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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.
Chrysostomou, Andreas C; Vrancken, Bram; Haralambous, Christos; Alexandrou, Maria; Aristokleous, Antonia; Christodoulou, Christina; Gregoriou, Ioanna; Ioannides, Marios; Kalakouta, Olga; Karagiannis, Christos; Koumbaris, George; Loizides, Charalambos; Mendris, Michail; Papastergiou, Panagiotis; Patsalis, Philippos C; Pieridou, Despo; Richter, Jan; Schmitt, Markus; Shammas, Christos; Stylianou, Dora C; Themistokleous, Giorgos; Lemey, Philippe; Kostrikis, Leondios G.
  • Chrysostomou AC; Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus.
  • Vrancken B; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium.
  • Haralambous C; Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium.
  • Alexandrou M; Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, Nicosia 1148, Cyprus.
  • Aristokleous A; Microbiology Department, Larnaca General Hospital, Larnaca 6301, Cyprus.
  • Christodoulou C; Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus.
  • Gregoriou I; Department of Molecular Virology, Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus.
  • Ioannides M; Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, Nicosia 1148, Cyprus.
  • Kalakouta O; NIPD Genetics, Nicosia 2409, Cyprus.
  • Karagiannis C; Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, Nicosia 1148, Cyprus.
  • Koumbaris G; Microbiology Department, Nicosia General Hospital, Nicosia 2029, Cyprus.
  • Loizides C; NIPD Genetics, Nicosia 2409, Cyprus.
  • Mendris M; NIPD Genetics, Nicosia 2409, Cyprus.
  • Papastergiou P; Microbiology Department, Limassol General Hospital, Limassol 4131, Cyprus.
  • Patsalis PC; Microbiology Department, Limassol General Hospital, Limassol 4131, Cyprus.
  • Pieridou D; NIPD Genetics, Nicosia 2409, Cyprus.
  • Richter J; Medical School, University of Nicosia, Nicosia 2417, Cyprus.
  • Schmitt M; Microbiology Department, Nicosia General Hospital, Nicosia 2029, Cyprus.
  • Shammas C; Department of Molecular Virology, Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus.
  • Stylianou DC; Eurofins Genomics Sequencing Europe, 85560 Ebersberg, Germany.
  • Themistokleous G; S.C.I.N.A Bioanalysis Sciomedical Centre Ltd., Limassol 4040, Cyprus.
  • The Comessar Network; Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus.
  • Lemey P; Microbiology Department, Larnaca General Hospital, Larnaca 6301, Cyprus.
Viruses ; 15(1)2022 Dec 30.
Article in English | MEDLINE | ID: covidwho-2228953
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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Experimental Studies / Observational study / Prognostic study / Randomized controlled trials Topics: Variants Limits: Humans Country/Region as subject: Europa Language: English Year: 2022 Document Type: Article Affiliation country: V15010108

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Experimental Studies / Observational study / Prognostic study / Randomized controlled trials Topics: Variants Limits: Humans Country/Region as subject: Europa Language: English Year: 2022 Document Type: Article Affiliation country: V15010108