Dispersal history of SARS-CoV-2 in Galicia, Spain

Abstract

The dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission are influenced by a variety of factors, including social restrictions and the emergence of distinct variants. In this study, we delve into the origins and dissemination of the Alpha, Delta, and Omicron-BA.1 variants of concern in Galicia, northwest Spain. For this, we leveraged genomic data collected by the EPICOVIGAL Consortium and from the GISAID database, along with mobility information from other Spanish regions and foreign countries. Our analysis indicates that initial introductions during the Alpha phase were predominantly from other Spanish regions and France. However, as the pandemic progressed, introductions from Portugal and the United States became increasingly significant. The number of detected introductions varied from 96 and 101 for Alpha and Delta to 39 for Omicron-BA.1. Most of these introductions left a low number of descendants (<10), suggesting a limited impact on the evolution of the pandemic in Galicia. Notably, Galicia's major coastal cities emerged as critical hubs for viral transmission, highlighting their role in sustaining and spreading the virus. This research emphasizes the critical role of regional connectivity in the spread of SARS-CoV-2 and offers essential insights for enhancing public health strategies and surveillance measures.

Keywords: SARS‐CoV‐2; dispersal; phylogeography; variants of concern.

Figure 1.. SARS-CoV-2 epidemic waves in Galicia from February 2020 to March 2022.

Number of samples available in the GISAID database (left-axis; bars) and diagnosed cases recorded by the Spanish National Epidemiology Center (CNE) (right-axis; black line) for Galicia from February 2020 to March 2022. Bar colors represent different lineages or variants, as explained in the legend.

Figure 2.. SARS-CoV-2 introductions into Galicia during the Alpha wave.

Left: Circular migration flow plot based on the Markov jumps between multiple countries and several Spanish regions, including Galicia. (A: Alpha; C: Delta; E: Omicron). Right: Mean and 95% highest posterior density (HPD) number of transitions from Spain and other countries to Galicia, computed from all the trees from the posterior distribution. (B: Alpha; D: Delta; F: Omicron). Correspondence between codes ISO 3166–2 and the complete name of the location in Supplementary Table 2.

Figure 3.. Continuous phylogeographic reconstruction of selected Alpha clusters.

A) Cluster 1–1; B) Cluster 1–2; C) Cluster 2; D) Cluster 3; E) Cluster 4. We map the maximum clade credibility (MCC) trees and overall 80% highest posterior density (HPD) regions reflecting the uncertainty related to the Bayesian phylogeographic inference. MCC trees and 80% HPD regions are based on 1,000 trees sampled from each posterior distribution and colored based on their time of occurrence. The direction of viral lineage movement is indicated by edge curvature (anti-clockwise).

Figure 4.. Continuous phylogeographic reconstruction of selected Delta clusters and Omicron - BA.1 cluster 1.

A) Delta Cluster 1–1, general vision; B) Delta Cluster 1–1, zoom in Vigo; C) Delta Cluster 1–2; D) Omicron - BA.1 Cluster 1. We map the maximum clade credibility (MCC) trees and overall 80% highest posterior density (HPD) regions, reflecting the uncertainty related to the Bayesian phylogeographic inference. MCC trees and 80% HPD regions are based on 1,000 trees sampled from each posterior distribution and colored based on their time of occurrence. The direction of viral lineage movement is indicated by edge curvature (anti-clockwise).