1
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Hu B, Guo H, Si H, Shi Z. Emergence of SARS and COVID-19 and preparedness for the next emerging disease X. Front Med 2024; 18:1-18. [PMID: 38561562 DOI: 10.1007/s11684-024-1066-6] [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: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 04/04/2024]
Abstract
Severe acute respiratory syndrome (SARS) and Coronavirus disease 2019 (COVID-19) are two human Coronavirus diseases emerging in this century, posing tremendous threats to public health and causing great loss to lives and economy. In this review, we retrospect the studies tracing the molecular evolution of SARS-CoV, and we sort out current research findings about the potential ancestor of SARS-CoV-2. Updated knowledge about SARS-CoV-2-like viruses found in wildlife, the animal susceptibility to SARS-CoV-2, as well as the interspecies transmission risk of SARS-related coronaviruses (SARSr-CoVs) are gathered here. Finally, we discuss the strategies of how to be prepared against future outbreaks of emerging or re-emerging coronaviruses.
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Affiliation(s)
- Ben Hu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Hua Guo
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Haorui Si
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhengli Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
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2
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Chandiwana N, Kruger C, Richardson N, Nxumalo S, Mashilo N, Dineka Y, Mudau N, Johnstone H, Kim W, Ju C, Arbe-Barnes S, Marrast AC, Flynn J, Venter WDF. Community-based management of a five-arm randomised clinical trial in COVID-19 outpatients in South Africa: challenges and opportunities. Trials 2023; 24:635. [PMID: 37794489 PMCID: PMC10548657 DOI: 10.1186/s13063-023-07577-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 08/04/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Repeated COVID-19 waves and corresponding mitigation measures have impacted health systems globally with exceptional challenges. In response to the pandemic, researchers, regulators, and funders rapidly pivoted to COVID-19 research activities. However, many clinical drug studies were not completed, due to often complex and rapidly evolving research conditions. METHODS We outline our experience of planning and managing a randomised, adaptive, open-label, phase 2 clinical trial to evaluate the safety and efficacy of four repurposed drug regimens versus standard-of-care (SOC) in outpatients with 'mild to moderate' COVID-19 in Johannesburg, South Africa, in the context of a partnership with multiple stakeholders. The study was conducted between 3 September 2020 and 23 August 2021 during changing COVID-19 restrictions, significant morbidity and mortality waves, and allied supply line, economic, and political instability. RESULTS Our clinical study design was pragmatic, including low-risk patients who were treated open label. There was built-in flexibility, including provision for some sample size adjustment and a range of secondary efficacy outcomes. Barriers to recruitment included the timing of waves, staff shortages due to illness, late presentation of patients, COVID-19 misinformation, and political unrest. Mitigations were the use of community health workers, deployment of mobile clinical units, and simplification of screening. Trial management required a radical reorganisation of logistics and processes to accommodate COVID-19 restrictions. These included the delivery of staff training and monitoring remotely, electronic consent, patient training and support to collect samples and report data at home, and the introduction of tele-medicine. These measures were successful for data collection, safe, and well received by patients. CONCLUSION Completing a COVID-19 trial in outpatients during the height of the pandemic required multiple innovations in nearly every aspect of clinical trial management, a high commitment level from study staff and patients, and support from study sponsors. Our experience has generated a more robust clinical research infrastructure, building in efficiencies to clinical trial management beyond the pandemic.
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Affiliation(s)
- Nomathemba Chandiwana
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Building C, 32 Princess of Wales Terrace, Johannesburg, 2001, South Africa.
| | - Chelsea Kruger
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Building C, 32 Princess of Wales Terrace, Johannesburg, 2001, South Africa
| | | | - Sibongiseni Nxumalo
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Building C, 32 Princess of Wales Terrace, Johannesburg, 2001, South Africa
| | - Nkoleleng Mashilo
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Building C, 32 Princess of Wales Terrace, Johannesburg, 2001, South Africa
| | - Yengiwe Dineka
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Building C, 32 Princess of Wales Terrace, Johannesburg, 2001, South Africa
| | - Ntanganedzeni Mudau
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Building C, 32 Princess of Wales Terrace, Johannesburg, 2001, South Africa
| | | | - Wookyung Kim
- Shin Poong Pharm. Co. Ltd, Seoul, Republic of Korea
| | - Chung Ju
- Shin Poong Pharm. Co. Ltd, Seoul, Republic of Korea
- Graduate School of Clinical Pharmacy, CHA University, Pocheon-Si, Gyeonggi-Do, Republic of Korea
| | | | | | - Julia Flynn
- Medicines for Malaria Venture, Geneva, Switzerland
| | - Willem D Francois Venter
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Building C, 32 Princess of Wales Terrace, Johannesburg, 2001, South Africa
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3
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Sandholtz SH, Drocco JA, Zemla AT, Torres MW, Silva MS, Allen JE. A Computational Pipeline to Identify and Characterize Binding Sites and Interacting Chemotypes in SARS-CoV-2. ACS OMEGA 2023; 8:21871-21884. [PMID: 37309388 PMCID: PMC10254058 DOI: 10.1021/acsomega.3c01621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/17/2023] [Indexed: 06/14/2023]
Abstract
Minimizing the human and economic costs of the COVID-19 pandemic and future pandemics requires the ability to develop and deploy effective treatments for novel pathogens as soon as possible after they emerge. To this end, we introduce a new computational pipeline for the rapid identification and characterization of binding sites in viral proteins along with the key chemical features, which we call chemotypes, of the compounds predicted to interact with those same sites. The composition of source organisms for the structural models associated with an individual binding site is used to assess the site's degree of structural conservation across different species, including other viruses and humans. We propose a search strategy for novel therapeutics that involves the selection of molecules preferentially containing the most structurally rich chemotypes identified by our algorithm. While we demonstrate the pipeline on SARS-CoV-2, it is generalizable to any new virus, as long as either experimentally solved structures for its proteins are available or sufficiently accurate predicted structures can be constructed.
