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

doi:10.3390/life11030219

. 2021 Mar 9;11(3):219.

doi: 10.3390/life11030219.

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

Maria Bousali¹, Aristea Dimadi¹, Evangelia-Georgia Kostaki², Sotirios Tsiodras³, Georgios K Nikolopoulos⁴, Dionyssios N Sgouras⁵, Gkikas Magiorkinis², George Papatheodoridis⁶, Vasiliki Pogka^{1

5}, Giota Lourida⁷, Aikaterini Argyraki⁷, Emmanouil Angelakis^{5

8}, George Sourvinos⁹, Apostolos Beloukas^{10

11}, Dimitrios Paraskevis², Timokratis Karamitros^{1

5}

Affiliations

¹ Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece.
² Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, 15772 Athens, Greece.
³ 4th Department of Internal Medicine & Infectious Diseases, School of Medicine, National and Kapodistrian University of Athens, 15772 Athens, Greece.
⁴ Medical School, University of Cyprus, 2029 Nicosia, Cyprus.
⁵ Laboratory of Medical Microbiology, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece.
⁶ Department of Gastroenterology, Medical School of National and Kapodistrian University of Athens, "Laiko" General Hospital of Athens, 11527 Athens, Greece.
⁷ Infectious Diseases Clinic A, Sotiria Chest Diseases Hospital, 11527 Athens, Greece.
⁸ IRD, APHM, VITROME, IHU-Mediterranean Infections, Aix Marseille University, 13005 Marseille, France.
⁹ Laboratory of Clinical Virology, School of Medicine, University of Crete, 71500 Heraklion, Greece.
¹⁰ Department of Biomedical Sciences, University of West Attica, 12243 Athens, Greece.
¹¹ Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, UK.

PMID: 33803490
PMCID: PMC8001481
DOI: 10.3390/life11030219

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

Maria Bousali et al. Life (Basel). 2021.

. 2021 Mar 9;11(3):219.

doi: 10.3390/life11030219.

Authors

Affiliations

¹ Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece.
² Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, 15772 Athens, Greece.
³ 4th Department of Internal Medicine & Infectious Diseases, School of Medicine, National and Kapodistrian University of Athens, 15772 Athens, Greece.
⁴ Medical School, University of Cyprus, 2029 Nicosia, Cyprus.
⁵ Laboratory of Medical Microbiology, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece.
⁶ Department of Gastroenterology, Medical School of National and Kapodistrian University of Athens, "Laiko" General Hospital of Athens, 11527 Athens, Greece.
⁷ Infectious Diseases Clinic A, Sotiria Chest Diseases Hospital, 11527 Athens, Greece.
⁸ IRD, APHM, VITROME, IHU-Mediterranean Infections, Aix Marseille University, 13005 Marseille, France.
⁹ Laboratory of Clinical Virology, School of Medicine, University of Crete, 71500 Heraklion, Greece.
¹⁰ Department of Biomedical Sciences, University of West Attica, 12243 Athens, Greece.
¹¹ Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, UK.

PMID: 33803490
PMCID: PMC8001481
DOI: 10.3390/life11030219

Abstract

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.

Keywords: COVID-19; SARS-CoV-2; clusters; molecular epidemiology; molecular transmission clusters; pandemic; phylodynamics; phylogenetics; transmission.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

**Figure 1**
Rooted phylogenetic inference of full genome SARS-CoV-2 sequences from 10 European geographical regions (a–j) and a globally sampled dataset (in grey). Nodes significantly enriched in geographical region’s specific sequences representing molecular transmission clusters (MTCs) are colored in orange, while nodes with geographical region’s specific unclustered sequences are in blue.

**Figure 2**
Distribution of total sequenced cases (five-color inner circle) and clustered sequences (belonging to MTCs—outer circle) according to age group. Density of population, containment measures, total levels of clustering and averages temperature range for each geographical region are also presented.

**Figure 3**
Distribution of clustered and unclustered sequences for each age group during the containment measures of schools’ closure (blue), the lockdown (red) and closure of national borders (orange). The virus symbol refers to the first case reported in each of the geographical regions.

See this image and copyright information in PMC

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

Affiliations

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

Authors

Affiliations

Abstract

Conflict of interest statement

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