PreprintCited by 1,611SARS-CoV-2 and COVID-19 ResearchCOVID-19 epidemiological studiesSARS-CoV-2 detection and testing

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Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data

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Volz, Erik, Mishra, Swapnil, Chand, Meera, Barrett, Jeffrey C., Johnson, Robert, Geidelberg, Lily, Hinsley, Wes R, Laydon, Daniel J, Dabrera, Gavin, O’Toole, Áine, Amato, Roberto, Ragonnet-Cronin, Manon, 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, Sillitoe, John, Kwiatkowski, Dominic P., The COVID-19 Genomics UK (COG-UK) consortium, Flaxman, Seth, Ratmann, Oliver, Bhatt, Samir, Hopkins, Susan, Gandy, Axel, Rambaut, Andrew, Ferguson, Neil M·2021·Nature

DOI 10.1101/2020.12.30.20249034

Preprint — published as 10.1038/s41586-021-03470-x · Paper page

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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.

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Predictive and interpretable machine learning for COVID-19 resurgences: the role of SARS-CoV-2 variants in the post-pandemic era
Ferreira, R. S., Colnago, M., & Casaca, W. C. D. O. (2025) · BMC Infectious Diseases · doi:10.1186/s12879-025-12366-4 · Cited by 1
“For instance, the Alpha variant (B.1.1.7) was linked to increased transmissibility [6], Delta (B.1.617.2) to greater virulence and immune escape [7], and Omicron (B0.”
Influential
How severe would prioritization-induced bottlenecks need to be offset the benefits from prioritizing COVID-19 vaccination to those most at risk in New York City?
Kim, H., Bershteyn, A., McGillen, J. B., et al. (2023) · BMC Public Health · doi:10.1186/s12889-022-14846-7 · Cited by 3
Targeting Viral ORF3a Protein: A New Approach to Mitigate COVID-19 Induced Immune Cell Apoptosis and Associated Respiratory Complications
Minu Treeza, M., Augustine, S., Mathew, A. A., Kanthlal, S. K., & Panonnummal, R. (2023) · Advanced Pharmaceutical Bulletin · doi:10.34172/apb.2023.069 · Cited by 3
Potential Therapeutic Role of Mesenchymal-Derived Stem Cells as an Alternative Therapy to Combat COVID-19 through Cytokines Storm
Upadhyay, T. K., Trivedi, R., Khan, F., Pandey, P., Sharangi, A. B., Goel, H., Saeed, M., Park, M. N., & Kim, B. (2022) · Cells · doi:10.3390/cells11172686 · Cited by 3
Density functional theory computation of the binding free energies between various mutations of SARS-CoV-2 RBD and human ACE2: molecular level roots of the contagiousness
Yamaçli, S., & Avcı, M. (2022) · Heliyon · doi:10.1016/j.heliyon.2022.e10128 · Cited by 2
“…strain, and iv) the binding free energy of the SARS-CoV-2 S-UK variant (B.1.1.7) with A570D and N501Y mutations – ACE2 complex (7EDJ) has the lowest value meaning that SARS-CoV-2 S-UK variant is the most favourable strain, as also observed by the signi ﬁ cant spread of this variant [13,44].”
Influential
Genomic Epidemiology of Imported Cases of COVID-19 in Guangdong Province, China, October 2020 - May 2021.
Liang, D., Wang, T., Li, J. J., Guan, D. W., Zhang, G. T., Liang, Y. F., Li, A. A., Hong, W. S., Wang, L., Chen, M. L., et al. (2022) · PubMed Central · doi:10.3967/bes2022.055 · Cited by 2
RT-PCR detection of SARS-CoV-2 in nasopharyngeal and salivary specimens: contribution of alternative collection systems and extraction processes to cope with mass screening. Interpretation of low viral loads
