Tracing the First Days of the SARS-CoV-2 Pandemic in Greece and the Role of the First Imported Group of Travelers

Abstract

The first SARS-CoV-2 case in Greece was confirmed on February 26, 2020, and since then, multiple strains have circulated the country, leading to regional and country-wide outbreaks. Our aim is to enlighten the events that took place during the first days of the SARS-CoV-2 pandemic in Greece, focusing on the role of the first imported group of travelers. We used whole-genome SARS-CoV-2 sequences obtained from the infected travelers of the group as well as Greece-derived and globally subsampled sequences and applied dedicated phylogenetics and phylodynamics tools as well as in-house-developed bioinformatics pipelines. Our analyses reveal the genetic variants circulating in Greece during the first days of the pandemic and the role of the group's imported strains in the course of the first pandemic wave in Greece. The strain that dominated in Greece throughout the first wave, bearing the D614G mutation, was primarily imported from a certain group of travelers, while molecular and clinical data suggest that the infection of the travelers occurred in Egypt. Founder effects early in the pandemic are important for the success of certain strains, as those arriving early, several times, and to diverse locations lead to the formation of large transmission clusters that can be estimated using molecular epidemiology approaches and can be a useful surveillance tool for the prioritization of nonpharmaceutical interventions and combating present and future outbreaks. IMPORTANCE The strain that dominated in Greece during the first pandemic wave was primarily imported from a group of returning travelers in February 2020, while molecular and clinical data suggest that the origin of the transmission was Egypt. The observed molecular transmission clusters reflect the transmission dynamics of this particular strain bearing the D614G mutation while highlighting the necessity of their use as a surveillance tool for the prioritization of nonpharmaceutical interventions and combating present and future outbreaks.

Keywords: SARS-CoV-2; infectious disease surveillance; molecular epidemiology; phylodynamics; phylogenetics; transmission clusters.

FIG 1

Epidemic curves presenting (A) the log-scaled confirmed cases in the world (gray), Europe (blue), and Greece (yellow) during the first pandemic wave, focusing on the first days of the SARS-CoV-2 pandemic in Greece (Feb 26, 2020 to March 14, 2020) and (B) the confirmed cases in Greece from February 26, 2020 (first confirmed case) to March 14, 2020 (7 days after the travelers’ group arrival in Greece).

FIG 2

Geographical distribution of the total sequences collected in Greece, along with the proportion of them that were imported from the group that visited Egypt and Israel (left). Maximum likelihood phylogenetic tree consisting of 2,451 unique sequences, 138 (5.63%) of which were collected in Greece, focusing on the clusters (presented in light-blue triangles) that consist of more than five sequences and at least 50% of them are Greece-derived (right). The molecular taxonomy presented for each MTC is based on Nextstrain’s Clade nomenclature. The depicted map was generated in R (Version 4.1.3) (43) after loading the open-source JavaScript library Leaflet version 2.1.1 (47).

FIG 3

Phylodynamic tree generated with the sequences falling withing Greece-enriched clusters, along with the nucleotide substitution profiles of each sequence depicted as a heatmap. Yellow arrows depict the Nextstrain’s Clade in which the sequences are classified.

FIG 4

Phylodynamic tree generated from the sequences collected from the cases of the imported group and all of the available sequences from Egypt, Israel, and Palestine from February 23, 2020 to March 13, 2020 (+/– 2 weeks from the collection date of the first group’s sequence). Yellow arrows depict the Nextstrain’s Clade in which the sequences are classified.