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

Volz, E. et al. (2021) Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature, 593(7858), pp. 266-269. (doi: 10.1038/s41586-021-03470-x) (PMID:33767447)

Abstract

The SARS-CoV-2 lineage B.1.1.7, designated variant of concern (VOC) 202012/01 by Public Health England1, was first identified in the UK in late summer to early autumn 20202. 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.

• Item Type: Articles
• Additional Information: University of Glasgow staff are members of The COVID-19 Genomics UK (COG-UK) consortium.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Shah, Dr Rajiv and Li, Dr Kathy and Aranday-Cortes, Dr Elihu and Robertson, Professor David and Singer, Dr Josh and Asamaphan, Dr Patawee and Nickbakhsh, Dr Sema and Mair, Mr Daniel and Tong, Dr Lily and Orton, Dr Richard and Jesudason, Dr Natasha and Gunson, Dr Rory and Blacow, Dr Rachel and Da Silva Filipe, Dr Ana and Shepherd, Dr James and Hughes, Dr Joseph and Mollett, Mr Guy and Broos, Ms Alice and Vattipally, Dr Sreenu and Carmichael, Dr Stephen and Nichols, Mrs Jenna and Nomikou, Dr Kyriaki and Thomson, Professor Emma and Bradley-Stewart, Dr Amanda and Johnson, Miss Natasha and Smollett, Dr Katherine and MacLean, Dr Alasdair and Niebel, Dr Marc
• Authors: Volz, E., Mishra, S., Chand, M., Barrett, J. C., Johnson, R., Geidelberg, L., Hinsley, W. R., Laydon, D. J., Dabrera, G., O’Toole, Á., Amato, R., Ragonnet-Cronin, M., Harrison, I., Jackson, B., Ariani, C. V., Boyd, O., Loman, N. J., McCrone, J. T., Gonçalves, S., Jorgensen, D., Myers, R., Hill, V., Jackson, D. K., Gaythorpe, K., Groves, N., Sillitoe, J., Kwiatkowski, D. P., Flaxman, S., Ratmann, O., Bhatt, S., Hopkins, S., Gandy, A., Rambaut, A., Ferguson, N. M., Smollett, K., Thomson, E. C., Shepherd, J. G., Asamaphan, P., Niebel, M. O., Li, K. K., Shah, R. N., Jesudason, N. G., Tong, L., Broos, A., Mair, D., Nichols, J., Carmichael, S. N., Nomikou, K., Aranday-Cortes, E., Johnson, N., Starinskij, I., da Silva Filipe, A., Robertson, D. L., Orton, R. J., Hughes, J., Vattipally, S., Singer, J. B., Nickbakhsh, S., Bradley, A., Maclean, A., Mollett, G., Blacow, R., and Gunson, R. N.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity; College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
• Journal Name: Nature
• Publisher: Nature Research
• ISSN: 0028-0836
• ISSN (Online): 1476-4687
• Published Online: 25 March 2021