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Marascio N, Cilburunoglu M, Torun EG, Centofanti F, Mataj E, Equestre M, Bruni R, Quirino A, Matera G, Ciccaglione AR, Yalcinkaya KT. Molecular Characterization and Cluster Analysis of SARS-CoV-2 Viral Isolates in Kahramanmaraş City, Turkey: The Delta VOC Wave within One Month. Viruses 2023; 15:v15030802. [PMID: 36992510 PMCID: PMC10054778 DOI: 10.3390/v15030802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/13/2023] [Accepted: 03/20/2023] [Indexed: 03/31/2023] Open
Abstract
The SARS-CoV-2 pandemic has seriously affected the population in Turkey. Since the beginning, phylogenetic analysis has been necessary to monitor public health measures against COVID-19 disease. In any case, the analysis of spike (S) and nucleocapsid (N) gene mutations was crucial in determining their potential impact on viral spread. We screened S and N regions to detect usual and unusual substitutions, whilst also investigating the clusters among a patient cohort resident in Kahramanmaraş city, in a restricted time span. Sequences were obtained by Sanger methods and genotyped by the PANGO Lineage tool. Amino acid substitutions were annotated comparing newly generated sequences to the NC_045512.2 reference sequence. Clusters were defined using phylogenetic analysis with a 70% cut-off. All sequences were classified as Delta. Eight isolates carried unusual mutations on the S protein, some of them located in the S2 key domain. One isolate displayed the unusual L139S on the N protein, while few isolates carried the T24I and A359S N substitutions able to destabilize the protein. Phylogeny identified nine monophyletic clusters. This study provided additional information about SARS-CoV-2 epidemiology in Turkey, suggesting local transmission of infection in the city by several transmission routes, and highlighting the necessity to improve the power of sequencing worldwide.
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Affiliation(s)
- Nadia Marascio
- Department of Health Sciences, Institute of Microbiology, "Magna Grecia" University, 88100 Catanzaro, Italy
| | - Merve Cilburunoglu
- Microbiology Department, Faculty of Medicine, Kahramanmaras Sutcü Imam University, 46050 Kahramanmaras, Turkey
| | - Elif Gulsum Torun
- Microbiology Department, Faculty of Medicine, Kahramanmaras Sutcü Imam University, 46050 Kahramanmaras, Turkey
| | - Federica Centofanti
- Department of Applied Clinical Sciences and Biotechnology, University of Aquila, 67100 L'Aquila, Italy
| | - Elida Mataj
- Instituti i Shendetit Publik (ISHP), 1000 Tirana, Albania
| | - Michele Equestre
- Department of Neurosciences, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Roberto Bruni
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Angela Quirino
- Department of Health Sciences, Institute of Microbiology, "Magna Grecia" University, 88100 Catanzaro, Italy
| | - Giovanni Matera
- Department of Health Sciences, Institute of Microbiology, "Magna Grecia" University, 88100 Catanzaro, Italy
| | | | - Kezban Tulay Yalcinkaya
- Microbiology Department, Faculty of Medicine, Kahramanmaras Sutcü Imam University, 46050 Kahramanmaras, Turkey
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