Aranday-Cortes, Elihu

Asamaphan, Patawee

Balaz, Daniel

Broos, Alice

Brunker, Kirstyn

Carmichael, Stephen

Colquhoun, Rachel M

Cotton, Seb

Dewar, Rebecca

Doherty, Thomas

Filipe, Ana da Silva

Gallagher, Michael D

Gunson, Rory

Hill, Verity

Holden, Matthew T.G.

Hughes, Joseph

Inward, Rhys

Jackson, Ben

Jesudason, Natasha

Johnson, Natasha

Kao, Rowland R

Li, Kathy

Lopez, Carlos Balcazar

Lu, Lu

Lycett, Samantha J

MacLean, Alasdair

Mair, Daniel

McCrone, John T

McDonald, Sarah E

McHugh, Martin P

Nichols, Jenna

Niebel, Marc

Nomikou, Kyriaki

O’Toole, Áine

Parr, Yasmin A

Rambaut, Andrew

Robertson, David L

Rooke, Stefan

Rossi, Gianluigi

Scher, Emily

Shaaban, Sharif

Shah, Rajiv

Shepherd, Amy

Shepherd, James G

Smollett, Katherine

Sreenu, Vattipally B

Stanton, Tom

Starinskij, Igor

Templeton, Kate

Thomson, Emma C

Tong, Lily

Williams, Thomas C

Williamson, Kathleen A

Woolhouse, Mark

English

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

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 &gt;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

Edinburgh Research Explorer

https://www.research.ed.ac.uk/files/199501738/2021.01.08.20248677v1.full.pdf

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

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