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Tolksdorf B, Heinze J, Niemeyer D, Röhrs V, Berg J, Drosten C, Kurreck J. Development of a highly stable, active small interfering RNA with broad activity against SARS-CoV viruses. Antiviral Res 2024; 226:105879. [PMID: 38599550 DOI: 10.1016/j.antiviral.2024.105879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/22/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
Treatment options for COVID-19 remain limited. Here, we report the optimization of an siRNA targeting the highly conserved leader region of SARS-CoV-2. The siRNA was rendered nuclease resistant by the introduction of modified nucleotides without loss of activity. Importantly, the siRNA also retained its inhibitory activity against the emerged omicron sublineage variant BA.2, which occurred after the siRNA was designed and is resistant to other antiviral agents such as antibodies. In addition, we show that a second highly active siRNA designed against the viral 5'-UTR can be applied as a rescue molecule, to minimize the spread of escape mutations. We therefore consider our siRNA-based molecules to be promising broadly active candidates for the treatment of current and future SARS-CoV-2 variants.
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Affiliation(s)
- Beatrice Tolksdorf
- Chair of Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, Berlin, 10623, Germany
| | - Julian Heinze
- German Center for Infection Research (DZIF), Charitéplatz 1, 10117, Berlin, Germany; Institute of Virology, Charité-Universitätsmedizin Berlin, 10117, Germany
| | - Daniela Niemeyer
- German Center for Infection Research (DZIF), Charitéplatz 1, 10117, Berlin, Germany; Institute of Virology, Charité-Universitätsmedizin Berlin, 10117, Germany
| | - Viola Röhrs
- Chair of Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, Berlin, 10623, Germany
| | - Johanna Berg
- Chair of Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, Berlin, 10623, Germany
| | - Christian Drosten
- German Center for Infection Research (DZIF), Charitéplatz 1, 10117, Berlin, Germany; Institute of Virology, Charité-Universitätsmedizin Berlin, 10117, Germany
| | - Jens Kurreck
- Chair of Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, Berlin, 10623, Germany.
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2
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Valleriani F, Di Pancrazio C, Spedicato M, Di Teodoro G, Malatesta D, Petrova T, Profeta F, Colaianni ML, Berjaoui S, Puglia I, Caporale M, Rossi E, Marcacci M, Luciani M, Sacchini F, Portanti O, Bencivenga F, Decaro N, Bonfante F, Lorusso A. A cell-adapted SARS-CoV-2 mutant, showing a deletion in the spike protein spanning the furin cleavage site, has reduced virulence at the lung level in K18-hACE2 mice. Virology 2024; 592:109997. [PMID: 38324940 DOI: 10.1016/j.virol.2024.109997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 01/05/2024] [Accepted: 01/17/2024] [Indexed: 02/09/2024]
Abstract
Here we investigated the virulence properties of a unique cell-adapted SARS-CoV-2 mutant showing a ten-amino acid deletion encompassing the furin cleavage site of the spike protein (Δ680SPRAARSVAS689; Δ680-689-B.1) in comparison to its parental strain (wt-B.1) and two Delta variants (AY.122 and AY.21) of concern. After intranasal inoculation, transgenic K18-hACE2 mice were monitored for 14 days for weight change, lethality, and clinical score; oral swabs were daily collected and tested for the presence of N protein subgenomic RNA. At 3 and 7 dpi mice were also sacrificed and organs collected for molecular, histopathological, and immune response profile investigations. The Δ680-689-B.1-infected mice exhibited reduced shedding, lower virulence at the lung level, and milder pulmonary lesions. In the lung, infection with Δ680-689-B.1 was associated with a significant lower expression of some cytokines at 3 dpi (IL-4, IL-27, and IL-28) and 7 dpi (IL-4, IL-27, IL-28, IFN-γ and IL-1α).
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Affiliation(s)
- Fabrizia Valleriani
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise (IZSAM), Teramo-Italy; IZSVe-IZSAM Joint FAO Reference Centre for Zoonotic Coronaviruses, Italy
| | - Chiara Di Pancrazio
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise (IZSAM), Teramo-Italy; IZSVe-IZSAM Joint FAO Reference Centre for Zoonotic Coronaviruses, Italy
| | - Massimo Spedicato
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise (IZSAM), Teramo-Italy; IZSVe-IZSAM Joint FAO Reference Centre for Zoonotic Coronaviruses, Italy
| | - Giovanni Di Teodoro
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise (IZSAM), Teramo-Italy; IZSVe-IZSAM Joint FAO Reference Centre for Zoonotic Coronaviruses, Italy
| | - Daniela Malatesta
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise (IZSAM), Teramo-Italy; IZSVe-IZSAM Joint FAO Reference Centre for Zoonotic Coronaviruses, Italy
| | - Tetyana Petrova
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise (IZSAM), Teramo-Italy; IZSVe-IZSAM Joint FAO Reference Centre for Zoonotic Coronaviruses, Italy
| | - Francesca Profeta
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise (IZSAM), Teramo-Italy; IZSVe-IZSAM Joint FAO Reference Centre for Zoonotic Coronaviruses, Italy
| | | | - Shadia Berjaoui
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise (IZSAM), Teramo-Italy; IZSVe-IZSAM Joint FAO Reference Centre for Zoonotic Coronaviruses, Italy
| | - Ilaria Puglia
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise (IZSAM), Teramo-Italy; IZSVe-IZSAM Joint FAO Reference Centre for Zoonotic Coronaviruses, Italy
| | - Marialuigia Caporale
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise (IZSAM), Teramo-Italy; IZSVe-IZSAM Joint FAO Reference Centre for Zoonotic Coronaviruses, Italy
| | - Emanuela Rossi
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise (IZSAM), Teramo-Italy; IZSVe-IZSAM Joint FAO Reference Centre for Zoonotic Coronaviruses, Italy
| | - Maurilia Marcacci
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise (IZSAM), Teramo-Italy; IZSVe-IZSAM Joint FAO Reference Centre for Zoonotic Coronaviruses, Italy
| | - Mirella Luciani
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise (IZSAM), Teramo-Italy; IZSVe-IZSAM Joint FAO Reference Centre for Zoonotic Coronaviruses, Italy
| | - Flavio Sacchini
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise (IZSAM), Teramo-Italy; IZSVe-IZSAM Joint FAO Reference Centre for Zoonotic Coronaviruses, Italy
| | - Ottavio Portanti
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise (IZSAM), Teramo-Italy; IZSVe-IZSAM Joint FAO Reference Centre for Zoonotic Coronaviruses, Italy
| | | | - Nicola Decaro
- Department of Veterinary Medicine, University of Bari, Valenzano-Italy
| | - Francesco Bonfante
- IZSVe-IZSAM Joint FAO Reference Centre for Zoonotic Coronaviruses, Italy; Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro-Italy
| | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise (IZSAM), Teramo-Italy; IZSVe-IZSAM Joint FAO Reference Centre for Zoonotic Coronaviruses, Italy.
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Vu Thi H, Tran LT, Nguyen HQ, Chu DT. RNA therapeutics for respiratory diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 203:257-271. [PMID: 38360002 DOI: 10.1016/bs.pmbts.2023.12.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
It has become increasingly common to utilize RNA treatment to treat respiratory illnesses. Experimental research on both people and animals has advanced quickly since the turn of the twenty-first century in an effort to discover a treatment for respiratory ailments that could not be accomplished with earlier techniques, specifically in treating prevalent respiratory diseases such as lung cancer, chronic obstructive pulmonary disease (COPD), respiratory infections caused by viruses, and asthma. This chapter has provided a comprehensive overview of the scientific evidence in applying RNA therapy to treat respiratory diseases. The chapter describes the development of this therapy for respiratory diseases. At the same time, the types of RNA therapy for respiratory diseases have been highlighted. In addition, the mechanism of this therapy for respiratory diseases has also been covered. These insights are indispensable if this therapy is to be developed widely.
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Affiliation(s)
- Hue Vu Thi
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam
| | - Linh Thao Tran
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Huy Quang Nguyen
- LMI DRISA, Department of Life Sciences, University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Dinh-Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam.
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Mubashshir M, Ahmad N, Negi T, Rawal R, Singhvi N, Khatoon H, Laxmi V, Dubey O, Sharma RB, Negi G, Ovais M. Therapeutic Benefits of Melatonin against COVID-19. Neuroimmunomodulation 2023; 30:196-205. [PMID: 37336193 PMCID: PMC10614475 DOI: 10.1159/000531550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/02/2023] [Indexed: 06/21/2023] Open
Abstract
The assumption of the pineal hormone melatonin as a therapeutic use for COVID-19-affected people seems promising. Its intake has shown significant improvement in the patients' conditions. Higher melatonin titers in children may provide a protective shield against this disease. The hormone melatonin works as an anti-inflammatory, antioxidant, immunomodulator, and strategically slows down the cytokine release which is observed in the COVID-19 disease, thereby improving the overall health of afflicted patients. The medical community is expected shortly to use remedial attributes like anti-inflammatory, antioxidant, antivirals, etc., of melatonin in the successful prevention and cure of COVID-19 morbidity. Thus, the administration of melatonin seems auspicious in the cure and prevention of this COVID-19 fatality. Moreover, melatonin does not seem to reduce the efficiency of approved vaccines against the SARS-CoV-2 virus. Melatonin increases the production of inflammatory cytokines and Th1 and enhances both humoral and cell-mediated responses. Through the enhanced humoral immunity, melatonin exhibits antiviral activities by suppressing multiple inflammatory products such as IL-6, IL1β, and tumor necrosis factor α, which are immediately released during lung injury of severe COVID-19. Hence, the novel use of melatonin along with other antivirals as an early treatment option against COVID-19 infection is suggested. Here, we have chalked out the invasion mechanisms and appropriate implications of the latest findings concerned with melatonin against the virus SARS-CoV-2. Nevertheless, within the setting of a clinical intervention, the promising compounds must go through a series of studies before their recommendation. In the clinical field, this is done in a time-ordered sequence, in line with the phase label affixed to proper protocol of trials: phase I-phase II and the final phase III. Nevertheless, while medical recommendations can only be made on the basis of reassuring evidence, there are still three issues worth considering before implementation: representativeness, validity, and lastly generalizability.
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Affiliation(s)
- Muhammad Mubashshir
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, India
| | - Nabeel Ahmad
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, India
| | - Tripti Negi
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, India
| | - Renu Rawal
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, India
| | - Nirjara Singhvi
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, India
| | - Hina Khatoon
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, India
| | - Vijya Laxmi
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, India
| | - Om Dubey
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, India
| | - Renu Bala Sharma
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, India
| | - Ganga Negi
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, India
| | - Mohd Ovais
- Department of Bio-Science, Barkatullah University, Bhopal, India
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Ning L, Liu M, Gou Y, Yang Y, He B, Huang J. Development and application of ribonucleic acid therapy strategies against COVID-19. Int J Biol Sci 2022; 18:5070-5085. [PMID: 35982905 PMCID: PMC9379410 DOI: 10.7150/ijbs.72706] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 07/16/2022] [Indexed: 11/17/2022] Open
Abstract
The Coronavirus disease 2019 (COVID-19) pandemic is caused by the severe acute respiratory syndrome 2 coronavirus (SARS-CoV-2), remaining a global health crisis since its outbreak until now. Advanced biotechnology and research findings have revealed many suitable viral and host targets for a wide range of therapeutic strategies. The emerging ribonucleic acid therapy can modulate gene expression by post-transcriptional gene silencing (PTGS) based on Watson-Crick base pairing. RNA therapies, including antisense oligonucleotides (ASO), ribozymes, RNA interference (RNAi), aptamers, etc., were used to treat SARS-CoV whose genome is similar to SARV-CoV-2, and the past experience also applies for the treatment of COVID-19. Several studies against SARS-CoV-2 based on RNA therapeutic strategy have been reported, and a dozen of relevant preclinical or clinical trials are in process globally. RNA therapy has been a very active and important part of COVID-19 treatment. In this review, we focus on the progress of ribonucleic acid therapeutic strategies development and application, discuss corresponding problems and challenges, and suggest new strategies and solutions.
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Affiliation(s)
- Lin Ning
- School of Healthcare Technology, Chengdu Neusoft University, Sichuan, China.,School of Life Science and Technology, University of Electronic Science and Technology of China, Sichuan, China
| | - Mujiexin Liu
- Ineye Hospital of Chengdu University of TCM, Sichuan, China
| | - Yushu Gou
- School of Life Science and Technology, University of Electronic Science and Technology of China, Sichuan, China
| | - Yue Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Sichuan, China
| | - Bifang He
- Medical College, Guizhou University, Guizhou, China
| | - Jian Huang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Sichuan, China
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Toseef M, Kiran A, Zhuo S, Jahangir M, Riaz S, Wei Z, Ghauri TA, Ullah I, Ahmad SB. Inspirational Leadership and Innovative Communication in Sustainable Organizations: A Mediating Role of Mutual Trust. Front Psychol 2022; 13:846128. [PMID: 36003091 PMCID: PMC9394427 DOI: 10.3389/fpsyg.2022.846128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
The possibility of accomplishing sustainable objectives is largely connected to the management and flourishing of an organizational system which keeps human capital engaged and committed. Our study investigated the association of inspirational leadership and innovative communication with employee engagement and commitment under the lens of leader member exchange theory. Specifically, we emphasized the mediating role of mutual trust in connection to social sustainability facets. A survey of data from employees in the manufacturing sector of Yunnan, China was utilized to test the hypothesized model. The study findings reported a significant association and came to the conclusion that a leader’s inspirational behavior coupled with innovative communication is a significant predictor of engagement and commitment in socially sustainable organizations. Moreover, mutual trust significantly mediated the relationship of innovative communication and inspirational leadership with employee engagement and commitment reaching the social perspective of sustainability. The current study added to the literature of sustainable organization by pointing out the social dimensions of sustainability.
