BIOLOGYTURKISH JOURNAL OF

http://journals.tubitak.gov.tr/biology/

VOLUME

44 2020YEAR

ISSN 1300-0152 • E-ISSN 1303-6092

3ISSUE

Published by the Scientific and Technological Research Council of Turkey

SPECIAL ISSUE

Special Issue on COVID-19

Editor-in-ChiefProf. Dr. Alaattin ŞEN

Asst. Editor-in-ChiefProf. Dr. Armağan KOÇER

Asst. Editor-in-ChiefAsst. Prof. Dr. Şerife AYAZ GÜNER

TURKISH JOURNAL OF BIOLOGY

• TheTurkishJournalofBiologyispublishedelectronically6timesayearbytheScientificandTechnologicalResearchCouncilofTurkey(TÜBİTAK).

• AcceptsEnglish-languagemanuscripts concerningall kindsofbiologicalprocesses includingbiochemistryandbio-synthesis,physiologyandmetabolism,moleculargenetics,molecularbiology,environmentalbiology,microbiology,neurobiology,genomics,proteomics,molecularfarming,biotechnology/genetictransformation,nanobiotechnology,bioinformaticsandsystemsbiology,cellanddevelopmentalbiology,stemcellbiology,andreproductivebiology.

• Contributionisopentoresearchersofallnationalities.• Letterstotheeditorreflecttheopinionsofotherresearchersonarticlespublishedinthejournal.• Theeditormayinvitesurveyreviewsconcerningrecentdevelopmentsinparticularareasofinterest.

• ScienceCitationIndexExpanded• PubMed PMC• Scopus• AcademicSearchComplete

• Ahmet KOÇ, Inonu University, Turkey• Ahmet ONAY, Dicle University, Turkey• Ali ERGÜL, Ankara University, Turkey• Ali Osman BELDÜZ, Karadeniz Technical University, Turkey• Ana Cristina da SILVA FIGUEIRDO, University of Lisbon, Portugal• Ataç UZEL, Ege University, Turkey• Atalay SÖKMEN, Karadeniz Technical University, Turkey• Bekir Uğur ERGÜR, Dokuz Eylul University, Turkey• Bektaş TEPE, Kilis 7 Aralık University, Turkey• Belma ASLIM, Gazi University, Turkey• Bülent GÜNDÜZ, Çanakkale Onsekiz Mart University, Turkey• Bülent KAYA, Akdeniz University, Turkey• Devrim GÖZÜAÇIK, Sabancı University, Turkey• Dilek TELCİ, Yeditepe University, Turkey• Dilek Turgut BALIK, Yıldız Technical Üniversity, Turkey• Ekrem GÜREL, Abant İzzet Baysal University, Turkey• Engin ULUKAYA, Istinye University, Turkey• Erdal BEDİR, İzmir Institute of Technology, Turkey• Esra ÇAĞAVİ, Istanbul Medipol University, Turkey• Fatih KOCABAŞ, Yeditepe University, Turkey• Feride SEVERCAN, Altinbaş University, Turkey• Fernao Castro BRAGA, Universidade Federal de Minas Gerais, Brazil• Gökhan SADİ, Karamanoğlu Mehmetbey University, Turkey• Hikmet GEÇKİL, İnönü University, Turkey• İbrahim Halil KAVAKLI, Koç University, Turkey• İhsan GÜRSEL, Bilkent University, Turkey• İsmail TÜRKAN, Ege University, Turkey• Jaswinder SINGH, McGill University, Canada• Jose A PARIENTE, University of Extramadura, Spain• Kemal GÜVEN, Dicle University, Turkey• Kemal KAZAN, CSIRO Plant Industry, Australia• Leyla AÇIK, Gazi University, Turkey