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Affiliation(s)
- Sarah H. Sandholtz
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
of America
| | - Jeffrey A. Drocco
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
of America
| | - Adam T. Zemla
- Global
Security Computing Applications Division, Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
of America
| | - Marisa W. Torres
- Global
Security Computing Applications Division, Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
of America
| | - Mary S. Silva
- Global
Security Computing Applications Division, Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
of America
| | - Jonathan E. Allen
- Global
Security Computing Applications Division, Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
of America
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4
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Patil S, Vijayanand S, Joshi D, Menon I, Braz Gomes K, Kale A, Bagwe P, Yacoub S, Uddin MN, D'Souza MJ. Subunit microparticulate vaccine delivery using microneedles trigger significant SARS-spike-specific humoral and cellular responses in a preclinical murine model. Int J Pharm 2023; 632:122583. [PMID: 36610521 PMCID: PMC9811858 DOI: 10.1016/j.ijpharm.2023.122583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 12/29/2022] [Accepted: 01/02/2023] [Indexed: 01/06/2023]
Abstract
The objective of this "proof-of-concept" study was to evaluate the synergistic effect of a subunit microparticulate vaccine and microneedles (MN) assisted vaccine delivery system against a human coronavirus. Here, we formulated PLGA polymeric microparticles (MPs) encapsulating spike glycoprotein (GP) of SARS-CoV as the model antigen. Similarly, we formulated adjuvant MPs encapsulating Alhydrogel® and AddaVax™. The antigen/adjuvant MPs were characterized and tested in vitro for immunogenicity. We found that the antigen/adjuvant MPs were non-cytotoxic in vitro. The spike GP MPs + Alhydrogel® MPs + AddaVax™ MPs showed enhanced immunogenicity in vitro as confirmed through the release of nitrite, autophagy, and antigen presenting molecules with their co-stimulatory molecules. Next, we tested the in vivo efficacy of the spike GP MP vaccine with and without adjuvant MPs in mice vaccinated using MN. The spike GP MPs + Alhydrogel® MPs + AddaVax™ MPs induced heightened spike GP-specific IgG, IgG1 and IgG2a antibodies in mice. Also, spike GP MPs + Alhydrogel® MPs + AddaVax™ MPs enhanced expression of CD4+ and CD8+ T cells in secondary lymphoid organ like spleen. These results indicated spike GP-specific humoral immunity and cellular immunity in vivo. Thus, we employed the benefits of both the subunit vaccine MPs and dissolving MN to form a non-invasive and effective vaccination strategy against human coronaviruses.
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Affiliation(s)
- Smital Patil
- Center for Drug Delivery Research, Vaccine Nanotechnology Laboratory, College of Pharmacy, Mercer University, Atlanta, GA 30341, USA
| | - Sharon Vijayanand
- Center for Drug Delivery Research, Vaccine Nanotechnology Laboratory, College of Pharmacy, Mercer University, Atlanta, GA 30341, USA
| | - Devyani Joshi
- Center for Drug Delivery Research, Vaccine Nanotechnology Laboratory, College of Pharmacy, Mercer University, Atlanta, GA 30341, USA
| | - Ipshita Menon
- Center for Drug Delivery Research, Vaccine Nanotechnology Laboratory, College of Pharmacy, Mercer University, Atlanta, GA 30341, USA
| | - Keegan Braz Gomes
- Center for Drug Delivery Research, Vaccine Nanotechnology Laboratory, College of Pharmacy, Mercer University, Atlanta, GA 30341, USA
| | - Akanksha Kale
- Center for Drug Delivery Research, Vaccine Nanotechnology Laboratory, College of Pharmacy, Mercer University, Atlanta, GA 30341, USA
| | - Priyal Bagwe
- Center for Drug Delivery Research, Vaccine Nanotechnology Laboratory, College of Pharmacy, Mercer University, Atlanta, GA 30341, USA
| | - Shadi Yacoub
- Center for Drug Delivery Research, Vaccine Nanotechnology Laboratory, College of Pharmacy, Mercer University, Atlanta, GA 30341, USA
| | - Mohammad N Uddin
- Center for Drug Delivery Research, Vaccine Nanotechnology Laboratory, College of Pharmacy, Mercer University, Atlanta, GA 30341, USA
| | - Martin J D'Souza
- Center for Drug Delivery Research, Vaccine Nanotechnology Laboratory, College of Pharmacy, Mercer University, Atlanta, GA 30341, USA.
