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. 2022 Aug 23;10(9):1688.
doi: 10.3390/microorganisms10091688.

Introduction, Spread and Impact of the SARS-CoV-2 Omicron Variants BA.1 and BA.2 in Cyprus

Jan Richter  1 , Dana Koptides  1 , Christina Tryfonos  1 , Denise Alexandrou  2 , Christina Christodoulou  1
Affiliations

Introduction, Spread and Impact of the SARS-CoV-2 Omicron Variants BA.1 and BA.2 in Cyprus

Jan Richter et al. Microorganisms. .

Abstract

The aim of this study was to investigate and obtain insights into the appearance, spread and impact of the Omicron variants and their sub-lineages in Cyprus by analyzing 611 high-coverage full-genome sequences for the period from November 2021 until April 2022. All viruses sequenced were identified to belong to either Delta (B.1.617.2) or Omicron (lineage BA.1 and BA.2, respectively), with a variety of different sub-lineages. A detailed analysis of the mutational profile is presented and discussed. The Omicron variant BA.1 was shortly followed by BA.2; despite emerging against a background of high vaccination (81% of adult population) and pre-existing natural immunity, they gave rise to the largest waves of infection, with daily numbers rising dramatically, highlighting their increased ability for immune evasion. Within a period of only five months, the percentage of the Cypriot population with a confirmed infection increased from ~15% of the total population to >57%. Despite unprecedented case numbers, a significant reduction in hospital burden and mortality was observed. Our findings highlight the role of the importation of new variants through travel 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.

Keywords: COVID-19; Cyprus; Omicron; SARS-CoV-2; epidemiology; whole-genome sequencing.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Number of daily positive SARS-CoV-2 cases as well as the number of recorded COVID-19-associated deaths in Cyprus since the detection of the first case in March 2020 until April 2022 (https://www.data.gov.cy/, accessed on 30 May 2022).
Figure 2
Figure 2
Bubble chart illustrating the weekly frequency of SARS-CoV-2 sub-lineages over time. The size of the circle is proportional to the percentage of each sub-lineage detected each week.
Figure 3
Figure 3
Phylogenetic tree of Cypriot full-genome sequences (n = 611) analyzed between November 2021 and April 2022 aligned against the reference genome hCoV-19/Wuhan/Hu-1/2019 (NC_045512.2). Bootstrap values >80% indicate the percentages of replicate trees, in which the associated taxa clustered together in the ultrafast bootstrap test (1000 replicates) are indicated by blue circles.
Figure 4
Figure 4
Time course of the frequency of the SARS-CoV-2 VOC identified in Cyprus in relation to the number of daily positive cases recorded between November 2021 and April 2022.
See this image and copyright information in PMC

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