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Affiliation(s)
- Muhammad Toseef
- Faculty of Management and Economics, Kunming University of Science and Technology, Kunming, China
- Department of Management Sciences, University College of Zhob, Balochistan University of Information Technology, Engineering & Management Sciences (BUITEMS), Zhob, Pakistan
| | - Alina Kiran
- Faculty of Technology Management and Technopreneurship, Universiti Teknikal Malaysia, Malacca, Malaysia
| | - Sufan Zhuo
- Business School, University of International Business and Economics, Beijing, China
- *Correspondence: Sufan Zhuo,
| | - Mahad Jahangir
- School of Business Administration, University of Lakki Marwat, Lakki Marwat, Pakistan
| | - Sidra Riaz
- School of Governance and Public Policy, National University of Modern Languages, Islamabad, Pakistan
| | - Zong Wei
- School of Ethnology and Sociology, Minzu University of China, Beijing, China
- South Asian Studies Center Institute of Area Studies, Honghe University, Mengzi, China
| | - Tauqir Ahmad Ghauri
- School of Business Administration, Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Irfan Ullah
- School of Management and Economics, Beijing Institute of Technology, Beijing, China
- *Correspondence: Sufan Zhuo,
| | - Suraya Binti Ahmad
- Faculty of Technology Management and Technopreneurship, Universiti Teknikal Malaysia, Malacca, Malaysia
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Ur Rehman M, Sajjad Naqvi S, Ullah R, Arshad N, Ammad M, Ul Ain Q, Razzak A, Yousaf M, Hussain A, Hasan TN. Elucidation of correlation between SARS-CoV-2 RdRp and N gene cycle threshold (Ct) by RT-PCR with age and gender. Clin Chim Acta 2022; 533:42-47. [PMID: 35714938 PMCID: PMC9195597 DOI: 10.1016/j.cca.2022.06.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/05/2022] [Indexed: 11/05/2022]
Abstract
Background Coronavirus disease 2019 (COVID19) caused by the new severe acute respiratory syndrome coronavirus 2 (SARSCoV2) is a global public health emergency. Age and gender are two important factors related to the risk and outcome of various diseases. Cycle threshold (Ct) value is believed to have relation with age and gender. Objective This study has been conducted to investigates the association between SARS-CoV-2 cycle threshold to age and gender of COVID-19 patients, to investigate whether the population-wide change of SARSCoV2 RTPCR Ct value over time is corelated to the number of new COVID19 cases and to investigate the dynamic of RdRp and N genes. Methods 72,811 individuals from second wave of COVID19, were observed in current study at Pure Health Lab, Mafraq Hospital, Abu Dhabi, UAE. Results 15,201/72,811 (21 %) positivity was observed. COVID-19 were more prevalent in males (59.35%) as compared to female (40.65%). The Positivity rate were significantly higher in Male than in Female cases (p-Value = 0.04). The Ct values for both targets of all the samples were ranged from 4.57 to 29.73. Longitudinal analysis showed significant increased during the study period from starting to end as were hypothesized. Interestingly, both the targets (RdRp and N) were present in age < 1 year. Which may indicate that mutated strains are not prevalent in children’s < 1 year. Conclusion There was no statistically significant difference in viral loads in between age-groups. Males were tending to higher viral load compared to females. The findings have implications for preventive strategies.
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Affiliation(s)
- Mati Ur Rehman
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates.
| | - Syed Sajjad Naqvi
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates.
| | - Rooh Ullah
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates.
| | - Narmeen Arshad
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates.
| | - Muhammad Ammad
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates.
| | - Qurat Ul Ain
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates.
| | - Anam Razzak
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates.
| | - Muhammad Yousaf
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates.
| | - Arif Hussain
- School of Life Science, Manipal Academy of Higher Education, Dubai, UAE.
| | - Tarique N Hasan
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates; School of Life Science, Manipal Academy of Higher Education, Dubai, UAE.
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Alavizadeh SH, Doagooyan M, Zahedipour F, Torghabe SY, Baharieh B, Soleymani F, Gheybi F. Antisense technology as a potential strategy for the treatment of coronaviruses infection: With focus on COVID-19. IET Nanobiotechnol 2022; 16:67-77. [PMID: 35274474 PMCID: PMC9007150 DOI: 10.1049/nbt2.12079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 01/25/2022] [Accepted: 02/14/2022] [Indexed: 11/20/2022] Open
Abstract
After the outbreak of coronavirus disease 2019 (COVID-19) in December 2019 and the increasing number of SARS-CoV-2 infections all over the world, researchers are struggling to investigate effective therapeutic strategies for the treatment of this infection. Targeting viral small molecules that are involved in the process of infection is a promising strategy. Since many host factors are also used by SARS-CoV-2 during various stages of infection, down-regulating or silencing these factors can serve as an effective therapeutic tool. Several nucleic acid-based technologies including short interfering RNAs, antisense oligonucleotides, aptamers, DNAzymes, and ribozymes have been suggested for the control of SARS-CoV-2 as well as other respiratory viruses. The antisense technology also plays an indispensable role in the treatment of many other diseases including cancer, influenza, and acquired immunodeficiency syndrome. In this review, we summarised the potential applications of antisense technology for the treatment of coronaviruses and specifically COVID-19 infection.
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Affiliation(s)
- Seyedeh Hoda Alavizadeh
- Nanotechnology Research CenterPharmaceutical Technology InstituteMashhad University of Medical SciencesMashhadIran
- Department of Pharmaceutical NanotechnologySchool of PharmacyMashhad University of Medical SciencesMashhadIran
| | - Maham Doagooyan
- Department of Medical Biotechnology and NanotechnologyFaculty of MedicineMashhad University of Medical SciencesMashhadIran
- Department of Molecular MedicineBiotechnology Research CenterPasteur Institute of IranTehranIran
| | - Fatemeh Zahedipour
- Department of Medical Biotechnology and NanotechnologyFaculty of MedicineMashhad University of Medical SciencesMashhadIran
- Student Research CommitteeFaculty of MedicineMashhad University of Medical SciencesMashhadIran
| | - Shima Yahoo Torghabe
- Department of Basic SciencesSari Agricultural Sciences and Natural Resources UniversitySariIran
| | - Bahare Baharieh
- Department of Medical Biotechnology and NanotechnologyFaculty of MedicineMashhad University of Medical SciencesMashhadIran
| | - Firooze Soleymani
- Department of Medical Biotechnology and NanotechnologyFaculty of MedicineMashhad University of Medical SciencesMashhadIran
| | - Fatemeh Gheybi
- Nanotechnology Research CenterPharmaceutical Technology InstituteMashhad University of Medical SciencesMashhadIran
- Department of Medical Biotechnology and NanotechnologyFaculty of MedicineMashhad University of Medical SciencesMashhadIran
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Gautam P, Paul D, Suroliya V, Garg R, Agarwal R, Das S, Kaur US, Pandey A, Bhugra A, Tarai B, Bihari C, Sarin SK, Gupta E. SARS-CoV-2 Lineage Tracking, and Evolving Trends Seen during Three Consecutive Peaks of Infection in Delhi, India: a Clinico-Genomic Study. Microbiol Spectr 2022; 10:e0272921. [PMID: 35311567 PMCID: PMC9045110 DOI: 10.1128/spectrum.02729-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/17/2022] [Indexed: 11/20/2022] Open
Abstract
Since its advent, the pandemic has caused havoc in multiple waves due partly to amplified transmissibility and immune escape to vaccines. Delhi, India also witnessed brutal multiple peaks causing exponential rise in cases. Here we had retrospectively investigated clade variation, emergence of new lineages and varied clinical characteristics during those three peaks in order to understand the trajectory of the ongoing pandemic. In this study, a total of 123,378 samples were collected for a time span of 14 months (1 June 2020 to 3 August 2021) encompassing three different peaks in Delhi. A subset of 747 samples was processed for sequencing. Complete clinical and demographic details of all the enrolled cases were also collected. We detected 26 lineages across three peaks nonuniformly from 612 quality passed samples. The first peak was driven by diverse early variants, while the second one by B.1.36 and B.1.617.2, unlike third peak caused entirely by B.1.617.2. A total of 18,316 mutations with median of 34 were reported. Majority of mutations were present in less than 1% of samples. Differences in clinical characteristics across three peaks was also reported. To be ahead of the frequently changing course of the ongoing pandemic, it is of utmost importance that novel lineages be tracked continuously. Prioritized sequencing of sudden local outburst and community hot spots must be done to swiftly detect a novel mutation/lineage of potential clinical importance. IMPORTANCE Genome surveillance of the Delhi data provides a more detailed picture of diverse circulating lineages. The added value that the current study provides by clinical details of the patients is of importance. We looked at the shifting patterns of lineages, clinical characteristics and mutation types and mutation load during each successive infection surge in Delhi. The importance of widespread genomic surveillance cannot be stressed enough to timely detect new variants so that appropriate policies can be immediately implemented upon to help control the infection spread. The entire idea of genomic surveillance is to arm us with the clues as to how the novel mutations and/or variants can prove to be more transmissible and/or fatal. In India, the densely populated cities have an added concern of the huge burden that even the milder variants of the virus combined with co-morbidity can have on the community/primary health care centers.
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Affiliation(s)
- Pramod Gautam
- Genome Sequencing Laboratory, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Diptanu Paul
- Department of Clinical Virology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Varun Suroliya
- Genome Sequencing Laboratory, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Rahul Garg
- Department of Clinical Virology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Reshu Agarwal
- Department of Clinical Virology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Santanu Das
- Department of Pathology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Urvinder S. Kaur
- Department of Pathology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Amit Pandey
- Department of Clinical Virology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Arjun Bhugra
- Department of Clinical Virology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Bansidhar Tarai
- Max Super Speciality Hospital, Max Healthcare, New Delhi, India
| | - Chhagan Bihari
- Department of Pathology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - S. K. Sarin
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Ekta Gupta
- Department of Clinical Virology, Institute of Liver and Biliary Sciences, New Delhi, India
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SARS-CoV-2 Spike Protein Binding of Glycated Serum Albumin-Its Potential Role in the Pathogenesis of the COVID-19 Clinical Syndromes and Bias towards Individuals with Pre-Diabetes/Type 2 Diabetes and Metabolic Diseases. Int J Mol Sci 2022; 23:ijms23084126. [PMID: 35456942 PMCID: PMC9030890 DOI: 10.3390/ijms23084126] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/04/2022] [Accepted: 04/06/2022] [Indexed: 01/08/2023] Open
Abstract
The immune response to SARS-CoV-2 infection requires antibody recognition of the spike protein. In a study designed to examine the molecular features of anti-spike and anti-nucleocapsid antibodies, patient plasma proteins binding to pre-fusion stabilised complete spike and nucleocapsid proteins were isolated and analysed by matrix-assisted laser desorption ionisation–time of flight (MALDI-ToF) mass spectrometry. Amongst the immunoglobulins, a high affinity for human serum albumin was evident in the anti-spike preparations. Careful mass comparison revealed the preferential capture of advanced glycation end product (AGE) forms of glycated human serum albumin by the pre-fusion spike protein. The ability of bacteria and viruses to surround themselves with serum proteins is a recognised immune evasion and pathogenic process. The preference of SARS-CoV-2 for AGE forms of glycated serum albumin may in part explain the severity and pathology of acute respiratory distress and the bias towards the elderly and those with (pre)diabetic and atherosclerotic/metabolic disease.
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11
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Saba AA, Adiba M, Chakraborty S, Nabi AN. Prediction of putative potential siRNAs for inhibiting SARS-CoV-2 strains, including variants of concern and interest. Future Microbiol 2022; 17:449-463. [PMID: 35285248 PMCID: PMC8958991 DOI: 10.2217/fmb-2021-0130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Aim: To predict siRNAs as a therapeutic intervention for highly infectious new variants of SARS-CoV-2. Methods: Conserved coding sequence regions of 11 SARS-CoV-2 proteins were used to construct siRNAs through sampling of metadata comprising 214,256 sequences. Results: Predicted siRNAs S1: 5′-UCAUUGAGAAAUGUUUACGCA-3′ and S2: 5′-AAAGACAUCAGCAUACUCCUG-3′ against RdRp of SARS-CoV-2 satisfied all the stringent filtering processes and showed good binding characteristics. The designed siRNAs are expected to inhibit viral replication and transcription of various coronavirus strains encompassing variants of concern and interest. Conclusion: The predicted siRNAs are expected to be potent against SARS-CoV-2, and following in vitro and in vivo validations may be considered as potential therapeutic measures.
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Affiliation(s)
- Abdullah Al Saba
- Department of Biochemistry and Molecular Biology, Laboratory of Population Genetics, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Maisha Adiba
- Department of Biochemistry and Molecular Biology, Laboratory of Population Genetics, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Sajib Chakraborty
- Department of Biochemistry and Molecular Biology, Systems Cell-Signalling Laboratory, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Ahm Nurun Nabi
- Department of Biochemistry and Molecular Biology, Laboratory of Population Genetics, University of Dhaka, Dhaka, 1000, Bangladesh
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12
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Friedrich M, Pfeifer G, Binder S, Aigner A, Vollmer Barbosa P, Makert GR, Fertey J, Ulbert S, Bodem J, König EM, Geiger N, Schambach A, Schilling E, Buschmann T, Hauschildt S, Koehl U, Sewald K. Selection and Validation of siRNAs Preventing Uptake and Replication of SARS-CoV-2. Front Bioeng Biotechnol 2022; 10:801870. [PMID: 35309990 PMCID: PMC8925020 DOI: 10.3389/fbioe.2022.801870] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/07/2022] [Indexed: 12/16/2022] Open
Abstract
In 2019, the novel highly infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak rapidly led to a global pandemic with more than 346 million confirmed cases worldwide, resulting in 5.5 million associated deaths (January 2022). Entry of all SARS-CoV-2 variants is mediated by the cellular angisin-converting enzyme 2 (ACE2). The virus abundantly replicates in the epithelia of the upper respiratory tract. Beyond vaccines for immunization, there is an imminent need for novel treatment options in COVID-19 patients. So far, only a few drugs have found their way into the clinics, often with modest success. Specific gene silencing based on small interfering RNA (siRNA) has emerged as a promising strategy for therapeutic intervention, preventing/limiting SARS-CoV-2 entry into host cells or interfering with viral replication. Here, we pursued both strategies. We designed and screened nine siRNAs (siA1-9) targeting the viral entry receptor ACE2. SiA1, (siRNA against exon1 of ACE2 mRNA) was most efficient, with up to 90% knockdown of the ACE2 mRNA and protein for at least six days. In vitro, siA1 application was found to protect Vero E6 and Huh-7 cells from infection with SARS-CoV-2 with an up to ∼92% reduction of the viral burden indicating that the treatment targets both the endosomal and the viral entry at the cytoplasmic membrane. Since the RNA-encoded genome makes SARS-CoV-2 vulnerable to RNA interference (RNAi), we designed and analysed eight siRNAs (siV1-8) directly targeting the Orf1a/b region of the SARS-CoV-2 RNA genome, encoding for non-structural proteins (nsp). As a significant hallmark of this study, we identified siV1 (siRNA against leader protein of SARS-CoV-2), which targets the nsp1-encoding sequence (a.k.a. ‘host shutoff factor’) as particularly efficient. SiV1 inhibited SARS-CoV-2 replication in Vero E6 or Huh-7 cells by more than 99% or 97%, respectively. It neither led to toxic effects nor induced type I or III interferon production. Of note, sequence analyses revealed the target sequence of siV1 to be highly conserved in SARS-CoV-2 variants. Thus, our results identify the direct targeting of the viral RNA genome (ORF1a/b) by siRNAs as highly efficient and introduce siV1 as a particularly promising drug candidate for therapeutic intervention.
