Jan Richter1,2, Pavlos Fanis2,3, Christina Tryfonos1,2, Dana Koptides1,2, George Krashias1,2, Stavros Bashiardes1,2, Andreas Hadjisavvas2,4, Maria Loizidou2,4, Anastasis Oulas2,5, Denise Alexandrou6, Olga Kalakouta6, Mihalis I Panayiotidis2,4, George M Spyrou2,5, Christina Christodoulou1,2. 1. Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus. 2. The Cyprus School of Molecular Medicine, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus. 3. Molecular Genetics, Function & Therapy Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus. 4. Cancer Genetics, Therapeutics & Ultrastructural Pathology Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus. 5. Bioinformatics Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus. 6. Medical and Public Health Services, Ministry of Health, Nicosia, Cyprus.
Abstract
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.
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 siene">nce then 33,567 confirmed cases and 230 n class="Disease">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.
Authors: Emma C Thomson; Laura E Rosen; James G Shepherd; Roberto Spreafico; Ana da Silva Filipe; Jason A Wojcechowskyj; Chris Davis; Luca Piccoli; David J Pascall; Josh Dillen; Spyros Lytras; Nadine Czudnochowski; Rajiv Shah; Marcel Meury; Natasha Jesudason; Anna De Marco; Kathy Li; Jessica Bassi; Aine O'Toole; Dora Pinto; Rachel M Colquhoun; Katja Culap; Ben Jackson; Fabrizia Zatta; Andrew Rambaut; Stefano Jaconi; Vattipally B Sreenu; Jay Nix; Ivy Zhang; Ruth F Jarrett; William G Glass; Martina Beltramello; Kyriaki Nomikou; Matteo Pizzuto; Lily Tong; Elisabetta Cameroni; Tristan I Croll; Natasha Johnson; Julia Di Iulio; Arthur Wickenhagen; Alessandro Ceschi; Aoife M Harbison; Daniel Mair; Paolo Ferrari; Katherine Smollett; Federica Sallusto; Stephen Carmichael; Christian Garzoni; Jenna Nichols; Massimo Galli; Joseph Hughes; Agostino Riva; Antonia Ho; Marco Schiuma; Malcolm G Semple; Peter J M Openshaw; Elisa Fadda; J Kenneth Baillie; John D Chodera; Suzannah J Rihn; Samantha J Lycett; Herbert W Virgin; Amalio Telenti; Davide Corti; David L Robertson; Gyorgy Snell Journal: Cell Date: 2021-01-28 Impact factor: 66.850
Authors: James Hadfield; Colin Megill; Sidney M Bell; John Huddleston; Barney Potter; Charlton Callender; Pavel Sagulenko; Trevor Bedford; Richard A Neher Journal: Bioinformatics Date: 2018-12-01 Impact factor: 6.931
Authors: George Krashias; Elie Deeba; Astero Constantinou; Maria Hadjiagapiou; Dana Koptides; Jan Richter; Christina Tryfonos; Stavros Bashiardes; Anastasia Lambrianides; Maria A Loizidou; Andreas Hadjisavvas; Mihalis I Panayiotidis; Christina Christodoulou Journal: Microorganisms Date: 2021-12-31