Epidemic waves of COVID-19 in Scotland: a genomic perspective on the impact of the introduction and relaxation of lockdown on SARS-CoV-2

Abstract

The second SARS virus, SARS-CoV-2, emerged in December 2019, and within a month was globally distributed. It was first introduced into Scotland in February 2020 associated with returning travellers and visitors. By March it was circulating in communities across the UK, and to control COVID-19 cases, and prevent overwhelming of the National Health Service (NHS), a ‘lockdown’ was introduced on 23rd March 2020 with a restriction of people’s movements. To augment the public health efforts a large-scale genome epidemiology effort (as part of the COVID-19 Genomics UK (COG-UK) consortium) resulted in the sequencing of over 5000 SARS-CoV-2 genomes by 18th August 2020 from Scottish cases, about a quarter of the estimated number of cases at that time. Here we quantify the geographical origins of the first wave introductions into Scotland from abroad and other UK regions, the spread of these SARS-CoV-2 lineages to different regions within Scotland (defined at the level of NHS Health Board) and the effect of lockdown on virus ‘success’. We estimate that approximately 300 introductions seeded lineages in Scotland, with around 25% of these lineages composed of more than five viruses, but by June circulating lineages were reduced to low levels, in line with low numbers of recorded positive cases. Lockdown was, thus, associated with a dramatic reduction in infection numbers and the extinguishing of most virus lineages. Unfortunately since the summer cases have been rising in Scotland in a second wave, with >1000 people testing positive on a daily basis, and hospitalisation of COVID-19 cases on the rise again. Examining the available Scottish genome data from the second wave, and comparing it to the first wave, we find that while some UK lineages have persisted through the summer, the majority of lineages responsible for the second wave are new introductions from outside of Scotland and many from outside of the UK. This indicates that, while lockdown in Scotland is directly linked with the first wave case numbers being brought under control, travel-associated imports (mostly from Europe or other parts of the UK) following the easing of lockdown are responsible for seeding the current epidemic population. This demonstrates that the impact of stringent public health measures can be compromised if following this, movements from regions of high to low prevalence are not minimised.

Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

“…For the phylodynamic analysis, Scottish ''introduction'' lineages with ten or more sequences were identified (Lycett et al, 2021), and the skygrowth package in R was used to estimate the effective population size over time (using up to ten time intervals), and the growth rates of the lineages within Scotland (Volz and Frost, 2017). The data used for analysis were sampled between Feb 28, 2020 and Aug 18, 2020.…”

SCoVMod – a spatially explicit mobility and deprivation adjusted model of first wave COVID-19 transmission dynamics

“…Our model also estimates the number of individuals with infection in early March, with the most likely case being on the order of 1500 infected individuals in Scotland at this time. While our approach is crude and does not take account of continuing importation of individuals over time, it is substantially greater than the estimate of 113 introductions of COVID-19 into Scotland based on viral sequence data 29 , but is plausible if one takes into account the additional infections these introductions would have caused by the start of our simulations.…”

Conference Outbreak March 2020 Incident Management Team report

“…A similar pattern of multiple introductions into Scotland was observed for the second wave. Analysis by Lycett et al (12) of sequences available to 21 October 2020, showed that most of the latter were novel lineages, rather than persisting wave one lineages. While some of the wave two lineages were re-introductions from other parts of the UK, the majority were introductions from outside the UK.…”