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Affiliation(s)
- Maik Friedrich
- Institute of Clinical Immunology, Faculty of Leipzig University of Leipzig, Max-Bürger-Forschungszentrum (MBFZ), Leipzig, Germany
- Department of Vaccines and Infection Models, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
- *Correspondence: Maik Friedrich,
| | - Gabriele Pfeifer
- Institute of Clinical Immunology, Faculty of Leipzig University of Leipzig, Max-Bürger-Forschungszentrum (MBFZ), Leipzig, Germany
| | - Stefanie Binder
- Institute of Clinical Immunology, Faculty of Leipzig University of Leipzig, Max-Bürger-Forschungszentrum (MBFZ), Leipzig, Germany
| | - Achim Aigner
- Rudolf Boehm Institute for Pharmacology and Toxicology, Clinical Pharmacology, Leipzig University, Faculty of Medicine, Leipzig, Germany
| | | | - Gustavo R. Makert
- Department of Vaccines and Infection Models, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Jasmin Fertey
- Department of Vaccines and Infection Models, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Sebastian Ulbert
- Department of Vaccines and Infection Models, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Jochen Bodem
- Institute of Virology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Eva-Maria König
- Institute of Virology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Nina Geiger
- Institute of Virology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
- REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
- Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Erik Schilling
- Institute of Clinical Immunology, Faculty of Leipzig University of Leipzig, Max-Bürger-Forschungszentrum (MBFZ), Leipzig, Germany
| | - Tilo Buschmann
- Institute of Clinical Immunology, Faculty of Leipzig University of Leipzig, Max-Bürger-Forschungszentrum (MBFZ), Leipzig, Germany
| | | | - Ulrike Koehl
- Institute of Clinical Immunology, Faculty of Leipzig University of Leipzig, Max-Bürger-Forschungszentrum (MBFZ), Leipzig, Germany
- Department of Vaccines and Infection Models, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
- REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
- Institute for Cellular Therapeutics, Hannover Medical School, Hannover, Germany
| | - Katherina Sewald
- Fraunhofer Institute of Toxicology and Experimental Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH) of the German Center for Lung Research (DZL), Hannover, Germany
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13
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Saadat KASM. RNAi-mediated siRNA sequences to combat the COVID-19 pandemic with the inhibition of SARS-CoV2. GENE REPORTS 2022; 26:101512. [PMID: 35071824 PMCID: PMC8760737 DOI: 10.1016/j.genrep.2022.101512] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 01/11/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Khandakar A S M Saadat
- Department of Medical Biology, Faculty of Medicine, Gaziantep University, Gaziantep 27310, Turkey
- Department of Medical Biology and Genetics, Institute of Health Sciences, Gaziantep University, Gaziantep 27310, Turkey
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14
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Zhang Y, Almazi JG, Ong HX, Johansen MD, Ledger S, Traini D, Hansbro PM, Kelleher AD, Ahlenstiel CL. Nanoparticle Delivery Platforms for RNAi Therapeutics Targeting COVID-19 Disease in the Respiratory Tract. Int J Mol Sci 2022; 23:2408. [PMID: 35269550 PMCID: PMC8909959 DOI: 10.3390/ijms23052408] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/14/2022] [Accepted: 02/18/2022] [Indexed: 02/06/2023] Open
Abstract
Since December 2019, a pandemic of COVID-19 disease, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has rapidly spread across the globe. At present, the Food and Drug Administration (FDA) has issued emergency approval for the use of some antiviral drugs. However, these drugs still have limitations in the specific treatment of COVID-19, and as such, new treatment strategies urgently need to be developed. RNA-interference-based gene therapy provides a tractable target for antiviral treatment. Ensuring cell-specific targeted delivery is important to the success of gene therapy. The use of nanoparticles (NPs) as carriers for the delivery of small interfering RNA (siRNAs) to specific tissues or organs of the human body could play a crucial role in the specific therapy of severe respiratory infections, such as COVID-19. In this review, we describe a variety of novel nanocarriers, such as lipid NPs, star polymer NPs, and glycogen NPs, and summarize the pre-clinical/clinical progress of these nanoparticle platforms in siRNA delivery. We also discuss the application of various NP-capsulated siRNA as therapeutics for SARS-CoV-2 infection, the challenges with targeting these therapeutics to local delivery in the lung, and various inhalation devices used for therapeutic administration. We also discuss currently available animal models that are used for preclinical assessment of RNA-interference-based gene therapy. Advances in this field have the potential for antiviral treatments of COVID-19 disease and could be adapted to treat a range of respiratory diseases.
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Affiliation(s)
- Yuan Zhang
- Kirby Institute, UNSW, Sydney, NSW 2052, Australia; (Y.Z.); (S.L.); (A.D.K.)
| | - Juhura G. Almazi
- Respiratory Technology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia; (J.G.A.); (H.X.O.); (D.T.)
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Ryde, NSW 2109, Australia
| | - Hui Xin Ong
- Respiratory Technology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia; (J.G.A.); (H.X.O.); (D.T.)
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Ryde, NSW 2109, Australia
| | - Matt D. Johansen
- Centre for Inflammation, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, NSW 2050, Australia; (M.D.J.); (P.M.H.)
| | - Scott Ledger
- Kirby Institute, UNSW, Sydney, NSW 2052, Australia; (Y.Z.); (S.L.); (A.D.K.)
| | - Daniela Traini
- Respiratory Technology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia; (J.G.A.); (H.X.O.); (D.T.)
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Ryde, NSW 2109, Australia
| | - Philip M. Hansbro
- Centre for Inflammation, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, NSW 2050, Australia; (M.D.J.); (P.M.H.)
| | - Anthony D. Kelleher
- Kirby Institute, UNSW, Sydney, NSW 2052, Australia; (Y.Z.); (S.L.); (A.D.K.)
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15
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Hussein M, Andrade dos Ramos Z, Berkhout B, Herrera-Carrillo E. In Silico Prediction and Selection of Target Sequences in the SARS-CoV-2 RNA Genome for an Antiviral Attack. Viruses 2022; 14:v14020385. [PMID: 35215977 PMCID: PMC8880226 DOI: 10.3390/v14020385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 12/10/2022] Open
Abstract
The SARS-CoV-2 pandemic has urged the development of protective vaccines and the search for specific antiviral drugs. The modern molecular biology tools provides alternative methods, such as CRISPR-Cas and RNA interference, that can be adapted as antiviral approaches, and contribute to this search. The unique CRISPR-Cas13d system, with the small crRNA guide molecule, mediates a sequence-specific attack on RNA, and can be developed as an anti-coronavirus strategy. We analyzed the SARS-CoV-2 genome to localize the hypothetically best crRNA-annealing sites of 23 nucleotides based on our extensive expertise with sequence-specific antiviral strategies. We considered target sites of which the sequence is well-conserved among SARS-CoV-2 isolates. As we should prepare for a potential future outbreak of related viruses, we screened for targets that are conserved between SARS-CoV-2 and SARS-CoV. To further broaden the search, we screened for targets that are conserved between SARS-CoV-2 and the more distantly related MERS-CoV, as well as the four other human coronaviruses (OC43, 229E, NL63, HKU1). Finally, we performed a search for pan-corona target sequences that are conserved among all these coronaviruses, including the new Omicron variant, that are able to replicate in humans. This survey may contribute to the design of effective, safe, and escape-proof antiviral strategies to prepare for future pandemics.
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Affiliation(s)
| | | | - Ben Berkhout
- Correspondence: (B.B.); (E.H.-C.); Tel.: +31-20-566-4822 (B.B.); +31-20-566-4865 (E.H.-C.)
| | - Elena Herrera-Carrillo
- Correspondence: (B.B.); (E.H.-C.); Tel.: +31-20-566-4822 (B.B.); +31-20-566-4865 (E.H.-C.)
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16
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Loss of Detection of sgN Precedes Viral Abridged Replication in COVID-19-Affected Patients-A Target for SARS-CoV-2 Propagation. Int J Mol Sci 2022; 23:ijms23041941. [PMID: 35216056 PMCID: PMC8878976 DOI: 10.3390/ijms23041941] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/24/2022] [Accepted: 02/07/2022] [Indexed: 02/05/2023] Open
Abstract
The development of prophylactic agents against the SARS-CoV-2 virus is a public health priority in the search for new surrogate markers of active virus replication. Early detection markers are needed to follow disease progression and foresee patient negativization. Subgenomic RNA transcripts (with a focus on sgN) were evaluated in oro/nasopharyngeal swabs from COVID-19-affected patients with an analysis of 315 positive samples using qPCR technology. Cut-off Cq values for sgN (Cq < 33.15) and sgE (Cq < 34.06) showed correlations to high viral loads. The specific loss of sgN in home-isolated and hospitalized COVID-19-positive patients indicated negativization of patient condition, 3–7 days from the first swab, respectively. A new detection kit for sgN, gene E, gene ORF1ab, and gene RNAse P was developed recently. In addition, in vitro studies have shown that 2’-O-methyl antisense RNA (related to the sgN sequence) can impair SARS-CoV-2 N protein synthesis, viral replication, and syncytia formation in human cells (i.e., HEK-293T cells overexpressing ACE2) upon infection with VOC Alpha (B.1.1.7)-SARS-CoV-2 variant, defining the use that this procedure might have for future therapeutic actions against SARS-CoV-2.
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17
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Biswas S, Mahmud S, Mita MA, Afrose S, Hasan MR, Sultana Shimu MS, Saleh MA, Mostafa-Hedeab G, Alqarni M, Obaidullah AJ, Batiha GES. Molecular Docking and Dynamics Studies to Explore Effective Inhibitory Peptides Against the Spike Receptor Binding Domain of SARS-CoV-2. Front Mol Biosci 2022; 8:791642. [PMID: 35187069 PMCID: PMC8851422 DOI: 10.3389/fmolb.2021.791642] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/24/2021] [Indexed: 01/15/2023] Open
Abstract
The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a pandemic due to the high transmission and mortality rate of this virus. The world health and economic sectors have been severely affected by this deadly virus, exacerbated by the lack of sufficient efficient vaccines. The design of effective drug candidates and their rapid development is necessary to combat this virus. In this study, we selected 23 antimicrobial peptides from the literature and predicted their structure using PEP-FOLD 3.5. In addition, we docked them to the SARS-CoV-2 spike protein receptor-binding domain (RBD) to study their capability to inhibit the RBD, which plays a significant role in virus binding, fusion and entry into the host cell. We used several docking programs including HDOCK, HPEPDOCK, ClusPro, and HawkDock to calculate the binding energy of the protein-peptide complexes. We identified four peptides with high binding free energy and docking scores. The docking results were further verified by molecular dynamics (MD) simulations to characterize the protein-peptide complexes in terms of their root-mean-square fluctuation (RMSF), root-mean-square deviation (RMSD), radius of gyration (Rg), solvent-accessible surface area (SASA), and hydrogen bond formation. Allergenicity and toxicity predictions suggested that the peptides we identified were non-allergenic and non-toxic. This study suggests that these four antimicrobial peptides could inhibit the RBD of SARS-CoV-2. Future in vitro and in vivo studies are necessary to confirm this.
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Affiliation(s)
- Suvro Biswas
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Shafi Mahmud
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Mohasana Akter Mita
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Shamima Afrose
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Robiul Hasan
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | | | - Md. Abu Saleh
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Gomaa Mostafa-Hedeab
- Pharmacology Department and Health Research Unit-medical College, Jouf University, Jouf, Saudi Arabia
- Pharmacology Department, Faculty of Medicine, Beni-Suef University, Beni Suef, Egypt
| | - Mohammed Alqarni
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Ahmad J. Obaidullah
- Drug Exploration and Development Chair (DEDC), Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
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18
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Ambike S, Cheng CC, Feuerherd M, Velkov S, Baldassi D, Afridi SQ, Porras-Gonzalez D, Wei X, Hagen P, Kneidinger N, Stoleriu MG, Grass V, Burgstaller G, Pichlmair A, Merkel OM, Ko C, Michler T. Targeting genomic SARS-CoV-2 RNA with siRNAs allows efficient inhibition of viral replication and spread. Nucleic Acids Res 2021; 50:333-349. [PMID: 34928377 PMCID: PMC8754636 DOI: 10.1093/nar/gkab1248] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 11/10/2021] [Accepted: 12/05/2021] [Indexed: 01/08/2023] Open
Abstract
A promising approach to tackle the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) could be small interfering (si)RNAs. So far it is unclear, which viral replication steps can be efficiently inhibited with siRNAs. Here, we report that siRNAs can target genomic RNA (gRNA) of SARS-CoV-2 after cell entry, and thereby terminate replication before start of transcription and prevent virus-induced cell death. Coronaviruses replicate via negative sense RNA intermediates using a unique discontinuous transcription process. As a result, each viral RNA contains identical sequences at the 5′ and 3′ end. Surprisingly, siRNAs were not active against intermediate negative sense transcripts. Targeting common sequences shared by all viral transcripts allowed simultaneous suppression of gRNA and subgenomic (sg)RNAs by a single siRNA. The most effective suppression of viral replication and spread, however, was achieved by siRNAs that targeted open reading frame 1 (ORF1) which only exists in gRNA. In contrast, siRNAs that targeted the common regions of transcripts were outcompeted by the highly abundant sgRNAs leading to an impaired antiviral efficacy. Verifying the translational relevance of these findings, we show that a chemically modified siRNA that targets a highly conserved region of ORF1, inhibited SARS-CoV-2 replication ex vivo in explants of the human lung. Our work encourages the development of siRNA-based therapies for COVID-19 and suggests that early therapy start, or prophylactic application, together with specifically targeting gRNA, might be key for high antiviral efficacy.
