1
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Paramonova NM, Chepur SV, Pervak MО, Myasnikov VA, Tyunin MA, Ilinskiy NS, Kanevskij BA, Smirnova AV. [An electron microscopic study of neocortex of Syrian hamsters ( Mesocricetus auratus) infected with SARS-CoV-2 (Coronaviridae: Coronavirinae: Betacoronavirus: Sarbecovirus)]. Vopr Virusol 2022; 67:403-413. [PMID: 36515286 DOI: 10.36233/0507-4088-130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Indexed: 12/07/2022]
Abstract
INTRODUCTION Convalescent COVID-19 patients have various signs of central nervous system damage, including those directly associated with SARS-CoV-2. Hence, studies of SARS-COV-2 related morphological changes in neocortex are particularly relevant for understanding the mechanisms of their formation and development of approaches to preclinical evaluation of the effectiveness of antiviral drugs. The purpose of the research is a longitudinal study of the ultrastructural alterations in Syrian hamsters neocortex after experimental SARS-CoV-2 infection. MATERIALS AND METHODS Male Syrian hamsters weighing 80100 g, aged 4 to 6 weeks, were infected with 26 l SARS-CoV-2 intranasally with 4104 TCD50/ml of viral particles. The animals were euthanized on days 3, 7 or 28 post-infection, the brain was extracted with the cortex excision. The material analysis was performed using transmission electron microscopy. RESULTS AND DISCUSSION On day 3 post-infection, the number of moderately hyperchromic neurons in neocortex increased, while by the day 7 the number of apoptotic cells significantly increased. Simultaneously, an increased signs of neuronophagy and representation of atypical glia were observed. Increased number of altered oligodendrocytes was observed on day 28 post-infection. Viral invasion was accompanied by changes in neocortical cells since day 3 post-infection, such as transformation of their nucleus, the rough endoplasmic reticulum and the Golgi vesicles as well as microvascular spasm with perivascular edema. CONCLUSION As a result of electron microscopic study, the ultrastructural alterations in neocortex were described in an experimental model of SARS-CoV-2 infection. The findings can be used to identify the mechanisms of infection pathogenesis and to search for the new directions in development of medicines.
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Affiliation(s)
- N M Paramonova
- State Research Testing Institute of Military Medicine of the Ministry of Defense of the Russian Federation.,Sechenov Institute of Evolutionary Physiology and Biochemistry of the Russian Academy of Sciences
| | - S V Chepur
- State Research Testing Institute of Military Medicine of the Ministry of Defense of the Russian Federation
| | - M О Pervak
- State Research Testing Institute of Military Medicine of the Ministry of Defense of the Russian Federation
| | - V A Myasnikov
- State Research Testing Institute of Military Medicine of the Ministry of Defense of the Russian Federation
| | - M A Tyunin
- State Research Testing Institute of Military Medicine of the Ministry of Defense of the Russian Federation
| | - N S Ilinskiy
- State Research Testing Institute of Military Medicine of the Ministry of Defense of the Russian Federation
| | - B A Kanevskij
- State Research Testing Institute of Military Medicine of the Ministry of Defense of the Russian Federation
| | - A V Smirnova
- State Research Testing Institute of Military Medicine of the Ministry of Defense of the Russian Federation
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2
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Arisan ED, Dart DA, Grant GH, Dalby A, Kancagi DD, Turan RD, Yurtsever B, Karakus GS, Ovali E, Lange S, Uysal-Onganer P. microRNA 1307 Is a Potential Target for SARS-CoV-2 Infection: An in Vitro Model. ACS OMEGA 2022; 7:38003-38014. [PMID: 36275122 PMCID: PMC9578367 DOI: 10.1021/acsomega.2c05245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
microRNAs (miRs) are proposed as critical molecular targets in SARS-CoV-2 infection. Our recent in silico studies identified seven SARS-CoV-2 specific miR-like sequences, which are highly conserved with humans, including miR-1307-3p, with critical roles in COVID-19. In this current study, Vero cells were infected with SARS-CoV-2, and miR expression profiles were thereafter confirmed by qRT-PCR. miR-1307-3p was the most highly expressed miR in the infected cells; we, therefore, transiently inhibited its expression in both infected and uninfected cells. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) cell proliferation assay assessed cell viability following SARS-CoV-2 infection, identifying that miR-1307 expression is inversely correlated with cell viability. Lastly, changes in miR-1307-dependent pathways were analyzed through a detailed miRNOME and associated in silico analysis. In addition to our previously identified miRs, including miR-1307-3p, the upregulation of miR-193a-5p, miR-5100, and miR-23a-5p and downregulation of miR-130b-5p, miR34a-5p, miR-505-3p, miR181a-2-3p, miR-1271-5p, miR-598-3p, miR-34c-3p, and miR-129-5p were also established in Vero cells related to general lung disease-related genes following SARS-CoV-2 infection. Targeted anti-miR-1307-3p treatment rescued cell viability in infection when compared to SARS CoV-2 mediated cell cytotoxicity only. We furthermore identified by in silico analysis that miR-1307-3p is conserved in all SARS-CoV-2 sequences/strains, except in the BA.2 variant, possibly contributing to the lower disease severity of this variant, which warrants further investigation. Small RNA seq analysis was next used to evaluate alterations in the miRNOME, following miR-1307-3p manipulation, identifying critical pathobiological pathways linked to SARS-CoV-2 infection-mediated upregulation of this miR. On the basis of our findings, miRNAs like miR-1307-3p play a critical role in SARS-CoV-2 infection, including via effects on disease progression and severity.
