{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T16:21:40Z","timestamp":1761582100982,"version":"build-2065373602"},"reference-count":82,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2021,6,9]],"date-time":"2021-06-09T00:00:00Z","timestamp":1623196800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Regional Development Fund and the Republic of Cyprus through the Cyprus Research and Innovation Foundation and the Structural Funds 2021-2027","award":["Project: CONCEPT-COVID_0420_0024"],"award-info":[{"award-number":["Project: CONCEPT-COVID_0420_0024"]}]},{"DOI":"10.13039\/100012996","name":"University of Cyprus","doi-asserted-by":"publisher","award":["Research Saves Lives campaign"],"award-info":[{"award-number":["Research Saves Lives campaign"]}],"id":[{"id":"10.13039\/100012996","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>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, \u0394H69\/V70, S898F, \u0394Y144, 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.<\/jats:p>","DOI":"10.3390\/v13061098","type":"journal-article","created":{"date-parts":[[2021,6,9]],"date-time":"2021-06-09T04:22:22Z","timestamp":1623212542000},"page":"1098","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["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"],"prefix":"10.3390","volume":"13","author":[{"given":"Andreas C.","family":"Chrysostomou","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6547-5283","authenticated-orcid":false,"given":"Bram","family":"Vrancken","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"George","family":"Koumbaris","sequence":"additional","affiliation":[{"name":"NIPD Genetics Limited, Nicosia 2409, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"George","family":"Themistokleous","sequence":"additional","affiliation":[{"name":"Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, Paralimni 5386, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Antonia","family":"Aristokleous","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christina","family":"Masia","sequence":"additional","affiliation":[{"name":"Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, Paralimni 5386, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christina","family":"Eleftheriou","sequence":"additional","affiliation":[{"name":"Department of Health and Safety, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Costakis","family":"I\u03bfannou","sequence":"additional","affiliation":[{"name":"Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, Paralimni 5386, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dora C.","family":"Stylianou","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marios","family":"Ioannides","sequence":"additional","affiliation":[{"name":"NIPD Genetics Limited, Nicosia 2409, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5104-579X","authenticated-orcid":false,"given":"Panagiotis","family":"Petrou","sequence":"additional","affiliation":[{"name":"Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, Paralimni 5386, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2342-5226","authenticated-orcid":false,"given":"Vasilis","family":"Georgiou","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9482-4024","authenticated-orcid":false,"given":"Amalia","family":"Hatziyianni","sequence":"additional","affiliation":[{"name":"Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, Paralimni 5386, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Philippe","family":"Lemey","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6594-2766","authenticated-orcid":false,"given":"Anne-Mieke","family":"Vandamme","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium"},{"name":"Center for Global Health and Tropical Medicine, Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, 1349-008 Lisbon, Portugal"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Philippos P.","family":"Patsalis","sequence":"additional","affiliation":[{"name":"NIPD Genetics Limited, Nicosia 2409, Cyprus"},{"name":"Medical School, University of Nicosia, Nicosia 2417, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5340-7109","authenticated-orcid":false,"given":"Leondios G.","family":"Kostrikis","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2021,6,9]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1016\/S0140-6736(20)30251-8","article-title":"Genomic characterisation and epidemiology of 2019 novel coronavirus: 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