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Affiliation(s)
- Shubhankar Ambike
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | - Cho-Chin Cheng
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | - Martin Feuerherd
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | - Stoyan Velkov
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | - Domizia Baldassi
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, Ludwig-Maximilians-Universität München, Butenandtstraße 5, 81377 Munich, Germany
| | - Suliman Qadir Afridi
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | - Diana Porras-Gonzalez
- Institute of Lung Biology and Disease (ILBD) and Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Xin Wei
- Institute of Lung Biology and Disease (ILBD) and Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Philipp Hagen
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | - Nikolaus Kneidinger
- Department of Medicine V, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Mircea Gabriel Stoleriu
- Center for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich (LMU) and Asklepios Pulmonary Hospital; Marchioninistraße 15, 81377 Munich and Robert-Koch-Allee 2, 82131 Gauting, Germany
| | - Vincent Grass
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | - Gerald Burgstaller
- Institute of Lung Biology and Disease (ILBD) and Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Andreas Pichlmair
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany.,German Center for Infection Research (DZIF), Munich partner site, Germany
| | - Olivia M Merkel
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, Ludwig-Maximilians-Universität München, Butenandtstraße 5, 81377 Munich, Germany.,Institute of Lung Biology and Disease (ILBD) and Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Chunkyu Ko
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany.,Infectious Diseases Therapeutic Research Center, Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology (KRICT), 34114 Daejeon, Republic of Korea
| | - Thomas Michler
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany.,German Center for Infection Research (DZIF), Munich partner site, Germany
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19
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Potential of cell-penetrating peptides (CPPs) in delivery of antiviral therapeutics and vaccines. Eur J Pharm Sci 2021; 169:106094. [PMID: 34896590 DOI: 10.1016/j.ejps.2021.106094] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022]
Abstract
Viral infections are a great threat to human health. Currently, there are no effective vaccines and antiviral drugs against the majority of viral diseases, suggesting the need to develop novel and effective antiviral agents. Since the intracellular delivery of antiviral agents, particularly the impermeable molecules, such as peptides, proteins, and nucleic acids, are essential to exert their therapeutic effects, using a delivery system is highly required. Among various delivery systems, cell-penetrating peptides (CPPs), a group of short peptides with the unique ability of crossing cell membrane, offer great potential for the intracellular delivery of various biologically active cargoes. The results of numerous in vitro and in vivo studies with CPP conjugates demonstrate their promise as therapeutic agents in various medical fields including antiviral therapy. The CPP-mediated delivery of various antiviral agents including peptides, proteins, nucleic acids, and nanocarriers have been associated with therapeutic efficacy both in vitro and in vivo. This review describes various aspects of viruses including their biology, pathogenesis, and therapy and briefly discusses the concept of CPP and its potential in drug delivery. Particularly, it will highlight a variety of CPP applications in the management of viral infections.
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20
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Tiwari S, Juneja S, Ghosal A, Bandara N, Khan R, Wallen S, Ramakrishna S, Kaushik A. Antibacterial and antiviral high-performance nano-systems to mitigate new SARS-CoV-2 variants of concerns. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2021; 21:100363. [PMID: 34869963 PMCID: PMC8632437 DOI: 10.1016/j.cobme.2021.100363] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/10/2021] [Accepted: 11/22/2021] [Indexed: 02/08/2023]
Abstract
The increased severity of COVID-19 infection due to new SARS-CoV-2 variants have resonated pandemic strategies to re-evaluate effectiveness of pandemic management strategies. This becomes critical due to the shortcomings in the existing global healthcare system in all the developed countries. The designing of high-performance nanosystems (NSs) with tunable performances seems to be the most efficient method to tackle infectious SARS-CoV-2 variants. The opinion projects the versatile functionalized NSs and their innovative potential to mitigate SARS-CoV-2 pathways by sensitization of virus, anti-pathogenicity, photocatalysis, photo-thermal, immune response, and development of ultrasensitive assays for SARS-CoV-2 or associated selective biomarkers identification. In this direction, we propose the fabrication of nano-enabled protective gears, masks, gloves, sheets, filtration units, nano-emulsified disinfectants, paints, and detection systems to facilitate improved quarantine or antiviral spaces. Functional protective gears can even tackle the aerosol distribution of infectious strains transmitted through respiratory fluids and pollutants within droplets, aerosols, air, and particulates.
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Affiliation(s)
- Shivani Tiwari
- School of Basic and Applied Science, Galgotias University, Greater Noida 201310, Uttar Pradesh, India
| | - Subhavna Juneja
- NanoBiotechnology Lab, School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067
| | - Anujit Ghosal
- Department of Food & Human Nutritional Sciences, The University of Manitoba, MB. R3T 2N2, Canada.,Richardson Centre for Functional Foods and Nutraceuticals, The University of Manitoba, MB. R3T 6C5, Canada
| | - Nandika Bandara
- Department of Food & Human Nutritional Sciences, The University of Manitoba, MB. R3T 2N2, Canada.,Richardson Centre for Functional Foods and Nutraceuticals, The University of Manitoba, MB. R3T 6C5, Canada
| | - Raju Khan
- Microfluidics & MEMS Centre, CSIR - Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal 462026, India
| | - Scott Wallen
- NanoBioTech Laboratory, Health System Engineering, Department of Environmental Engineering, Florida Polytechnic University, Lakeland, Florida 33805, USA
| | - Seeram Ramakrishna
- Center for Nanotechnology and Sustainability, National University of Singapore, 119260 Singapore
| | - Ajeet Kaushik
- NanoBioTech Laboratory, Health System Engineering, Department of Environmental Engineering, Florida Polytechnic University, Lakeland, Florida 33805, USA
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21
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Ramesh S, Govindarajulu M, Parise RS, Neel L, Shankar T, Patel S, Lowery P, Smith F, Dhanasekaran M, Moore T. Emerging SARS-CoV-2 Variants: A Review of Its Mutations, Its Implications and Vaccine Efficacy. Vaccines (Basel) 2021; 9:1195. [PMID: 34696303 PMCID: PMC8537675 DOI: 10.3390/vaccines9101195] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/26/2021] [Accepted: 10/08/2021] [Indexed: 12/21/2022] Open
Abstract
The widespread increase in multiple severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants is causing a significant health concern in the United States and worldwide. These variants exhibit increased transmissibility, cause more severe disease, exhibit evasive immune properties, impair neutralization by antibodies from vaccinated individuals or convalescence sera, and reinfection. The Centers for Disease Control and Prevention (CDC) has classified SARS-CoV-2 variants into variants of interest, variants of concern, and variants of high consequence. Currently, four variants of concern (B.1.1.7, B.1.351, P.1, and B.1.617.2) and several variants of interests (B.1.526, B.1.525, and P.2) are characterized and are essential for close monitoring. In this review, we discuss the different SARS-CoV-2 variants, emphasizing variants of concern circulating the world and highlight the various mutations and how these mutations affect the characteristics of the virus. In addition, we discuss the most common vaccines and the various studies concerning the efficacy of these vaccines against different variants of concern.
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Affiliation(s)
- Sindhu Ramesh
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
| | - Manoj Govindarajulu
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
| | - Rachel S. Parise
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
| | - Logan Neel
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
| | - Tharanath Shankar
- Department of Internal Medicine, Ramaiah Medical College and Hospital, Bengaluru 560054, Karnataka, India;
| | - Shriya Patel
- Department of Neuroscience, Middlebury College, Middlebury, VT 05753, USA;
| | - Payton Lowery
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
| | - Forrest Smith
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
| | - Muralikrishnan Dhanasekaran
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
| | - Timothy Moore
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
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22
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Tolksdorf B, Nie C, Niemeyer D, Röhrs V, Berg J, Lauster D, Adler JM, Haag R, Trimpert J, Kaufer B, Drosten C, Kurreck J. Inhibition of SARS-CoV-2 Replication by a Small Interfering RNA Targeting the Leader Sequence. Viruses 2021; 13:v13102030. [PMID: 34696460 PMCID: PMC8539227 DOI: 10.3390/v13102030] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/04/2021] [Accepted: 10/06/2021] [Indexed: 12/16/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected almost 200 million people worldwide and led to approximately 4 million deaths as of August 2021. Despite successful vaccine development, treatment options are limited. A promising strategy to specifically target viral infections is to suppress viral replication through RNA interference (RNAi). Hence, we designed eight small interfering RNAs (siRNAs) targeting the highly conserved 5′-untranslated region (5′-UTR) of SARS-CoV-2. The most promising candidate identified in initial reporter assays, termed siCoV6, targets the leader sequence of the virus, which is present in the genomic as well as in all subgenomic RNAs. In assays with infectious SARS-CoV-2, it reduced replication by two orders of magnitude and prevented the development of a cytopathic effect. Moreover, it retained its activity against the SARS-CoV-2 alpha variant and has perfect homology against all sequences of the delta variant that were analyzed by bioinformatic means. Interestingly, the siRNA was even highly active in virus replication assays with the SARS-CoV-1 family member. This work thus identified a very potent siRNA with a broad activity against various SARS-CoV viruses that represents a promising candidate for the development of new treatment options.
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Affiliation(s)
- Beatrice Tolksdorf
- Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany; (B.T.); (V.R.); (J.B.)
| | - Chuanxiong Nie
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany; (C.N.); (D.L.); (R.H.)
| | - Daniela Niemeyer
- German Centre for Infection Research (DZIF), Charitéplatz 1, 10117 Berlin, Germany; (D.N.); (C.D.)
- Institute of Virology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Viola Röhrs
- Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany; (B.T.); (V.R.); (J.B.)
| | - Johanna Berg
- Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany; (B.T.); (V.R.); (J.B.)
| | - Daniel Lauster
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany; (C.N.); (D.L.); (R.H.)
| | - Julia M. Adler
- Department of Veterinary Medicine, Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany; (J.M.A.); (J.T.); (B.K.)
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Rainer Haag
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany; (C.N.); (D.L.); (R.H.)
| | - Jakob Trimpert
- Department of Veterinary Medicine, Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany; (J.M.A.); (J.T.); (B.K.)
| | - Benedikt Kaufer
- Department of Veterinary Medicine, Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany; (J.M.A.); (J.T.); (B.K.)
| | - Christian Drosten
- German Centre for Infection Research (DZIF), Charitéplatz 1, 10117 Berlin, Germany; (D.N.); (C.D.)
- Institute of Virology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Jens Kurreck
- Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany; (B.T.); (V.R.); (J.B.)
- Correspondence: ; Tel.:+ 49-30-314-27581
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23
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Khaitov M, Nikonova A, Shilovskiy I, Kozhikhova K, Kofiadi I, Vishnyakova L, Nikolskii A, Gattinger P, Kovchina V, Barvinskaia E, Yumashev K, Smirnov V, Maerle A, Kozlov I, Shatilov A, Timofeeva A, Andreev S, Koloskova O, Kuznetsova N, Vasina D, Nikiforova M, Rybalkin S, Sergeev I, Trofimov D, Martynov A, Berzin I, Gushchin V, Kovalchuk A, Borisevich S, Valenta R, Khaitov R, Skvortsova V. Silencing of SARS-CoV-2 with modified siRNA-peptide dendrimer formulation. Allergy 2021; 76:2840-2854. [PMID: 33837568 PMCID: PMC8251148 DOI: 10.1111/all.14850] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/09/2021] [Accepted: 03/15/2021] [Indexed: 12/12/2022]
Abstract
Background First vaccines for prevention of Coronavirus disease 2019 (COVID‐19) are becoming available but there is a huge and unmet need for specific forms of treatment. In this study we aimed to evaluate the anti‐SARS‐CoV‐2 effect of siRNA both in vitro and in vivo. Methods To identify the most effective molecule out of a panel of 15 in silico designed siRNAs, an in vitro screening system based on vectors expressing SARS‐CoV‐2 genes fused with the firefly luciferase reporter gene and SARS‐CoV‐2‐infected cells was used. The most potent siRNA, siR‐7, was modified by Locked nucleic acids (LNAs) to obtain siR‐7‐EM with increased stability and was formulated with the peptide dendrimer KK‐46 for enhancing cellular uptake to allow topical application by inhalation of the final formulation – siR‐7‐EM/KK‐46. Using the Syrian Hamster model for SARS‐CoV‐2 infection the antiviral capacity of siR‐7‐EM/KK‐46 complex was evaluated. Results We identified the siRNA, siR‐7, targeting SARS‐CoV‐2 RNA‐dependent RNA polymerase (RdRp) as the most efficient siRNA inhibiting viral replication in vitro. Moreover, we showed that LNA‐modification and complexation with the designed peptide dendrimer enhanced the antiviral capacity of siR‐7 in vitro. We demonstrated significant reduction of virus titer and lung inflammation in animals exposed to inhalation of siR‐7‐EM/KK‐46 in vivo. Conclusions Thus, we developed a therapeutic strategy for COVID‐19 based on inhalation of a modified siRNA‐peptide dendrimer formulation. The developed medication is intended for inhalation treatment of COVID‐19 patients.
