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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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.
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SciScore for 10.1101/2021.01.08.20248677: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Library pools were loaded onto R9.4.1 flow cells and sequenced in MinION or GridION devices using MinKNOW version 19.12.5 and 19.12.6, respectively. MinKNOWsuggested: NoneThe ARTIC nCoV-2019 environment utilising RAMPART v1.0.5 and v1.1.0 was used to visualise read mapping in real time. RAMPARTsuggested: (Rampart, RRID:SCR_016742)MinION generated raw FAST5 files were subsequently base called using Guppy version 3.4.5 in high accuracy mode and using a minimum quality score of 7. Mi…SciScore for 10.1101/2021.01.08.20248677: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Library pools were loaded onto R9.4.1 flow cells and sequenced in MinION or GridION devices using MinKNOW version 19.12.5 and 19.12.6, respectively. MinKNOWsuggested: NoneThe ARTIC nCoV-2019 environment utilising RAMPART v1.0.5 and v1.1.0 was used to visualise read mapping in real time. RAMPARTsuggested: (Rampart, RRID:SCR_016742)MinION generated raw FAST5 files were subsequently base called using Guppy version 3.4.5 in high accuracy mode and using a minimum quality score of 7. MinIONsuggested: (MinION, RRID:SCR_017985)Following the ARTIC-nCov-2019 bioinformatics protocol, reads were initially size filtered, then demultiplexed and trimmed with Porechop (18), and mapped against reference strain Wuhan-Hu-1 (GenBank accession number MN908947.3), followed by clipping of primer regions. Porechopsuggested: (Porechop, RRID:SCR_016967)All consensus genomes are available from the GISAID database (https://www.gisaid.org), the COG-UK consortium website (https://www.cogconsortium.uk/data/) and BAM files from the European Nucleotide Archive’s Sequence Read Archive service, BioProject PRJEB37886 (https://www.ebi.ac.uk/ena/data/view/PRJEB37886). BioProjectsuggested: (NCBI BioProject, RRID:SCR_004801)Briefly, the sequences are aligned to the reference sequence Wuhan-Hu_1 (MN908947.3) using minimap2 (Li, 2018) and a maximum-likelihood phylogenetic tree is constructed using Fasttree http://www.microbesonline.org/fasttree/. Fasttreesuggested: (FastTree, RRID:SCR_015501)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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SciScore for 10.1101/2021.01.08.20248677: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Library pools were loaded onto R9.4.1 flow cells and sequenced in MinION or GridION devices using MinKNOW version 19.12.5 and 19.12.6, respectively. MinKNOWsuggested: NoneThe ARTIC nCoV-2019 environment utilising RAMPART v1.0.5 and v1.1.0 was used to visualise read mapping in real time. RAMPARTsuggested: (Rampart, RRID:SCR_016742)MinION generated raw … SciScore for 10.1101/2021.01.08.20248677: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Library pools were loaded onto R9.4.1 flow cells and sequenced in MinION or GridION devices using MinKNOW version 19.12.5 and 19.12.6, respectively. MinKNOWsuggested: NoneThe ARTIC nCoV-2019 environment utilising RAMPART v1.0.5 and v1.1.0 was used to visualise read mapping in real time. RAMPARTsuggested: (Rampart, RRID:SCR_016742)MinION generated raw FAST5 files were subsequently base called using Guppy version 3.4.5 in high accuracy mode and using a minimum quality score of 7. MinIONsuggested: (MinION, RRID:SCR_017985)Following the ARTIC-nCov-2019 bioinformatics protocol, reads were initially size filtered, then demultiplexed and trimmed with Porechop (18), and mapped against reference strain Wuhan-Hu-1 (GenBank accession number MN908947.3), followed by clipping of primer regions. Porechopsuggested: (Porechop, RRID:SCR_016967)All consensus genomes are available from the GISAID database (https://www.gisaid.org), the COG-UK consortium website (https://www.cogconsortium.uk/data/) and BAM files from the European Nucleotide Archive’s Sequence Read Archive service, BioProject PRJEB37886 ( BioProjectsuggested: (NCBI BioProject, RRID:SCR_004801)Briefly, the sequences are aligned to the reference sequence Wuhan-Hu_1 (MN908947.3) using minimap2 (Li, 2018) and a maximum-likelihood phylogenetic tree is constructed using Fasttree http://www.microbesonline.org/fasttree/. Fasttreesuggested: (FastTree, RRID:SCR_015501)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
About SciScore
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