TY - JOUR
T1 - Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England
AU - The COVID-19 Genomics UK (COG-UK) consortium
AU - Volz, Erik
AU - Mishra, Swapnil
AU - Chand-Kumar, Meera
AU - Barrett, Jeffrey C.
AU - Johnson, Robert
AU - Geidelberg, Lily
AU - Hinsley, Wes R.
AU - Laydon, Daniel J.
AU - Dabrera, Gavin
AU - O’Toole, Áine
AU - Amato, Roberto
AU - Ragonnet-Cronin, Manon
AU - Harrison, Ian
AU - Jackson, Ben
AU - Ariani, Cristina V.
AU - Boyd, Olivia
AU - Loman, Nicholas J.
AU - McCrone, John T.
AU - Gonçalves, Sónia
AU - Jorgensen, David
AU - Myers, Richard
AU - Hill, Verity
AU - Jackson, David K.
AU - Gaythorpe, Katy
AU - Groves, Natalie
AU - Sillitoe, John
AU - Kwiatkowski, Dominic P.
AU - Flaxman, Seth
AU - Ratmann, Oliver
AU - Bhatt, Samir
AU - Hopkins, Susan
AU - Gandy, Axel
AU - Rambaut, Andrew
AU - Ferguson, Neil M.
N1 - Publisher Copyright:
© 2021, The Author(s), under exclusive licence to Springer Nature Limited.
PY - 2021/5/13
Y1 - 2021/5/13
N2 - 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.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.
AB - 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.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.
UR - http://www.scopus.com/inward/record.url?scp=85103190451&partnerID=8YFLogxK
U2 - 10.1038/s41586-021-03470-x
DO - 10.1038/s41586-021-03470-x
M3 - Article
AN - SCOPUS:85103190451
SN - 0028-0836
VL - 593
SP - 266-+
JO - Nature
JF - Nature
IS - 7858
ER -