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Affiliation(s)
| | - Alexandra Nikonova
- NRC Institute of Immunology FMBA Moscow Russia
- Mechnikov Research Institute for Vaccines and Sera Moscow Russia
| | | | | | | | | | | | | | | | | | | | | | | | - Ivan Kozlov
- NRC Institute of Immunology FMBA Moscow Russia
| | | | | | | | | | - Nadezhda Kuznetsova
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology named after Honorary Academician N. F.Gamaleya” of the Ministry of Health of the Russian Federation Moscow Russia
| | - Daria Vasina
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology named after Honorary Academician N. F.Gamaleya” of the Ministry of Health of the Russian Federation Moscow Russia
| | - Maria Nikiforova
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology named after Honorary Academician N. F.Gamaleya” of the Ministry of Health of the Russian Federation Moscow Russia
| | | | | | | | | | - Igor Berzin
- Federal Medico‐biological Agency of Russia (FMBA Russia) Moscow Russia
| | - Vladimir Gushchin
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology named after Honorary Academician N. F.Gamaleya” of the Ministry of Health of the Russian Federation Moscow Russia
| | - Aleksey Kovalchuk
- 48 Central Research Institute of the Ministry of Defense of the Russian Federation Moscow Russia
| | - Sergei Borisevich
- 48 Central Research Institute of the Ministry of Defense of the Russian Federation Moscow Russia
| | - Rudolf Valenta
- NRC Institute of Immunology FMBA Moscow Russia
- Medical University of Vienna Vienna Austria
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24
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Maharjan PM, Cheon J, Jung J, Kim H, Lee J, Song M, Jeong GU, Kwon Y, Shim B, Choe S. Plant-Expressed Receptor Binding Domain of the SARS-CoV-2 Spike Protein Elicits Humoral Immunity in Mice. Vaccines (Basel) 2021; 9:978. [PMID: 34579215 PMCID: PMC8472882 DOI: 10.3390/vaccines9090978] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 12/20/2022] Open
Abstract
The current 15-month coronavirus disease-19 (COVID-19) pandemic caused by SARS-CoV-2 has accounted for 3.77 million deaths and enormous worldwide social and economic losses. A high volume of vaccine production is urgently required to eliminate COVID-19. Inexpensive and robust production platforms will improve the distribution of vaccines to resource-limited countries. Plant species offer such platforms, particularly through the production of recombinant proteins to serve as immunogens. To achieve this goal, here we expressed the receptor binding domain (RBD) of the SARS-CoV-2 spike (S) protein in the glycoengineered-tobacco plant Nicotiana benthamiana to provide a candidate subunit vaccine. This recombinant RBD elicited humoral immunity in mice via induction of highly neutralizing antibodies. These findings provide a strong foundation to further advance the development of plant-expressed RBD antigens for use as an effective, safe, and inexpensive SARS-CoV-2 vaccine. Moreover, our study further highlights the utility of plant species for vaccine development.
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Affiliation(s)
- Puna Maya Maharjan
- G+FLAS Life Sciences, 123 Uiryodanji-gil, Osong-eup, Heungdeok-gu, Cheongju-si 28161, Korea; (P.M.M.); (J.L.); (M.S.)
- School of Biological Sciences, College of Natural Sciences, Seoul National University, Gwanak-gu, Seoul 08826, Korea
| | - Jinyeong Cheon
- G+FLAS Life Sciences, 38 Nakseongdae-ro, Gwanak-gu, Seoul 08790, Korea; (J.C.); (J.J.); (H.K.)
| | - Jiyun Jung
- G+FLAS Life Sciences, 38 Nakseongdae-ro, Gwanak-gu, Seoul 08790, Korea; (J.C.); (J.J.); (H.K.)
| | - Haerim Kim
- G+FLAS Life Sciences, 38 Nakseongdae-ro, Gwanak-gu, Seoul 08790, Korea; (J.C.); (J.J.); (H.K.)
| | - Jaewon Lee
- G+FLAS Life Sciences, 123 Uiryodanji-gil, Osong-eup, Heungdeok-gu, Cheongju-si 28161, Korea; (P.M.M.); (J.L.); (M.S.)
| | - Minjeong Song
- G+FLAS Life Sciences, 123 Uiryodanji-gil, Osong-eup, Heungdeok-gu, Cheongju-si 28161, Korea; (P.M.M.); (J.L.); (M.S.)
| | - Gi Uk Jeong
- Center for Convergent Research for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea; (G.U.J.); (Y.K.)
| | - Youngchan Kwon
- Center for Convergent Research for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea; (G.U.J.); (Y.K.)
| | - Byoungshik Shim
- International Vaccine Institute, SNU Research Park, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea;
| | - Sunghwa Choe
- School of Biological Sciences, College of Natural Sciences, Seoul National University, Gwanak-gu, Seoul 08826, Korea
- G+FLAS Life Sciences, 38 Nakseongdae-ro, Gwanak-gu, Seoul 08790, Korea; (J.C.); (J.J.); (H.K.)
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25
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Sajid M, Moazzam M, Cho Y, Kato S, Xu A, Way JJ, Lohan S, Tiwari RK. siRNA Therapeutics for the Therapy of COVID-19 and Other Coronaviruses. Mol Pharm 2021; 18:2105-2121. [PMID: 33945284 PMCID: PMC9896947 DOI: 10.1021/acs.molpharmaceut.0c01239] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The ongoing pandemic of global concern has killed about three million humans and affected around 151 million people worldwide, as of April 30, 2021. Although recently approved vaccines for COVID-19 are engendering hope, finding new ways to cure the viral pandemic is still a quest for researchers worldwide. Major pandemics in history have been of viral origin, such as SARS, MERS, H1NI, Spanish flu, and so on. A larger emphasis has been on discovering potential vaccines, novel antiviral drugs, and agents that can mitigate the viral infection symptoms; however, a relatively new area, RNA interference (RNAi), has proven effective as an antiviral agent. The RNAi phenomenon has been largely exploited to cure cancer, neurodegenerative diseases, and some rare diseases. The U.S. Food and Drug Administration has recently approved three siRNA products for human use that garner significant hope in siRNA therapeutics for coronaviruses. There have been some commentaries and communications addressing this area. We have summarized and illustrated the significance and the potential of the siRNA therapeutics available as of April 30, 2021 to combat the ongoing viral pandemic and the emerging new variants such as B.1.1.7 and B.1.351. Numerous successful in vitro studies and several investigations to address the clinical application of siRNA therapeutics provide great hope in this field. This seminal Review describes the significance of siRNA-based therapy to treat diverse viral infections in addition to the current coronavirus challenge. In addition, we have thoroughly reviewed the patents approved for coronaviruses, the major challenges in siRNA therapy, and the potential approaches to address them, followed by innovation and prospects.
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Affiliation(s)
- Muhammad
Imran Sajid
- Center
for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical
Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, California 92618, United States
- Faculty
of Pharmacy, University of Central Punjab, Lahore 54700, Pakistan
| | - Muhammad Moazzam
- Faculty
of Pharmacy, University of Central Punjab, Lahore 54700, Pakistan
| | - Yeseom Cho
- Center
for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical
Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, California 92618, United States
- Department
of Biochemistry and Molecular Biology, Schmid College of Science and
Technology, Chapman University, Orange, California 92866, United States
| | - Shun Kato
- Center
for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical
Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, California 92618, United States
- Department
of Biochemistry and Molecular Biology, Schmid College of Science and
Technology, Chapman University, Orange, California 92866, United States
| | - Ava Xu
- Center
for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical
Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, California 92618, United States
| | - J. J. Way
- Center
for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical
Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, California 92618, United States
| | - Sandeep Lohan
- Center
for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical
Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, California 92618, United States
| | - Rakesh K. Tiwari
- Center
for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical
Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, California 92618, United States
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26
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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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27
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Parasher A. COVID-19: Current understanding of its Pathophysiology, Clinical presentation and Treatment. Postgrad Med J 2021; 97:312-320. [PMID: 32978337 PMCID: PMC10017004 DOI: 10.1136/postgradmedj-2020-138577] [Citation(s) in RCA: 344] [Impact Index Per Article: 114.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/09/2020] [Accepted: 07/18/2020] [Indexed: 01/08/2023]
Abstract
BACKGROUND The severe acute respiratory syndrome (SARS) coronavirus-2 is a novel coronavirus belonging to the family Coronaviridae and is now known to be responsible for the outbreak of a series of recent acute atypical respiratory infections originating in Wuhan, China. The disease caused by this virus, termed coronavirus disease 19 or simply COVID-19, has rapidly spread throughout the world at an alarming pace and has been declared a pandemic by the WHO on March 11, 2020. In this review, an update on the pathophysiology, clinical presentation and the most recent management strategies for COVID-19 has been described. MATERIALS AND METHODS A search was conducted for literature and various articles/case reports from 1997 to 2020 in PUBMED/MEDLINE for the keywords coronavirus, SARS, Middle East respiratory syndrome and mRNA virus. RESULTS AND CONCLUSIONS COVID-19 has now spread globally with increasing morbidity and mortality among all populations. In the absence of a proper and effective antibody test, the diagnosis is presently based on a reverse-transcription PCR of nasopharyngeal and oropharyngeal swab samples. The clinical spectrum of the disease presents in the form of a mild, moderate or severe illness. Most patients are either asymptomatic carriers who despite being without symptoms have the potential to be infectious to others coming in close contact, or have a mild influenza-like illness which cannot be differentiated from a simple upper respiratory tract infection. Moderate and severe cases require hospitalisation as well as intensive therapy which includes non-invasive as well as invasive ventilation, along with antipyretics, antivirals, antibiotics and steroids. Complicated cases may require treatment by immunomodulatory drugs and plasma exchange therapy. The search for an effective vaccine for COVID-19 is presently in full swing, with pharmaceutical corporations having started human trials in many countries.
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Mehta A, Michler T, Merkel OM. siRNA Therapeutics against Respiratory Viral Infections-What Have We Learned for Potential COVID-19 Therapies? Adv Healthc Mater 2021; 10:e2001650. [PMID: 33506607 PMCID: PMC7995229 DOI: 10.1002/adhm.202001650] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 01/06/2021] [Indexed: 12/30/2022]
Abstract
Acute viral respiratory tract infections (AVRIs) are a major burden on human health and global economy and amongst the top five causes of death worldwide resulting in an estimated 3.9 million lives lost every year. In addition, new emerging respiratory viruses regularly cause outbreaks such as SARS-CoV-1 in 2003, the "Swine flu" in 2009, or most importantly the ongoing SARS-CoV-2 pandemic, which intensely impact global health, social life, and economy. Despite the prevalence of AVRIs and an urgent need, no vaccines-except for influenza-or effective treatments were available at the beginning of the COVID-19 pandemic. However, the innate RNAi pathway offers the ability to develop nucleic acid-based antiviral drugs. siRNA sequences against conserved, essential regions of the viral genome can prevent viral replication. In addition, viral infection can be averted prophylactically by silencing host genes essential for host-viral interactions. Unfortunately, delivering siRNAs to their target cells and intracellular site of action remains the principle hurdle toward their therapeutic use. Currently, siRNA formulations and chemical modifications are evaluated for their delivery. This progress report discusses the selection of antiviral siRNA sequences, delivery techniques to the infection sites, and provides an overview of antiviral siRNAs against respiratory viruses.
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Affiliation(s)
- Aditi Mehta
- Department of PharmacyPharmaceutical Technology and BiopharmaceuticsLudwig‐Maximilians‐Universität MünchenButenandtstraße 5Munich81377Germany
| | - Thomas Michler
- Institute of VirologyTechnische Universität MünchenTrogerstr. 30Munich81675Germany
| | - Olivia M. Merkel
- Department of PharmacyPharmaceutical Technology and BiopharmaceuticsLudwig‐Maximilians‐Universität MünchenButenandtstraße 5Munich81377Germany
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29
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Pandey AK, Verma S. An in silico analysis of effective siRNAs against COVID-19 by targeting the leader sequence of SARS-CoV-2. ACTA ACUST UNITED AC 2021; 4:e107. [PMID: 33786418 PMCID: PMC7995175 DOI: 10.1002/acg2.107] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/31/2021] [Accepted: 02/09/2021] [Indexed: 12/15/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a retrovirus having genome size of around 30 kb. Its genome contains a highly conserved leader sequence at its 5' end, which is added to all subgenomic mRNAs at their 5' terminus by a discontinuous transcription mechanism and regulates their translation. Targeting the leader sequence by RNA interference can be an effective approach to inhibit the viral replication. In the present study an in-silico prediction of highly effective siRNAs was performed to target the leader sequence using the online software siDirect version 2.0. Low seed-duplex stability, exact complementarity with target, at least three mismatches with any off-target and least number of off-targets, were considered as effective criteria for highly specific siRNA. Further validation of siRNA affinity for the target was accomplished by molecular docking by HNADOCK online server. Our results revealed four potential siRNAs, of which siRNA having guide strand sequence 5'GUUUAGAGAACAGAUCUACAA3' met almost all specificity criteria with no off-targets for guide strand. Molecular docking of all predicted siRNAs (guide strand) with the target leader sequence depicted highest binding score of -327.45 for above-mentioned siRNA. Furthermore, molecular docking of the passenger strand of the best candidate with off-target sequences gave significantly low binding scores. Hence, 5'GUUUAGAGAACAGAUCUACAA3' siRNA possess great potential to silence the leader sequence of SARS-CoV-2 with least off-target effect. Present study provides great scope for development of gene therapy against the prevailing COVID-19 disease, thus further research in this concern is urgently demanded.