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Affiliation(s)
- Elif Damla Arisan
- Gebze
Technical University, Institute of Biotechnology, Gebze, Kocaeli 41400, Turkiye
| | - D. Alwyn Dart
- Institute
of Medical and Biomedical Education, St
George’s University of London, Cranmer Terrace, Tooting, London SW17
0RE, United Kingdom
| | - Guy H. Grant
- School
of Life Sciences, University of Bedfordshire, Park Square, Luton LU1
3JU, United Kingdom
| | - Andrew Dalby
- School
of Life Sciences, University of Westminster, London W1W 6UW, United Kingdom
| | | | - Raife Dilek Turan
- Acibadem
Labcell Cellular Therapy Laboratory, İstanbul 34457, Turkiye
- Yeditepe
University, Institute of Biotechnology, İstanbul 34755, Turkiye
| | - Bulut Yurtsever
- Acibadem
Labcell Cellular Therapy Laboratory, İstanbul 34457, Turkiye
| | - Gozde Sir Karakus
- Acibadem
Labcell Cellular Therapy Laboratory, İstanbul 34457, Turkiye
| | - Ercument Ovali
- Acibadem
Labcell Cellular Therapy Laboratory, İstanbul 34457, Turkiye
| | - Sigrun Lange
- Tissue
Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, United Kingdom
| | - Pinar Uysal-Onganer
- Cancer
Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, United Kingdom
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3
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Identification, propagation and molecular characterization of SARS-CoV-2 delta variant isolated from Egyptian COVID-19 patients. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 100:105278. [PMID: 35367360 PMCID: PMC8968185 DOI: 10.1016/j.meegid.2022.105278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 12/14/2022]
Abstract
The recently emerging coronavirus, severe acute respiratory syndrome coronavirus 2, (SARS-CoV-2) is the causative agent of the Coronavirus disease 2019 (COVID-19) pandemic. Since its discovery in the city of Wahan, China, SARS-CoV-2 has spread rapidly to invade all countries. In addition to its rapid transmission rate, it is characterized by high genetic mutation rates. The aim of this study is to provide an effective method for the isolation and propagation of SARS-CoV-2 in cell lines without any induction of genetic variations. In this study, we isolated SARS-CoV-2 from oro-nasopharyngeal swabs collected from Egyptian patients who were clinically diagnosed with COVID-19. Molecular identification of SARS-CoV-2 was performed by Real-Time Quantitative Reverse Transcription PCR (RT-qPCR). The isolated virus was propagated on Vero E6 cells without applying serial viral passages to avoid any variation of the viral genome. The replication and propagation were confirmed by the results of both RT-qPCR and the cytopathic effect (CPE). Moreover, SARS-CoV-2 was completely inactivated chemically using beta-propiolactone (βPL). Whole genome sequencing (WGS) of the propagated virus was performed in order to investigate mutational patterns. The genome sequences recovered in 2020 (n = 18) were similar to the reference strain, Wuhan-Hu-1, and were clustered as clade 20A. However, the genomic sequences recovered in 2021 (n = 2) were clustered as clade 21J. These two sequences are considered the first Delta (B.1.617.2) variants detected in Egypt. This study provides a reference for researchers in Egypt to isolate and propagate SARS-CoV-2 easily and efficiently. Furthermore, the prevalence of the SARS-CoV-2 delta variant in Egypt necessitates continuous monitoring of the efficacy of the applied treatment protocol and the effectiveness of current vaccines against such variants of concern (VOC).
