Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence

Moritz U. G. Kraemer; Verity Hill; Christopher Ruis; Simon Dellicour; Sumali Bajaj; John T. McCrone; Guy Baele; Kris V. Parag; Anya Lindström Battle; Bernardo Gutierrez; Ben Jackson; Rachel Colquhoun; Áine O’Toole; Brennan Klein; Alessandro Vespignani; Erik Volz; Nuno R. Faria; David M. Aanensen; Nicholas J. Loman; Louis Du Plessis; Simon Cauchemez; Andrew Rambaut; Samuel V. Scarpino; Oliver G. Pybus

doi:10.1126/science.abj0113

Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence

Moritz U. G. Kraemer, Verity Hill, Christopher Ruis, Simon Dellicour, Sumali Bajaj, John T. McCrone, Guy Baele, Kris V. Parag, Anya Lindström Battle, Bernardo Gutierrez, Ben Jackson, Rachel Colquhoun, Áine O’Toole, Brennan Klein, Alessandro Vespignani, Erik Volz, Nuno R. Faria, David M. Aanensen, Nicholas J. Loman, Louis Du PlessisSimon Cauchemez, Andrew Rambaut, Samuel V. Scarpino, Oliver G. Pybus

School of Biological Sciences

Research output: Contribution to journal › Article › peer-review

Abstract

Understanding the causes and consequences of the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern is crucial to pandemic control yet difficult to achieve because they arise in the context of variable human behavior and immunity. We investigated the spatial invasion dynamics of lineage B.1.1.7 by jointly analyzing UK human mobility, virus genomes, and community-based polymerase chain reaction data. We identified a multistage spatial invasion process in which early B.1.1.7 growth rates were associated with mobility and asymmetric lineage export from a dominant source location, enhancing the effects of B.1.1.7’s increased intrinsic transmissibility. We further explored how B.1.1.7 spread was shaped by nonpharmaceutical interventions and spatial variation in previous attack rates. Our findings show that careful accounting of the behavioral and epidemiological context within which variants of concern emerge is necessary to interpret correctly their observed relative growth rates.

Original language	English
Pages (from-to)	889-895
Number of pages	7
Journal	Science
Volume	373
Issue number	6557
Early online date	19 Aug 2021
DOIs	https://doi.org/10.1126/science.abj0113
Publication status	Published - 20 Aug 2021

Access to Document

10.1126/science.abj0113Licence: Creative Commons: Attribution (CC-BY)

PybusEtalS2022SpatiotemporalInvasionDynamicsOfSARS-CoV-2Final published version, 1.68 MBLicence: Creative Commons: Attribution (CC-BY)

Cite this

Kraemer, M. U. G., Hill, V., Ruis, C., Dellicour, S., Bajaj, S., McCrone, J. T., Baele, G., Parag, K. V., Battle, A. L., Gutierrez, B., Jackson, B., Colquhoun, R., O’Toole, Á., Klein, B., Vespignani, A., Volz, E., Faria, N. R., Aanensen, D. M., Loman, N. J., ... Pybus, O. G. (2021). Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence. Science, 373(6557), 889-895. https://doi.org/10.1126/science.abj0113

@article{5d17a48c458842129d3e5ff5901a72d2,

title = "Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence",

abstract = "Understanding the causes and consequences of the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern is crucial to pandemic control yet difficult to achieve because they arise in the context of variable human behavior and immunity. We investigated the spatial invasion dynamics of lineage B.1.1.7 by jointly analyzing UK human mobility, virus genomes, and community-based polymerase chain reaction data. We identified a multistage spatial invasion process in which early B.1.1.7 growth rates were associated with mobility and asymmetric lineage export from a dominant source location, enhancing the effects of B.1.1.7{\textquoteright}s increased intrinsic transmissibility. We further explored how B.1.1.7 spread was shaped by nonpharmaceutical interventions and spatial variation in previous attack rates. Our findings show that careful accounting of the behavioral and epidemiological context within which variants of concern emerge is necessary to interpret correctly their observed relative growth rates.",

author = "Kraemer, {Moritz U. G.} and Verity Hill and Christopher Ruis and Simon Dellicour and Sumali Bajaj and McCrone, {John T.} and Guy Baele and Parag, {Kris V.} and Battle, {Anya Lindstr{\"o}m} and Bernardo Gutierrez and Ben Jackson and Rachel Colquhoun and {\'A}ine O{\textquoteright}Toole and Brennan Klein and Alessandro Vespignani and Erik Volz and Faria, {Nuno R.} and Aanensen, {David M.} and Loman, {Nicholas J.} and {Du Plessis}, Louis and Simon Cauchemez and Andrew Rambaut and Scarpino, {Samuel V.} and Pybus, {Oliver G.}",