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Affiliation(s)
- Anand Kumar Pandey
- Department of Biotechnology Engineering Institute of Engineering and Technology Bundelkhand University Jhansi India
| | - Shalja Verma
- Department of Biotechnology Engineering Institute of Engineering and Technology Bundelkhand University Jhansi India.,Department of Biochemical Engineering and Biotechnology Indian Institute of Technology New Delhi India.,NIMR-ICMR New Delhi India
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30
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Rohani N, Ahmadi Moughari F, Eslahchi C. DisCoVering potential candidates of RNAi-based therapy for COVID-19 using computational methods. PeerJ 2021; 9:e10505. [PMID: 33680575 PMCID: PMC7919535 DOI: 10.7717/peerj.10505] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/15/2020] [Indexed: 01/04/2023] Open
Abstract
The ongoing pandemic of a novel coronavirus (SARS-CoV-2) leads to international concern; thus, emergency interventions need to be taken. Due to the time-consuming experimental methods for proposing useful treatments, computational approaches facilitate investigating thousands of alternatives simultaneously and narrow down the cases for experimental validation. Herein, we conducted four independent analyses for RNA interference (RNAi)-based therapy with computational and bioinformatic methods. The aim is to target the evolutionarily conserved regions in the SARS-CoV-2 genome in order to down-regulate or silence its RNA. miRNAs are denoted to play an important role in the resistance of some species to viral infections. A comprehensive analysis of the miRNAs available in the body of humans, as well as the miRNAs in bats and many other species, were done to find efficient candidates with low side effects in the human body. Moreover, the evolutionarily conserved regions in the SARS-CoV-2 genome were considered for designing novel significant siRNA that are target-specific. A small set of miRNAs and five siRNAs were suggested as the possible efficient candidates with a high affinity to the SARS-CoV-2 genome and low side effects. The suggested candidates are promising therapeutics for the experimental evaluations and may speed up the procedure of treatment design. Materials and implementations are available at: https://github.com/nrohani/SARS-CoV-2.
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Affiliation(s)
- Narjes Rohani
- Department of Computer and Data Sciences, Faculty of Mathematical Sciences, Shahid Beheshti University, Tehran, Iran
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
| | - Fatemeh Ahmadi Moughari
- Department of Computer and Data Sciences, Faculty of Mathematical Sciences, Shahid Beheshti University, Tehran, Iran
| | - Changiz Eslahchi
- Department of Computer and Data Sciences, Faculty of Mathematical Sciences, Shahid Beheshti University, Tehran, Iran
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
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31
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Kalhori MR, Saadatpour F, Arefian E, Soleimani M, Farzaei MH, Aneva IY, Echeverría J. The Potential Therapeutic Effect of RNA Interference and Natural Products on COVID-19: A Review of the Coronaviruses Infection. Front Pharmacol 2021; 12:616993. [PMID: 33716745 PMCID: PMC7953353 DOI: 10.3389/fphar.2021.616993] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/14/2021] [Indexed: 01/08/2023] Open
Abstract
The SARS-CoV-2 virus was reported for the first time in Wuhan, Hubei Province, China, and causes respiratory infection. This pandemic pneumonia killed about 1,437,835 people out of 61,308,161cases up to November 27, 2020. The disease's main clinical complications include fever, recurrent coughing, shortness of breath, acute respiratory syndrome, and failure of vital organs that could lead to death. It has been shown that natural compounds with antioxidant, anticancer, and antiviral activities and RNA interference agents could play an essential role in preventing or treating coronavirus infection by inhibiting the expression of crucial virus genes. This study aims to introduce a summary of coronavirus's genetic and morphological structure and determine the role of miRNAs, siRNAs, chemical drugs, and natural compounds in stimulating the immune system or inhibiting the virus's structural and non-structural genes that are essential for replication and infection of SARS-CoV-2.
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Affiliation(s)
- Mohammad Reza Kalhori
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Fatemeh Saadatpour
- Molecular Virology Lab, Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Ehsan Arefian
- Molecular Virology Lab, Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Masoud Soleimani
- Department of Hematology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Hosien Farzaei
- Medical Technology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ina Yosifova Aneva
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Javier Echeverría
- Departamento de Ciencias del Ambiente, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
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32
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Wang R, Chen J, Gao K, Hozumi Y, Yin C, Wei GW. Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Commun Biol 2021; 4:228. [PMID: 33589648 PMCID: PMC7884689 DOI: 10.1038/s42003-021-01754-6] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 has been mutating since it was first sequenced in early January 2020. Here, we analyze 45,494 complete SARS-CoV-2 geneome sequences in the world to understand their mutations. Among them, 12,754 sequences are from the United States. Our analysis suggests the presence of four substrains and eleven top mutations in the United States. These eleven top mutations belong to 3 disconnected groups. The first and second groups consisting of 5 and 8 concurrent mutations are prevailing, while the other group with three concurrent mutations gradually fades out. Moreover, we reveal that female immune systems are more active than those of males in responding to SARS-CoV-2 infections. One of the top mutations, 27964C > T-(S24L) on ORF8, has an unusually strong gender dependence. Based on the analysis of all mutations on the spike protein, we uncover that two of four SASR-CoV-2 substrains in the United States become potentially more infectious.
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Affiliation(s)
- Rui Wang
- grid.17088.360000 0001 2150 1785Department of Mathematics, Michigan State University, East Lansing, MI 48824 USA
| | - Jiahui Chen
- grid.17088.360000 0001 2150 1785Department of Mathematics, Michigan State University, East Lansing, MI 48824 USA
| | - Kaifu Gao
- grid.17088.360000 0001 2150 1785Department of Mathematics, Michigan State University, East Lansing, MI 48824 USA
| | - Yuta Hozumi
- grid.17088.360000 0001 2150 1785Department of Mathematics, Michigan State University, East Lansing, MI 48824 USA
| | - Changchuan Yin
- grid.185648.60000 0001 2175 0319Department of Mathematics, Statistics, and Computer Science, University of Illinois at Chicago, Chicago, IL 60607 USA
| | - Guo-Wei Wei
- grid.17088.360000 0001 2150 1785Department of Mathematics, Michigan State University, East Lansing, MI 48824 USA ,grid.17088.360000 0001 2150 1785Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI 48824 USA ,grid.17088.360000 0001 2150 1785Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824 USA
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33
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Yang D. Application of Nanotechnology in the COVID-19 Pandemic. Int J Nanomedicine 2021; 16:623-649. [PMID: 33531805 PMCID: PMC7847377 DOI: 10.2147/ijn.s296383] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/08/2021] [Indexed: 12/12/2022] Open
Abstract
COVID-19, caused by SARS-CoV-2 infection, has been prevalent worldwide for almost a year. In early 2000, there was an outbreak of SARS-CoV, and in early 2010, a similar dissemination of infection by MERS-CoV occurred. However, no clear explanation for the spread of SARS-CoV-2 and a massive increase in the number of infections has yet been proposed. The best solution to overcome this pandemic is the development of suitable and effective vaccines and therapeutics. Fortunately, for SARS-CoV-2, the genome sequence and protein structure have been published in a short period, making research and development for prevention and treatment relatively easy. In addition, intranasal drug delivery has proven to be an effective method of administration for treating viral lung diseases. In recent years, nanotechnology-based drug delivery systems have been applied to intranasal drug delivery to overcome various limitations that occur during mucosal administration, and advances have been made to the stage where effective drug delivery is possible. This review describes the accumulated knowledge of the previous SARS-CoV and MERS-CoV infections and aims to help understand the newly emerged SARS-CoV-2 infection. Furthermore, it elucidates the achievements in developing COVID-19 vaccines and therapeutics to date through existing approaches. Finally, the applicable nanotechnology approach is described in detail, and vaccines and therapeutic drugs developed based on nanomedicine, which are currently undergoing clinical trials, have presented the potential to become innovative alternatives for overcoming COVID-19.
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Affiliation(s)
- Dongki Yang
- Department of Physiology, College of Medicine, Gachon University, Incheon, 21999, South Korea
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34
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Emerging Technologies for the Treatment of COVID-19. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1321:81-96. [PMID: 33656715 DOI: 10.1007/978-3-030-59261-5_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The new coronavirus, named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), turned into a pandemic affecting more than 200 countries. Due to the high rate of transmission and mortality, finding specific and effective treatment options for this infection is currently of urgent importance. Emerging technologies have created a promising platform for developing novel treatment options for various viral diseases such as the SARS-CoV-2 virus. Here, we have described potential novel therapeutic options based on the structure and pathophysiological mechanism of the SARS-CoV-2 virus, as well as the results of previous studies on similar viruses such as SARS and MERS. Many of these approaches can be used for controlling viral infection by reducing the viral damage or by increasing the potency of the host response. Owing to their high sensitivity, specificity, and reproducibility, siRNAs, aptamers, nanobodies, neutralizing antibodies, and different types of peptides can be used for interference with viral replication or for blocking internalization. Receptor agonists and interferon-inducing agents are also potential options to balance and enhance the innate immune response against SARS-CoV-2. Solid evidence on the efficacy and safety of such novel technologies is yet to be established although many well-designed clinical trials are underway to address these issues.
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35
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Rahimi A, Mirzazadeh A, Tavakolpour S. Genetics and genomics of SARS-CoV-2: A review of the literature with the special focus on genetic diversity and SARS-CoV-2 genome detection. Genomics 2021; 113:1221-1232. [PMID: 33007398 PMCID: PMC7525243 DOI: 10.1016/j.ygeno.2020.09.059] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/26/2020] [Accepted: 09/28/2020] [Indexed: 02/06/2023]
Abstract
The outbreak of 2019-novel coronavirus disease (COVID-19), caused by SARS-CoV-2, started in late 2019; in a short time, it has spread rapidly all over the world. Although some possible antiviral and anti-inflammatory medications are available, thousands of people are dying daily. Well-understanding of the SARS-CoV-2 genome is not only essential for the development of new treatments/vaccines, but it also can be used for improving the sensitivity and specificity of current approaches for virus detection. Accordingly, we reviewed the most critical findings related to the genetics of the SARS-CoV-2, with a specific focus on genetic diversity and reported mutations, molecular-based diagnosis assays, using interfering RNA technology for the treatment of patients, and genetic-related vaccination strategies. Additionally, considering the unanswered questions or uncertainties in these regards, different topics were discussed.
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Affiliation(s)
- Azadeh Rahimi
- Department of Genetics and Molecular Biology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Azin Mirzazadeh
- Department of Medical Genetics, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran,Joint Bioinformatics Graduate Program, University of Arkansas Little Rock and University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Soheil Tavakolpour
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, United States.
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36
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Henzinger H, Barth DA, Klec C, Pichler M. Non-Coding RNAs and SARS-Related Coronaviruses. Viruses 2020; 12:E1374. [PMID: 33271762 PMCID: PMC7761185 DOI: 10.3390/v12121374] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/25/2020] [Accepted: 11/28/2020] [Indexed: 02/07/2023] Open
Abstract
The emergence of SARS-CoV-2 in 2019 has caused a major health and economic crisis around the globe. Gaining knowledge about its attributes and interactions with human host cells is crucial. Non-coding RNAs (ncRNAs) are involved in the host cells' innate antiviral immune response. In RNA interference, microRNAs (miRNAs) may bind to complementary sequences of the viral RNA strand, forming an miRNA-induced silencing complex, which destroys the viral RNA, thereby inhibiting viral protein expression. There are several targets for human miRNAs on SARS-CoV-2's RNA, most of which are in the 5' and 3' untranslated regions. Mutations of the viral genome causing the creation or loss of miRNA binding sites may have crucial effects on SARS-CoV-2 pathogenicity. In addition to mediating immunity, the ncRNA landscape of host cells further influences their susceptibility to virus infection, as certain miRNAs are essential in the regulation of cellular receptors that are necessary for virus invasion. Conversely, virus infection also changes the host ncRNA expression patterns, possibly augmenting conditions for viral replication and dissemination. Hence, ncRNAs typically upregulated in SARS-CoV-2 infection could be useful biomarkers for disease progression and severity. Understanding these mechanisms could provide further insight into the pathogenesis and possible treatment options against COVID-19.
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Affiliation(s)
- Hanna Henzinger
- Comprehensive Cancer Center Graz, Research Unit of Non-Coding RNAs and Genome Editing, Department of Internal Medicine, Division of Clinical Oncology, Medical University of Graz, 8036 Graz, Austria; (H.H.); (D.A.B.); (C.K.)
| | - Dominik A. Barth
- Comprehensive Cancer Center Graz, Research Unit of Non-Coding RNAs and Genome Editing, Department of Internal Medicine, Division of Clinical Oncology, Medical University of Graz, 8036 Graz, Austria; (H.H.); (D.A.B.); (C.K.)
| | - Christiane Klec
- Comprehensive Cancer Center Graz, Research Unit of Non-Coding RNAs and Genome Editing, Department of Internal Medicine, Division of Clinical Oncology, Medical University of Graz, 8036 Graz, Austria; (H.H.); (D.A.B.); (C.K.)
| | - Martin Pichler
- Comprehensive Cancer Center Graz, Research Unit of Non-Coding RNAs and Genome Editing, Department of Internal Medicine, Division of Clinical Oncology, Medical University of Graz, 8036 Graz, Austria; (H.H.); (D.A.B.); (C.K.)
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Lorusso A, Calistri P, Mercante MT, Monaco F, Portanti O, Marcacci M, Cammà C, Rinaldi A, Mangone I, Di Pasquale A, Iommarini M, Mattucci M, Fazii P, Tarquini P, Mariani R, Grimaldi A, Morelli D, Migliorati G, Savini G, Borrello S, D'Alterio N. A "One-Health" approach for diagnosis and molecular characterization of SARS-CoV-2 in Italy. One Health 2020; 10:100135. [PMID: 32313828 PMCID: PMC7166304 DOI: 10.1016/j.onehlt.2020.100135] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 04/16/2020] [Accepted: 04/16/2020] [Indexed: 01/08/2023] Open
Abstract
The current pandemic is caused by a novel coronavirus (CoV) called SARS-CoV-2 (species Severe acute respiratory syndrome-related coronavirus, subgenus Sarbecovirus, genus Betacoronavirus, family Coronaviridae). In Italy, up to the 2nd of April 2020, overall 139,422 confirmed cases and 17,669 deaths have been notified, while 26,491 people have recovered. Besides the overloading of hospitals, another issue to face was the capacity to perform thousands of tests per day. In this perspective, to support the National Health Care System and to minimize the impact of this rapidly spreading virus, the Italian Ministry of Health involved the Istituti Zooprofilattici Sperimentali (IZSs), Veterinary Public Health Institutes, in the diagnosis of SARS-CoV-2 by testing human samples. The Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise is currently testing more than 600 samples per day and performing whole genome sequencing from positive samples. Sequence analysis of these samples suggested that different viral variants may be circulating in Italy, and so in Abruzzo region. CoVs, and related diseases, are well known to veterinarians since decades. The experience that veterinarians operating within the Public Health system gained in the control and characterization of previous health issues of livestock and poultry including avian flu, bluetongue, foot and mouth disease, responsible for huge economic losses, is certainly of great help to minimize the impact of this global crisis.