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5
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COVID-19 Preventive Measure: A Study on “MASK-A Boon or a Bane”. Interdiscip Perspect Infect Dis 2022; 2022:2253656. [DOI: 10.1155/2022/2253656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/29/2022] [Accepted: 07/13/2022] [Indexed: 11/17/2022] Open
Abstract
Background. Mask wearing can restrict the spread of respiratory viral transmission during the third wave of the COVID-19 pandemic. Globally, governments have emphasized its use in workplaces and public areas to prevent the transmission routes of corona virus. In spite of the current awareness in the general population, the stringency of wearing the mask lies as an individual’s choices. Subject and Methods. This research work discusses available studies on the types and comparison of masks in the market for use. It includes a short survey conducted with 1,173 anonymized healthy participants primarily devoid of comorbidities. The survey includes the effects of mask wearing, while outdoor with minimal activities like walking and with mild activities like jogging and stretching. Our research further discusses various health effects of wearing a mask, including cardiac output, hypoxemia, hypoxia, and dyspnoea, and how such situations that pose a threat can be consciously avoided. Results. It was found that the majority of people use cloth/fabric reusable mask. There remains scope for better-designed masks and improving health in the mass population by inculcating healthy breathing habits and other relevant exercises that can help people cope up better in this fight against the deadly virus at a larger scale. Conclusion. For most of the survey questions, there was significant correlation between gender and the related responses as there was no significantly observable difference in the nonparametric, unpaired analyses of responses. The main objective of this research work is to initiate more discussions and enhance awareness in natural ways of staying healthy during the pandemic emphasizing mask use. Further progress in this aspect remains a whole new area for future exploration.
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6
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Seadawy MG, Binsuwaidan R, Alotaibi B, El-Masry TA, El-Harty BE, Gad AF, Elkhatib WF, El-Bouseary MM. The Mutational Landscape of SARS-CoV-2 Variants of Concern Recovered From Egyptian Patients in 2021. Front Microbiol 2022; 13:923137. [PMID: 35875574 PMCID: PMC9300961 DOI: 10.3389/fmicb.2022.923137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/16/2022] [Indexed: 11/22/2022] Open
Abstract
In December 2019, a mysterious viral pneumonia first developed in Wuhan, China, resulting in a huge number of fatal cases. This pneumonia, which was named COVID-19, was attributed to a novel coronavirus, SARS-CoV-2. The emerging SARS-CoV-2 mutations pose the greatest risk to human health because they could result in an increase in the COVID-19 severity or the failure of current vaccines. One of these notable mutations is the SARS-CoV-2 Delta variant (B.1.617) that was first detected in India and has rapidly expanded to 115 countries worldwide. Consequently, in this study, we performed next-generation sequencing and phylogenetic analysis of SARS-CoV-2 during the third wave of the pandemic to determine the SARS-CoV-2 variants of concern (VOC) prevalence in Egypt. We observed several mutational patterns, revealing that SARS-CoV-2 evolution has expanded in Egypt with a considerable increase in the number of VOC. Therefore, the Egyptian authorities should take an appropriate approach to investigate the compatibility of already employed vaccines with this VOC and to examine the efficacy of the existing therapeutic regimen against new SARS-CoV-2 variants.
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Affiliation(s)
| | - Reem Binsuwaidan
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Badriyah Alotaibi
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Thanaa A. El-Masry
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | | | - Ahmed F. Gad
- Biological Prevention Department, Egypt Army, Cairo, Egypt
| | - Walid F. Elkhatib
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Galala University, New Galala City, Egypt
| | - Maisra M. El-Bouseary
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Tanta University, Tanta, Egypt
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7
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Uvarova EA, Belavin PA, Deineko EV. Design and assembly of plant-based COVID-19 candidate vaccines: reсent development and future prospects. Vavilovskii Zhurnal Genet Selektsii 2022; 26:327-335. [PMID: 35795227 PMCID: PMC9177425 DOI: 10.18699/vjgb-22-39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 11/19/2022] Open
Abstract
An outbreak of a new variant of the coronavirus infection, known as COVID-19, occurred at the end of 2019 in China, in the city of Wuhan. It was caused by the SARS-CoV-2 virus. This variant of the virus is characterized by a high degree of variability and, as the current situation with its spread across different regions of the globe shows, it can lead to a progressive spread of infection among the human population and become the cause of a pandemic. The world scientific community is making tremendous efforts to develop means of protection,prevention and treatment of this disease based on modern advances in molecular biology, immunology and
vaccinology. This review provides information on the current state of research in the field of vaccine development
against COVID-19 with an emphasis on the role of plants in solving this complex problem. Although plants have
long been used by mankind as sources of various medicinal substances, in a pandemic, plant expression systems
become attractive as biofactories or bioreactors for the production of artificially created protein molecules
that include protective antigens against viral infection. The design and creation of such artificial molecules
underlies the development of recombinant subunit vaccines aimed at a rapid response against the spread of
infections with a high degree of variability. The review presents the state of research covering a period of just
over two years, i. e. since the emergence of the new outbreak of coronavirus infection. The authors tried to
emphasize the importance of rapid response of research groups from various scientific fields towards the use
of existing developments to create means of protection against various pathogens. With two plant expression
systems – stable and transient – as examples, the development of work on the creation of recombinant subunit
vaccines against COVID-19 in various laboratories and commercial companies is shown. The authors emphasize
that plant expression systems have promise for the development of not only protective means under conditions
of rapid response (subunit vaccines), but also therapeutic agents in the form of monoclonal antibodies against
COVID-19 synthesized in plant cells.