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4
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Artik Y, Coşğun AB, Cesur NP, Hızel N, Uyar Y, Sur H, Ayan A. Comparison of COVID-19 laboratory diagnosis by commercial kits: Effectivity of RT-PCR to the RT-LAMP. J Med Virol 2022; 94:1998-2007. [PMID: 34997587 PMCID: PMC9015626 DOI: 10.1002/jmv.27559] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 12/27/2021] [Indexed: 01/08/2023]
Abstract
Coronavirus disease 2019 or COVID-19 caused by novel coronavirus/severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 or 2019-nCoV) is an ongoing pandemic that has emerging global effects and requires rapid and reliable diagnostic testing. Quantitative reverse transcription-polymerase chain reaction (q-RT-PCR) is the gold standard method for SARS-CoV-2 detections. On the other hand, new approaches remedy the diagnosis difficulties gradually. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) as one of these novel approaches may also contribute to faster and cheaper field-based testing. The present study was designed to evaluate this rapid screening diagnostic test that can give results in 30-45 min and to compare the effectiveness of LAMP to the q-RT-PCR. The 30 randomly chosen patient samples were generated by nasopharyngeal swabs with a portion of the SARS-CoV-2 nucleic sequence. The sample of quantification cycle (Cq) values was tested using RT-LAMP as well as by conventional q-RT-PCR. The patient samples were tested with four different kits (SENSObiz COVID-19 [SARS-CoV-2] LAMP Assay, the QIAseq DIRECT SARS-CoV-2 kit, Biospeedy SARS-CoV-2 Variant Plus kit, and CoVirion-CV19-2 SARS-CoV-2 OneStep RT-PCR kit) and two different PCR devices (GDS Rotor-Gene Q Thermocycler and Inovia Technologies GenX series). Based on 30 patient samples, the positive/negative ratio (P/N) was 30/0 as Biospeedy and Covirion (positivity 100%), 28/2 as Qiagen kit (positivity 93.3%) for the samples studied on the Inovia device while the same samples on the Rotor-Gene device were 30/0 as Biospeedy and Covirion (positivity 100%), 29/1 as Qiagen kit at the first day (96.7%). On the fifth day, the samples were studied in the Inovia device and the respective results were obtained: 27/3 as Biospeedy (positivity 90%), 16/14 as Qiagen (positivity 53.3%), 28/2 as Covirion kit (positivity 93.3%). When these samples were studied in the Rotor-Gene device, it was 29/1 in Biospeedy and Covirion (positivity 96.7%), 19/11 in the Qiagen kit (positivity 63.3%). When these samples were compared with the LAMP method it was found to be 19/11 (positivity 63.3%) on the first day and 18/12 (positivity 60%) on the fifth day. SARS-CoV-2 test studies will contribute to a proactive approach to the development of rapid diagnosis systems. The LAMP approach presents promising results to monitor exposed individuals and also improves screening efforts in potential ports of entry.
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Affiliation(s)
- Yakup Artik
- Republic of Turkey, Ministry of Health, Health Institutes of Turkey (TUSEB), COVID-19 Diagnostic Center, University of Health Sciences, Kanuni Sultan Süleyman Training and Research Hospital, Istanbul, Küçükçekmece, Turkey.,Private Viromed Istanbul Central Laboratory and Imaging Center, COVID-19 Diagnostic Center, Istanbul, Şişli, Turkey.,Department of Molecular Biology and Genetics, Istanbul Kültür University, Faculty of Science and Letters, Istanbul, Bakırköy, Turkey
| | - Alp B Coşğun
- Private Viromed Istanbul Central Laboratory and Imaging Center, COVID-19 Diagnostic Center, Istanbul, Şişli, Turkey
| | - Nevra P Cesur
- Republic of Turkey, Ministry of Health, Health Institutes of Turkey (TUSEB), COVID-19 Diagnostic Center, University of Health Sciences, Kanuni Sultan Süleyman Training and Research Hospital, Istanbul, Küçükçekmece, Turkey.,Private Viromed Istanbul Central Laboratory and Imaging Center, COVID-19 Diagnostic Center, Istanbul, Şişli, Turkey
| | - Nedret Hızel
- Private Viromed Istanbul Central Laboratory and Imaging Center, COVID-19 Diagnostic Center, Istanbul, Şişli, Turkey.,Faculty of Medicine, Medical Biochemistry, Üsküdar University, Istanbul, Üsküdar, Turkey
| | - Yavuz Uyar
- Private Viromed Istanbul Central Laboratory and Imaging Center, COVID-19 Diagnostic Center, Istanbul, Şişli, Turkey
| | - Haydar Sur
- Department of Public Health, Faculty of Medicine, Üsküdar University, Istanbul, Üsküdar, Turkey
| | - Alp Ayan
- Department of Molecular Biology and Genetics, Istanbul Kültür University, Faculty of Science and Letters, Istanbul, Bakırköy, Turkey
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5
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Hatirnaz Ng O, Akyoney S, Sahin I, Soykam HO, Bayram Akcapinar G, Ozdemir O, Kancagi DD, Sir Karakus G, Yurtsever B, Kocagoz AS, Ovali E, Ozbek U. Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. PLoS One 2021; 16:e0260438. [PMID: 34871297 PMCID: PMC8648120 DOI: 10.1371/journal.pone.0260438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/10/2021] [Indexed: 12/11/2022] Open
Abstract
The Coronavirus Disease 2019 (COVID-19) was declared a pandemic in March 2020 by the World Health Organization (WHO). As of May 25th, 2021 there were 2.059.941 SARS-COV2 genome sequences that have been submitted to the GISAID database, with numerous variations. Here, we aim to analyze the SARS-CoV-2 genome data submitted to the GISAID database from Turkey and to determine the variant and clade distributions by the end of May 2021, in accordance with their appearance timeline. We compared these findings to USA, Europe, and Asia data as well. We have also evaluated the effects of spike protein variations, detected in a group of genome sequences of 13 patients who applied to our clinic, by using 3D modeling algorithms. For this purpose, we analyzed 4607 SARS-CoV-2 genome sequences submitted by different lab centers from Turkey to the GISAID database between March 2020 and May 2021. Described mutations were also introduced in silico to the spike protein structure to analyze their isolated impacts on the protein structure. The most abundant clade was GR followed by G, GH, and GRY and we did not detect any V clade. The most common variant was B.1, followed by B.1.1, and the UK variant, B.1.1.7. Our results clearly show a concordance between the variant distributions, the number of cases, and the timelines of different variant accumulations in Turkey. The 3D simulations indicate an increase in the surface hydrophilicity of the reference spike protein and the detected mutations. There was less surface hydrophilicity increase in the Asp614Gly mutation, which exhibits a more compact conformation around the ACE-2 receptor binding domain region, rendering the structure in a “down” conformation. Our genomic findings can help to model vaccination programs and protein modeling may lead to different approaches for COVID-19 treatment strategies.
