Whole Genome Sequencing and Phylogenetic Analysis of SARS‑CoV‑2 strains in Turkey

  • Onur Tokgun Pamukkale University, Faculty of Medicine, Department of Medical Genetics, Denizli, Turkey
  • Ahmet Caliskan Pamukkale University, Faculty of Medicine, Department of Medical Microbiology, Denizli, Turkey
  • Cagil Coskun Cukurova University, Faculty of Medicine, Department of Biophysics, Adana, Turkey
  • Pervin Elvan Tokgun Pamukkale University, Faculty of Medicine, Department of Medical Genetics, Denizli, Turkey
  • Hakan Akca Pamukkale University, Faculty of Medicine, Department of Medical Genetics, Denizli, Turkey
Keywords: Coronaviruses, SARS-CoV-2, NGS, clade, lineage

Abstract

Introduction: Coronaviruses which are single-stranded RNAs, are members of a large family of viruses that may be important pathogens for humans. SARS-CoV-2 was found to cause the severe respiratory syndrome, and on January 22, 2020 first human-to-human transmission was reported. We aimed to reveal the complete genomes of 19 SARS-CoV-2 isolates from Denizli province and identify Turkish patients' genetic similarities.

Methodology: 15 samples with the highest viral loads resulting from RT-PCR were selected for NGS analysis. Fifteen SARS-CoV-2 complete genome sequences were then subjected to phylogenetic analysis and uploaded to the GISAID database. Phylogenetic trees were constructed by the Neighbor-Joining method using MEGAX software.

Results: Whole-genome sequencing of the viral RNA samples revealed 32 missense, 21 synonymous, and 4 non-coding alleles. In all samples c.1-25C>T (5’UTR), c.14144C>T (ORF1ab), c.2772C>T (ORF1ab) and c.1841A>G(S) mutations were detected. Phylogenetic analysis revealed that most of the present study's genomes are in 20B clade while the two are in 20A. The phylogenetic tree constructed with all complete SARS-CoV-2 genomes of Turkey showed that the viruses were spread nearly homogenous on eastern (around Kars) and western (around Istanbul) sides.

Conclusions: Here, we reported the viral genomes in Denizli comprehensively for the first time. We identified 11 rare missense mutations in the virus compared to the reference genome. Phylogenetic analysis revealed that while most of our isolates were similar to European sequences, some had different sublineages depending on their genomic variants.

Published
2021-04-30
How to Cite
1.
Tokgun O, Caliskan A, Coskun C, Tokgun PE, Akca H (2021) Whole Genome Sequencing and Phylogenetic Analysis of SARS‑CoV‑2 strains in Turkey. J Infect Dev Ctries 15:470-477. doi: 10.3855/jidc.14560
Section
Coronavirus Pandemic