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Affiliation(s)
- E. A. Uvarova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - P. A. Belavin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - E. V. Deineko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Tomsk State University
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8
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Ordoñez R, Solano D, Granizo G. T and B Cells Immune Response and the importance of vaccines Against SARS-CoV-2. BIONATURA 2022. [DOI: 10.21931/rb/2022.07.01.36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 has become a global pandemic because it is a severe respiratory syndrome that attacks many people worldwide and can lead to death depending on the severity. In recent years, the study of the acquired immune response (T cells) and innate (B cells) has increased to better treat the disease from the quantitative cell count. A picture has begun to emerge revealing that CD4+ T cells, CD8+ T cells, and neutralizing antibodies contribute to the control of SARS-CoV-2 in COVID-19 cases. This work studies the three fundamental components of the adaptive immune system: B cells (the source of antibodies), CD4+T cells, and CD8+T cells and their function against SARS-CoV2. The importance of vaccines and the different types of existing vaccines are discussed. Implications of covid-19 variants on Immunity and vaccine types are also analyzed to understand how the action of the immune system will help treat the disease.
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Affiliation(s)
- Ronny Ordoñez
- School of Biological Science and Engineering, Yachay Tech University, Hacienda San José s/n, San Miguel de Urcuquí 100119, Ecuador
| | - Dulexy Solano
- School of Biological Science and Engineering, Yachay Tech University, Hacienda San José s/n, San Miguel de Urcuquí 100119, Ecuador
| | - Gustavo Granizo
- School of Biological Science and Engineering, Yachay Tech University, Hacienda San José s/n, San Miguel de Urcuquí 100119, Ecuador
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9
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Conserved Residues Adjacent to ß-Barrel and Loop Intersection among Enterovirus VP1 Affect Viral Replication: Potential Target for Anti-Enteroviral Development. Viruses 2022; 14:v14020364. [PMID: 35215957 PMCID: PMC8877150 DOI: 10.3390/v14020364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/05/2022] [Accepted: 02/07/2022] [Indexed: 11/17/2022] Open
Abstract
Enterovirus genus has over one hundred genotypes and could cause several kinds of severe animal and human diseases. Understanding the role of conserved residues in the VP1 capsid protein among the enterovirus genus may lead to anti-enteroviral drug development. The highly conserved residues were found to be located at the loop and ß-barrel intersections. To elucidate the role of these VP1 residues among the enterovirus genus, alanine substitution reverse genetics (rg) variants were generated, and virus properties were investigated for their impact. Six highly conserved residues were identified as located near the inside of the canyon, and four of them were close to the ß-barrel and loop intersection. The variants rgVP1-R86A, rgVP1-P193A, rgVP1-G231A, and rgVP1-K256A were unable to be obtained, which may be due to disruption in the virus replication process. In contrast, rgVP1-E134A and rgVP1-P157A replicated well and rgVP1-P157A showed smaller plaque size, lower viral growth kinetics, and thermal instability at 39.5°C when compared to the rg wild type virus. These findings showed that the conserved residues located at the ß-barrel and loop junction play roles in modulating viral replication, which may provide a pivotal role for pan-enteroviral inhibitor candidate.
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10
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Tan S, Banwell MG, Ye WC, Lan P, White LV. The Inhibition of RNA Viruses by Amaryllidaceae Alkaloids: Opportunities for the Development of Broad-Spectrum Anti-Coronavirus Drugs. Chem Asian J 2022; 17:e202101215. [PMID: 35032358 DOI: 10.1002/asia.202101215] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 12/06/2021] [Indexed: 12/16/2022]
Abstract
The global COVID-19 pandemic has claimed the lives of millions and disrupted nearly every aspect of human society. Currently, vaccines remain the only widely available medical means to address the cause of the pandemic, the SARS-CoV-2 virus. Unfortunately, current scientific consensus deems the emergence of vaccine-resistant SARS-CoV-2 variants highly likely. In this context, the design and development of broad-spectrum, small-molecule based antiviral drugs has been described as a potentially effective, alternative medical strategy to address circulating and re-emerging CoVs. Small molecules are well-suited to target the least-rapidly evolving structures within CoVs such as highly conserved RNA replication enzymes, and this renders them less vulnerable to evolved drug resistance. Examination of the vast literature describing the inhibition of RNA viruses by Amaryllidaceae alkaloids suggests that future, broad-spectrum anti-CoV drugs may be derived from this family of natural products.
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Affiliation(s)
- Shen Tan
- The Institute for Advanced and Applied Chemical Synthesis, Jinan University, Guangzhou, 510632, P. R. China
| | - Martin G Banwell
- The Institute for Advanced and Applied Chemical Synthesis, Jinan University, Guangzhou, 510632, P. R. China
| | - Wen-Cai Ye
- College of Pharmacy, Jinan University, Guangzhou, 510632, P. R. China
| | - Ping Lan
- The Institute for Advanced and Applied Chemical Synthesis, Jinan University, Guangzhou, 510632, P. R. China
| | - Lorenzo V White
- The Institute for Advanced and Applied Chemical Synthesis, Jinan University, Guangzhou, 510632, P. R. China
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Shukla P, Pandey P, Prasad B, Robinson T, Purohit R, D'Cruz LG, Tambuwala MM, Mutreja A, Harkin J, Rai TS, Murray EK, Gibson DS, Bjourson AJ. Immuno-informatics analysis predicts B and T cell consensus epitopes for designing peptide vaccine against SARS-CoV-2 with 99.82% global population coverage. Brief Bioinform 2021; 23:6484513. [PMID: 34962259 PMCID: PMC8769887 DOI: 10.1093/bib/bbab496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 10/03/2021] [Accepted: 10/30/2021] [Indexed: 01/03/2023] Open
Abstract
The current global pandemic due to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has taken a substantial number of lives across the world. Although few vaccines have been rolled-out, a number of vaccine candidates are still under clinical trials at various pharmaceutical companies and laboratories around the world. Considering the intrinsic nature of viruses in mutating and evolving over time, persistent efforts are needed to develop better vaccine candidates. In this study, various immuno-informatics tools and bioinformatics databases were deployed to derive consensus B-cell and T-cell epitope sequences of SARS-CoV-2 spike glycoprotein. This approach has identified four potential epitopes which have the capability to initiate both antibody and cell-mediated immune responses, are non-allergenic and do not trigger autoimmunity. These peptide sequences were also evaluated to show 99.82% of global population coverage based on the genotypic frequencies of HLA binding alleles for both MHC class-I and class-II and are unique for SARS-CoV-2 isolated from human as a host species. Epitope number 2 alone had a global population coverage of 98.2%. Therefore, we further validated binding and interaction of its constituent T-cell epitopes with their corresponding HLA proteins using molecular docking and molecular dynamics simulation experiments, followed by binding free energy calculations with molecular mechanics Poisson–Boltzmann surface area, essential dynamics analysis and free energy landscape analysis. The immuno-informatics pipeline described and the candidate epitopes discovered herein could have significant impact upon efforts to develop globally effective SARS-CoV-2 vaccines.
