Mary Wilson
Well-known member
This is an unedited manuscript that has been accepted for publication.
Nature Research are providing this early version of the manuscript as a service to our authors and readers.
Published: 25 March 2021
DOI: https://doi.org/10.1038/s41586-021-03470-x
Erik Volz, Swapnil Mishra, Neil M. Ferguson
Abstract
The SARS-CoV-2 lineage B.1.1.7, designated a Variant of Concern 202012/01 (VOC) by Public Health England[SUP]1[/SUP], originated in the UK in late Summer to early Autumn 2020[SUP]2[/SUP]. 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.
PDF Format:
https://www.nature.com/articles/s41586-021-03470-x_reference.pdf
Nature Research are providing this early version of the manuscript as a service to our authors and readers.
Published: 25 March 2021
DOI: https://doi.org/10.1038/s41586-021-03470-x
Erik Volz, Swapnil Mishra, Neil M. Ferguson
Abstract
The SARS-CoV-2 lineage B.1.1.7, designated a Variant of Concern 202012/01 (VOC) by Public Health England[SUP]1[/SUP], originated in the UK in late Summer to early Autumn 2020[SUP]2[/SUP]. 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.
PDF Format:
https://www.nature.com/articles/s41586-021-03470-x_reference.pdf