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[Preprint]. 2024 Jul 1:2024.07.01.24309632.

doi: 10.1101/2024.07.01.24309632.

Dispersal history of SARS-CoV-2 variants Alpha, Delta, and Omicron (BA.1) in Spain

Pilar Gallego-García^{1

2}, Samuel L Hong³, Nena Bollen³, Simon Dellicour^{3

4}, Guy Baele³, Marc A Suchard^{5

6

7}, Philippe Lemey^{3

8}, David Posada^{1

2

9}

Affiliations

¹ CINBIO, Universidade de Vigo, 36310 Vigo, Spain.
² Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO.
³ Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Epidemiological Virology, KU Leuven - University of Leuven, 3000 Leuven, Belgium.
⁴ Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Brussels, Belgium.
⁵ Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA.
⁶ Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.
⁷ Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.
⁸ Global Virus Network (GVN), Baltimore, MD 21201, USA.
⁹ Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, Vigo 36310, Spain.

PMID: 39006420
PMCID: PMC11245079
DOI: 10.1101/2024.07.01.24309632

Dispersal history of SARS-CoV-2 variants Alpha, Delta, and Omicron (BA.1) in Spain

Pilar Gallego-García et al. medRxiv. 2024.

[Preprint]. 2024 Jul 1:2024.07.01.24309632.

doi: 10.1101/2024.07.01.24309632.

Authors

Pilar Gallego-García^{1

2}, Samuel L Hong³, Nena Bollen³, Simon Dellicour^{3

4}, Guy Baele³, Marc A Suchard^{5

6

7}, Philippe Lemey^{3

8}, David Posada^{1

2

9}

Affiliations

¹ CINBIO, Universidade de Vigo, 36310 Vigo, Spain.
² Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO.
³ Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Epidemiological Virology, KU Leuven - University of Leuven, 3000 Leuven, Belgium.
⁴ Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Brussels, Belgium.
⁵ Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA.
⁶ Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.
⁷ Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.
⁸ Global Virus Network (GVN), Baltimore, MD 21201, USA.
⁹ Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, Vigo 36310, Spain.

PMID: 39006420
PMCID: PMC11245079
DOI: 10.1101/2024.07.01.24309632

Update in

International importance and spread of SARS-CoV-2 variants Alpha, Delta, and Omicron BA.1 into Spain.
Gallego-García P, Hong SL, Bollen N, Dellicour S, Baele G, Suchard MA, Lemey P, Posada D. Gallego-García P, et al. Commun Med (Lond). 2025 May 30;5(1):209. doi: 10.1038/s43856-025-00912-9. Commun Med (Lond). 2025. PMID: 40447716 Free PMC article.

Abstract

Different factors influence the spread of SARS-CoV-2, from the inherent transmission capabilities of the different variants to the control measurements put in place. Here we studied the introduction of the Alpha, Delta, and Omicron-BA.1 variants of concern (VOCs) into Spain. For this, we collected genomic data from the GISAID database and combined it with connectivity data from different countries with Spain to perform a phylodynamic Bayesian analysis of the introductions. Our findings reveal that the introductions of these VOCs predominantly originated from France, especially in the case of Alpha. As travel restrictions were eased during the Delta and Omicron-BA.1 waves, the number of introductions from distinct countries increased, with the United Kingdom and Germany becoming significant sources of the virus. The largest number of introductions detected corresponded to the Delta wave, which was associated with fewer restrictions and the summer period, when Spain receives a considerable number of tourists. This research underscores the importance of monitoring international travel patterns and implementing targeted public health measures to manage the spread of SARS-CoV-2.

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Conflict of interest statement

Declaration of interest There are no conflicting interests.

Figures

**Figure 1.. SARS-CoV-2 epidemic waves in Spain from February 2020 to April 2022.**
A) Number of sequences from Spain available in the GISAID database until June 11, 2022. Bar colors represent different lineages or variants, as explained in the legend. B) Number of diagnosed cases (left-axis; black line) and deaths (right-axis; red line) of COVID-19 in Spain. Data taken from OurWorldInData (Mathieu et al., 2020). C) Spain’s Oxford Stringency Index (Hale et al., 2021), representing how strict the measures were in Spain at any given moment (the index represents the response level of the strictest region within Spain). Data taken from OurWorldInData (https://ourworldindata.org/). Shaded areas represent periods in which masks were mandatory outside.

**Figure 2.. SARS-CoV-2 introduction events into Spain.**
Circular migration flow plots based on the Markov jumps between different countries and Spain (A: Alpha; C: Delta; E: Omicron-BA.1). Mean and 95% highest posterior density (HPD) number of transitions from those countries to Spain, computed from all the trees from the posterior distribution (B: Alpha; D: Delta; F: Omicron-BA.1). Codes ISO 3166–2 AD, IN, and US correspond with Andorra, India, and the USA respectively.

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References

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This is a preprint.

Dispersal history of SARS-CoV-2 variants Alpha, Delta, and Omicron (BA.1) in Spain

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Dispersal history of SARS-CoV-2 variants Alpha, Delta, and Omicron (BA.1) in Spain

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