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Affiliation(s)
- Ozden Hatirnaz Ng
- Department of Medical Biology, Acibadem Mehmet Ali Aydinlar University School of Medicine, Istanbul, Turkey
- Acibadem Mehmet Ali Aydinlar University Rare Diseases and Orphan Drugs Application and Research Center (ACURARE), Istanbul, Turkey
| | - Sezer Akyoney
- Department of Medical Biology, Acibadem Mehmet Ali Aydinlar University School of Medicine, Istanbul, Turkey
- Department of Biostatistics and Bioinformatics, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Ilayda Sahin
- Department of Medical Biotechnology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Department of Medical Genetics, Acibadem Mehmet Ali Aydinlar University School of Medicine, Istanbul, Turkey
| | - Huseyin Okan Soykam
- Department of Biostatistics and Bioinformatics, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Gunseli Bayram Akcapinar
- Department of Medical Biotechnology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Ozkan Ozdemir
- Acibadem Mehmet Ali Aydinlar University Rare Diseases and Orphan Drugs Application and Research Center (ACURARE), Istanbul, Turkey
- Department of Genome Studies, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | | | | | - Bulut Yurtsever
- Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey
| | - Ayse Sesin Kocagoz
- Department of Infectious Diseases and Clinical Microbiology, Acibadem Mehmet Ali Aydinlar University School of Medicine, Istanbul, Turkey
| | - Ercument Ovali
- Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey
| | - Ugur Ozbek
- Acibadem Mehmet Ali Aydinlar University Rare Diseases and Orphan Drugs Application and Research Center (ACURARE), Istanbul, Turkey
- Department of Medical Genetics, Acibadem Mehmet Ali Aydinlar University School of Medicine, Istanbul, Turkey
- * E-mail:
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6
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Farag EA, Islam MM, Enan K, El-Hussein ARM, Bansal D, Haroun M. SARS-CoV-2 at the human-animal interphase: A review. Heliyon 2021; 7:e08496. [PMID: 34869934 PMCID: PMC8626158 DOI: 10.1016/j.heliyon.2021.e08496] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 09/29/2021] [Accepted: 11/24/2021] [Indexed: 12/15/2022] Open
Abstract
Since its emergence in China in December 2019, COVID-19 remains the recent leading disease of concern drawing the public health attention globally. The disease is known of viral origin and zoonotic nature originating from animals. However, to date neither the source of the spillover nor the intermediate hosts are identified. Moreover, the public health situation is intermittently aggravated by identification of new animals susceptible to the SARS-CoV-2 infection, potentially replicating the virus and maintaining intra and interspecies spread of the disease. Although the role of a given animal and/or its produce is important to map the disease pattern, continuous efforts should be undertaken to further understand the epidemiology of SARS-CoV-2, a vital step to establish effective disease prevention and control strategy. This manuscript attempted to review updates regarding SARS-CoV-2 infection at the human-animal interface with consideration to postulations on the genetic relatedness and origin of the different SARS-CoV-2 variants isolated from different animal species. Also, the review addresses the possible role of different animal species and their produce in transmission of the disease. Also, the manuscript discussed the contamination potentiality of the virus and its environmental stability. Finally, we reviewed the currently instituted measures to prevent and manage the spread of SARS-CoV-2 infection. The manuscript suggested the One Health based control measures that could prove of value for the near future.
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Affiliation(s)
| | - Md Mazharul Islam
- Department of Animal Resources, Ministry of Municipality and Environment, Doha, Qatar
| | - Khalid Enan
- Department of Animal Resources, Ministry of Municipality and Environment, Doha, Qatar
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7
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KOCABAŞ F, USLU M. The current state of validated small molecules inhibiting SARS-CoV-2 nonstructural proteins. Turk J Biol 2021; 45:469-483. [PMID: 34803448 PMCID: PMC8573838 DOI: 10.3906/biy-2106-42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 08/06/2021] [Indexed: 11/03/2022] Open
Abstract
The current COVID-19 outbreak has had a profound influence on public health and daily life. Despite all restrictions and vaccination programs, COVID-19 still can lead to fatality due to a lack of COVID-19-specific treatments. A number of studies have demonstrated the feasibility to develop therapeutics by targeting underlying components of the viral proteome. Here we reviewed recently developed and validated small molecule inhibitors of SARS-CoV-2's nonstructural proteins. We described the validation level of identified compounds specific for SARS-CoV-2 in the presence of in vitro and in vivo supporting data. The mechanisms of pharmacological activity, as well as approaches for developing improved SARS-CoV-2 NSP inhibitors have been emphasized.
