Molecular Characterization and Cluster Analysis of SARS-CoV-2 Viral Isolates in Kahramanmaraş City, Turkey: The Delta VOC Wave within One Month

• Published in: Viruses 2023-03, Vol.15 (3), p.802
• Main Authors: Marascio, Nadia, Cilburunoglu, Merve, Torun, Elif Gulsum, Centofanti, Federica, Mataj, Elida, Equestre, Michele, Bruni, Roberto, Quirino, Angela, Matera, Giovanni, Ciccaglione, Anna Rita, Yalcinkaya, Kezban Tulay
• Format: Article
• Language: English
• Subjects: Causes of; Cluster Analysis; cluster identification; Coronaviruses; COVID-19; COVID-19 - epidemiology; COVID-19 vaccines; delta VOC; Disease; Epidemics; Epidemiology; Genes; Genomes; Humans; Infections; Laboratories; Mutation; N protein; Nucleocapsids; Pandemics; Phylogenetics; Phylogeny; Proteins; Public health; SARS-CoV-2; SARS-CoV-2 - genetics; Severe acute respiratory syndrome coronavirus 2; Turkey; Turkey - epidemiology; unusual mutations
• ISSN: 1999-4915; 1999-4915
• DOI: 10.3390/v15030802

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.