Molecular epidemiology of SARS-CoV-2 in Cyprus.
Whole genome sequencing of viral specimens following molecular diagnosis is a powerful analytical tool of molecular epidemiology that can critically assist in resolving chains of transmission, identifying of new variants or assessing pathogen evolution and allows a real-time view into the dynamics o...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2021-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0248792 |
| _version_ | 1819012520623472640 |
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| author | Jan Richter Pavlos Fanis Christina Tryfonos Dana Koptides George Krashias Stavros Bashiardes Andreas Hadjisavvas Maria Loizidou Anastasis Oulas Denise Alexandrou Olga Kalakouta Mihalis I Panayiotidis George M Spyrou Christina Christodoulou |
| author_facet | Jan Richter Pavlos Fanis Christina Tryfonos Dana Koptides George Krashias Stavros Bashiardes Andreas Hadjisavvas Maria Loizidou Anastasis Oulas Denise Alexandrou Olga Kalakouta Mihalis I Panayiotidis George M Spyrou Christina Christodoulou |
| author_sort | Jan Richter |
| collection | DOAJ |
| description | Whole genome sequencing of viral specimens following molecular diagnosis is a powerful analytical tool of molecular epidemiology that can critically assist in resolving chains of transmission, identifying of new variants or assessing pathogen evolution and allows a real-time view into the dynamics of a pandemic. In Cyprus, the first two cases of COVID-19 were identified on March 9, 2020 and since then 33,567 confirmed cases and 230 deaths were documented. In this study, viral whole genome sequencing was performed on 133 SARS-CoV-2 positive samples collected between March 2020 and January 2021. Phylogenetic analysis was conducted to evaluate the genomic diversity of circulating SARS-CoV-2 lineages in Cyprus. 15 different lineages were identified that clustered into three groups associated with the spring, summer and autumn/winter wave of SARS-CoV-2 incidence in Cyprus, respectively. The majority of the Cypriot samples belonged to the B.1.258 lineage first detected in September that spread rapidly and largely dominated the autumn/winter wave with a peak prevalence of 86% during the months of November and December. The B.1.1.7 UK variant (VOC-202012/01) was identified for the first time at the end of December and spread rapidly reaching 37% prevalence within one month. Overall, we describe the changing pattern of circulating SARS-CoV-2 lineages in Cyprus since the beginning of the pandemic until the end of January 2021. These findings highlight the role of importation of new variants through travel towards the emergence of successive waves of incidence in Cyprus and demonstrate the importance of genomic surveillance in determining viral genetic diversity and the timely identification of new variants for guiding public health intervention measures. |
| first_indexed | 2024-12-21T01:45:22Z |
| format | Article |
| id | doaj.art-575849ed4506438aa08b64729e613158 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-21T01:45:22Z |
| publishDate | 2021-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-575849ed4506438aa08b64729e6131582022-12-21T19:20:02ZengPublic Library of Science (PLoS)PLoS ONE1932-62032021-01-01167e024879210.1371/journal.pone.0248792Molecular epidemiology of SARS-CoV-2 in Cyprus.Jan RichterPavlos FanisChristina TryfonosDana KoptidesGeorge KrashiasStavros BashiardesAndreas HadjisavvasMaria LoizidouAnastasis OulasDenise AlexandrouOlga KalakoutaMihalis I PanayiotidisGeorge M SpyrouChristina ChristodoulouWhole genome sequencing of viral specimens following molecular diagnosis is a powerful analytical tool of molecular epidemiology that can critically assist in resolving chains of transmission, identifying of new variants or assessing pathogen evolution and allows a real-time view into the dynamics of a pandemic. In Cyprus, the first two cases of COVID-19 were identified on March 9, 2020 and since then 33,567 confirmed cases and 230 deaths were documented. In this study, viral whole genome sequencing was performed on 133 SARS-CoV-2 positive samples collected between March 2020 and January 2021. Phylogenetic analysis was conducted to evaluate the genomic diversity of circulating SARS-CoV-2 lineages in Cyprus. 15 different lineages were identified that clustered into three groups associated with the spring, summer and autumn/winter wave of SARS-CoV-2 incidence in Cyprus, respectively. The majority of the Cypriot samples belonged to the B.1.258 lineage first detected in September that spread rapidly and largely dominated the autumn/winter wave with a peak prevalence of 86% during the months of November and December. The B.1.1.7 UK variant (VOC-202012/01) was identified for the first time at the end of December and spread rapidly reaching 37% prevalence within one month. Overall, we describe the changing pattern of circulating SARS-CoV-2 lineages in Cyprus since the beginning of the pandemic until the end of January 2021. These findings highlight the role of importation of new variants through travel towards the emergence of successive waves of incidence in Cyprus and demonstrate the importance of genomic surveillance in determining viral genetic diversity and the timely identification of new variants for guiding public health intervention measures.https://doi.org/10.1371/journal.pone.0248792 |
| spellingShingle | Jan Richter Pavlos Fanis Christina Tryfonos Dana Koptides George Krashias Stavros Bashiardes Andreas Hadjisavvas Maria Loizidou Anastasis Oulas Denise Alexandrou Olga Kalakouta Mihalis I Panayiotidis George M Spyrou Christina Christodoulou Molecular epidemiology of SARS-CoV-2 in Cyprus. PLoS ONE |
| title | Molecular epidemiology of SARS-CoV-2 in Cyprus. |
| title_full | Molecular epidemiology of SARS-CoV-2 in Cyprus. |
| title_fullStr | Molecular epidemiology of SARS-CoV-2 in Cyprus. |
| title_full_unstemmed | Molecular epidemiology of SARS-CoV-2 in Cyprus. |
| title_short | Molecular epidemiology of SARS-CoV-2 in Cyprus. |
| title_sort | molecular epidemiology of sars cov 2 in cyprus |
| url | https://doi.org/10.1371/journal.pone.0248792 |
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