Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus from November 2020 to October 2021: The Passage of Waves of Alpha and Delta Variants of Concern

Viruses. 2022 Dec 30;15(1):108. doi: 10.3390/v15010108.

Abstract

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019 resulted in the coronavirus disease 2019 (COVID-19) pandemic, which has had devastating repercussions for public health. Over the course of this pandemic, the virus has continuously been evolving, resulting in new, more infectious variants that have frequently led to surges of new SARS-CoV-2 infections. In the present study, we performed detailed genetic, phylogenetic, phylodynamic and phylogeographic analyses to examine the SARS-CoV-2 epidemic in Cyprus using 2352 SARS-CoV-2 sequences from infected individuals in Cyprus during November 2020 to October 2021. During this period, a total of 61 different lineages and sublineages were identified, with most falling into three groups: B.1.258 & sublineages, Alpha (B.1.1.7 & Q. sublineages), and Delta (B.1.617.2 & AY. sublineages), each encompassing a set of S gene mutations that primarily confer increased transmissibility as well as immune evasion. Specifically, these lineages were coupled with surges of new infections in Cyprus, resulting in the following: the second wave of SARS-CoV-2 infections in Cyprus, comprising B.1.258 & sublineages, during late autumn 2020/beginning of winter 2021; the third wave, comprising Alpha (B.1.1.7 & Q. sublineages), during spring 2021; and the fourth wave, comprising Delta (B.1.617.2 & AY. sublineages) during summer 2021. Additionally, it was identified that these lineages were primarily imported from and exported to the UK, Greece, and Sweden; many other migration links were also identified, including Switzerland, Denmark, Russia, and Germany. Taken together, the results of this study indicate that the SARS-CoV-2 epidemic in Cyprus was characterized by successive introduction of new lineages from a plethora of countries, resulting in the generation of waves of infection. Overall, this study highlights the importance of investigating the spatiotemporal evolution of the SARS-CoV-2 epidemic in the context of Cyprus, as well as the impact of protective measures placed to mitigate transmission of the virus, providing necessary information to safeguard public health.

Keywords: COVID-19; Cyprus; SARS-CoV-2; molecular epidemiology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • COVID-19* / epidemiology
  • Cyprus / epidemiology
  • Genomics
  • Humans
  • Pandemics
  • Phylogeny
  • SARS-CoV-2* / genetics

Supplementary concepts

  • SARS-CoV-2 variants

Grants and funding

This work was co-funded by the Ministry of Health of the Republic of Cyprus, the University of Cyprus and the Cyprus Academy of Sciences, Letters, and Arts through research funds awarded to Leondios G. Kostrikis. Bram Vrancken was supported by a postdoctoral grant (12U7121N) of the Research Foundation—Flanders (Fonds voor Wetenschappelijk Onderzoek). Philippe Lemey acknowledges support from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725422—ReservoirDOCS), the EU grant 874850 MOOD and from the Research Foundation—Flanders (‘Fonds voor Wetenschappelijk Onderzoek—Vlaanderen’, G066215N, G0D5117N and G0B9317N).