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Affiliation(s)
- Priyank Shukla
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, Ulster University, C-TRIC Building, Altnagelvin Area Hospital, Glenshane Road, Derry/Londonderry, BT47 6SB, UK
| | - Preeti Pandey
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Bodhayan Prasad
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, Ulster University, C-TRIC Building, Altnagelvin Area Hospital, Glenshane Road, Derry/Londonderry, BT47 6SB, UK
| | - Tony Robinson
- School of Computing, Engineering and Intelligent Systems, Ulster University, Magee Campus, Derry/Londonderry, BT48 7JL, UK
| | - Rituraj Purohit
- Structural Bioinformatics Lab, Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh-176061, India
| | - Leon G D'Cruz
- Respiratory Medicine Department and Clinical Trials Unit, Queen Alexandra Hospital, Portsmouth, PO6 3LY, UK
| | - Murtaza M Tambuwala
- School of Pharmacy and Pharmaceutical Sciences, Ulster University, Coleraine Campus, Coleraine, BT52 1SA, UK
| | - Ankur Mutreja
- Department of Medicine, University of Cambridge, Level 5, Addenbrookes Hospital, Cambridge, CB2 0QQ, UK
| | - Jim Harkin
- School of Computing, Engineering and Intelligent Systems, Ulster University, Magee Campus, Derry/Londonderry, BT48 7JL, UK
| | - Taranjit Singh Rai
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, Ulster University, C-TRIC Building, Altnagelvin Area Hospital, Glenshane Road, Derry/Londonderry, BT47 6SB, UK
| | - Elaine K Murray
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, Ulster University, C-TRIC Building, Altnagelvin Area Hospital, Glenshane Road, Derry/Londonderry, BT47 6SB, UK
| | - David S Gibson
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, Ulster University, C-TRIC Building, Altnagelvin Area Hospital, Glenshane Road, Derry/Londonderry, BT47 6SB, UK
| | - Anthony J Bjourson
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, Ulster University, C-TRIC Building, Altnagelvin Area Hospital, Glenshane Road, Derry/Londonderry, BT47 6SB, UK
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12
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Peng XL, Cheng JSY, Gong HL, Yuan MD, Zhao XH, Li Z, Wei DX. Advances in the design and development of SARS-CoV-2 vaccines. Mil Med Res 2021; 8:67. [PMID: 34911569 PMCID: PMC8674100 DOI: 10.1186/s40779-021-00360-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 11/15/2021] [Indexed: 01/18/2023] Open
Abstract
Since the end of 2019, coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide. The RNA genome of SARS-CoV-2, which is highly infectious and prone to rapid mutation, encodes both structural and nonstructural proteins. Vaccination is currently the only effective method to prevent COVID-19, and structural proteins are critical targets for vaccine development. Currently, many vaccines are in clinical trials or are already on the market. This review highlights ongoing advances in the design of prophylactic or therapeutic vaccines against COVID-19, including viral vector vaccines, DNA vaccines, RNA vaccines, live-attenuated vaccines, inactivated virus vaccines, recombinant protein vaccines and bionic nanoparticle vaccines. In addition to traditional inactivated virus vaccines, some novel vaccines based on viral vectors, nanoscience and synthetic biology also play important roles in combating COVID-19. However, many challenges persist in ongoing clinical trials.
