Genomic Surveillance and Molecular Characterization of SARS-CoV-2 Variants During the Peak of the Pandemic in Türkiye.

Autor: Akçeşme FB; Division of Biostatistics and Medical Informatics, Department of Basic Medical Sciences, Hamidiye Faculty of Medicine, University of Health Sciences, Istanbul, Turkey., Köprülü TK; Division of Medical Laboratory Techniques, Department of Medical Services and Techniques, Hamidiye Health Services Vocational School, University of Health Sciences, Istanbul, Turkey.; Experimental Medicine Application and Research Center, University of Health Sciences, Istanbul, Turkey., Çam BE; Department of Molecular Biology and Genetics, Faculty of Science and Letters, Yıldız Technical University, Istanbul, Turkey., İş Ş; Division of Bioinformatics, Department of Molecular Biotechnology, Faculty of Science, Turkish-German University, Istanbul, Turkey.; Division of Medical Biology, Department of Basic Medical Sciences, Hamidiye Faculty of Medicine, University of Health Sciences, Istanbul, Turkey., Keskin BC; Genome Research Center, Life Sciences, Marmara Research Center, TUBITAK, Kocaeli, Turkey., Akçeşme B; Division of Medical Biology, Department of Basic Medical Sciences, Hamidiye Faculty of Medicine, University of Health Sciences, Istanbul, Turkey. betul.akcesme@sbu.edu.tr., Baydili KN; Department of Biostatistics and Medical Informatics, Hamidiye Faculty of Medicine, University of Health Sciences, Istanbul, Turkey., Gezer B; Experimental Medicine Application and Research Center, University of Health Sciences, Istanbul, Turkey.; Department of Molecular Medicine, Hamidiye Faculty of Health Sciences, University of Health Sciences, Istanbul, Turkey., Balkan J; Experimental Medicine Application and Research Center, University of Health Sciences, Istanbul, Turkey.; Department of Molecular Medicine, Hamidiye Faculty of Health Sciences, University of Health Sciences, Istanbul, Turkey., Uçar B; Genome Research Center, Life Sciences, Marmara Research Center, TUBITAK, Kocaeli, Turkey.; Department of Biology, Faculty of Science, Marmara University, Istanbul, Turkey., Gürsoy O; Department of Computer Sciences and Engineering, Faculty of Engineering and Natural Sciences, International University of Sarajevo, Sarajevo, Bosnia and Herzegovina., Yıldız MT; Hamidiye Institute of Science, Molecular Medicine, Hamidiye Health Services Vocational School, University of Health Sciences, Istanbul, Turkey., Kurt H; Department of Medical Biology, Hamidiye International Faculty of Medicine, University of Health Sciences, Istanbul, Turkey., Ünal N; Department of Microbiology, Adana City Training and Research Hospital, Adana, Turkey., Korkmaz C; Division of Thoracic Diseases, Department of Internal Medicine, Faculty of Medicine, Necmettin Erbakan University, Konya, Turkey., Saral ÖB; Clinic for Infectious Diseases and Clinical Microbiology, Trabzon Kanuni Training and Research Hospital, Trabzon, Turkey., Demirkol B; Department of Chest Diseases, Basaksehir Cam and Sakura City Hospital, University of Health Sciences, Istanbul, Turkey., Çağ Y; Division of Infectious Diseases and Clinical Microbiology, Department of Internal Medicine, Faculty of Medicine, İstanbul Medeniyet University, Istanbul, Turkey., Abakay H; Clinic for Infectious Diseases, İzmir Tepecik Training and Research Hospital, İzmir, Turkey., Köse Ş; Division of Infectious Diseases, Department of Internal Medicine, Dokuz Eylül Univesity, İzmir, Turkey., Türkez H; Department of Medical Biology, Faculty of Medicine, Atatürk University, Erzurum, Turkey., Çadırcı K; Department of Internal Medicine, Erzurum Regional Education and Research Hospital, Erzurum, Turkey., Altındiş M; Division of Medical Microbiology, Department of Basic Medical Sciences, Faculty of Medicine, Sakarya University, Sakarya, Turkey., Gülseren YD; Department of Medical Microbiology, Balıkesir Atatürk City Hospital, Balıkesir, Turkey., Aslan N; Emergency Service, Sakarya University Training and Research Hospital, Sakarya, Turkey., Özel A; Experimental Medicine Application and Research Center, University of Health Sciences, Istanbul, Turkey.; Dr. Orhan Öcalgiray Molecular Biology-Biotechnology and Genetics Research Center (ITU-MOBGAM), Faculty of Science and Letters, İstanbul Technical University, Istanbul, Turkey., Karagöl MA; Department of Chest Diseases, Basaksehir Cam and Sakura City Hospital, University of Health Sciences, Istanbul, Turkey., Mutluay N; Department of Medical Microbiology, Adana City Training and Research Hospital, Adana, Turkey.; Division of Medical Microbiology, Department of Basic Medical Sciences, Faculty of Medicine, Çukurova University, Adana, Turkey., Tekin Ş; Division of Medical Biology, Department of Basic Medical Sciences, Hamidiye Faculty of Medicine, University of Health Sciences, Istanbul, Turkey.
Jazyk: angličtina
Zdroj: Biochemical genetics [Biochem Genet] 2024 Nov 08. Date of Electronic Publication: 2024 Nov 08.
DOI: 10.1007/s10528-024-10962-8
Abstrakt: SARS-CoV-2 is a highly transmissible coronavirus and has caused a pandemic of acute respiratory disease. Genomic characterization of SARS-CoV-2 is important for monitoring and assessing its evolution. A total of 1.346 nasopharyngeal swab samples were collected but only 879 SARS-CoV-2 high-quality genomes were isolated, subjected to Next Generation Sequencing and analyzed both statistically and regarding mutations comprehensively. The distribution of clades and lineages in different cities of Türkiye and the association of SARS-CoV-2 variants with age groups and clinical characteristics of COVID-19 were also examined. Furthermore, the frequency of the clades and lineages was observed in 10 months. Finally, non-synonymous mutations not defined in specific SARS-CoV-2 variants (during that period) were identified by performing mutation analysis. B.1.1.7 (Alpha) and B.1.617.2 (Delta) SARS-CoV-2 variants which have also been identified in our study from March to December 2021. We observed a significant association of SARS-CoV-2 variants with age groups and cities. Also, E:T9I, S:A27S, S:A67V, S:D796Y, S:K417N, S:N440K, S:R158X, S:S477N (below 1%-frequency) were determined as specific mutations belonging and shared with the Omicron variant that appeared later. Our study has highlighted the importance of constant monitoring of the genetic diversity of SARS-CoV-2 to provide better prevention strategies and it contributes to the understanding of SARS-CoV-2 from the past to the present.
(© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)
Databáze: MEDLINE
Externí odkaz: