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Whole Genome Sequencing and Phylogenetic Analysis of SARS­CoV­2 strains in Turkey.
Tokgun, Onur; Caliskan, Ahmet; Coskun, Cagil; Tokgun, Pervin Elvan; Akca, Hakan.
  • Tokgun O; Pamukkale University, Faculty of Medicine, Department of Medical Genetics, Denizli, Turkey. otokgun@pau.edu.tr.
  • Caliskan A; Pamukkale University, Faculty of Medicine, Department of Medical Microbiology, Denizli, Turkey.
  • Coskun C; Cukurova University, Faculty of Medicine, Department of Biophysics, Adana, Turkey.
  • Tokgun PE; Pamukkale University, Faculty of Medicine, Department of Medical Genetics, Denizli, Turkey.
  • Akca H; Pamukkale University, Faculty of Medicine, Department of Medical Genetics, Denizli, Turkey.
J Infect Dev Ctries ; 15(4): 470-477, 2021 04 30.
Article in English | MEDLINE | ID: covidwho-1218644
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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Phylogeny / SARS-CoV-2 Type of study: Randomized controlled trials Topics: Variants Limits: Humans Language: English Journal: J Infect Dev Ctries Journal subject: Communicable Diseases Year: 2021 Document Type: Article Affiliation country: Jidc.14560

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Phylogeny / SARS-CoV-2 Type of study: Randomized controlled trials Topics: Variants Limits: Humans Language: English Journal: J Infect Dev Ctries Journal subject: Communicable Diseases Year: 2021 Document Type: Article Affiliation country: Jidc.14560