Molecular Epidemiology of SARS-CoV-2 in 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-CoV2 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.

In depth analysis of Cyprus-specific mutations of SARS-CoV-2 strains using computational approaches

“…This work was based on the analysis of a small number (N=144) of viral strains from the Cypriot population. To this end we initially perform basic phylogenetic and lineage analysis as previously reported for these samples [9]. We extend previous work by selecting for 18 Cyprus-specific mutations exhibiting a high frequency of occurrence that is unique to Cyprus compared to the rest of the world.…”

“…Multiple national studies have been undertaken by a plethora of countries throughout the world, in order to generate and analyse high throughput sequencing country-specific data for SARs-CoV-2 strains [1–8]. Recently, the Cyprus Institute of Neurology and Genetics (CING) also published a study based on 144 NGS samples obtained from the Cypriot population representing the first documented genomic and epidemiological characterization of these samples [9]. In this study we expand on this work, by initially performing basic lineage analysis, as previously reported [9], to identify the dominant SARS-CoV-2 lineage(s) in Cyprus as well as a phylogenetic tree analysis to map the Cypriot strains against other strains present throughout the world.…”

“…Recently, the Cyprus Institute of Neurology and Genetics (CING) also published a study based on 144 NGS samples obtained from the Cypriot population representing the first documented genomic and epidemiological characterization of these samples [9]. In this study we expand on this work, by initially performing basic lineage analysis, as previously reported [9], to identify the dominant SARS-CoV-2 lineage(s) in Cyprus as well as a phylogenetic tree analysis to map the Cypriot strains against other strains present throughout the world. We further perform a more thorough, in depth genomic analysis of these samples by implementing variant-calling and displaying an overview of the genomic variation and reported frequencies in the Cypriot strains.…”