Dataset Information

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

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.

SUBMITTER: Marascio N

PROVIDER: S-EPMC10054778 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature

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

Marascio Nadia N Cilburunoglu Merve M Torun Elif Gulsum EG Centofanti Federica F Mataj Elida E Equestre Michele M Bruni Roberto R Quirino Angela A Matera Giovanni G Ciccaglione Anna Rita AR Yalcinkaya Kezban Tulay KT

Viruses 20230321 3

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 ...[more]

PMID: 36992510

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Dataset Information

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

Publications

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

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