Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 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 Bousali  1 , Aristea Dimadi  1 , Evangelia-Georgia Kostaki  2 , Sotirios Tsiodras  3 , Georgios K Nikolopoulos  4 , Dionyssios N Sgouras  5 , Gkikas Magiorkinis  2 , George Papatheodoridis  6 , Vasiliki Pogka  1   5 , Giota Lourida  7 , Aikaterini Argyraki  7 , Emmanouil Angelakis  5   8 , George Sourvinos  9 , Apostolos Beloukas  10   11 , Dimitrios Paraskevis  2 , Timokratis Karamitros  1   5
Affiliations

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

Maria Bousali et al. Life (Basel). .

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.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
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
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
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

References

    1. Cui J., Li F., Shi Z.-L. Origin and evolution of pathogenic coronaviruses. Nat. Rev. Microbiol. 2018;17:181–192. doi: 10.1038/s41579-018-0118-9. - DOI - PMC - PubMed
    1. Zhou H., Chen X., Hu T., Li J., Song H., Liu Y., Wang P., Liu D., Yang J., Holmes E.C., et al. A novel bat coronavirus closely related to SARS-CoV-2 contains natural insertions at the S1/S2 cleavage site of the spike protein. Curr. Biol. 2020;30:2196–2203. doi: 10.1016/j.cub.2020.05.023. - DOI - PMC - PubMed
    1. Wu F., Zhao S., Yu B., Chen Y.M., Wang W., Song Z.G., Hu Y., Tao Z.W., Tian J.H., Pei Y.Y., et al. A new coronavirus associated with human respiratory disease in China. Nature. 2020;579:265–269. doi: 10.1038/s41586-020-2008-3. - DOI - PMC - PubMed
    1. Drosten C., Preiser W., Günther S., Schmitz H., Doerr H.W. Severe acute respiratory syndrome: Identification of the etiological agent. Trends Mol. Med. 2003;9:325–327. doi: 10.1016/S1471-4914(03)00133-3. - DOI - PMC - PubMed
    1. Gandhi R.T., Lynch J.B., del Rio C. Mild or moderate Covid-19. N. Engl. J. Med. 2020;383:1757–1766. doi: 10.1056/NEJMcp2009249. - DOI - PubMed

LinkOut - more resources