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
Andreas C. Chrysostomou,
Bram Vrancken,
Christos Haralambous,
Maria Alexandrou,
Antonia Aristokleous,
Christina Christodoulou,
Ioanna Gregoriou,
Marios Ioannides,
Olga Kalakouta,
Christos Karagiannis,
George Koumbaris,
Charalambos Loizides,
Michail Mendris,
Panagiotis Papastergiou,
Philippos C. Patsalis,
Despo Pieridou,
Jan Richter,
Markus Schmitt,
Christos Shammas,
Dora C. Stylianou,
Giorgos Themistokleous,
the COMESSAR Network,
Philippe Lemey,
Leondios G. Kostrikis
Affiliations
Andreas C. Chrysostomou
Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus
Bram Vrancken
Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
Christos Haralambous
Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, Nicosia 1148, Cyprus
Maria Alexandrou
Microbiology Department, Larnaca General Hospital, Larnaca 6301, Cyprus
Antonia Aristokleous
Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus
Christina Christodoulou
Department of Molecular Virology, Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
Ioanna Gregoriou
Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, Nicosia 1148, Cyprus
Marios Ioannides
NIPD Genetics, Nicosia 2409, Cyprus
Olga Kalakouta
Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, Nicosia 1148, Cyprus
Christos Karagiannis
Microbiology Department, Nicosia General Hospital, Nicosia 2029, Cyprus
George Koumbaris
NIPD Genetics, Nicosia 2409, Cyprus
Charalambos Loizides
NIPD Genetics, Nicosia 2409, Cyprus
Michail Mendris
Microbiology Department, Limassol General Hospital, Limassol 4131, Cyprus
Panagiotis Papastergiou
Microbiology Department, Limassol General Hospital, Limassol 4131, Cyprus
Philippos C. Patsalis
NIPD Genetics, Nicosia 2409, Cyprus
Despo Pieridou
Microbiology Department, Nicosia General Hospital, Nicosia 2029, Cyprus
Jan Richter
Department of Molecular Virology, Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
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.