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A Case Report: Genetically Distinct Severe Acute Respiratory Syndrome Coronavirus-2 Variant Causing Reinfection
Hossain, M. E., Rahman, M. M., Alam, M. S., Sarmin, M., Karim, Y., Hasan, M., Hoque, A. F., Hasan, M. M., Rahman, M. Z., Chisti, M. J., et al. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.792514 · Cited by 2
Community transmission of SARS-CoV-2 with B.1.1.7 lineage in Mumbai, India
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“It has been designated as variant of concern due to its high transmissibility, with estimates ranging from 40 to 80% higher transmissibility.(2,3) During the first wave of pandemic in India, SARS-CoV-2 cases showed downward trend since September 2020; however it again started rising in March 2021 with the number of ca…”
Background
Mobility-Dependent and Mobility-Compensated Effective Reproduction Number of COVID-19 Viral Variants: New Metric for Infectivity EvaluationPreprint
Kodera, S., Rashed, E. A., & Hirata, A. (2021) · arXiv (Cornell University) · doi:10.48550/arxiv.2111.02961 · Cited by 2
“According to previous studies in the United Kingdom (Davies et al., 2021, Volz et al., 2021), the infectivity of the delta variant is higher than that of the alpha variant (43%–90%).”
Variant-specific interventions to slow down replacement and prevent outbreaks
Majeed, B. J., Tosato, M., & Wu, J. (2021) · Mathematical Biosciences · doi:10.1016/j.mbs.2021.108703 · Cited by 1
Rapid expansion of SARS-CoV-2 variants of concern is a result of adaptive epistasisPreprint
Garvin, M. R., Prates, E. T., Romero, J., Cliff, A., Gazolla, J. G. F. M., Pickholz, M., Pavicic, M., & Jacobson, D. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.08.03.454981 · Cited by 10
SARS-CoV-2 lineage B.1.1.7 is associated with greater disease severity among hospitalised women but not men
Stirrup, O., Boshier, F., Venturini, C., et al. (2021) · medRxiv · doi:10.1101/2021.06.24.21259107 · Cited by 2
Structural Proteomics-Driven Targeted Design of Favipiravir-Binding Site in The RdRp of SARS-CoV-2 Unravels Susceptible Hotspots and Resistance Mutations
Padhi, A., Dandapat, J., Uversky, V., et al. (2021) · doi:10.20944/preprints202105.0492.v1 · Cited by 2
Coming to America: Genomic surveillance and how B.1.1.7 arrived in the US
Qiu, X.-T., Hanage, W., & Taylor, B. (2021) · Cell · doi:10.1016/j.cell.2021.04.031 · Cited by 2
Magnetofluidic platform for rapid multiplexed screening of SARS-CoV-2 variants and respiratory pathogens
Trick, A. Y., Chen, F.-E., Chen, L., et al. (2021) · medRxiv · doi:10.1101/2021.05.10.21256995 · Cited by 2
Phylodynamic modelling of bacterial outbreaks using nanopore sequencing
Steinig, E., Duchêne, S., Aglua, I., et al. (2021) · bioRxiv · doi:10.1101/2021.04.30.442218 · Cited by 2
Impffortschritt in Deutschland und der Welt: Chancen und Risiken
Grimm, V., Lembcke, F. K., & Schwarz, M. (2021) · Wirtschaftsdienst · doi:10.1007/s10273-021-2894-5 · Cited by 5
“Die verfügbaren Impfstoffe könnten überdies an neue Varianten angepasst werden (Davies et al., 2021b; Tada et al., 2021; Volz et al., 2021).”
Background
Pattern of COVID-19 epidemics in Japan influenced by the control measures
Konishi, T. (2021) · medRxiv · doi:10.1101/2021.03.24.21253923 · Cited by 2
“The conditions for finding variants from each country are as follows (Konishi 2021): (original axes) group 0: -0.004 < PC1 < 0.004, PC2 < 0.004 England: PC198 > 0.002 Pan-European: PC62 > 0.0035, PC63 > 0.009 group 2: PC2 > 0.004 France: PC118 > 0.002 USA: PC28 > 0.01 (On axes considering the new variants in the UK an…”
