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)
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...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-09-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/15/9/1933 |
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| author | Andreas C. Chrysostomou Bram Vrancken Christos Haralambous Maria Alexandrou Ioanna Gregoriou Marios Ioannides Costakis Ioannou Olga Kalakouta Christos Karagiannis Markella Marcou Christina Masia Michail Mendris Panagiotis Papastergiou Philippos C. Patsalis Despo Pieridou Christos Shammas Dora C. Stylianou Barbara Zinieri Philippe Lemey The COMESSAR Network Leondios G. Kostrikis |
| author_facet | Andreas C. Chrysostomou Bram Vrancken Christos Haralambous Maria Alexandrou Ioanna Gregoriou Marios Ioannides Costakis Ioannou Olga Kalakouta Christos Karagiannis Markella Marcou Christina Masia Michail Mendris Panagiotis Papastergiou Philippos C. Patsalis Despo Pieridou Christos Shammas Dora C. Stylianou Barbara Zinieri Philippe Lemey The COMESSAR Network Leondios G. Kostrikis |
| author_sort | Andreas C. Chrysostomou |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T21:51:26Z |
| format | Article |
| id | doaj.art-5b4eaa5c0b60417bb302e60628c0cad7 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T21:51:26Z |
| publishDate | 2023-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-5b4eaa5c0b60417bb302e60628c0cad72023-11-19T13:23:46ZengMDPI AGViruses1999-49152023-09-01159193310.3390/v15091933Unraveling 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)Andreas C. Chrysostomou0Bram Vrancken1Christos Haralambous2Maria Alexandrou3Ioanna Gregoriou4Marios Ioannides5Costakis Ioannou6Olga Kalakouta7Christos Karagiannis8Markella Marcou9Christina Masia10Michail Mendris11Panagiotis Papastergiou12Philippos C. Patsalis13Despo Pieridou14Christos Shammas15Dora C. Stylianou16Barbara Zinieri17Philippe Lemey18The COMESSAR NetworkLeondios G. Kostrikis19Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, CyprusDepartment of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, BelgiumUnit for Surveillance and Control of Communicable Diseases, Ministry of Health, 1148 Nicosia, CyprusMicrobiology Department, Larnaca General Hospital, 6301 Larnaca, CyprusUnit for Surveillance and Control of Communicable Diseases, Ministry of Health, 1148 Nicosia, CyprusMedicover Genetics, 2409 Nicosia, CyprusMedical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, 5310 Paralimni, CyprusUnit for Surveillance and Control of Communicable Diseases, Ministry of Health, 1148 Nicosia, CyprusMicrobiology Department, Nicosia General Hospital, 2029 Nicosia, CyprusDepartment of Microbiology, Archbishop Makarios III Hospital, 2012 Nicosia, CyprusMedical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, 5310 Paralimni, CyprusMicrobiology Department, Limassol General Hospital, 4131 Limassol, CyprusMicrobiology Department, Limassol General Hospital, 4131 Limassol, CyprusMedicover Genetics, 2409 Nicosia, CyprusMicrobiology Department, Nicosia General Hospital, 2029 Nicosia, CyprusS.C.I.N.A. Bioanalysis Sciomedical Centre Ltd., 4040 Limassol, CyprusDepartment of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, CyprusMicrobiology Department, Paphos General Hospital, Achepans, 8026 Paphos, CyprusDepartment of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, BelgiumDepartment of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, CyprusCommencing 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.https://www.mdpi.com/1999-4915/15/9/1933SARS-CoV-2COVID-19genomic epidemiologyCyprus |
| spellingShingle | Andreas C. Chrysostomou Bram Vrancken Christos Haralambous Maria Alexandrou Ioanna Gregoriou Marios Ioannides Costakis Ioannou Olga Kalakouta Christos Karagiannis Markella Marcou Christina Masia Michail Mendris Panagiotis Papastergiou Philippos C. Patsalis Despo Pieridou Christos Shammas Dora C. Stylianou Barbara Zinieri Philippe Lemey The COMESSAR Network Leondios G. Kostrikis 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) Viruses SARS-CoV-2 COVID-19 genomic epidemiology Cyprus |
| title | 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) |
| title_full | 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) |
| title_fullStr | 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) |
| title_full_unstemmed | 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) |
| title_short | 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) |
| title_sort | 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 |
| topic | SARS-CoV-2 COVID-19 genomic epidemiology Cyprus |
| url | https://www.mdpi.com/1999-4915/15/9/1933 |
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