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Affiliation(s)
- Fatih KOCABAŞ
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, İstanbulTurkey
| | - Merve USLU
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, İstanbulTurkey
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8
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Gamma-irradiated SARS-CoV-2 vaccine candidate, OZG-38.61.3, confers protection from SARS-CoV-2 challenge in human ACEII-transgenic mice. Sci Rep 2021; 11:15799. [PMID: 34349145 PMCID: PMC8339061 DOI: 10.1038/s41598-021-95086-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 07/21/2021] [Indexed: 11/29/2022] Open
Abstract
The SARS-CoV-2 virus caused the most severe pandemic around the world, and vaccine development for urgent use became a crucial issue. Inactivated virus formulated vaccines such as Hepatitis A and smallpox proved to be reliable approaches for immunization for prolonged periods. In this study, a gamma-irradiated inactivated virus vaccine does not require an extra purification process, unlike the chemically inactivated vaccines. Hence, the novelty of our vaccine candidate (OZG-38.61.3) is that it is a non-adjuvant added, gamma-irradiated, and intradermally applied inactive viral vaccine. Efficiency and safety dose (either 1013 or 1014 viral RNA copy per dose) of OZG-38.61.3 was initially determined in BALB/c mice. This was followed by testing the immunogenicity and protective efficacy of the vaccine. Human ACE2-encoding transgenic mice were immunized and then infected with the SARS-CoV-2 virus for the challenge test. This study shows that vaccinated mice have lowered SARS-CoV-2 viral RNA copy numbers both in oropharyngeal specimens and in the histological analysis of the lung tissues along with humoral and cellular immune responses, including the neutralizing antibodies similar to those shown in BALB/c mice without substantial toxicity. Subsequently, plans are being made for the commencement of Phase 1 clinical trial of the OZG-38.61.3 vaccine for the COVID-19 pandemic.
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9
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Berber B, Aydin C, Kocabas F, Guney-Esken G, Yilancioglu K, Karadag-Alpaslan M, Caliseki M, Yuce M, Demir S, Tastan C. Gene editing and RNAi approaches for COVID-19 diagnostics and therapeutics. Gene Ther 2021; 28:290-305. [PMID: 33318646 PMCID: PMC7734466 DOI: 10.1038/s41434-020-00209-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 10/20/2020] [Accepted: 10/27/2020] [Indexed: 01/29/2023]
Abstract
The novel coronavirus pneumonia (COVID-19) is a highly infectious acute respiratory disease caused by Severe Acute Respiratory Syndrome-Related Coronavirus (SARS-CoV-2) (Prec Clin Med 2020;3:9-13, Lancet 2020;395:497-506, N. Engl J Med 2020a;382:1199-207, Nature 2020;579:270-3). SARS-CoV-2 surveillance is essential to controlling widespread transmission. However, there are several challenges associated with the diagnostic of the COVID-19 during the current outbreak (Liu and Li (2019), Nature 2020;579:265-9, N. Engl J Med 2020;382:727-33). Firstly, the high number of cases overwhelms diagnostic test capacity and proposes the need for a rapid solution for sample processing (Science 2018;360:444-8). Secondly, SARS-CoV-2 is closely related to other important coronavirus species and subspecies, so detection assays can give false-positive results if they are not efficiently specific to SARS-CoV-2. Thirdly, patients with suspected SARS-CoV-2 infection sometimes have a different respiratory viral infection or co-infections with SARS-CoV-2 and other respiratory viruses (MedRxiv 2020a;1-18). Confirmation of the COVID-19 is performed mainly by virus isolation followed by RT-PCR and sequencing (N. Engl J Med 2020;382:727-33, MedRxiv 2020a, Turkish J Biol 2020;44:192-202). The emergence and outbreak of the novel coronavirus highlighted the urgent need for new therapeutic technologies that are fast, precise, stable, easy to manufacture, and target-specific for surveillance and treatment. Molecular biology tools that include gene-editing approaches such as CRISPR-Cas12/13-based SHERLOCK, DETECTR, CARVER and PAC-MAN, antisense oligonucleotides, antisense peptide nucleic acids, ribozymes, aptamers, and RNAi silencing approaches produced with cutting-edge scientific advances compared to conventional diagnostic or treatment methods could be vital in COVID-19 and other future outbreaks. Thus, in this review, we will discuss potent the molecular biology approaches that can revolutionize diagnostic of viral infections and therapies to fight COVID-19 in a highly specific, stable, and efficient way.
