Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England
File(s)2020.12.30.20249034v2.full.pdf (2.44 MB)
Accepted version
Author(s)
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.
Date Issued
2021-05-13
Date Acceptance
2021-03-18
ISSN
0028-0836
Publisher
Nature Research
Start Page
266
End Page
269
Journal / Book Title
Nature
Volume
593
Copyright Statement
Copyright © 2021, The Author(s), under exclusive licence to Springer Nature Limited.
Sponsor
Medical Research Council
Bill & Melinda Gates Foundation
Medical Research Council (MRC)
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/33767447
10.1038/s41586-021-03470-x
Grant Number
MR/R015600/1
1705CR001/LD1
MR/R015600/1
Subjects
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
Coverage Spatial
England
Date Publish Online
2021-03-25