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

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 the...

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Bibliographic Details
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
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Summary: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.
ISSN:1999-4915
1999-4915
DOI:10.3390/v15030802