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Affiliation(s)
- Xue-Liang Peng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Department of Life Sciences and Medicine, Northwest University, Xi’an, 710069 China
| | - Ji-Si-Yu Cheng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Department of Life Sciences and Medicine, Northwest University, Xi’an, 710069 China
| | - Hai-Lun Gong
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Department of Life Sciences and Medicine, Northwest University, Xi’an, 710069 China
| | - Meng-Di Yuan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Department of Life Sciences and Medicine, Northwest University, Xi’an, 710069 China
| | - Xiao-Hong Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Department of Life Sciences and Medicine, Northwest University, Xi’an, 710069 China
| | - Zibiao Li
- Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, Innovis, #08-03, Singapore, 138634 Singapore
| | - Dai-Xu Wei
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Department of Life Sciences and Medicine, Northwest University, Xi’an, 710069 China
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13
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Wu S, Xia Y, Hu Y, Ma G. Bio-mimic particles for the enhanced vaccinations: Lessons learnt from the natural traits and pathogenic invasion. Adv Drug Deliv Rev 2021; 176:113871. [PMID: 34311014 DOI: 10.1016/j.addr.2021.113871] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/30/2021] [Accepted: 07/11/2021] [Indexed: 12/21/2022]
Abstract
In the combat against pathogens, the immune systems were evolved with the immune recognitions against the various danger signals, which responded vigorously upon the pathogen invasions and elicited potent antibodies or T cell engagement against the re-infections. Envisage with the prevailing pandemics and increasing demands for cancer vaccines, bio-mimic particles were developed to imitate the natural traits of the pathogens, which conferred the optimal strategies to stimulate the immune engagement and let to the increased vaccine efficacy. Here, the recent development in bio-mimic particles, as well as the natural cues from the pathogens were discussed. As such, the designing principles that adapted from the physiochemical properties of the pathogens were unfolded as the surface characteristics (hydrophobic, nano-pattern, antigen display, charge), properties (size, shape, softness) and the delivered components (peptide, protein, nuclear acids, toll-like receptor (TLR) agonist, antibody). Additionally, the strategies for the efficient delivery, regarding the biodistribution, internalization and presentation of the antigens were also illustrated. Through reviewing the state-of-art in biomimetic particles, the lesson learnt from the natural traits and pathogenic invasion may shed light on the rational design for the enhanced vaccinations.
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14
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Zheng B, Peng W, Guo M, Huang M, Gu Y, Wang T, Ni G, Ming D. Inhalable nanovaccine with biomimetic coronavirus structure to trigger mucosal immunity of respiratory tract against COVID-19. CHEMICAL ENGINEERING JOURNAL (LAUSANNE, SWITZERLAND : 1996) 2021; 418:129392. [PMID: 33762883 PMCID: PMC7972832 DOI: 10.1016/j.cej.2021.129392] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/22/2021] [Accepted: 03/12/2021] [Indexed: 05/16/2023]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 seriously threatens global public health. It has previously been confirmed that SARS-CoV-2 is mainly transmitted between people through "respiratory droplets". Therefore, the respiratory tract mucosa is the first barrier to prevent virus invasion. It is very important to stimulate mucosal immunity to protect the body from respiratory virus infection. Inspired by this, we designed a bionic-virus nanovaccine, which can induce mucosal immunity by nasal delivery to prevent virus infection from respiratory tract. The nanovaccine that mimic virosome is composed of poly(I:C) mimicking viral genetic material as immune adjuvant, biomimetic pulmonary surfactant (bio-PS) liposomes as capsid structure of virus and the receptor binding domains (RBDs) of SARS-CoV-2 as "spike" to completely simulate the structure of the coronavirus. The nanovaccine can be administered by inhaling to imitate the process of SARS-CoV-2 infection through the respiratory tract. Our results demonstrated that the inhalable nanovaccine with bionic virus-like structure has a stronger mucosal protective effect than routine muscle and subcutaneous inoculation. In particular, high titer of secretory immunoglobulin A (sIgA) was detected in respiratory secretions, which effectively neutralize the virus and prevent it from entering the body through the respiratory tract. Through imitating the structure and route of infection, this inhalable nanovaccine strategy might inspire a new approach to the precaution of respiratory viruses.
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Affiliation(s)
- Bin Zheng
- Academy of Medical Engineering and Translational Medicine, Tianjin Key Laboratory of Brain Science and Neural Engineering, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, PR China
| | - Wenchang Peng
- Academy of Medical Engineering and Translational Medicine, Tianjin Key Laboratory of Brain Science and Neural Engineering, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, PR China
| | - Mingming Guo
- Academy of Medical Engineering and Translational Medicine, Tianjin Key Laboratory of Brain Science and Neural Engineering, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, PR China
| | - Mengqian Huang
- School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, PR China
| | - Yuxuan Gu
- Academy of Medical Engineering and Translational Medicine, Tianjin Key Laboratory of Brain Science and Neural Engineering, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, PR China
| | - Tao Wang
- School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, PR China
| | - Guangjian Ni
- Academy of Medical Engineering and Translational Medicine, Tianjin Key Laboratory of Brain Science and Neural Engineering, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, PR China
| | - Dong Ming
- Academy of Medical Engineering and Translational Medicine, Tianjin Key Laboratory of Brain Science and Neural Engineering, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, PR China
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15
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S N N, B N R, C P, K S S, Ramakrishnappa T, B T K, S M J, M M, N A, Yallappa, D DP, T V R, E G, Bagoji M, Chandaragi SS. SARS-CoV 2 spike protein S1 subunit as an ideal target for stable vaccines: A bioinformatic study. MATERIALS TODAY. PROCEEDINGS 2021; 49:904-912. [PMID: 34307057 PMCID: PMC8279943 DOI: 10.1016/j.matpr.2021.07.163] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The Covid-19 a pandemic infectious disease and affected life across the world resulting in over 188.65 million confirmed cases across 223 countries, territories and areas with 4.06 million deaths. It is caused by a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and spike (S) protein of SARS-CoV-2, which plays a key role in the receptor recognition and cell membrane fusion process, is composed of two subunits, S1 and S2. The S1 subunit contains a receptor-binding domain (RBD) that recognizes and binds to the host receptor angiotensin-converting enzyme 2 (ACE2), while the S2 subunit mediates viral cell membrane fusion. Hence, it is a key target for developing neutralizing antibodies. Here, we have performed phylogenetic analysis and structural modeling of the SARS-CoV-2 spike glycoprotein, which is found highly conserved. The overall percent protein sequence identity from the SARS-CoV-2 spike protein sequences from the NCBI database was 99.68%. The functional domains of the S protein reveal that the S1 subunit was highly conserved (99.70%) than the S2 subunit (99.66%). Further, the 319-541 residues (RBD) of amino acids within the S1 domain were 100% similar among the spike protein. The 3D modeling of SARS-CoV-2 spike glycoprotein indicated that S protein has four domains with five protein units and the S1 subunit from 1 to 289 amino acid of domain 1 is highly conserved without any change in the ligand interaction site. This analysis clearly suggests that the S1 subunit (RBD 319-541) can be used as a target region for stable and safe vaccine development.