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Affiliation(s)
- Burak Berber
- Department of Biology, Faculty of Science, Eskisehir Technical University, Eskisehir, Turkey
| | - Cihan Aydin
- Department of Molecular Biology and Genetics, Faculty of Engineering and Natural Sciences, Istanbul Medeniyet University, Istanbul, Turkey
| | - Fatih Kocabas
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Gulen Guney-Esken
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Kaan Yilancioglu
- Institute of Addiction and Forensic Sciences, Uskudar University, Istanbul, Turkey
- Transgenic Cell Technologies and Epigenetics Application and Research Center (TRGENMER), Uskudar University, Istanbul, Turkey
| | - Medine Karadag-Alpaslan
- Department of Medical Genetics, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey
| | - Mehmet Caliseki
- Department of Molecular Biology, Genetics and Bioengineering, Graduate School of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Melek Yuce
- Center for Stem Cell Research, Ondokuz Mayis University, Samsun, Turkey
| | - Sevda Demir
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Cihan Tastan
- Transgenic Cell Technologies and Epigenetics Application and Research Center (TRGENMER), Uskudar University, Istanbul, Turkey.
- Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey.
- Faculty of Science and Letters, Department of Molecular Biology and Genetics, Istanbul Kultur University, Istanbul, Turkey.
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10
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Sir Karakus G, Tastan C, Dilek Kancagi D, Yurtsever B, Tumentemur G, Demir S, Turan RD, Abanuz S, Cakirsoy D, Seyis U, Ozer S, Elibol O, Elek M, Ertop G, Arbak S, Acikel Elmas M, Hemsinlioglu C, Kocagoz AS, Hatirnaz Ng O, Akyoney S, Sahin I, Ozbek U, Telci D, Sahin F, Yalcin K, Ratip S, Ovali E. Preclinical efficacy and safety analysis of gamma-irradiated inactivated SARS-CoV-2 vaccine candidates. Sci Rep 2021; 11:5804. [PMID: 33707532 PMCID: PMC7970959 DOI: 10.1038/s41598-021-83930-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/04/2021] [Indexed: 12/27/2022] Open
Abstract
COVID-19 outbreak caused by SARS-CoV-2 created an unprecedented health crisis since there is no vaccine for this novel virus. Therefore, SARS-CoV-2 vaccines have become crucial for reducing morbidity and mortality. In this study, in vitro and in vivo safety and efficacy analyzes of lyophilized vaccine candidates inactivated by gamma-irradiation were performed. The candidate vaccines in this study were OZG-3861 version 1 (V1), an inactivated SARS-CoV-2 virus vaccine, and SK-01 version 1 (V1), a GM-CSF adjuvant added vaccine. The candidate vaccines were applied intradermally to BALB/c mice to assess toxicity and immunogenicity. Preliminary results in vaccinated mice are reported in this study. Especially, the vaccine models containing GM-CSF caused significant antibody production with neutralization capacity in absence of the antibody-dependent enhancement feature, when considered in terms of T and B cell responses. Another important finding was that the presence of adjuvant was more important in T cell in comparison with B cell response. Vaccinated mice showed T cell response upon restimulation with whole inactivated SARS-CoV-2 or peptide pool. This study shows that the vaccines are effective and leads us to start the challenge test to investigate the gamma-irradiated inactivated vaccine candidates for infective SARS-CoV-2 virus in humanized ACE2 + mice.
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Affiliation(s)
| | - Cihan Tastan
- Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey
- Molecular Biology and Genetics Department, Uskudar University, Istanbul, Turkey
| | | | - Bulut Yurtsever
- Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey
| | - Gamze Tumentemur
- Vocational School of Health Services, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Sevda Demir
- Genetic and Bioengineering Department, Yeditepe University, Istanbul, Turkey
| | - Raife Dilek Turan
- Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey
- Genetic and Bioengineering Department, Yeditepe University, Istanbul, Turkey
| | - Selen Abanuz
- Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey
- Medical Biochemistry Department, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Didem Cakirsoy
- Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey
- Medical Biotechnology Department, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Utku Seyis
- Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey
| | - Samed Ozer
- Animal Application and Research Center, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Omer Elibol
- Acibadem Altunizade Hospital, Istanbul, Turkey
| | - Muhammer Elek
- Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey
- Genetic and Bioengineering Department, Yeditepe University, Istanbul, Turkey
| | - Gurcan Ertop
- Vocational School of Health Services, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Serap Arbak
- Histology and Embryology Department, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Merve Acikel Elmas
- Histology and Embryology Department, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | | | | | - Ozden Hatirnaz Ng
- Medical Biology Department, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Sezer Akyoney
- Medical Biology Department, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Biostatistics and Bioinformatics Department, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Ilayda Sahin
- Medical Biotechnology Department, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Medical Genetics Department, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Ugur Ozbek
- Medical Genetics Department, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Dilek Telci
- Genetic and Bioengineering Department, Yeditepe University, Istanbul, Turkey
| | - Fikrettin Sahin
- Genetic and Bioengineering Department, Yeditepe University, Istanbul, Turkey
| | - Koray Yalcin
- Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey
- Medical Park Goztepe Hospital, Pediatric Bone Marrow Transplantation Unit, Istanbul, Turkey
| | - Siret Ratip
- Hematology Department, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Ercument Ovali
- Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey.
