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

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.

Detection of Circulating SARS-CoV-2 Variants of Concern (VOCs) Using a Multiallelic Spectral Genotyping Assay

“…In addition to the EVAg panel of reference samples, the assay was tested using clinical samples ( Table 2 ) that were derived from the study of the Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus ([ 66 ] and manuscript in preparation for publication), which were collected under the ongoing collaboration between our laboratory (BMV UCY), the Ministry of Health, NIPD Genetics, and the other members of the Cypriot Comprehensive Molecular Epidemiological Study on SARS-CoV-2 (COMESSAR) Network. Bioethical approval for the use of these samples was granted by the Cyprus National Bioethics Committee (EEBK 21.1.04.43.01).…”

“…b The panel of freeze-dried SARS-CoV-2 variants grown in cell culture and the purified RNA of Coronavirus strain BetaCoV/Germany/BavPat1/2020 p.1 grown in cell culture were received from the EVAg (European Virus Archive goes Global) Organization. c The clinical samples that were selected to be tested by the present assay are part of the study of the Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus ([ 66 ] and manuscript in preparation for publication), which were collected under the ongoing collaboration between the BMV UCY and the Ministry of Health. Bioethical approval was received by the Cyprus National Bioethics Committee (EEBK 21.1.04.43.01) for the use of these samples.…”

Unraveling the Dynamics of Omicron (BA.1, BA.2, and BA.5) Waves and Emergence of the Deltacron Variant: Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus (Oct 2021–Oct 2022)

“…Sample collection, RNA extraction, and SARS-CoV-2 real-time RT-PCR were performed as explained in our previously published studies [ 24 , 25 ]. In brief, nasopharyngeal and/or oropharyngeal swab samples in transport medium were collected or received by medical facilities situated in Cyprus for diagnostic purposes.…”

“…The insights gained have been instrumental in informing public health responses to the pandemic [ 18 , 19 , 20 , 21 , 22 , 23 ]. In Cyprus, the impact of SARS-CoV-2 has been diligently studied since the early stages of the COVID-19 pandemic from April 2020 to October 2021 [ 24 , 25 ]. During this period, four consecutive waves of SARS-CoV-2 infections were identified, represented by specific lineages.…”

“…The first wave was represented by B.1.1 (specifically B.1.1.29), prevalent from April to June 2020, and the second wave, with B.1.258 and sublineages, was from September 2020 to January 2021. The waves that followed were represented by VOCs, with the third wave being characterized by the Alpha variant and sublineages, prevalent from February to May 2021, while the fourth wave was characterized by the Delta variant and sublineages, prevalent from June to September 2021 [ 24 , 25 ].…”