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Mr. Berk Turhan
Sabanci University

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Research Keywords & Expertise

0 Bioinformatics
0 COVID 19
0 Mutation analysis
0 Next generation sequence data analysis
0 Influenza and respiratory viruses

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Short Biography

Undergraduate Student at Sabanci University, Istanbul, Turkey.

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Journal article
Published: 02 March 2021 in Viruses
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Understanding SARS-CoV-2 evolution is a fundamental effort in coping with the COVID-19 pandemic. The virus genomes have been broadly evolving due to the high number of infected hosts world-wide. Mutagenesis and selection are two inter-dependent mechanisms of virus diversification. However, which mechanisms contribute to the mutation profiles of SARS-CoV-2 remain under-explored. Here, we delineate the contribution of mutagenesis and selection to the genome diversity of SARS-CoV-2 isolates. We generated a comprehensive phylogenetic tree with representative genomes. Instead of counting mutations relative to the reference genome, we identified each mutation event at the nodes of the phylogenetic tree. With this approach, we obtained the mutation events that are independent of each other and generated the mutation profile of SARS-CoV-2 genomes. The results suggest that the heterogeneous mutation patterns are mainly reflections of host (i) antiviral mechanisms that are achieved through APOBEC, ADAR, and ZAP proteins, and (ii) probable adaptation against reactive oxygen species.

ACS Style

Cem Azgari; Zeynep Kilinc; Berk Turhan; Defne Circi; Ogun Adebali. The Mutation Profile of SARS-CoV-2 Is Primarily Shaped by the Host Antiviral Defense. Viruses 2021, 13, 394 .

AMA Style

Cem Azgari, Zeynep Kilinc, Berk Turhan, Defne Circi, Ogun Adebali. The Mutation Profile of SARS-CoV-2 Is Primarily Shaped by the Host Antiviral Defense. Viruses. 2021; 13 (3):394.

Chicago/Turabian Style

Cem Azgari; Zeynep Kilinc; Berk Turhan; Defne Circi; Ogun Adebali. 2021. "The Mutation Profile of SARS-CoV-2 Is Primarily Shaped by the Host Antiviral Defense." Viruses 13, no. 3: 394.

Journal article
Published: 21 June 2020 in TURKISH JOURNAL OF BIOLOGY
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COVID-19 has effectively spread worldwide. As of May 2020, Turkey is among the top ten countries with the most cases. A comprehensive genomic characterization of the virus isolates in Turkey is yet to be carried out. Here, we built a phylogenetic tree with globally obtained 15,277 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes. We identified the subtypes based on the phylogenetic clustering in comparison with the previously annotated classifications. We performed a phylogenetic analysis of the first 30 SARS-CoV-2 genomes isolated and sequenced in Turkey. We suggest that the first introduction of the virus to the country is earlier than the first reported case of infection. Virus genomes isolated from Turkey are dispersed among most types in the phylogenetic tree. We find 2 of the seventeen subclusters enriched with the isolates of Turkey, which likely have spread expansively in the country. Finally, we traced virus genomes based on their phylogenetic placements. This analysis suggested multiple independent international introductions of the virus and revealed a hub for the inland transmission. We released a web application to track the global and interprovincial virus spread of the isolates from Turkey in comparison to thousands of genomes worldwide.

ACS Style

Ogün Adebali; Aylin Bircan; Defne Çirci; Burak Işlek; Zeynep Kilinç; Berkay Selçuk; Berk Turhan. Phylogenetic analysis of SARS-CoV-2 genomes in Turkey. TURKISH JOURNAL OF BIOLOGY 2020, 44, 146 -156.

AMA Style

Ogün Adebali, Aylin Bircan, Defne Çirci, Burak Işlek, Zeynep Kilinç, Berkay Selçuk, Berk Turhan. Phylogenetic analysis of SARS-CoV-2 genomes in Turkey. TURKISH JOURNAL OF BIOLOGY. 2020; 44 (3):146-156.

Chicago/Turabian Style

Ogün Adebali; Aylin Bircan; Defne Çirci; Burak Işlek; Zeynep Kilinç; Berkay Selçuk; Berk Turhan. 2020. "Phylogenetic analysis of SARS-CoV-2 genomes in Turkey." TURKISH JOURNAL OF BIOLOGY 44, no. 3: 146-156.

Preprint content
Published: 15 May 2020
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COVID-19 has effectively spread worldwide. As of May 2020, Turkey is among the top ten countries with the most cases. A comprehensive genomic characterization of the virus isolates in Turkey is yet to be carried out. Here, we built a phylogenetic tree with globally obtained 15,277 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes. We identified the subtypes based on the phylogenetic clustering in comparison with the previously annotated classifications. We performed a phylogenetic analysis of the first thirty SARS-CoV-2 genomes isolated and sequenced in Turkey. We suggest that the first introduction of the virus to the country is earlier than the first reported case of infection. Virus genomes isolated from Turkey are dispersed among most types in the phylogenetic tree. We find two of the seventeen sub-clusters enriched with the isolates of Turkey, which likely have spread expansively in the country. Finally, we traced virus genomes based on their phylogenetic placements. This analysis suggested multiple independent international introductions of the virus and revealed a hub for the inland transmission. We released a web application to track the global and interprovincial virus spread of the isolates from Turkey in comparison to thousands of genomes worldwide.

ACS Style

Ogün Adebalı; Aylin Bırcan; Defne Çırcı; Burak Işlek; Zeynep Kilinç; Berkay Selçuk; Berk Turhan. Phylogenetic Analysis of SARS-CoV-2 Genomes in Turkey. 2020, 1 .

AMA Style

Ogün Adebalı, Aylin Bırcan, Defne Çırcı, Burak Işlek, Zeynep Kilinç, Berkay Selçuk, Berk Turhan. Phylogenetic Analysis of SARS-CoV-2 Genomes in Turkey. . 2020; ():1.

Chicago/Turabian Style

Ogün Adebalı; Aylin Bırcan; Defne Çırcı; Burak Işlek; Zeynep Kilinç; Berkay Selçuk; Berk Turhan. 2020. "Phylogenetic Analysis of SARS-CoV-2 Genomes in Turkey." , no. : 1.