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)
Author:
Chrysostomou Andreas1ORCID, Vrancken Bram23ORCID, Haralambous Christos4, Alexandrou Maria5, Gregoriou Ioanna4, Ioannides Marios6, Ioannou Costakis7, Kalakouta Olga4, Karagiannis Christos8, Marcou Markella9, Masia Christina7, Mendris Michail10, Papastergiou Panagiotis10, Patsalis Philippos611, Pieridou Despo8, Shammas Christos12, Stylianou Dora1, Zinieri Barbara13, Lemey Philippe2, Kostrikis Leondios114ORCID,
Affiliation:
1. Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus 2. Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium 3. Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium 4. Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, 1148 Nicosia, Cyprus 5. Microbiology Department, Larnaca General Hospital, 6301 Larnaca, Cyprus 6. Medicover Genetics, 2409 Nicosia, Cyprus 7. Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, 5310 Paralimni, Cyprus 8. Microbiology Department, Nicosia General Hospital, 2029 Nicosia, Cyprus 9. Department of Microbiology, Archbishop Makarios III Hospital, 2012 Nicosia, Cyprus 10. Microbiology Department, Limassol General Hospital, 4131 Limassol, Cyprus 11. Medical School, University of Nicosia, 2417 Nicosia, Cyprus 12. S.C.I.N.A. Bioanalysis Sciomedical Centre Ltd., 4040 Limassol, Cyprus 13. Microbiology Department, Paphos General Hospital, Achepans, 8026 Paphos, Cyprus 14. Cyprus Academy of Sciences, Letters, and Arts, 60-68 Phaneromenis Street, 1011 Nicosia, Cyprus
Abstract
Commencing in December 2019 with the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), three years of the coronavirus disease 2019 (COVID-19) pandemic have transpired. The virus has consistently demonstrated a tendency for evolutionary adaptation, resulting in mutations that impact both immune evasion and transmissibility. This ongoing process has led to successive waves of infections. This study offers a comprehensive assessment spanning genetic, phylogenetic, phylodynamic, and phylogeographic dimensions, focused on the trajectory of the SARS-CoV-2 epidemic in Cyprus. Based on a dataset comprising 4700 viral genomic sequences obtained from affected individuals between October 2021 and October 2022, our analysis is presented. Over this timeframe, a total of 167 distinct lineages and sublineages emerged, including variants such as Delta and Omicron (1, 2, and 5). Notably, during the fifth wave of infections, Omicron subvariants 1 and 2 gained prominence, followed by the ascendancy of Omicron 5 in the subsequent sixth wave. Additionally, during the fifth wave (December 2021–January 2022), a unique set of Delta sequences with genetic mutations associated with Omicron variant 1, dubbed “Deltacron”, was identified. The emergence of this phenomenon initially evoked skepticism, characterized by concerns primarily centered around contamination or coinfection as plausible etiological contributors. These hypotheses were predominantly disseminated through unsubstantiated assertions within the realms of social and mass media, lacking concurrent scientific evidence to validate their claims. Nevertheless, the exhaustive molecular analyses presented in this study have demonstrated that such occurrences would likely lead to a frameshift mutation—a genetic aberration conspicuously absent in our provided sequences. This substantiates the accuracy of our initial assertion while refuting contamination or coinfection as potential etiologies. Comparable observations on a global scale dispelled doubt, eventually leading to the recognition of Delta-Omicron variants by the scientific community and their subsequent monitoring by the World Health Organization (WHO). As our investigation delved deeper into the intricate dynamics of the SARS-CoV-2 epidemic in Cyprus, a discernible pattern emerged, highlighting the major role of international connections in shaping the virus’s local trajectory. Notably, the United States and the United Kingdom were the central conduits governing the entry and exit of the virus to and from Cyprus. Moreover, notable migratory routes included nations such as Greece, South Korea, France, Germany, Brazil, Spain, Australia, Denmark, Sweden, and Italy. These empirical findings underscore that the spread of SARS-CoV-2 within Cyprus was markedly influenced by the influx of new, highly transmissible variants, triggering successive waves of infection. This investigation elucidates the emergence of new waves of infection subsequent to the advent of highly contagious and transmissible viral variants, notably characterized by an abundance of mutations localized within the spike protein. Notably, this discovery decisively contradicts the hitherto hypothesis of seasonal fluctuations in the virus’s epidemiological dynamics. This study emphasizes the importance of meticulously examining molecular genetics alongside virus migration patterns within a specific region. Past experiences also emphasize the substantial evolutionary potential of viruses such as SARS-CoV-2, underscoring the need for sustained vigilance. However, as the pandemic’s dynamics continue to evolve, a balanced approach between caution and resilience becomes paramount. This ethos encourages an approach founded on informed prudence and self-preservation, guided by public health authorities, rather than enduring apprehension. Such an approach empowers societies to adapt and progress, fostering a poised confidence rooted in well-founded adaptation.
Funder
Ministry of Health of the Republic of Cyprus University of Cyprus the Research Foundation—Flanders the European Research Council EU
Subject
Virology,Infectious Diseases
Reference124 articles.
1. Rabi, F.A., Al Zoubi, M.S., Al-Nasser, A.D., Kasasbeh, G.A., and Salameh, D.M. (2020). Sars-cov-2 and coronavirus disease 2019: What we know so far. Pathogens, 9. 2. The socio-economic implications of the coronavirus pandemic (COVID-19): A review;Nicola;Int. J. Surg.,2020 3. An interactive web-based dashboard to track COVID-19 in real time;Dong;Lancet Infect. Dis.,2020 4. (2023, August 15). Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (JHU). COVID-19 Dashboard. Available online: https://gisanddata.maps.arcgis.com/apps/dashboards/bda7594740fd40299423467b48e9ecf6. 5. (2023, May 03). The World Health Organization (WHO) Tracking SARS-CoV-2 Variants. Available online: https://www.who.int/activities/tracking-SARS-CoV-2-variants.
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