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Affiliation(s)
- Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise “G. Caporale”, Teramo, Italy
| | - Paolo Calistri
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise “G. Caporale”, Teramo, Italy
| | - Maria Teresa Mercante
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise “G. Caporale”, Teramo, Italy
| | - Federica Monaco
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise “G. Caporale”, Teramo, Italy
| | - Ottavio Portanti
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise “G. Caporale”, Teramo, Italy
| | - Maurilia Marcacci
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise “G. Caporale”, Teramo, Italy
| | - Cesare Cammà
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise “G. Caporale”, Teramo, Italy
| | - Antonio Rinaldi
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise “G. Caporale”, Teramo, Italy
| | - Iolanda Mangone
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise “G. Caporale”, Teramo, Italy
| | - Adriano Di Pasquale
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise “G. Caporale”, Teramo, Italy
| | | | | | - Paolo Fazii
- Reparto di Microbiologia e Virologia clinica, Ospedale Civile Spirito Santo, Pescara, Italy
| | | | - Rinalda Mariani
- UOC Malattie Infettive Ospedale SS Filippo e Nicola, Avezzano (L' Aquila), Italy
| | | | - Daniela Morelli
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise “G. Caporale”, Teramo, Italy
| | - Giacomo Migliorati
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise “G. Caporale”, Teramo, Italy
| | - Giovanni Savini
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise “G. Caporale”, Teramo, Italy
| | - Silvio Borrello
- Direzione Generale della Sanita' Animale e dei Farmaci Veterinari, Ministero della Salute, Roma, Italy
| | - Nicola D'Alterio
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise “G. Caporale”, Teramo, Italy
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Aljabali AAA, Bakshi HA, Satija S, Metha M, Prasher P, Ennab RM, Chellappan DK, Gupta G, Negi P, Goyal R, Sharma A, Mishra V, Dureja H, Dua K, Tambuwala MM. COVID-19: Underpinning Research for Detection, Therapeutics, and Vaccines Development. Pharm Nanotechnol 2020; 8:323-353. [PMID: 32811406 DOI: 10.2174/2211738508999200817163335] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/22/2020] [Accepted: 07/15/2020] [Indexed: 01/08/2023]
Abstract
BACKGROUND The newly emerged coronavirus SARS-CoV-2, first reported in December 2019, has infected about five and a half million people globally and resulted in nearly 9063264 deaths until the 24th of June 2020. Nevertheless, the highly contagious virus has instigated an unimaginably rapid response from scientific and medical communities. OBJECTIVES Pioneering research on molecular mechanisms underlying the viral transmission, molecular pathogenicity, and potential treatments will be highlighted in this review. The development of antiviral drugs specific to SARS-CoV-2 is a complicated and tedious process. To accelerate scientific discoveries and advancement, researchers are consolidating available data from associated coronaviruses into a single pipeline, which can be readily made available to vaccine developers. METHODS In order to find studies evaluating the COVID-19 virus epidemiology, repurposed drugs and potential vaccines, web searches and bibliographical bases have been used with keywords that matches the content of this review. RESULTS The published results of SARS-CoV-2 structures and interactomics have been used to identify potential therapeutic candidates. We illustrate recent publications on SARS-CoV-2, concerning its molecular, epidemiological, and clinical characteristics, and focus on innovative diagnostics technologies in the production pipeline. This objective of this review is to enhance the comprehension of the unique characteristics of SARS-CoV-2 and strengthen future control measures. Lay Summary An innovative analysis is evaluating the nature of the COVID-19 pandemic. The aim is to increase knowledge of possible viral detection methods, which highlights several new technology limitations and advantages. We have assessed some drugs currently for patients (Lopinavir, Ritonavir, Anakinra and Interferon beta 1a), as the feasibility of COVID-19 specific antivirals is not presently known. The study explores the race toward vaccine development and highlights some significant trials and candidates in various clinical phases. This research addresses critical knowledge gaps by identifying repurposed drugs currently under clinical trials. Findings will be fed back rapidly to the researchers interested in COVID 19 and support the evidence and potential of possible therapeutics and small molecules with their mode of action.
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Affiliation(s)
- Alaa A A Aljabali
- Faculty of Pharmacy, Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University, Irbid 566, Jordan
| | - Hamid A Bakshi
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, County Londonderry, Northern Ireland, United Kingdom
| | - Saurabh Satija
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara-144411, Punjab, India
| | - Meenu Metha
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara-144411, Punjab, India
| | - Parteek Prasher
- Department of Chemistry, University of Petroleum & Energy Studies, Dehradun 248007, India
| | - Raed M Ennab
- Department of Clinical sciences, Faculty of Medicine, Yarmouk University, Irbid 566, Jordan
| | - Dinesh K Chellappan
- Department of Life Sciences, School of Pharmacy, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia
| | - Gaurav Gupta
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, Jaipur 302017, India
| | - Poonam Negi
- School of Pharmaceutical Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, India
| | - Rohit Goyal
- Neuropharmacology Laboratory, School of Pharmaceutical Sciences, Shoolini University, Solan 173 212, Himachal Pradesh, India
| | - Ashish Sharma
- Neuropharmacology Laboratory, School of Pharmaceutical Sciences, Shoolini University, Solan 173 212, Himachal Pradesh, India
| | - Vijay Mishra
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara-144411, Punjab, India
| | - Harish Dureja
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak 124001, India
| | - Kamal Dua
- School of Pharmaceutical Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, India
| | - Murtaza M Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, County Londonderry, Northern Ireland, United Kingdom
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Alouane T, Laamarti M, Essabbar A, Hakmi M, Bouricha EM, Chemao-Elfihri MW, Kartti S, Boumajdi N, Bendani H, Laamarti R, Ghrifi F, Allam L, Aanniz T, Ouadghiri M, El Hafidi N, El Jaoudi R, Benrahma H, Attar JE, Mentag R, Sbabou L, Nejjari C, Amzazi S, Belyamani L, Ibrahimi A. Genomic Diversity and Hotspot Mutations in 30,983 SARS-CoV-2 Genomes: Moving Toward a Universal Vaccine for the "Confined Virus"? Pathogens 2020; 9:E829. [PMID: 33050463 PMCID: PMC7600297 DOI: 10.3390/pathogens9100829] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic has been ongoing since its onset in late November 2019 in Wuhan, China. Understanding and monitoring the genetic evolution of the virus, its geographical characteristics, and its stability are particularly important for controlling the spread of the disease and especially for the development of a universal vaccine covering all circulating strains. From this perspective, we analyzed 30,983 complete SARS-CoV-2 genomes from 79 countries located in the six continents and collected from 24 December 2019, to 13 May 2020, according to the GISAID database. Our analysis revealed the presence of 3206 variant sites, with a uniform distribution of mutation types in different geographic areas. Remarkably, a low frequency of recurrent mutations has been observed; only 169 mutations (5.27%) had a prevalence greater than 1% of genomes. Nevertheless, fourteen non-synonymous hotspot mutations (>10%) have been identified at different locations along the viral genome; eight in ORF1ab polyprotein (in nsp2, nsp3, transmembrane domain, RdRp, helicase, exonuclease, and endoribonuclease), three in nucleocapsid protein, and one in each of three proteins: Spike, ORF3a, and ORF8. Moreover, 36 non-synonymous mutations were identified in the receptor-binding domain (RBD) of the spike protein with a low prevalence (<1%) across all genomes, of which only four could potentially enhance the binding of the SARS-CoV-2 spike protein to the human ACE2 receptor. These results along with intra-genomic divergence of SARS-CoV-2 could indicate that unlike the influenza virus or HIV viruses, SARS-CoV-2 has a low mutation rate which makes the development of an effective global vaccine very likely.
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Affiliation(s)
- Tarek Alouane
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Meriem Laamarti
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Abdelomunim Essabbar
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Mohammed Hakmi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - El Mehdi Bouricha
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - M. W. Chemao-Elfihri
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Souad Kartti
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Nasma Boumajdi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Houda Bendani
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Rokia Laamarti
- Medical Biotechnology Center, Moroccan Foundation for Science, Innovation & Research (MAScIR), Rabat 10100, Morocco;
| | - Fatima Ghrifi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Loubna Allam
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Tarik Aanniz
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Mouna Ouadghiri
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Naima El Hafidi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Rachid El Jaoudi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Houda Benrahma
- Faculty of Medicine, Mohammed VI University of Health Sciences (UM6SS), Casablanca 82403, Morocco;
| | - Jalil El Attar
- Riad Laboratory, City Center Hay Riad, Rabat 10112, Morocco;
| | - Rachid Mentag
- Biotechnology Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Rabat 10101, Morocco;
| | - Laila Sbabou
- Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat 10000, Morocco;
| | - Chakib Nejjari
- International School of Public Health, Mohammed VI University of Health Sciences (UM6SS), Casablanca 82403, Morocco;
| | - Saaid Amzazi
- Laboratory of Human Pathologies Biology, Faculty of Sciences, Mohammed V University, Rabat 10000, Morocco;
| | - Lahcen Belyamani
- Emergency Department, Military Hospital Mohammed V, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10112, Morocco;
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
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Beeraka NM, Sadhu SP, Madhunapantula SV, Rao Pragada R, Svistunov AA, Nikolenko VN, Mikhaleva LM, Aliev G. Strategies for Targeting SARS CoV-2: Small Molecule Inhibitors-The Current Status. Front Immunol 2020; 11:552925. [PMID: 33072093 PMCID: PMC7531039 DOI: 10.3389/fimmu.2020.552925] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/18/2020] [Indexed: 01/08/2023] Open
Abstract
Severe Acute Respiratory Syndrome-Corona Virus-2 (SARS-CoV-2) induced Coronavirus Disease - 19 (COVID-19) cases have been increasing at an alarming rate (7.4 million positive cases as on June 11 2020), causing high mortality (4,17,956 deaths as on June 11 2020) and economic loss (a 3.2% shrink in global economy in 2020) across 212 countries globally. The clinical manifestations of this disease are pneumonia, lung injury, inflammation, and severe acute respiratory syndrome (SARS). Currently, there is no vaccine or effective pharmacological agents available for the prevention/treatment of SARS-CoV2 infections. Moreover, development of a suitable vaccine is a challenging task due to antibody-dependent enhancement (ADE) and Th-2 immunopathology, which aggravates infection with SARS-CoV-2. Furthermore, the emerging SARS-CoV-2 strain exhibits several distinct genomic and structural patterns compared to other coronavirus strains, making the development of a suitable vaccine even more difficult. Therefore, the identification of novel small molecule inhibitors (NSMIs) that can interfere with viral entry or viral propagation is of special interest and is vital in managing already infected cases. SARS-CoV-2 infection is mediated by the binding of viral Spike proteins (S-protein) to human cells through a 2-step process, which involves Angiotensin Converting Enzyme-2 (ACE2) and Transmembrane Serine Protease (TMPRSS)-2. Therefore, the development of novel inhibitors of ACE2/TMPRSS2 is likely to be beneficial in combating SARS-CoV-2 infections. However, the usage of ACE-2 inhibitors to block the SARS-CoV-2 viral entry requires additional studies as there are conflicting findings and severe health complications reported for these inhibitors in patients. Hence, the current interest is shifted toward the development of NSMIs, which includes natural antiviral phytochemicals and Nrf-2 activators to manage a SARS-CoV-2 infection. It is imperative to investigate the efficacy of existing antiviral phytochemicals and Nrf-2 activators to mitigate the SARS-CoV-2-mediated oxidative stress. Therefore, in this review, we have reviewed structural features of SARS-CoV-2 with special emphasis on key molecular targets and their known modulators that can be considered for the development of NSMIs.
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Affiliation(s)
- Narasimha M. Beeraka
- Department of Biochemistry, Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR), JSS Academy of Higher Education & Research (JSS AHER), Mysore, India
| | - Surya P. Sadhu
- AU College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, India
| | - SubbaRao V. Madhunapantula
- Department of Biochemistry, Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR), JSS Academy of Higher Education & Research (JSS AHER), Mysore, India
- Special Interest Group in Cancer Biology and Cancer Stem Cells (SIG-CBCSC), JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysore, India
| | | | - Andrey A. Svistunov
- I. M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia
| | - Vladimir N. Nikolenko
- I. M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia
- Department of Normal and Topographic Anatomy, M.V. Lomonosov Moscow State University, Moscow, Russia
| | | | - Gjumrakch Aliev
- Research Institute of Human Morphology, Moscow, Russia
- Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
- Institute of Physiologically Active Compounds, Russian Academy of Sciences, Moscow, Russia
- GALLY International Research Institute, San Antonio, TX, United States
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Campos EVR, Pereira AES, de Oliveira JL, Carvalho LB, Guilger-Casagrande M, de Lima R, Fraceto LF. How can nanotechnology help to combat COVID-19? Opportunities and urgent need. J Nanobiotechnology 2020; 18:125. [PMID: 32891146 PMCID: PMC7474329 DOI: 10.1186/s12951-020-00685-4] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/28/2020] [Indexed: 12/11/2022] Open
Abstract
Incidents of viral outbreaks have increased at an alarming rate over the past decades. The most recent human coronavirus known as COVID-19 (SARS-CoV-2) has already spread around the world and shown R0 values from 2.2 to 2.68. However, the ratio between mortality and number of infections seems to be lower in this case in comparison to other human coronaviruses (such as severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV)). These outbreaks have tested the limits of healthcare systems and have posed serious questions about management using conventional therapies and diagnostic tools. In this regard, the use of nanotechnology offers new opportunities for the development of novel strategies in terms of prevention, diagnosis and treatment of COVID-19 and other viral infections. In this review, we discuss the use of nanotechnology for COVID-19 virus management by the development of nano-based materials, such as disinfectants, personal protective equipment, diagnostic systems and nanocarrier systems, for treatments and vaccine development, as well as the challenges and drawbacks that need addressing.