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Affiliation(s)
- Nagesha S N
- Department of Biotechnology, College of Agriculture, Hassan, University of Agricultural Sciences, Bangalore 560065, Karnataka, India
| | - Ramesh B N
- Department of Biotechnology, College of Agriculture, Hassan, University of Agricultural Sciences, Bangalore 560065, Karnataka, India
| | - Pradeep C
- Department of Biotechnology, College of Agriculture, Hassan, University of Agricultural Sciences, Bangalore 560065, Karnataka, India
| | - Shashidhara K S
- Department of Genetics and Plant Breeding, College of Agriculture, Hassan, University of Agricultural Sciences, Bangalore 560065, Karnataka, India
| | - Thippeswamy Ramakrishnappa
- Department of Chemistry, BMS Institute of Technology and Management, Avalahalli, Yelahanka, Bengaluru 560064, Karnataka, India
| | - Krishnaprasad B T
- Department of Biotechnology, College of Agriculture, Hassan, University of Agricultural Sciences, Bangalore 560065, Karnataka, India
| | - Jnanashree S M
- Department of Biotechnology, College of Agriculture, Hassan, University of Agricultural Sciences, Bangalore 560065, Karnataka, India
| | - Manohar M
- Department of Biotechnology, College of Agriculture, Hassan, University of Agricultural Sciences, Bangalore 560065, Karnataka, India
| | - Arunkumar N
- Department of Biotechnology, College of Agriculture, Hassan, University of Agricultural Sciences, Bangalore 560065, Karnataka, India
| | - Yallappa
- Department of Biotechnology, College of Agriculture, Hassan, University of Agricultural Sciences, Bangalore 560065, Karnataka, India
| | - Dhanush Patel D
- Department of Biotechnology, College of Agriculture, Hassan, University of Agricultural Sciences, Bangalore 560065, Karnataka, India
| | - Rakesh T V
- Department of Biotechnology, College of Agriculture, Hassan, University of Agricultural Sciences, Bangalore 560065, Karnataka, India
| | - Girish E
- Department of Biotechnology, College of Agriculture, Hassan, University of Agricultural Sciences, Bangalore 560065, Karnataka, India
| | - Mahantesh Bagoji
- Department of Biotechnology, College of Agriculture, Hassan, University of Agricultural Sciences, Bangalore 560065, Karnataka, India
| | - Shreeram S Chandaragi
- Department of Biotechnology, College of Agriculture, Hassan, University of Agricultural Sciences, Bangalore 560065, Karnataka, India
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16
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Shrivastava T, Singh B, Rizvi ZA, Verma R, Goswami S, Vishwakarma P, Jakhar K, Sonar S, Mani S, Bhattacharyya S, Awasthi A, Surjit M. Comparative Immunomodulatory Evaluation of the Receptor Binding Domain of the SARS-CoV-2 Spike Protein; a Potential Vaccine Candidate Which Imparts Potent Humoral and Th1 Type Immune Response in a Mouse Model. Front Immunol 2021; 12:641447. [PMID: 34108961 PMCID: PMC8182375 DOI: 10.3389/fimmu.2021.641447] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/12/2021] [Indexed: 12/18/2022] Open
Abstract
The newly emerged novel coronavirus, SARS-CoV-2, the causative agent of COVID-19 has proven to be a threat to the human race globally, thus, vaccine development against SARS-CoV-2 is an unmet need driving mass vaccination efforts. The receptor binding domain of the spike protein of this coronavirus has multiple neutralizing epitopes and is associated with viral entry. Here we have designed and characterized the SARS-CoV-2 spike protein fragment 330-526 as receptor binding domain 330-526 (RBD330-526) with two native glycosylation sites (N331 and N343); as a potential subunit vaccine candidate. We initially characterized RBD330-526 biochemically and investigated its thermal stability, humoral and T cell immune response of various RBD protein formulations (with or without adjuvant) to evaluate the inherent immunogenicity and immunomodulatory effect. Our result showed that the purified RBD immunogen is stable up to 72 h, without any apparent loss in affinity or specificity of interaction with the ACE2 receptor. Upon immunization in mice, RBD generates a high titer humoral response, elevated IFN-γ producing CD4+ cells, cytotoxic T cells, and robust neutralizing antibodies against live SARS-CoV-2 virus. Our results collectively support the potential of RBD330-526 as a promising vaccine candidate against SARS-CoV-2.
