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[Genomic Characterization of SARS-CoV-2 Isolates Obtained from Antalya, Türkiye]
Aylin Erman Daloğlu1, Erley Lizarazo Forero2, Nevgün Sepin Özen1
1University of Health Sciences, Antalya Training and Research Hospital, Medical Microbiology Clinic, Antalya, Türkiye.
Mikrobiyoloji Bulteni
|January 2, 2025
Summary
This study analyzed severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) mutations and clades in Türkiye, revealing Delta and Omicron variants were most frequent. Findings emphasize proactive molecular surveillance for future pandemic preparedness.
Area of Science:
- Virology and Molecular Epidemiology
- Genomic surveillance of respiratory viruses
- Next-generation sequencing applications in public health
Context:
- Ongoing circulation of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) necessitates continuous monitoring.
- Shift from broad social restrictions to individual-level measures requires adaptable diagnostic strategies.
- Integration of SARS-CoV-2 into routine respiratory pathogen panels highlights its sustained public health importance.
Purpose:
- To perform whole-genome sequencing and analyze mutation profiles of SARS-CoV-2.
- To determine the clade distribution of SARS-CoV-2 in randomly selected positive samples from different pandemic periods.
- To investigate the genetic diversity and evolutionary patterns of SARS-CoV-2 in the Mediterranean Region of Türkiye.
Summary:
- Eighty-four SARS-CoV-2 positive samples underwent whole-genome sequencing using a commercial next-generation sequencing kit.
- Nextstrain clades identified included 21J (Delta), 21L (Omicron), 20B, 20A, 21K (Omicron), 19A, and 22B (Omicron), with Delta and Omicron variants being most prevalent.
- A total of 2829 distinct mutations were detected, predominantly in the Spike gene, indicating ongoing viral evolution.
Impact:
- Provides the first comprehensive SARS-CoV-2 genome analysis from the pandemic period in Antalya, Türkiye.
- Identifies potential viral entry routes into Türkiye by comparing sequences with international data, highlighting links to Germany and the UK.
- Underscores the critical need for proactive molecular surveillance and data sharing, especially from developing countries, for effective pandemic control and preparedness.