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11
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Akan S, Ediz C, Kızılkan YE, Alcin A, Tavukcu HH, Yilmaz O. COVID-19 infection threat in patients with high-risk non-muscle invasive bladder cancer receiving intravesical BCG therapy. Int J Clin Pract 2021; 75:e13752. [PMID: 33064918 PMCID: PMC7646056 DOI: 10.1111/ijcp.13752] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 10/03/2020] [Indexed: 01/08/2023] Open
Abstract
AIM We evaluated the COVID-19 infection threat in patients receiving intravesical BCG therapy which has immunotherapeutic effects and is of vital importance in most of the individuals with high-risk non-muscle-invasive bladder cancer (NMIBC) and investigated the need for postponement of this therapy. METHODS A total of 71 patients, who were diagnosed with high-risk NMIBC and on intravesical BCG treatment regularly (induction or maintenance), were enrolled in the study. The patients were classified into two groups depending on whether they were diagnosed with COVID-19 during the pandemic period or not. RESULTS Of 71 patients, 26 underwent a COVID-19 polymerase chain reaction test with clinical suspicion during the pandemic period. Of these 26 patients, 4 were diagnosed with COVID-19. Age of the patients, working status (working/retired), compliance with containment measures against the pandemic, number of BCG courses, adverse effects after BCG therapy and systemic immune-inflammation index, which is an inflammation-related parameter, were not different between groups (P > .05). Neutrophil/lymphocyte ratio was significantly higher in the COVID-19 positive group (P < .05). COVID-19 positivity was higher in age groups 50-64 (6.6%) and 65-80 (5.8%) years than that in similar age groups of the normal population. CONCLUSION Every effort should be made to administer intravesical BCG treatment in high-risk NMIBC patients even during the pandemic period. However, increased risk of COVID-19 transmission should be kept in mind and protective measures against COVID-19 for healthcare providers and patients before the procedure should be taken optimally. The procedure should be postponed in patients with lymphopenia in recent complete blood count.
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Affiliation(s)
- Serkan Akan
- Department of UrologyUniversity of Health SciencesSultan Abdulhamid Han Training and Research HospitalIstanbulTurkey
| | - Caner Ediz
- Department of UrologyUniversity of Health SciencesSultan Abdulhamid Han Training and Research HospitalIstanbulTurkey
| | - Yunus Emre Kızılkan
- Department of UrologyUniversity of Health SciencesSultan Abdulhamid Han Training and Research HospitalIstanbulTurkey
| | - Adem Alcin
- Department of UrologyUniversity of Health SciencesSultan Abdulhamid Han Training and Research HospitalIstanbulTurkey
| | - Hasan Huseyin Tavukcu
- Department of UrologyUniversity of Health SciencesSultan Abdulhamid Han Training and Research HospitalIstanbulTurkey
| | - Omer Yilmaz
- Department of UrologyUniversity of Health SciencesSultan Abdulhamid Han Training and Research HospitalIstanbulTurkey
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12
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Karamitros T, Papadopoulou G, Bousali M, Mexias A, Tsiodras S, Mentis A. SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies. J Clin Virol 2020; 131:104585. [PMID: 32818852 PMCID: PMC7418792 DOI: 10.1016/j.jcv.2020.104585] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 08/05/2020] [Accepted: 08/09/2020] [Indexed: 12/19/2022]
Abstract
In December 2019, an outbreak of atypical pneumonia (Coronavirus disease 2019 -COVID-19) associated with a novel coronavirus (SARS-CoV-2) was reported in Wuhan city, Hubei province, China. The outbreak was traced to a seafood wholesale market and human to human transmission was confirmed. The rapid spread and the death toll of the new epidemic warrants immediate intervention. The intra-host genomic variability of SARS-CoV-2 plays a pivotal role in the development of effective antiviral agents and vaccines, as well as in the design of accurate diagnostics. We analyzed NGS data derived from clinical samples of three Chinese patients infected with SARS-CoV-2, in order to identify small- and large-scale intra-host variations in the viral genome. We identified tens of low- or higher- frequency single nucleotide variations (SNVs) with variable density across the viral genome, affecting 7 out of 10 protein-coding viral genes. The majority of these SNVs (72/104) corresponded to missense changes. The annotation of the identified SNVs but also of all currently circulating strain variations revealed colocalization of intra-host as well as strain specific SNVs with primers and probes currently used in molecular diagnostics assays. Moreover, we de-novo assembled the viral genome, in order to isolate and validate intra-host structural variations and recombination breakpoints. The bioinformatics analysis disclosed genomic rearrangements over poly-A / poly-U regions located in ORF1ab and spike (S) gene, including a potential recombination hot-spot within S gene. Our results highlight the intra-host genomic diversity and plasticity of SARS-CoV-2, pointing out genomic regions that are prone to alterations. The isolated SNVs and genomic rearrangements reflect the intra-patient capacity of the polymorphic quasispecies, which may arise rapidly during the outbreak, allowing immunological escape of the virus, offering resistance to anti-viral drugs and affecting the sensitivity of the molecular diagnostics assays.
