Journal Article

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

Gonçalves, Sónia, Volz, Erik, Chand, Meera, Johnson, Robert, Jackson, Ben, Flaxman, Seth, Hinsley, Wes R., Myers, Richard, Loman, Nicholas J., Harrison, Ian, Amato, Robert, Gandy, Axel, Laydon, Daniel J., Mishra, Swapnil, Groves, Natalie, Bhatt, Samir, Barrett, Jeffrey C., Gaythorpe, Katy, Rambaut, Andrew, Geidelberg, Lily, Jackson, David K., Kwiatkowski, Dominic P., McCrone, John T., Dabrera, Gavin, Ragonnet-Cronin, Manon, Ariani, Cristina V., Boyd, Olivia, Ratmann, Oliver, Ferguson, Neil M., Jorgensen, David, Hopkins, Susan, O’Toole, Áine, Hill, Verity, Sillitoe, John

2021

Overview

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. Genetic and testing data from England show that the SARS-CoV-2 variant of concern B.1.1.7 has a transmission advantage over other lineages.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 45 / 631/181/457 / 631/326/596/4130 / 692/699/255/2514 / Adolescent / Adult / Age / Age composition / Age Distribution / Age groups / Aged / Aged, 80 and over / Autumn / Basic Reproduction Number / Biomarkers / Child / Child, Preschool / Coronaviruses / COVID-19 / COVID-19 - diagnosis / COVID-19 - epidemiology / COVID-19 - transmission / COVID-19 - virology / COVID-19 diagnostic tests / Diagnostic systems / Disease transmission / England - epidemiology / Evolution, Molecular / Genome, Viral - genetics / Genomes / Humanities and Social Sciences / Humans / Infant / Infant, Newborn / Latent period / Middle Aged / multidisciplinary / Nucleotide sequence / Phylogeny / Proteins / Public health / S gene / SARS-CoV-2 - classification / SARS-CoV-2 - genetics / SARS-CoV-2 - isolation & purification / SARS-CoV-2 - pathogenicity / Science / Science (multidisciplinary) / Severe acute respiratory syndrome coronavirus 2 / Spike Glycoprotein, Coronavirus - analysis / Spike Glycoprotein, Coronavirus - genetics / Time Factors / Trends / Young Adult