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-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.

Fig 1. Daily number of positive SARS-CoV-2 cases in Cyprus identified between March 2020 and January 2021 (https://covid19.ucy.ac.cy/).

The start of the implementation as well as the lifting of important governmental pandemic control measures are indicated.

Fig 2. Bubble chart illustrating the pattern of SARS-CoV-2 lineages identified per month.

The size of the circle is proportional to the number of samples.

Fig 3. Phylogenetic analysis of full genome sequences of 133 Cypriot strains aligned against the reference genome hCoV-19/Wuhan/Hu-1/2019 (NC_045512.2).

Sample names consist of internal laboratory code followed by the date of sampling. The percentages of replicate trees in which the associated taxa clustered together in the standard bootstrap test (1000 replicates) are shown next to the branches. Only bootstrap values >70% are shown.