highly transmissible variant lineage b.1.1.7 OC frequency inferred from genetic data correspond

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.

The SARS-CoV-2 lineage B.1.1.7 spread rapidly across England between November 2020 and January 2021. This variant possesses a large number of non-synonymous substitutions of immunological importance². The N501Y replacement on the spike protein has been shown to increase ACE2 binding^3,4 and cell infectivity in animal models⁵, and the P618H replacement on the spike protein adjoins the furin-cleavage site⁶. B.1.1.7 also possesses a deletion at positions 69 and 70 of the spike protein (Δ69–70) that has been associated with failure of diagnostic tests using the ThermoFisher TaqPath probe, which targets the spike protein⁷.

Although other variants with Δ69–70 are also circulating in the UK, the absence of detection of the S gene target in an otherwise positive PCR test appears to be a highly specific biomarker for the B.1.1.7 lineage. Data from national community testing in November 2020 showed a rapid increase in SGTF during PCR testing for SARS-CoV-2, coinciding with a rapid increase in the frequency of B.1.1.7 observed in genomic surveillance. The B.1.1.7 lineage was designated VOC 202012/01 by Public Health England (PHE) in December 2020.

We examined whole-genome SARS-CoV-2 sequences from randomly sampled residual materials obtained from community-based COVID-19 testing in England, collected between 1 October 2020 and 16 January 2021. These data included 31,390 B.1.1.7 sequences for which the time and location of sample collection were known.

Over the same period, 52,795 non-VOC genomes were collected. VOC sequences were initially concentrated in London (n = 9,134), the South East (n = 5,609), and the East of England (n = 4,413), but is now widely distributed across England. Overall, we estimate the median posterior additive difference in growth rates between B.1.1.7 and co-circulating variants to be 0.69 per week (95% credible interval (CrI) 0.61–0.76) (Fig. 1a, Extended Data Fig. 1, Supplementary Methods section 2), and this difference was largest in November. However, in tandem with geographic expansion of the VOC and imposition of lockdown measures in 2021, this difference declined gradually to 0.43 per week (95% CrI 0.33–0.52) for the week ending 16 January.