Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data

Abstract

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. Fourth, we assess the association of VOC frequency with independent estimates of the overall SARS-CoV-2 reproduction number through time. Finally, we fit a semi-mechanistic model directly to local VOC and non-VOC case incidence to estimate the reproduction numbers over time for each. There is a consensus among all analyses that the VOC has a substantial transmission advantage, with the estimated difference in reproduction numbers between VOC and non-VOC ranging between 0.4 and 0.7, and the ratio of reproduction numbers varying between 1.4 and 1.8. We note that these estimates of transmission advantage apply to a period where high levels of social distancing were in place in England; extrapolation to other transmission contexts therefore requires caution.

Priorities for the COVID-19 pandemic at the start of 2021: statement of the Lancet COVID-19 Commission

“…The high rates of community transmission (>100 new COVID-19 cases per million per day) 2 in the USA, Europe, South Africa, and other countries show the emergence of new variants of SARS-CoV-2, such as lineage B.1.1.7 in the UK, [3][4][5][6][7] 501Y.V2 in South Africa, 8 and additional variants emerging in California, USA, 9,10 and in Brazil. 11,12 New lineages are increasing transmission of infection and raising risks in regions that have been less affected by COVID-19, including in sub-Saharan Africa.…”

Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging

“…Although this strain was detected in late September 2020, a rapid increase in its frequency has since been reported in December 2020 in England, and it has spread to other countries from the UK, Europe, Africa, Asia, Oceania and America [24][25][26]. This variant is roughly 50-56% more transmissible than other virus variants but does not cause more severe disease [27,28]. Its rapid spread has been associated with the N501Y and P681H substitutions, which could be implicated in viral infectivity [29].…”

Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677

“…Remarkably, a 19B cluster harboring the ostensibly less fit, 'ancestral' D614 Spike, which has been circulating at ≤2% of global frequency since August 2020, recently resurfaced as a newly reemergent lineage carrying N501Y together with 677H (Wagner, 2021). N501Y is therefore notably found in all three of the 'variants of concern' (Tegally et al, 2020;Faria et al, 2021;Lauring and Hodcroft, 2021;Naveca, Nascimento, et al, 2021;Volz, Mishra, et al, 2021). Acknowledging this observation is circumstantial, it further suggests that the 677H mutation may confer an evolutionary advantage to SARS-CoV-2.…”

“…In mid-December 2020, the United Kingdom reported a SARS-CoV-2 variant termed B.1.1.7 (20I/501Y.V1) that exhibited a rapid increase in its range and incidence following its initial detection in November (Andrew Rambaut,Nick Loman,Oliver Pybus,Wendy Barclay,Jeff Barrett,Alesandro Carabelli,Tom Connor,Tom Peacock,David L Robertson,Erik Volz, Genomics Consortium UK (CoG-UK), 2020; Volz, Mishra, et al, 2021). Since then, additional "variants of concern" have emerged, namely lineages B.1.351 (20H/501Y.V2) from S Africa (Tegally et al, 2020) and P.1 (20J/501Y.V3) and P.2 from Brazil (Voloch et al, 2020;Faria et al, 2021;Naveca, da Costa, et al, 2021;Sabino et al, 2021).…”