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Affiliation(s)
- Estefânia V R Campos
- Human and Natural Sciences Center, Federal University of ABC. Av. dos Estados, 5001. Bl. A, T3 Lab. 503-3. Bangú, Santo André, SP, Brazil
| | - Anderson E S Pereira
- São Paulo State University-UNESP, Institute of Science and Technology, Sorocaba, SP, Brazil
| | | | | | | | - Renata de Lima
- Universidade de Sorocaba, Rodovia Raposo Tavares km 92,5, Sorocaba, São Paulo, Brazil.
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Baldassarre A, Paolini A, Bruno SP, Felli C, Tozzi AE, Masotti A. Potential use of noncoding RNAs and innovative therapeutic strategies to target the 5'UTR of SARS-CoV-2. Epigenomics 2020; 12:1349-1361. [PMID: 32875809 PMCID: PMC7466951 DOI: 10.2217/epi-2020-0162] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
After the increasing number of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections all over the world, researchers and clinicians are struggling to find a vaccine or innovative therapeutic strategies to treat this viral infection. The severe acute respiratory syndrome coronavirus infection that occurred in 2002, Middle East respiratory syndrome (MERS) and other more common infectious diseases such as hepatitis C virus, led to the discovery of many RNA-based drugs. Among them, siRNAs and antisense locked nucleic acids have been demonstrated to have effective antiviral effects both in animal models and humans. Owing to the high genomic homology of SARS-CoV-2 and severe acute respiratory syndrome coronavirus (80–82%) the use of these molecules could be employed successfully also to target this emerging coronavirus. Trying to translate this approach to treat COVID-19, we analyzed the common structural features of viral 5’UTR regions that can be targeted by noncoding RNAs and we also identified miRNAs binding sites suitable for designing RNA-based drugs to be employed successfully against SARS-CoV-2.
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Affiliation(s)
- Antonella Baldassarre
- Children's Hospital Bambino Gesù-IRCCS, Research Laboratories; Multifactorial & Complex Phenotype Research Area, V.le di San Paolo 15, Rome 00146, Italy
| | - Alessandro Paolini
- Children's Hospital Bambino Gesù-IRCCS, Research Laboratories; Multifactorial & Complex Phenotype Research Area, V.le di San Paolo 15, Rome 00146, Italy
| | - Stefania Paola Bruno
- Children's Hospital Bambino Gesù-IRCCS, Research Laboratories; Multifactorial & Complex Phenotype Research Area, V.le di San Paolo 15, Rome 00146, Italy
| | - Cristina Felli
- Children's Hospital Bambino Gesù-IRCCS, Research Laboratories; Multifactorial & Complex Phenotype Research Area, V.le di San Paolo 15, Rome 00146, Italy
| | - Alberto Eugenio Tozzi
- Children's Hospital Bambino Gesù-IRCCS, Research Laboratories; Multifactorial & Complex Phenotype Research Area, V.le di San Paolo 15, Rome 00146, Italy
| | - Andrea Masotti
- Children's Hospital Bambino Gesù-IRCCS, Research Laboratories; Multifactorial & Complex Phenotype Research Area, V.le di San Paolo 15, Rome 00146, Italy
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RNA interference as a promising treatment against SARS-CoV-2. Int Microbiol 2020; 24:123-124. [PMID: 32875426 PMCID: PMC7462657 DOI: 10.1007/s10123-020-00146-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 08/25/2020] [Accepted: 08/28/2020] [Indexed: 11/03/2022]
Abstract
Until now, there is no current vaccine or treatment against SARS-CoV-2. There are previous successful RNAi studies performed on SARS-CoV. Therefore, similar line of investigation against SARS-CoV-2 could be successful.
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Uludağ H, Parent K, Aliabadi HM, Haddadi A. Prospects for RNAi Therapy of COVID-19. Front Bioeng Biotechnol 2020; 8:916. [PMID: 32850752 PMCID: PMC7409875 DOI: 10.3389/fbioe.2020.00916] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/15/2020] [Indexed: 12/12/2022] Open
Abstract
COVID-19 caused by the SARS-CoV-2 virus is a fast emerging disease with deadly consequences. The pulmonary system and lungs in particular are most prone to damage caused by the SARS-CoV-2 infection, which leaves a destructive footprint in the lung tissue, making it incapable of conducting its respiratory functions and resulting in severe acute respiratory disease and loss of life. There were no drug treatments or vaccines approved for SARS-CoV-2 at the onset of pandemic, necessitating an urgent need to develop effective therapeutics. To this end, the innate RNA interference (RNAi) mechanism can be employed to develop front line therapies against the virus. This approach allows specific binding and silencing of therapeutic targets by using short interfering RNA (siRNA) and short hairpin RNA (shRNA) molecules. In this review, we lay out the prospect of the RNAi technology for combatting the COVID-19. We first summarize current understanding of SARS-CoV-2 virology and the host response to viral entry and duplication, with the purpose of revealing effective RNAi targets. We then summarize the past experience with nucleic acid silencers for SARS-CoV, the predecessor for current SARS-CoV-2. Efforts targeting specific protein-coding regions within the viral genome and intragenomic targets are summarized. Emphasizing non-viral delivery approaches, molecular underpinnings of design of RNAi agents are summarized with comparative analysis of various systems used in the past. Promising viral targets as well as host factors are summarized, and the possibility of modulating the immune system are presented for more effective therapies. We place special emphasis on the limitations of past studies to propel the field faster by focusing on most relevant models to translate the promising agents to a clinical setting. Given the urgency to address lung failure in COVID-19, we summarize the feasibility of delivering promising therapies by the inhalational route, with the expectation that this route will provide the most effective intervention to halt viral spread. We conclude with the authors' perspectives on the future of RNAi therapeutics for combatting SARS-CoV-2. Since time is of the essence, a strong perspective for the path to most effective therapeutic approaches are clearly articulated by the authors.
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Affiliation(s)
- Hasan Uludağ
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Kylie Parent
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada
| | | | - Azita Haddadi
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, SK, Canada
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Decaro N, Lorusso A. Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses. Vet Microbiol 2020; 244:108693. [PMID: 32402329 PMCID: PMC7195271 DOI: 10.1016/j.vetmic.2020.108693] [Citation(s) in RCA: 231] [Impact Index Per Article: 57.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/10/2020] [Accepted: 04/10/2020] [Indexed: 12/16/2022]
Abstract
The recent pandemic caused by the novel human coronavirus, referrred to as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), not only is having a great impact on the health care systems and economies in all continents but it is also causing radical changes of common habits and life styles. The novel coronavirus (CoV) recognises, with high probability, a zoonotic origin but the role of animals in the SARS-CoV-2 epidemiology is still largely unknown. However, CoVs have been known in animals since several decades, so that veterinary coronavirologists have a great expertise on how to face CoV infections in animals, which could represent a model for SARS-CoV-2 infection in humans. In the present paper, we provide an up-to-date review of the literature currently available on animal CoVs, focusing on the molecular mechanisms that are responsible for the emergence of novel CoV strains with different antigenic, biologic and/or pathogenetic features. A full comprehension of the mechanisms driving the evolution of animal CoVs will help better understand the emergence, spreading, and evolution of SARS-CoV-2.
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Affiliation(s)
- Nicola Decaro
- Department of Veterinary Medicine, University of Bari, Valenzano, Bari, Italy.
| | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise 'G. Caporale', Teramo, Italy
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Yin C. Genotyping coronavirus SARS-CoV-2: methods and implications. Genomics 2020; 112:3588-3596. [PMID: 32353474 PMCID: PMC7184998 DOI: 10.1016/j.ygeno.2020.04.016] [Citation(s) in RCA: 176] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/13/2020] [Accepted: 04/22/2020] [Indexed: 01/08/2023]
Abstract
The emerging global infectious COVID-19 disease by novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) presents critical threats to global public health and the economy since it was identified in late December 2019 in China. The virus has gone through various pathways of evolution. To understand the evolution and transmission of SARS-CoV-2, genotyping of virus isolates is of great importance. This study presents an accurate method for effectively genotyping SARS-CoV-2 viruses using complete genomes. The method employs the multiple sequence alignments of the genome isolates with the SARS-CoV-2 reference genome. The single-nucleotide polymorphism (SNP) genotypes are then measured by Jaccard distances to track the relationship of virus isolates. The genotyping analysis of SARS-CoV-2 isolates from the globe reveals that specific multiple mutations are the predominated mutation type during the current epidemic. The proposed method serves an effective tool for monitoring and tracking the epidemic of pathogenic viruses in their global and local genetic variations. The genotyping analysis shows that the genes encoding the S proteins and RNA polymerase, RNA primase, and nucleoprotein, undergo frequent mutations. These mutations are critical for vaccine development in disease control.
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Affiliation(s)
- Changchuan Yin
- Department of Mathematics, Statistics, and Computer Science, University of Illinois at Chicago, Chicago, IL 60607, USA.
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Computational Identification of Small Interfering RNA Targets in SARS-CoV-2. Virol Sin 2020; 35:359-361. [PMID: 32297156 PMCID: PMC7157830 DOI: 10.1007/s12250-020-00221-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/03/2020] [Indexed: 01/08/2023] Open
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Development of small-molecule viral inhibitors targeting various stages of the life cycle of emerging and re-emerging viruses. Front Med 2017; 11:449-461. [PMID: 29170916 PMCID: PMC7089273 DOI: 10.1007/s11684-017-0589-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 09/22/2017] [Indexed: 01/22/2023]
Abstract
In recent years, unexpected outbreaks of infectious diseases caused by emerging and re-emerging viruses have become more frequent, which is possibly due to environmental changes. These outbreaks result in the loss of life and economic hardship. Vaccines and therapeutics should be developed for the prevention and treatment of infectious diseases. In this review, we summarize and discuss the latest progress in the development of small-molecule viral inhibitors against highly pathogenic coronaviruses, including severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus, Ebola virus, and Zika virus. These viruses can interfere with the specific steps of viral life cycle by blocking the binding between virus and host cells, disrupting viral endocytosis, disturbing membrane fusion, and interrupting viral RNA replication and translation, thereby demonstrating potent therapeutic effect against various emerging and re-emerging viruses. We also discuss some general strategies for developing small-molecule viral inhibitors.
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Liu YY, Chen LJ, Zhong Y, Shen MX, Ma N, Liu BY, Luo F, Hou W, Yang ZQ, Xiong HR. Specific interference shRNA-expressing plasmids inhibit Hantaan virus infection in vitro and in vivo. Acta Pharmacol Sin 2016; 37:497-504. [PMID: 26972493 PMCID: PMC4820803 DOI: 10.1038/aps.2015.165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 12/15/2015] [Indexed: 01/28/2023] Open
Abstract
AIM To investigate the antiviral effects of vectors expressing specific short hairpin RNAs (shRNAs) against Hantaan virus (HTNV) infection in vitro and in vivo. METHODS Based on the effects of 4 shRNAs targeting different regions of HTNV genomic RNA on viral replication, the most effective RNA interference fragments of the S and M genes were constructed in pSilencer-3.0-H1 vectors, and designated pSilencer-S and pSilencer-M, respectively. The antiviral effect of pSilencer-S/M against HTNV was evaluated in both HTNV-infected Vero-E6 cells and mice. RESULTS In HTNV-infected Vero-E6 cells, pSilencer-S and pSilencer-M targeted the viral nucleocapsid proteins and envelope glycoproteins, respectively, as revealed in the immunofluorescence assay. Transfection with pSilencer-S or pSilencer-M (1, 2, 4 μg) markedly inhibited the viral antigen expression in dose- and time-dependent manners. Transfection with either plasmid (2 μg) significantly decreased HTNV-RNA level at 3 day postinfectin (dpi) and the progeny virus titer at 5 dpi. In mice infected with lethal doses of HTNV, intraperitoneal injection of pSilencer-S or pSilencer-M (30 μg) considerably increased the survival rates and mean time to death, and significantly reduced the mean virus yields and viral RNA level, and alleviated virus-induced pathological lesions in lungs, brains and kidneys. CONCLUSION Plasmid-based shRNAs potently inhibit HTNV replication in vitro and in vivo. Our results provide a basis for development of shRNA as therapeutics for HTNV infections in humans.
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Ballarín-González B, Thomsen TB, Howard KA. Clinical translation of RNAi-based treatments for respiratory diseases. Drug Deliv Transl Res 2015; 3:84-99. [PMID: 25787868 PMCID: PMC7097609 DOI: 10.1007/s13346-012-0098-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The ability to harness the RNA interference (RNAi) mechanism as a potential potent therapeutic has attracted great interest from academia and industry. Numerous preclinical and recent clinical trials have demonstrated the effectiveness of RNAi triggers such as synthetic small interfering RNA (siRNA). Chemical modification and delivery technologies can be utilized to avoid immune stimulation and improve the bioactivity and pharmacokinetics. Local application to the respiratory epithelia allows direct access to the site of respiratory pathogens that include influenza and respiratory syncytial virus (RSV). This review outlines the essential steps required for the clinical translation of RNAi-based respiratory therapies including disease and RNA target selection, siRNA design, respiratory barriers, and delivery solutions. Attention is given to antiviral therapies and preclinical evaluation with focus on the current status of anti-RSV clinical trials.
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Affiliation(s)
- Borja Ballarín-González
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, University of Aarhus, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Troels Bo Thomsen
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, University of Aarhus, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Kenneth Alan Howard
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, University of Aarhus, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
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