Carla López-Causapé 1, 2, Pablo A Fraile-Ribot 1, 2, Santiago Jiménez-Serrano 1 , Gabriel Cabot 1, 2, Ester Del Barrio-Tofiño 1, 2, M Carmen Prado 1, Juana María Linares 1, Aranzazu López 4, Adoración Hurtado 4, Elena Riera 5, Antoni Serra 5, Eva Roselló 6, Lluis Carbó 6, M Victoria Fernández-Baca 7, Carmen Gallegos 7, Juan Saurina 8, Emilio Arteaga 8, M Magdalena Salom 9, Antonia Salvá 10, Antoni Nicolau 9, Fernando González-Candelas 11, 12, Iñaki Comas 3, 12, Antonio Oliver 1, 2
1 Servicio de Microbiología and Unidad de Investigación, Hospital Universitari Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain.
2 CIBER en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain.
3 Instituto de Biomedicina de Valencia, Valencia, Spain.
4 Servicio de Microbiología, Hospital Can Misses, Ibiza, Spain.
5 Servicio de Microbiología, Hospital de Manacor, Manacor, Spain.
6 Servicio de Microbiología, Hospital Mateu Orfila, Mahón, Spain.
7 Servicio de Microbiología, Hospital Universitari Son Llàtzer, Palma, Spain.
8 Servicio de Microbiología, Hospital Comarcal de Inca, Inca, Spain.
9 Servicio de Epidemiología de las Islas Baleares, Palma, Spain.
10 Gabinete Técnico-Asistencial, Servicio de Salud de las Islas Baleares, Palma, Spain.
11 Unidad Mixta de Investigación «Infección y Salud Pública» FISABIO-Universidad de Valencia, Instituto de Biología Integrativa de Sistemas (I2SysBIO, CSIC-UV), Valencia, Spain.
12 CIBER en Epidemiología y Salud Publica (CIBERESP), Madrid, Spain.
Abstract:
Objective: To analyze the SARS-CoV-2 genomic epidemiology in the Balearic Islands, a unique setting in which the course of the pandemic has been influenced by a complex interplay between insularity, severe social restrictions and tourism travels.
Methods: Since the onset of the pandemic, more than 2,700 SARS-CoV-2 positive respiratory samples have been randomly selected and sequenced in the Balearic Islands. Genetic diversity of circulating variants was assessed by lineage assignment of consensus whole genome sequences with PANGOLIN and investigation of additional spike mutations.
Results: Consensus sequences were assigned to 46 different PANGO lineages and 75% of genomes were classified within a VOC, VUI, or VUM variant according to the WHO definitions. Highest genetic diversity was documented in the island of Majorca (42 different lineages detected). Globally, lineages B.1.1.7 and B.1.617.2/AY.X were identified as the 2 major lineages circulating in the Balearic Islands during the pandemic, distantly followed by lineages B.1.177/B.1.177.X. However, in Ibiza/Formentera lineage distribution was slightly different and lineage B.1.221 was the third most prevalent. Temporal distribution analysis showed that B.1 and B.1.5 lineages dominated the first epidemic wave, lineage B.1.177 dominated the second and third, and lineage B.1.617.2 the fourth. Of note, lineage B.1.1.7 became the most prevalent circulating lineage during first half of 2021; however, it was not associated with an increased in COVID-19 cases likely due to severe social restrictions and limited travels. Additional spike mutations were rarely documented with the exception of mutation S:Q613H which has been detected in several genomes (n = 25) since July 2021.
Conclusion: Virus evolution, mainly driven by the acquisition and selection of spike substitutions conferring biological advantages, social restrictions, and size population are apparently key factors for explaining the epidemic patterns registered in the Balearic Islands.
Front Microbiol. 2022 Jan 12;12:803827. doi: 10.3389/fmicb.2021.803827.
Link to Frontiers in Microbiology