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Article

SARS-CoV-2 Molecular Transmission Clusters and Containment Measures in Ten European Regions during the First Pandemic Wave

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Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece
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Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, 15772 Athens, Greece
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4th Department of Internal Medicine & Infectious Diseases, School of Medicine, National and Kapodistrian University of Athens, 15772 Athens, Greece
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Medical School, University of Cyprus, 2029 Nicosia, Cyprus
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Laboratory of Medical Microbiology, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece
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IRD, APHM, VITROME, IHU-Mediterranean Infections, Aix Marseille University, 13005 Marseille, France
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Department of Gastroenterology, Medical School of National and Kapodistrian University of Athens, “Laiko” General Hospital of Athens, 11527 Athens, Greece
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Infectious Diseases Clinic A, Sotiria Chest Diseases Hospital, 11527 Athens, Greece
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Laboratory of Clinical Virology, School of Medicine, University of Crete, 71500 Heraklion, Greece
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Department of Biomedical Sciences, University of West Attica, 12243 Athens, Greece
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Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, UK
*
Authors to whom correspondence should be addressed.
Academic Editor: Daniele Focosi
Life 2021, 11(3), 219; https://doi.org/10.3390/life11030219
Received: 18 January 2021 / Revised: 12 February 2021 / Accepted: 3 March 2021 / Published: 9 March 2021
(This article belongs to the Special Issue Ecology, Evolution and Epidemiology of Coronaviruses)
Background: The spatiotemporal profiling of molecular transmission clusters (MTCs) using viral genomic data can effectively identify transmission networks in order to inform public health actions targeting SARS-CoV-2 spread. Methods: We used whole genome SARS-CoV-2 sequences derived from ten European regions belonging to eight countries to perform phylogenetic and phylodynamic analysis. We developed dedicated bioinformatics pipelines to identify regional MTCs and to assess demographic factors potentially associated with their formation. Results: The total number and the scale of MTCs varied from small household clusters identified in all regions, to a super-spreading event found in Uusimaa-FI. Specific age groups were more likely to belong to MTCs in different regions. The clustered sequences referring to the age groups 50–100 years old (y.o.) were increased in all regions two weeks after the establishment of the lockdown, while those referring to the age group 0–19 y.o. decreased only in those regions where schools’ closure was combined with a lockdown. Conclusions: The spatiotemporal profiling of the SARS-CoV-2 MTCs can be a useful tool to monitor the effectiveness of the interventions and to reveal cryptic transmissions that have not been identified through contact tracing. View Full-Text
Keywords: SARS-CoV-2; COVID-19; pandemic; transmission; clusters; phylodynamics; phylogenetics; molecular epidemiology; molecular transmission clusters SARS-CoV-2; COVID-19; pandemic; transmission; clusters; phylodynamics; phylogenetics; molecular epidemiology; molecular transmission clusters
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MDPI and ACS Style

Bousali, M.; Dimadi, A.; Kostaki, E.-G.; Tsiodras, S.; Nikolopoulos, G.K.; Sgouras, D.N.; Magiorkinis, G.; Papatheodoridis, G.; Pogka, V.; Lourida, G.; Argyraki, A.; Angelakis, E.; Sourvinos, G.; Beloukas, A.; Paraskevis, D.; Karamitros, T. SARS-CoV-2 Molecular Transmission Clusters and Containment Measures in Ten European Regions during the First Pandemic Wave. Life 2021, 11, 219. https://doi.org/10.3390/life11030219

AMA Style

Bousali M, Dimadi A, Kostaki E-G, Tsiodras S, Nikolopoulos GK, Sgouras DN, Magiorkinis G, Papatheodoridis G, Pogka V, Lourida G, Argyraki A, Angelakis E, Sourvinos G, Beloukas A, Paraskevis D, Karamitros T. SARS-CoV-2 Molecular Transmission Clusters and Containment Measures in Ten European Regions during the First Pandemic Wave. Life. 2021; 11(3):219. https://doi.org/10.3390/life11030219

Chicago/Turabian Style

Bousali, Maria, Aristea Dimadi, Evangelia-Georgia Kostaki, Sotirios Tsiodras, Georgios K. Nikolopoulos, Dionyssios N. Sgouras, Gkikas Magiorkinis, George Papatheodoridis, Vasiliki Pogka, Giota Lourida, Aikaterini Argyraki, Emmanouil Angelakis, George Sourvinos, Apostolos Beloukas, Dimitrios Paraskevis, and Timokratis Karamitros. 2021. "SARS-CoV-2 Molecular Transmission Clusters and Containment Measures in Ten European Regions during the First Pandemic Wave" Life 11, no. 3: 219. https://doi.org/10.3390/life11030219

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