17
IRUS Total
Downloads

Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England

File Description SizeFormat 
2020.12.30.20249034v2.full.pdfAccepted version2.5 MBAdobe PDFView/Open
Title: Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England
Authors: Volz, E
Mishra, S
Chand, M
Barrett, JC
Johnson, R
Geidelberg, L
Hinsley, WR
Laydon, DJ
Dabrera, G
O'Toole, Á
Amato, R
Ragonnet-Cronin, M
Harrison, I
Jackson, B
Ariani, CV
Boyd, O
Loman, NJ
McCrone, JT
Gonçalves, S
Jorgensen, D
Myers, R
Hill, V
Jackson, DK
Gaythorpe, K
Groves, N
Sillitoe, J
Kwiatkowski, DP
COVID-19 Genomics UK (COG-UK) consortium
Flaxman, S
Ratmann, O
Bhatt, S
Hopkins, S
Gandy, A
Rambaut, A
Ferguson, NM
Item Type: Journal Article
Abstract: The SARS-CoV-2 lineage B.1.1.7, designated a Variant of Concern 202012/01 (VOC) by Public Health England1, originated in the UK in late Summer to early Autumn 20202. Whole genome SARS-CoV-2 sequence data collected from community-based diagnostic testing shows an unprecedentedly rapid expansion of the B.1.1.7 lineage during Autumn 2020, suggesting a selective advantage. 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. Analysis of trends in SGTF and non-SGTF case numbers in local areas across England shows that the VOC has higher transmissibility than non-VOC lineages, even if the VOC has a different latent period or generation time. The SGTF data indicate a transient shift in the age composition of reported cases, with a larger share of under 20 year olds among reported VOC than non-VOC cases. Time-varying reproduction numbers for the VOC and cocirculating lineages were estimated using SGTF and genomic data. The best supported models did not indicate a substantial difference in VOC transmissibility among different age groups. There is a consensus among all analyses that the VOC has a substantial transmission advantage with a 50% to 100% higher reproduction number.
Issue Date: 13-May-2021
Date of Acceptance: 18-Mar-2021
URI: http://hdl.handle.net/10044/1/87474
DOI: 10.1038/s41586-021-03470-x
ISSN: 0028-0836
Publisher: Nature Research
Start Page: 266
End Page: 269
Journal / Book Title: Nature
Volume: 593
Replaces: 10044/1/85239
http://hdl.handle.net/10044/1/85239
Copyright Statement: Copyright © 2021, The Author(s), under exclusive licence to Springer Nature Limited.
Sponsor/Funder: Medical Research Council
Bill & Melinda Gates Foundation
Medical Research Council (MRC)
Funder's Grant Number: MR/R015600/1
1705CR001/LD1
MR/R015600/1
Keywords: Science & Technology
Multidisciplinary Sciences
Science & Technology - Other Topics
Adolescent
Adult
Age Distribution
Aged
Aged, 80 and over
Basic Reproduction Number
COVID-19
Child
Child, Preschool
England
Evolution, Molecular
Genome, Viral
Humans
Infant
Infant, Newborn
Middle Aged
Phylogeny
SARS-CoV-2
Spike Glycoprotein, Coronavirus
Time Factors
Young Adult
COVID-19 Genomics UK (COG-UK) consortium
Humans
Age Distribution
Evolution, Molecular
Phylogeny
Genome, Viral
Time Factors
Adolescent
Adult
Aged
Aged, 80 and over
Middle Aged
Child
Child, Preschool
Infant
Infant, Newborn
England
Basic Reproduction Number
Young Adult
Spike Glycoprotein, Coronavirus
COVID-19
SARS-CoV-2
The COVID-19 Genomics UK (COG-UK) consortium
General Science & Technology
Publication Status: Published
Conference Place: England
Open Access location: https://www.medrxiv.org/content/10.1101/2020.12.30.20249034v2
Online Publication Date: 2021-03-25
Appears in Collections:Mathematics
Department of Infectious Diseases
Statistics
Faculty of Medicine
Imperial College London COVID-19
School of Public Health
Faculty of Natural Sciences