• Lixin ZHU, State University of New York at Buffalo, U.S.A.• Margaret BUCKINHAM, Pasteur Institute, France• Mario De TULLIO, University of Bari, Italy• Mehmet Cengiz BALOĞLU, Kastamonu University, Turkey• Mehmet İNAN, Akdeniz University, Turkey• Mehmet TUZCU, Fırat University, Turkey• Mehmet Yakup ARICA, Gazi University, Turkey• Merih KIVANÇ, Anadolu University, Turkey• Muhsin KONUK, Üsküdar University, Turkey• Murat ELİBOL, Ege University, Turkey• Murat KASAP, Kocaeli University, Turkey• Murat KAYA, Aksaray University, Turkey• Murat ÖZMEN, İnönü University, Turkey• Musa KAVAS, Ondokuz Mayıs University, Turkey• Mustafa NAZIROĞLU, Süleyman Demirel University, Turkey• Nesrin ÖZÖREN, Boğaziçi University, Turkey• Özgür ŞAHİN, Bilkent University, Turkey• Peggy G. LEMAUX , UC Berkeley, U.S.A.• Rajendra MEHTA, Cancer Biology IIT Research Institute, U.S.A.• Razan ALKHOURI , University of Buffalo, U.S.A.• Ren XU, University of Kentucky, U.S.A.• Serdar DURDAĞI, Bahçeşehir University, Turkey• Serhan KARVAR, Medical University of South Carolina, U.S.A.• Shuyang YU, University of Iowa, U.S.A.• Uygar Halis TAZEBAY, Gebze Technical University, Turkey• Volkan SEYRANTEPE, İzmir Institute of Technology, Turkey• Wolfgang KREIS, Friedrich Alexander Universitat Erlangen, Germany• Yan LI, University of Pennsylvania , U.S.A.• Yusuf BARAN, İzmir Institute of Technology, Turkey• Yusuf TUTAR, University of Health Sciences, Turkey• Zeki KAYA, Middle East Technical University, Turkey• Zeynep Petek ÇAKAR, İstanbul Technical University, Turkey

ABSTRACTED AND INDEXED

EDITORIAL BOARD

SCOPE OF JOURNAL

ISSN1300-0152•E-ISSN1303-6092VOLUME 44 ISSUE 3 2020Editor-in-Chief AlaattinŞEN,PamukkaleUniversity,Turkey

Assistant Editor-in-Chief ŞerifeAYAZGÜNER,AbdullahGülUniversity,Turkey ArmağanKOÇER,UniversityofTwente,Netherlands

CONTENTS

Covid-19: current knowledge, disease potential, prevention and clinical advances ..............................................................121Aftab ALAM , Mohd Faizan SIDDIQUI, Nikhat IMAM, Rafat ALI, Md. Mushtaque, Romana ISHRAT

Biosafety and biosecurity approaches to restrain/contain and counter SARS-CoV-2/COVID-19 pandemic: a rapid-review ...............................................................................................................................................................132Tauseef AHMAD, Haroon, Kuldeep DHAMA, Khan SHARUN, Fazal Mehmood KHAN, Irfan AHMED, Ruchi TIWARI, Taha Hussien MUSA, Muhammad KHAN, D. Katterine BONILLA-ALDANA, Alfonso J. RODRIGUEZ-MORALES, Jin HUI

Phylogenetic analysis of SARS-CoV-2 genomes in Turkey .......................................................................................................146Ogün ADEBALİ, Aylin BİRCAN, Defne ÇİRCİ, Burak İŞLEK, Zeynep KILINÇ, Berkay SELÇUK, Berk TURHAN

An updated analysis of variations in SARS-CoV-2 genome ......................................................................................................157Osman Mutluhan UGUREL , Oguz ATA, Dilek TURGUT-BALIK

Integration of transcriptomic profile of SARS-CoV-2 infected normal human bronchial epi-thelial cells with metabolic and protein-protein interaction networks ............................................................................168Hamza Umut KARAKURT, Pınar PİR

Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey ..................................................178Ayşe Banu DEMİR, Domenico BENVENUTO, Hakan ABACIOĞLU, Silvia ANGELETTI, Massimo CICCOZZI

Virtual drug repurposing study against SARS-CoV-2 TMPRSS2 target .................................................................................185Serdar DURDAĞI

SARS-CoV-2 isolation and propagation from Turkish COVID-19 patients ...........................................................................192Cihan TAŞTAN, Bulut YURTSEVER, Gözde SIR KARAKUŞ, Derya DİLEK KANÇAĞI, Sevda DEMİR, Selen ABANUZ, Utku SEYİS, Mülazim YILDIRIM, Recai KUZAY, Ömer ELİBOL, Serap ARBAK, Merve AÇIKEL ELMAS, Selçuk BİRDOĞAN, Osman Uğur SEZERMAN, Ayşe Sesin KOCAGÖZ, Koray YALÇIN, Ercüment OVALI

SARS-CoV-2 neutralizing antibody development strategies .....................................................................................................203Bertan Koray BALCIOĞLU, Melis DENİZCİ ÖNCÜ, Hasan Ümit ÖZTÜRK, Fatıma YÜCEL, Filiz KAYA, Müge SERHATLI, Hivda ÜLBEĞİ POLAT, Şaban TEKİN, Aylin ÖZDEMİR BAHADIR

