sharon sanders
Editor-in-Chief & President
Report 42 - Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: insights from linking epidemiological and genetic data
Key info
Date:
31 December 2020
Authors:
Erik Volz[SUP]1[/SUP], Swapnil Mishra, Meera Chand, Jeffrey C. Barrett, Robert Johnson, Lily Geidelberg, Wes R Hinsley, Daniel J Laydon, Gavin Dabrera, ?ine O’Toole, Roberto Amato, Manon Ragonnet-Cronin, Ian Harrison, Ben Jackson, Cristina V. Ariani, Olivia Boyd, Nick Loman, John T McCrone, S?nia Gon?alves, David Jorgensen, Richard Myers, Verity Hill, David K. Jackson, Katy Gaythorpe, Natalie Groves, John Sillitoe, Dominic P. Kwiatkowski, COG-UK, Seth Flaxman, Oliver Ratmann, Samir Bhatt, Susan Hopkins, Axel Gandy, Andrew Rambaut, Neil M Ferguson[SUP]1[/SUP]
[SUP]1[/SUP]Correspondence:
e.volz@imperial.ac.uk
neil.ferguson@imperial.ac.uk
Download the full PDF for Report 42See all reports
WHO Collaborating Centre for Infectious Disease Modelling, MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), in collaboration with the Department of Mathematics, Imperial College London, University of Edinburgh, Public Health England (PHE), the Wellcome Sanger Institute, University of Birmingham and the COVID-19 Genomics UK (COG-UK) Consortium+.
Summary
The SARS-CoV-2 lineage B.1.1.7, now designated Variant of Concern 202012/01 (VOC) by Public Health England, originated in the UK in late Summer to early Autumn 2020. We examine epidemiological evidence for this VOC having a transmission advantage from several perspectives. First, whole genome sequence data collected from community-based diagnostic testing provides an indication of changing prevalence of different genetic variants through time. Phylodynamic modelling additionally indicates that genetic diversity of this lineage has changed in a manner consistent with exponential growth. Second, 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. Third, we examine growth trends in SGTF and non-SGTF case numbers at local area level across England, and show that the VOC has higher transmissibility than non-VOC lineages, even if the VOC has a different latent period or generation time. Available SGTF data indicate a shift in the age composition of reported cases, with a larger share of under 20 year olds among reported VOC than non-VOC cases.
https://www.imperial.ac.uk/mrc-globa...cov-2-variant/
Key info
Date:
31 December 2020
Authors:
Erik Volz[SUP]1[/SUP], Swapnil Mishra, Meera Chand, Jeffrey C. Barrett, Robert Johnson, Lily Geidelberg, Wes R Hinsley, Daniel J Laydon, Gavin Dabrera, ?ine O’Toole, Roberto Amato, Manon Ragonnet-Cronin, Ian Harrison, Ben Jackson, Cristina V. Ariani, Olivia Boyd, Nick Loman, John T McCrone, S?nia Gon?alves, David Jorgensen, Richard Myers, Verity Hill, David K. Jackson, Katy Gaythorpe, Natalie Groves, John Sillitoe, Dominic P. Kwiatkowski, COG-UK, Seth Flaxman, Oliver Ratmann, Samir Bhatt, Susan Hopkins, Axel Gandy, Andrew Rambaut, Neil M Ferguson[SUP]1[/SUP]
[SUP]1[/SUP]Correspondence:
e.volz@imperial.ac.uk
neil.ferguson@imperial.ac.uk
Download the full PDF for Report 42See all reports
WHO Collaborating Centre for Infectious Disease Modelling, MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), in collaboration with the Department of Mathematics, Imperial College London, University of Edinburgh, Public Health England (PHE), the Wellcome Sanger Institute, University of Birmingham and the COVID-19 Genomics UK (COG-UK) Consortium+.
Summary
The SARS-CoV-2 lineage B.1.1.7, now designated Variant of Concern 202012/01 (VOC) by Public Health England, originated in the UK in late Summer to early Autumn 2020. We examine epidemiological evidence for this VOC having a transmission advantage from several perspectives. First, whole genome sequence data collected from community-based diagnostic testing provides an indication of changing prevalence of different genetic variants through time. Phylodynamic modelling additionally indicates that genetic diversity of this lineage has changed in a manner consistent with exponential growth. Second, 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. Third, we examine growth trends in SGTF and non-SGTF case numbers at local area level across England, and show that the VOC has higher transmissibility than non-VOC lineages, even if the VOC has a different latent period or generation time. Available SGTF data indicate a shift in the age composition of reported cases, with a larger share of under 20 year olds among reported VOC than non-VOC cases.
https://www.imperial.ac.uk/mrc-globa...cov-2-variant/
