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

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.

Molecular epidemiology of SARS-CoV-2 in Cyprus.

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.

Impact assessment of COVID-19 non-pharmaceutical interventions in long term care facilities in Cyprus: Safety improvement strategy.

The current COVID-19 crisis has changed our everyday lives almost in every aspect. Many people worldwide have died or hospitalised due to the severe impact of COVID-19 on the vulnerable population, and in particular to the elderly residents of long term care facilities (LTCF). The problem is amplified due to the fact that many of those occupants also suffer from comorbidities (e.g. respiratory and cardiovascular diseases, hypertension, etc.) and are therefore regarded as a susceptible host to severe COVID-19 disease. Impacts can be felt in the wider societal safety level. The aim of the present study is, therefore, to present the first National multimodal quality and safety improvement strategy plan for the LTCF in the Republic of Cyprus. The current program focused on the intensification of COVID-19 epidemiological surveillance, the promotion of educational training on best practises in infection control and prevention, and the implementation of additional non-pharmaceutical interventions (NPIs), according to the recommendations of ECDC (European Centre for Disease Prevention and Control) and WHO (World Health Organization). This innovative program fostered the interconnectivity and collaboration among the local authorities, academia and the local leaders of the LTCF. In addition, this program reinforced the importance of volunteerism and active participation of medical students in the National initiatives against the COVID-19 pandemic. The effectiveness of the adopted multimodal advanced care-safety planning program is appraised based on the reported new confirmed COVID-19 cases among LTCF healthcare workers and occupants, after the introducing and implementation of the selected NPIs. This multimodal strategy plan seems to be capable of reducing significantly the number of new cases of COVID-19 infections in LTCF and as a result, to also affect the residents' death number.