BackgroundInfluential
An upsurge of SARS CoV-2 B.1.1.7 Variant in Pakistan
Umair, M., Salman, M., Rehman, Z., et al. (2021) · medRxiv · doi:10.1101/2021.02.26.21252562 · Cited by 2
A two–strain SARS–COV–2 model for Germany - Evidence from a Linearization
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“In the linearized model (4) it holds that x + y = (R1 − 1)x+ (R2 − 1)zx and hence z(Ť ) = z0e (R2−R1)Ť = 1−R1 R2−1 > 0.”
Background
SARS-CoV-2 N501Y introductions and transmissions in Switzerland from beginning of October 2020 to February 2021 â implementation of Swiss-wide diagnostic screening and whole genome sequencing
Cabecinhas, T. R. A. R. G., Stange, C. B. M., Huber, A. R. M., et al. (2021) · medRxiv · doi:10.1101/2021.02.11.21251589 · Cited by 2
The feasibility of targeted test-trace-isolate for the control of B.1.1.7
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Epidemiology of COVID-19 in Latin America
Rodriguez-Morales, A. J., & Bonilla‐Aldana, D. K. (2021) · Elsevier eBooks · doi:10.1016/b978-0-323-85662-1.00012-4 · Cited by 1
Osmolality as a strong predictor of COVID-19 mortality and its possible links to other biomarkers
Çetin, Ş., Ülgen, A., Şıvgın, H., Çetin, M., & Li, W. (2025) · PLoS ONE · doi:10.1371/journal.pone.0331344 · Cited by 1
“The B.1.1.7 (alpha) variant was first reported in the UK in November 2020 and was known to spread fast in mid-December 2020 in UK [46,47] and elsewhere.”
Influential
Stochastic network to model the global spreading of respiratory diseases: From SARS-CoV-2 to pathogen X pandemic
López, L., & Rodó, X. (2024) · Ecological Informatics · doi:10.1016/j.ecoinf.2024.102827 · Cited by 1
Travel history among persons infected with SARS-CoV-2 variants of concern in the United States, December 2020—February 2021
Dunajcik, A., Haire, K., Thomas, J. D., Moriarty, L. F., Springer, Y. P., Villanueva, J. M., MacNeil, A., Silk, B. J., Nemhauser, J. B., Byrkit, R., et al. (2023) · PLOS Global Public Health · doi:10.1371/journal.pgph.0001252 · Cited by 1
Adolescent Stress Management Using Five-Finger Hypnotic Therapy during The Covid-19 Pandemic
Abidin, Z., Rahmawati, P. M., & Musviro, M. (2023) · JI-KES (Jurnal Ilmu Kesehatan) · doi:10.33006/jikes.v6i2.571 · Cited by 1
IT’S ALL ABOUT COVID-19: A REVIEW OF PATTERN OF WAVES IN PAKISTAN, DRUGS AND VACCINATION PROGRAMS
Shaikh, M., Channa, N., Arain, S., et al. (2023) · Liaquat Medical Research Journal · doi:10.38106/lmrj.2022.4.4-08 · Cited by 1
Assessment of Jordanian health care professionals’ perception towards new COVID-19 variants of concern
Sawan, H. M., Omari, S. M. A., Bahar, F. A., et al. (2022) · PLoS ONE · doi:10.1371/journal.pone.0265797 · Cited by 1
Dynamics of SARS-CoV-2 lineages in French Guiana in 2020–2021: 4 epidemic waves with cross-influences from Europe and South America
Miliu, A., Lavergne, A., Succo, T., Laizé, C., Andrieu, A., Enfissi, A., Enouf, V., van der Werf, S., Blanchet, D., Demar, M., et al. (2022) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2022.105370 · Cited by 3
“It has also been reported that the presence of the K417N, K417T, E484K and/or N501Y mutations results in a small but significant reduction in neutralization in individuals vaccinated or naturally infected with SARS-CoV-2 (Wang et al., 2021).”
