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. 2022 Jan 12:12:803827.
doi: 10.3389/fmicb.2021.803827. eCollection 2021.

A Genomic Snapshot of the SARS-CoV-2 Pandemic in the Balearic Islands

Carla López-Causapé  1   2 , Pablo A Fraile-Ribot  1   2 , Santiago Jiménez-Serrano  3 , 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
Affiliations

A Genomic Snapshot of the SARS-CoV-2 Pandemic in the Balearic Islands

Carla López-Causapé et al. Front Microbiol. .

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.

Keywords: SARS-CoV-2; genomic epidemiology; genomic evolution; spike mutations; variants.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Number of new reported cases and samples selected for sequencing by epidemiological week. Epidemic waves in the Balearic Islands are indicated in colors: dark blue (1st epidemic wave), purple (2nd epidemic wave), orange (3rd epidemic wave), and light blue (4th epidemic wave).
FIGURE 2
FIGURE 2
Geographical distribution of the 10 most frequently detected PANGO lineages. Most frequent lineages detected in (A) the Balearic Islands, (B) Menorca, (C) Ibiza/Formentera, and (D) Majorca are shown.
FIGURE 3
FIGURE 3
Temporal evolution of SARS-CoV-2 lineages. Lineage distribution in each of the epidemic waves (and intermediate periods) registered in the Balearic Islands.
See this image and copyright information in PMC

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