Genomic epidemiology of SARS-CoV-2 spread in Scotland highlights the role of European travel in COVID-19 emergence

Abstract

SARS-CoV-2, the causative agent of COVID-19, emerged in Wuhan, China in December 2019 and spread rapidly throughout the world. Understanding the introductions of this new coronavirus in different settings may assist control efforts and the establishment of frameworks to support rapid response in future infectious disease outbreaks. We investigated the first four weeks of emergence of the SARS-CoV-2 virus in Scotland after the first case reported on the 1st March 2020. We obtained full genome sequences from 452 individuals with a laboratory-confirmed diagnosis of COVID-19, representing 20% of all cases until 1st April 2020 (n=2310). This permitted a genomic epidemiology approach to study the introductions and spread of the SARS-2 virus in Scotland. From combined phylogenetic and epidemiological analysis, we estimated at least 113 introductions of SARS-CoV-2 into Scotland during this period. Clusters containing multiple sequences suggestive of onward transmission occurred in 48/86 (56%). 42/86 (51%) clusters had no known international travel history indicating undetected introductions. The majority of viral sequences were most closely related to those circulating in other European countries, including Italy, Austria and Spain. Travel-associated introductions of SARS-CoV-2 into Scotland predated travel restrictions in the UK and other European countries. The first local transmission occurred three days after the first case. A shift from travel-associated to sustained community transmission was apparent after only 11 days. Undetected introductions occurred prior to the first known case of COVID-19. Earlier travel restrictions and quarantine measures might have resulted in fewer introductions into Scotland, thereby reducing the number of cases and the subsequent burden on health services. The high number of introductions and transmission rates were likely to have impacted on national contact tracing efforts. Our results also demonstrate that local real-time genomic epidemiology can be used to monitor transmission clusters and facilitate control efforts to restrict the spread of COVID-19.

Phylogenetic pattern of SARS-CoV-2 from COVID-19 patients from Bosnia and Herzegovina: lessons learned to optimize future molecular and epidemiological approaches

“…Even though all four BiH sequences cluster mainly with European ones, the constructed phylogenetic tree indicates multiple independent introductions of COVID-19 in BiH. Those findings correspond with other COVID-19 WGS studies [13,14] and confirm the importance of travel-associated disease introduction events for BiH as well. The success of future mitigation measures related to this type of disease introduction will be highly challenging for BiH due to a significant proportion of BiH population living abroad.…”

Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore

“…Viral genomes can be used to estimate the rate of viral evolution, monitor circulating lineages as well as identifying any signs of adaptation to hosts, treatments or vaccines. Genome sequencing of SARS-CoV-2 has provided epidemiological insights into the early outbreak [7][8][9] and a number of studies have adopted our method [8,[10][11][12][13][14][15][16][17] . Rapid data sharing allows sequences to be compared across labs or public health authorities and can provide insight into routes of transmission and effectiveness of containment measures [18] .…”

COVID-19 in patients undergoing chronic kidney replacement therapy and kidney transplant recipients in Scotland: findings and experience from the Scottish renal registry

“…The first case of SARS-CoV-2 infection in Scotland was confirmed on 1st March 2020, although subsequent data suggest that the virus had been in circulation for weeks prior to this [14]. On 24th March, as part of the Scottish Government response to the pandemic, certain groups of patients were identified as the most vulnerable to developing severe illness and advised to "shield" meaning they were advised to remain at home and minimise all non-essential contact with other members of their household.…”