Spain has been one of the main epicenters for Covid-19 in Europe. The country is divided into 17 Autonomous Communities (AC) and two Autonomous Cities (ACi). This study aims to describe the epidemiology of SARS-CoV-2 in Spain across 3 study periods established from the beginning of the pandemic to the third epidemiologic wave, after analyzing genomes from all AC/ACi from February 2020 to March 2021.
All 14,256 available partial and complete Spanish SARS-CoV-2 human genomic sequences deposited in the GISAID repository (https://www.gisaid.org/) until 21 March 2021 were downloaded in nucleotides and classified according to the AC/ACi and to the epidemiological week by collection date. The sequences were assigned to the genetic lineages according to Pangolin COVID-19 Lineage Assigner (https://pangolin.cog-uk.io/). Epiweeks were grouped into three main periods adjusted to the Spanish epidemic curve, as informed in the National Epidemiological Surveillance Network (RENAVE, https://cnecovid.isciii.es). The first period comprised from the beginning of the pandemic to the end of the first state of emergency (June 2020). The second period included the second epidemic wave (June-December 2020), and the third period covered the third wave (December 2020-March 2021). Only AC with at least 10 sequences for each period were described in the results. The two ACi were considered together.
Before the national lockdown (14 March 2020), 11 SARS-CoV-2 lineages were circulating in Spain with A.2 lineage predominance. During the lockdown the SARS-CoV-2 variant diversity increased, decreasing during the confinement. During this period, B.1 was the main circulating variant. During summer 2020, B.1.177 became the main circulating variant. The third wave was characterized by the introduction and fast spread of the B.1.1.7 or Alpha Variant of Concern.
The reduction of diversity during the lockdown suggests this measure was effective in reducing the import of SARS-CoV-2 lineages. After the opening of borders within Europe during summer 2020, the variant diversity increased again and B.1.177 became the predominant variant, suggesting that despite the efforts to avoid SARS-CoV-2 spread between countries, travel restrictions during summer 2020 were not sufficient to control viral spreading. The variant distribution was heterogeneous among the AC and periods, reflecting different incidence and sequencing capacities across AC.