266-269
- ISSN
- 0028-0836 (ISSN-L)
- OpenAlex
- W3136588845
- Cited by
- 1,611
- References
- 28
- 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
