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Article

A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic

1
Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus
2
Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
3
NIPD Genetics Limited, Nicosia 2409, Cyprus
4
Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, Paralimni 5386, Cyprus
5
Department of Health and Safety, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus
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Center for Global Health and Tropical Medicine, Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, 1349-008 Lisbon, Portugal
7
Medical School, University of Nicosia, Nicosia 2417, Cyprus
*
Author to whom correspondence should be addressed.
Academic Editor: Vittorio Sambri
Viruses 2021, 13(6), 1098; https://doi.org/10.3390/v13061098
Received: 6 May 2021 / Revised: 28 May 2021 / Accepted: 4 June 2021 / Published: 9 June 2021
(This article belongs to the Special Issue State-of-the-Art Emerging Respiratory Viruses in Europe)
The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resulted in an extraordinary global public health crisis. In early 2020, Cyprus, among other European countries, was affected by the SARS-CoV-2 epidemic and adopted lockdown measures in March 2020 to limit the initial outbreak on the island. In this study, we performed a comprehensive retrospective molecular epidemiological analysis (genetic, phylogenetic, phylodynamic and phylogeographic analyses) of SARS-CoV-2 isolates in Cyprus from April 2020 to January 2021, covering the first ten months of the SARS-CoV-2 infection epidemic on the island. The primary aim of this study was to assess the transmissibility of SARS-CoV-2 lineages in Cyprus. Whole SARS-CoV-2 genomic sequences were generated from 596 clinical samples (nasopharyngeal swabs) obtained from community-based diagnostic testing centers and hospitalized patients. The phylogenetic analyses revealed a total of 34 different lineages in Cyprus, with B.1.258, B.1.1.29, B.1.177, B.1.2, B.1 and B.1.1.7 (designated a Variant of Concern 202012/01, VOC) being the most prevalent lineages on the island during the study period. Phylodynamic analysis showed a highly dynamic epidemic of SARS-CoV-2 infection, with three consecutive surges characterized by specific lineages (B.1.1.29 from April to June 2020; B.1.258 from September 2020 to January 2021; and B.1.1.7 from December 2020 to January 2021). Genetic analysis of whole SARS-CoV-2 genomic sequences of the aforementioned lineages revealed the presence of mutations within the S protein (L18F, ΔH69/V70, S898F, ΔY144, S162G, A222V, N439K, N501Y, A570D, D614G, P681H, S982A and D1118H) that confer higher transmissibility and/or antibody escape (immune evasion) upon the virus. Phylogeographic analysis indicated that the majority of imports and exports were to and from the United Kingdom (UK), although many other regions/countries were identified (southeastern Asia, southern Europe, eastern Europe, Germany, Italy, Brazil, Chile, the USA, Denmark, the Czech Republic, Slovenia, Finland, Switzerland and Pakistan). Taken together, these findings demonstrate that the SARS-CoV-2 infection epidemic in Cyprus is being maintained by a continuous influx of lineages from many countries, resulting in the establishment of an ever-evolving and polyphyletic virus on the island. View Full-Text
Keywords: SARS-CoV-2; Covid-19; Cyprus; molecular epidemiology SARS-CoV-2; Covid-19; Cyprus; molecular epidemiology
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MDPI and ACS Style

Chrysostomou, A.C.; Vrancken, B.; Koumbaris, G.; Themistokleous, G.; Aristokleous, A.; Masia, C.; Eleftheriou, C.; Iοannou, C.; Stylianou, D.C.; Ioannides, M.; Petrou, P.; Georgiou, V.; Hatziyianni, A.; Lemey, P.; Vandamme, A.-M.; Patsalis, P.P.; Kostrikis, L.G. A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. Viruses 2021, 13, 1098. https://doi.org/10.3390/v13061098

AMA Style

Chrysostomou AC, Vrancken B, Koumbaris G, Themistokleous G, Aristokleous A, Masia C, Eleftheriou C, Iοannou C, Stylianou DC, Ioannides M, Petrou P, Georgiou V, Hatziyianni A, Lemey P, Vandamme A-M, Patsalis PP, Kostrikis LG. A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. Viruses. 2021; 13(6):1098. https://doi.org/10.3390/v13061098

Chicago/Turabian Style

Chrysostomou, Andreas C., Bram Vrancken, George Koumbaris, George Themistokleous, Antonia Aristokleous, Christina Masia, Christina Eleftheriou, Costakis Iοannou, Dora C. Stylianou, Marios Ioannides, Panagiotis Petrou, Vasilis Georgiou, Amalia Hatziyianni, Philippe Lemey, Anne-Mieke Vandamme, Philippos P. Patsalis, and Leondios G. Kostrikis. 2021. "A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic" Viruses 13, no. 6: 1098. https://doi.org/10.3390/v13061098

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