An insight into the epitope-based peptide vaccine design strategy and studies against COVID-19 ...................................215Murat TOPUZOĞULLARI, Tayfun ACAR, Pelin PELİT ARAYICI, Burcu UÇAR, Erennur UĞUREL, Emrah Şefik ABAMOR, Tülin ARASOĞLU, Dilek TURGUT-BALIK, Serap DERMAN

Potentials of plant-based substance to inhabit and probable cure for the COVID-19 ..........................................................228Israt JAHAN, Ahmet ONAY

Interaction of certain monoterpenoid hydrocarbons with the receptor binding domain of 2019 novel coronavirus (2019-nCoV), transmembrane serine protease 2 (TMPRSS2), cathepsin B, and cathepsin L (CatB/L) and their pharmacokinetic properties .......................................................................242Erman Salih İSTİFLİ, Arzuhan ŞIHOĞLU TEPE, Cengiz SARIKÜRKCÜ, Bektaş TEPE

Gut-lung axis and dysbiosis in COVID-19 ..................................................................................................................................265Busra AKTAS, Belma ASLIM

Mesenchymal stem cell derived extracellular vesicles: promising immunomodulators against autoimmune, autoinflammatory disorders and SARS-CoV-2 infection ....................................................................273Özlem BULUT, İhsan GÜRSEL

Preface

The SARS-CoV-2 virus and associated COVID-19 pandemic have been one of the most devastating outbreaks in human history and affected millions of people and caused hundreds of thousands of deaths. Despite the intense scientific efforts, there are still many unknowns to be resolved and explained. As Turkish Journal of Biology (TJB), one of the respectful journals among the TÜBİTAK publishing, we would like to make a contribution to the scientific world by publishing a special COVID-19 issue. In this way, we believed to be a solution partner by contributing to a better understanding of the epidemiology of the COVID-19 by providing the data belonging to Turkish population that was presented by Turkish and as well as international scientists.

TJB COVID-19 special issue is an important 176-page inventory of studies provided by 14 respectable group leader scientists and their teams, and it will be an important resource for future studies. This special issue begins with two concise review on SARS-CoV-2 epidemiology, diagnosis and treatment, vaccine developments, socio-economic impacts and biosafety issues for controlling the outbreak. This general introductory review is followed by the original research studies involving the phylogenetic analysis of the first thirty SARS-CoV-2 genomes isolated and sequenced from Turkish patients and variations among the SARS-CoV-2 genomes using the software developed by the Turkish scientists in Turkey. Further original researches presenting the virtual drug repurposing studies using hybrid molecular modelling approach to identify new drugs against disease and analyses that integrating transcriptomics data with protein-protein interaction network to identify early responses to infection provide important data to the literature. Isolation and characterization of SARS-CoV-2 from naso- and oro-pharyngeal samples of patients diagnosed in Turkey offers further original contributions. Strategies to develop neutralizing antibodies and epitope-based peptide vaccines against SARS-CoV-2 were presented with subsequent review articles.

An interesting review paper discussing the antiviral potentials of medicinal plants to inhibit coronaviruses and original research studies investigating the molecular interactions between the monoterpenoids present in these medicinal plants with the spike protein of virus illuminated to the understanding of alternative and complementary therapeutics and their molecular mechanisms. As popular topic recently, the intestinal microbiota, a review paper discussing the effect microbiota dysbiosis of on SARS-CoV-2 infection and the faecal transmission of the virus were included. TJB-COVID-19 special issue ends with an excellent review presenting the results of pre-clinical and clinical trials of mesenchymal stem cell-derived extracellular vesicles as promising immunomodulators against autoimmune, autoinflammatory disorders and SARS-CoV-2 infection.

I believe that TJB-COVID-19 special issue will be a very important resource for both epidemiologic, in-silico and laboratory-based future studies. I present my sincere thanks to the respectable group leader scientists and their colleagues who have responded positively to our invitations and contributed to this special issue of TJB COVID-19, to our technical office and associate editors who have made an extraordinary effort to prepare the issue in a short time, to the reviewers for their comprehensive but quick peer evaluations, and to Prof. Dr. Hasan MANDAL, president of TÜBİTAK, for his kind support.

I wish that the COVID-19 epidemic will end soon with my belief that this COVID-19 special issue of the Turkish Journal of Biology will be an important contribution with this scope.

Best regards,Alaattin ŞEN, PhDEditor-in-Chief

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