International importance and spread of SARS-CoV-2 variants Alpha, Delta, and Omicron BA.1 into Spain

Abstract

Background: The spread of SARS-CoV-2 has been influenced by multiple factors, from the inherent transmission capabilities of the different variants to the control measurements put in place. Understanding how new variants enter a country is essential for managing future outbreaks. This study investigates how three major variants-Alpha, Delta, and Omicron (BA.1)-entered Spain and how different restrictions potentially affected their introduction.

Methods: We collected Spanish and international SARS-CoV-2 genomes from the GISAID database. Leveraging connectivity data from different countries with Spain, we performed a phylodynamic Bayesian analysis of the SARS-CoV-2 introductions into Spain.

Results: Most introductions of the Alpha variant originated from France. As travel restrictions eased, the number of introductions from different countries increased. During the Delta and Omicron waves, the United Kingdom and Germany became important sources of the virus. The highest number of introductions occurred during the Delta wave, coinciding with fewer travel restrictions and the summer season, when Spain receives a considerable number of tourists.

Conclusions: Our findings highlight the role of international travel in the spread of new variants. They underscore the importance of monitoring travel patterns and implementing targeted public health measures to manage the spread of SARS-CoV-2.

Fig. 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. Shaded areas represent the periods studied for each wave. b Number of diagnosed cases (left-axis; black line) and deaths (right-axis; red line) of COVID-19 in Spain. Data taken from OurWorldInData. c Spain’s Oxford Stringency Index, 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/) which adapted the original data collected by the Oxford Covid-19 Government Response Tracker (OxCGRT). Shaded areas represent periods in which masks were mandatory outside.

Fig. 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 number of transitions from those countries to Spain, computed from all the trees from the posterior distribution. The error bars represent the 95% highest posterior density (HPD). The width of the violin plots represents the density of observations, derived from 638 M, 794 M, and 1388 M generations for Alpha, Delta, and Omicron-BA.1, respectively (b: Alpha; d: Delta; f: Omicron-BA.1). Codes ISO 3166-2 AD, IN, UK, and US correspond with Andorra, India, the United Kingdom and the United States of America, respectively.