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Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England
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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.
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“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]
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“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]
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Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission
Aggarwal, D., Warne, B., Jahun, A. S., Hamilton, W. L., Fieldman, T., du Plessis, L., Hill, V., Blane, B., Watkins, E., Wright, E., et al. (2022) · Nature Communications · doi:10.1038/s41467-021-27942-w · Cited by 48
Self-citationKiem, C. T., Massonnaud, C., Lévy-Bruhl, D., Poletto, C., Colizza, V., Bosetti, P., Fontanet, A. L., Gabet, A., Olié, V., Zanetti, L. C. D. S., et al. (2021) · EClinicalMedicine · doi:10.1016/j.eclinm.2021.101001 · Cited by 57
The effect of COVID-19 vaccination in Italy and perspectives for living with the virus
Marziano, V., Guzzetta, G., Mammone, A., Riccardo, F., Poletti, P., Trentini, F., Manica, M., Siddu, A., Bella, A., Stefanelli, P., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-27532-w · Cited by 55
The way of SARS-CoV-2 vaccine development: success and challenges
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Protein post-translational modification in SARS-CoV-2 and host interaction
Cheng, N., Liu, M., Li, W., Sun, B., Liu, D., Wang, G., Shi, J., & Li, L. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2022.1068449 · Cited by 58
Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2
Huang, K.-Y. A., Chen, X., Mohapatra, A., Nguyen, H. T. V., Schimanski, L. M., Tan, T. K., Rijal, P., Vester, S. K., Hills, R. A., Howarth, M. R., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-35949-8 · Cited by 51
Dominance of Alpha and Iota variants in SARS-CoV-2 vaccine breakthrough infections in New York City
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Multiple Routes of Antibody-Dependent Enhancement of SARS-CoV-2 Infection
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Rapid characterization of spike variants via mammalian cell surface display
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Lung fibrosis: Post-COVID-19 complications and evidences
Hirawat, R., Jain, N., Saifi, M. A., Rachamalla, M., & Godugu, C. (2022) · International Immunopharmacology · doi:10.1016/j.intimp.2022.109418 · Cited by 54
SARS-CoV-2 diagnostic testing rates determine the sensitivity of genomic surveillance programs
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Vaccine escape in a heterogeneous population: insights for SARS-CoV-2 from a simple model
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From Bench to the Clinic: The Path to Translation of Nanotechnology-Enabled mRNA SARS-CoV-2 Vaccines
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Evolutionary implications of SARS-CoV-2 vaccination for the future design of vaccination strategies
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Emergence of SARS-CoV-2 Variants in the World: How Could This Happen?
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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
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