TY - UNPB
T1 - Genomic epidemiology of SARS-CoV-2 spread in Scotland highlights the role of European travel in COVID-19 emergence
AU - The COVID-19 Genomics UK (COG-UK) Consortium
AU - da Silva Filipe, Ana
AU - Shepherd, James
AU - Williams, Thomas
AU - Hughes, Joseph
AU - Aranday-Cortes, Elihu
AU - Asamaphan, Patawee
AU - Balcazar, Carlos
AU - Brunker, Kirstyn
AU - Carmichael, Stephen
AU - Dewar, Rebecca
AU - Gallagher, Michael D.
AU - Gunson, Rory
AU - Ho, Antonia
AU - Jesudason, Natasha
AU - Johnson, Natasha
AU - McWilliam Leitch, E Carol
AU - Li, Kathy
AU - MacLean, Alasdair
AU - Nomikou, Kyriaki
AU - Orton, Richard J.
AU - O’Toole, Áine
AU - Palmarini, Massimo
AU - Parr, Yasmin A.
AU - Rambaut, Andrew
AU - Rooke, Stefan
AU - Shaaban, Sharif
AU - Shah, Rajiv
AU - Singer, Joshua B.
AU - Smollett, Katherine
AU - Starinskij, Igor
AU - Tong, Lily
AU - Vattipally, Sreenu
AU - Wastnedge, Elizabeth
AU - Robertson, David L.
AU - Holden, Matthew T.G.
AU - Templeton, Kate
AU - Thomson, Emma
AU - Robson, Samuel
AU - Scarlett, Garry
AU - Bourgeois, Yann Xavier Claude
AU - Beckett, Angela Helen
AU - Loveson, Katie
PY - 2020/6/9
Y1 - 2020/6/9
N2 - 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.
AB - 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.
UR - https://www.medrxiv.org/content/10.1101/2020.06.08.20124834v1
U2 - 10.1101/2020.06.08.20124834
DO - 10.1101/2020.06.08.20124834
M3 - Working paper
BT - Genomic epidemiology of SARS-CoV-2 spread in Scotland highlights the role of European travel in COVID-19 emergence
PB - medRxiv
ER -
