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

Maria Bousali,Georgios K Nikolopoulos,Aristea Dimadi,Emmanouil Angelakis,George Sourvinos,Dimitrios Paraskevis,George Papatheodoridis,Timokratis Karamitros,Vasiliki Pogka,Gkikas Magiorkinis,Giota Lourida,Aikaterini Argyraki,Apostolos Beloukas,Evangelia-Georgia Kostaki,Sotirios Tsiodras,Dionyssios N Sgouras

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.

Highlights

Coronaviruses (CoVs) belong to the Nidovirales order, Coronaviridae family and Coronavirinae subfamily and are the largest known group of viruses
The percentage of clustered sequences was higher in Uusimaa and La Rioja (88.9% and 67.5%, respectively), while Saint Petersburg and Liege were found to have high percentage of sequences not belonging to molecular transmission clusters (MTCs)
We focused on the spatio-temporal characterization of SARS-CoV2 molecular transmission clusters in ten geographical regions of the European continent and we evaluated the effect of individual containment measures taken in each geographical region on the clustering patterns of the sequenced cases and the virus dispersal profiles

Summary

Introduction

Coronaviruses (CoVs) belong to the Nidovirales order, Coronaviridae family and Coronavirinae subfamily and are the largest known group of viruses. In December 2019, a novel Coronavirus was firstly reported in the city of Wuhan, Hubei province in China This novel coronavirus was further named as “2019-nCoV” by WHO [2] and later as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Viruses. The 11 January 2020, the first whole-genome sequence of SARS-CoV-2 was available and became the baseline for researchers to track SARS-CoV-2, as it spread through the world [3]. 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. 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

Methods

Results

Conclusion