Novel Mutations Associated with N-Gene Target Failure in SARS-COV-2 Genome in Iran, Case Series
Maleki, A., Fereydouni, Z., Tavakoli, M., et al. (2022) · Journal of Medical Microbiology and Infectious Diseases · doi:10.52547/jommid.10.3.141 · Cited by 1
“3 There are some deletions and some substitutions in these variants; the most important ones include 69-70 Del, N501Y, E484K, D614G, P681H, and so on [4, 5, 7].”
Background
Betriebliches SARS-CoV-2-Risikomanagement zur wirkungsvollen Eindämmung von Infektionsketten
Paaßen, A., Anderle, L., John, K., & Wilbrand, S. (2022) · Zentralblatt für Arbeitsmedizin Arbeitsschutz und Ergonomie · doi:10.1007/s40664-022-00467-9 · Cited by 1
Characterization of mutations modulating enhanced transmissibility of SARS-CoV-2 B.1.617+ (Delta) variant using In Silico tools
Shahhosseini, N. (2022) · Gene Reports · doi:10.1016/j.genrep.2022.101636 · Cited by 1
EMERGENCE OF NEW STRAINS OF SARS - COV - 2: AFRICA’S FATE AND ITS PREPAREDNESS AGAINST COVID - 19 INFECTION WAVE
Ohia, C., Solomon, B. A., Tauseef, A., Haroon, H., E., A. G. R. E., & Sridhar Mynepalli, K. C. (2022) · African Journal of Infectious Diseases · doi:10.21010/ajid.v16i2.1 · Cited by 1
“…rose sporadically to an average of 11,000 daily, these numbers portrayed the slower trend of the disease across the continent which came as a bit of relief (Wadvalla, 2020); given the already identified challenge of weak and over-burdened health system across African nations (Ohia et al., 2020).”
Background
Spatiotemporal analyses illuminate the competitive advantage of a SARS-CoV-2 variant of concern over a variant of interestPreprint
Russell, A., O’Connor, C., Lasek‐Nesselquist, E., Plitnick, J., Kelly, J. P., Lamson, D. M., & George, K. S. (2021) · medRxiv · doi:10.1101/2021.09.14.21262977 · Cited by 1
Genomic chronicle of SARS-CoV-2: a mutational analysis with over 1 million genome sequences
Uğurel, O. M., Ata, O., & Turgut‐Balik, D. (2021) · TURKISH JOURNAL OF BIOLOGY · doi:10.3906/biy-2106-8 · Cited by 2
“6 SNVs that cause substitutions on S protein, especially A23063T (N501Y), are reported as key mutations and associated with these 21 SNVs (Volz et al., 2021; O’Toole, 2021).”
Background
Low SARS-CoV-2 seroprevalence but high perception of risk among healthcare workers at children’s hospital before second pandemic wave in Germany
Neumann, M., Aigner, A., Rossow, E., Schwarz, D., Marschallek, M., Steinmann, J., Stücker, R., Königs, I., & Stock, P. (2021) · World Journal of Pediatrics · doi:10.1007/s12519-021-00447-8 · Cited by 3
Workplace risk management for SARS-CoV-2: a three-step early in-tervention strategy for effective containment of infection chains with special regards to virus variants with increased infectivityPreprint
Paaßen, A., Anderle, L., John, K., & Wilbrand, S. (2021) · medRxiv · doi:10.1101/2021.07.21.21260756
“Concerning virus variants, the value of R0 is adapted to recent estimates of the respective infectivity [9,10] (B 1.”
Background
Real-time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with Variants of Concern
Abdulnoor, M., Eshaghi, A., Perusini, S. J., et al. (2021) · medRxiv · doi:10.1101/2021.06.23.21258782 · Cited by 1

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)
DOI: 10.1101/2020.12.30.20249034
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

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Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data

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