year = "2021",

month = aug,

day = "20",

doi = "10.1126/science.abj0113",

language = "English",

volume = "373",

pages = "889--895",

journal = "Science",

issn = "0036-8075",

publisher = "AMER ASSOC ADVANCEMENT SCIENCE",

number = "6557",

}

Kraemer, MUG, Hill, V, Ruis, C, Dellicour, S, Bajaj, S, McCrone, JT, Baele, G, Parag, KV, Battle, AL, Gutierrez, B, Jackson, B, Colquhoun, R, O’Toole, Á, Klein, B, Vespignani, A, Volz, E, Faria, NR, Aanensen, DM, Loman, NJ, Du Plessis, L, Cauchemez, S, Rambaut, A, Scarpino, SV & Pybus, OG 2021, 'Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence', Science, vol. 373, no. 6557, pp. 889-895. https://doi.org/10.1126/science.abj0113

TY - JOUR

T1 - Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence

AU - Kraemer, Moritz U. G.

AU - Hill, Verity

AU - Ruis, Christopher

AU - Dellicour, Simon

AU - Bajaj, Sumali

AU - McCrone, John T.

AU - Baele, Guy

AU - Parag, Kris V.

AU - Battle, Anya Lindström

AU - Gutierrez, Bernardo

AU - Jackson, Ben

AU - Colquhoun, Rachel

AU - O’Toole, Áine

AU - Klein, Brennan

AU - Vespignani, Alessandro

AU - Volz, Erik

AU - Faria, Nuno R.

AU - Aanensen, David M.

AU - Loman, Nicholas J.

AU - Du Plessis, Louis

AU - Cauchemez, Simon

AU - Rambaut, Andrew

AU - Scarpino, Samuel V.

AU - Pybus, Oliver G.

PY - 2021/8/20

Y1 - 2021/8/20

N2 - Understanding the causes and consequences of the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern is crucial to pandemic control yet difficult to achieve because they arise in the context of variable human behavior and immunity. We investigated the spatial invasion dynamics of lineage B.1.1.7 by jointly analyzing UK human mobility, virus genomes, and community-based polymerase chain reaction data. We identified a multistage spatial invasion process in which early B.1.1.7 growth rates were associated with mobility and asymmetric lineage export from a dominant source location, enhancing the effects of B.1.1.7’s increased intrinsic transmissibility. We further explored how B.1.1.7 spread was shaped by nonpharmaceutical interventions and spatial variation in previous attack rates. Our findings show that careful accounting of the behavioral and epidemiological context within which variants of concern emerge is necessary to interpret correctly their observed relative growth rates.

AB - Understanding the causes and consequences of the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern is crucial to pandemic control yet difficult to achieve because they arise in the context of variable human behavior and immunity. We investigated the spatial invasion dynamics of lineage B.1.1.7 by jointly analyzing UK human mobility, virus genomes, and community-based polymerase chain reaction data. We identified a multistage spatial invasion process in which early B.1.1.7 growth rates were associated with mobility and asymmetric lineage export from a dominant source location, enhancing the effects of B.1.1.7’s increased intrinsic transmissibility. We further explored how B.1.1.7 spread was shaped by nonpharmaceutical interventions and spatial variation in previous attack rates. Our findings show that careful accounting of the behavioral and epidemiological context within which variants of concern emerge is necessary to interpret correctly their observed relative growth rates.

UR - https://github.com/COG-UK/B.1.1.7_spatial_analysis_UK

U2 - 10.1126/science.abj0113

DO - 10.1126/science.abj0113

M3 - Article

VL - 373

SP - 889

EP - 895

JO - Science

JF - Science

SN - 0036-8075

IS - 6557

ER -

Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence

Abstract

Access to Document

Other files and links

Fingerprint

The evolutionary dynamics of pathogen emergence and establishment: from Reservoir Detection to Outbreak Control

Wellcome Trust Four-Year PhD Studentship (Ms Aine O'Toole)

Cite this

Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence

Abstract

Access to Document

Other files and links

Fingerprint

Projects

The evolutionary dynamics of pathogen emergence and establishment: from Reservoir Detection to Outbreak Control

Wellcome Trust Four-Year PhD Studentship (Ms Aine O'Toole)

Cite this