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Affiliation(s)
- Timokratis Karamitros
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece.
| | - Gethsimani Papadopoulou
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | - Maria Bousali
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | - Anastasios Mexias
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | - Sotirios Tsiodras
- 4(th) Academic Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Andreas Mentis
- Public Health Laboratories, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
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13
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Sabino CP, Sellera FP, Sales-Medina DF, Machado RRG, Durigon EL, Freitas-Junior LH, Ribeiro MS. UV-C (254 nm) lethal doses for SARS-CoV-2. Photodiagnosis Photodyn Ther 2020; 32:101995. [PMID: 32916328 PMCID: PMC7477605 DOI: 10.1016/j.pdpdt.2020.101995] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/01/2020] [Accepted: 09/04/2020] [Indexed: 11/27/2022]
Abstract
We developed a controlled assay to investigate the UV-C inactivation kinetics for SARS-CoV-2. We established the UV-C lethal doses for the virus in vitro. LD90 for SARS-CoV-2 was reached at 0.016 mJ/cm2. LD99.999 was achieved at 108.714 mJ/cm2 with exposure time less than 50 s.
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Affiliation(s)
- Caetano P Sabino
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil; BioLambda, Scientific and Commercial LTD, São Paulo, Brazil.
| | - Fábio P Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil; School of Veterinary Medicine, Metropolitan University of Santos, Santos, Brazil
| | - Douglas F Sales-Medina
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Edison Luiz Durigon
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Lucio H Freitas-Junior
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Martha S Ribeiro
- Center for Lasers and Applications, Nuclear and Energy Research Institute (IPEN-CNEN/SP), São Paulo, SP, Brazil.
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14
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Okur HK, Yalcin K, Tastan C, Demir S, Yurtsever B, Karakus GS, Kancagi DD, Abanuz S, Seyis U, Zengin R, Hemsinlioglu C, Kara M, Yildiz ME, Deliceo E, Birgen N, Pelit NB, Cuhadaroglu C, Kocagoz AS, Ovali E. Preliminary report of in vitro and in vivo effectiveness of dornase alfa on SARS-CoV-2 infection. New Microbes New Infect 2020; 37:100756. [PMID: 32922804 PMCID: PMC7476504 DOI: 10.1016/j.nmni.2020.100756] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/02/2020] [Accepted: 09/02/2020] [Indexed: 12/21/2022] Open
Abstract
Dornase alfa, the recombinant form of the human DNase I enzyme, breaks down neutrophil extracellular traps (NET) that include a vast amount of DNA fragments, histones, microbicidal proteins and oxidant enzymes released from necrotic neutrophils in the highly viscous mucus of cystic fibrosis patients. Dornase alfa has been used for decades in patients with cystic fibrosis to reduce the viscoelasticity of respiratory tract secretions, to decrease the severity of respiratory tract infections, and to improve lung function. Previous studies have linked abnormal NET formations to lung diseases, especially to acute respiratory distress syndrome (ARDS). It is well known that novel coronavirus disease 2019 (COVID-19) pneumonia progresses to ARDS and even multiple organ failure. High blood neutrophil levels are an early indicator of COVID-19 and predict severe respiratory diseases. Also it is reported that mucus structure in COVID-19 is very similar to that in cystic fibrosis due to the accumulation of excessive NET in the lungs. In this study, we showed the recovery of three individuals with COVID-19 after including dornase alfa in their treatment. We followed clinical improvement in the radiological analysis (two of three cases), oxygen saturation (Spo2), respiratory rate, disappearance of dyspnoea, coughing and a decrease in NET formation and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load after the treatment. Also here, we share our preliminary results suggesting that dornase alfa has an anti-viral effect against SARS-CoV-2 infection in a green monkey kidney cell line, Vero, and a bovine kidney cell line, MDBK, without determined cytotoxicity on healthy peripheral blood mononuclear cells.
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Affiliation(s)
- H K Okur
- Acibadem Altunizade Hospital, Chest Disease Unit, Istanbul, Turkey
| | - K Yalcin
- Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey.,Medical Park Goztepe Hospital, Paediatric Bone Marrow Transplantation Unit, Istanbul, Turkey
| | - C Tastan
- Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey
| | - S Demir
- Genetic and Bioengineering Department, Yeditepe University, Istanbul, Turkey
| | - B Yurtsever
- Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey
| | - G S Karakus
- Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey
| | - D D Kancagi
- Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey
| | - S Abanuz
- Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey
| | - U Seyis
- Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey
| | - R Zengin
- Acibadem Altunizade Hospital, Infectious Disease Unit, Istanbul, Turkey
| | - C Hemsinlioglu
- Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey
| | - M Kara
- Acibadem Altunizade Hospital, Internal Medicine Unit Department of Endocrinology, Istanbul, Turkey
| | - M E Yildiz
- Acibadem Altunizade Hospital, Radiology Unit, Istanbul, Turkey
| | - E Deliceo
- Acibadem Mehmet Ali Aydinlar University, School of Medicine, Department of Pediatrics, Istanbul, Turkey
| | - N Birgen
- Acibadem Altunizade Hospital, Cellular Therapy Centre, Istanbul, Turkey
| | - N B Pelit
- Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey
| | - C Cuhadaroglu
- Acibadem Altunizade Hospital, Chest Disease Unit, Istanbul, Turkey
| | - A S Kocagoz
- Acibadem Altunizade Hospital, Infectious Disease Unit, Istanbul, Turkey
| | - E Ovali
- Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey
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