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Affiliation(s)
- Tripti Shrivastava
- Infection and Immunology, Translational Health Science & Technology Institute, National Capital Region (NCR) Biotech Science Cluster, Faridabad, India
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17
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Yan Y, Pang Y, Lyu Z, Wang R, Wu X, You C, Zhao H, Manickam S, Lester E, Wu T, Pang CH. The COVID-19 Vaccines: Recent Development, Challenges and Prospects. Vaccines (Basel) 2021; 9:349. [PMID: 33916489 PMCID: PMC8067284 DOI: 10.3390/vaccines9040349] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/21/2021] [Accepted: 03/22/2021] [Indexed: 12/24/2022] Open
Abstract
The highly infectious coronavirus disease 2019 (COVID-19) associated with the pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread to become a global pandemic. At present, the world is relying mainly on containment and hygiene-related measures, as well as repurposed drugs to control the outbreak. The development of COVID-19 vaccines is crucial for the world to return to pre-pandemic normalcy, and a collective global effort has been invested into protection against SARS-CoV-2. As of March 2021, thirteen vaccines have been approved for application whilst over 90 vaccine candidates are under clinical trials. This review focuses on the development of COVID-19 vaccines and highlights the efficacy and vaccination reactions of the authorised vaccines. The mechanisms, storage, and dosage specification of vaccine candidates at the advanced stage of development are also critically reviewed together with considerations for potential challenges. Whilst the development of a vaccine is, in general, in its infancy, current progress is promising. However, the world population will have to continue to adapt to the "new normal" and practice social distancing and hygienic measures, at least until effective vaccines are available to the general public.
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Affiliation(s)
- Yuxin Yan
- Department of Chemical and Environmental Engineering, University of Nottingham Ningbo China, Ningbo 315100, China; (Y.Y.); (Z.L.); (T.W.)
| | - Yoongxin Pang
- New Materials Institute, University of Nottingham Ningbo China, Ningbo 315042, China; (Y.P.); (R.W.); (X.W.)
| | - Zhuoyi Lyu
- Department of Chemical and Environmental Engineering, University of Nottingham Ningbo China, Ningbo 315100, China; (Y.Y.); (Z.L.); (T.W.)
| | - Ruiqi Wang
- New Materials Institute, University of Nottingham Ningbo China, Ningbo 315042, China; (Y.P.); (R.W.); (X.W.)
| | - Xinyun Wu
- New Materials Institute, University of Nottingham Ningbo China, Ningbo 315042, China; (Y.P.); (R.W.); (X.W.)
| | - Chong You
- Beijing International Center for Mathematical Research, Peking University, Beijing 100871, China;
| | - Haitao Zhao
- MITMECHE, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;
| | - Sivakumar Manickam
- Petroleum and Chemical Engineering, Faculty of Engineering, Universiti Teknologi Brunei, Bandar Seri Begawan BE1410, Brunei;
| | - Edward Lester
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, UK;
| | - Tao Wu
- Department of Chemical and Environmental Engineering, University of Nottingham Ningbo China, Ningbo 315100, China; (Y.Y.); (Z.L.); (T.W.)
- Key Laboratory for Carbonaceous Wastes Processing and Process Intensification Research of Zhejiang Province, University of Nottingham Ningbo China, Ningbo 315100, China
| | - Cheng Heng Pang
- New Materials Institute, University of Nottingham Ningbo China, Ningbo 315042, China; (Y.P.); (R.W.); (X.W.)
- Municipal Key Laboratory of Clean Energy Conversion Technologies, University of Nottingham Ningbo China, Ningbo 315100, China
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18
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Krumm ZA, Lloyd GM, Francis CP, Nasif LH, Mitchell DA, Golde TE, Giasson BI, Xia Y. Precision therapeutic targets for COVID-19. Virol J 2021; 18:66. [PMID: 33781287 PMCID: PMC8006140 DOI: 10.1186/s12985-021-01526-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/04/2021] [Indexed: 01/18/2023] Open
Abstract
Beginning in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged as a novel pathogen that causes coronavirus disease 2019 (COVID-19). SARS-CoV-2 has infected more than 111 million people worldwide and caused over 2.47 million deaths. Individuals infected with SARS-CoV-2 show symptoms of fever, cough, dyspnea, and fatigue with severe cases that can develop into pneumonia, myocarditis, acute respiratory distress syndrome, hypercoagulability, and even multi-organ failure. Current clinical management consists largely of supportive care as commonly administered treatments, including convalescent plasma, remdesivir, and high-dose glucocorticoids. These have demonstrated modest benefits in a small subset of hospitalized patients, with only dexamethasone showing demonstrable efficacy in reducing mortality and length of hospitalization. At this time, no SARS-CoV-2-specific antiviral drugs are available, although several vaccines have been approved for use in recent months. In this review, we will evaluate the efficacy of preclinical and clinical drugs that precisely target three different, essential steps of the SARS-CoV-2 replication cycle: the spike protein during entry, main protease (MPro) during proteolytic activation, and RNA-dependent RNA polymerase (RdRp) during transcription. We will assess the advantages and limitations of drugs that precisely target evolutionarily well-conserved domains, which are less likely to mutate, and therefore less likely to escape the effects of these drugs. We propose that a multi-drug cocktail targeting precise proteins, critical to the viral replication cycle, such as spike protein, MPro, and RdRp, will be the most effective strategy of inhibiting SARS-CoV-2 replication and limiting its spread in the general population.
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Affiliation(s)
- Zachary A Krumm
- Department of Neuroscience, College of Medicine, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
- Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Grace M Lloyd
- Department of Neuroscience, College of Medicine, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
- Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Connor P Francis
- College of Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA
- Lillian S. Wells Department of Neurosurgery, University of Florida, Gainesville, FL, 32610, USA
- UF Clinical and Translational Science Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Lith H Nasif
- Department of Neuroscience, College of Medicine, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
- Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Duane A Mitchell
- College of Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA
- Lillian S. Wells Department of Neurosurgery, University of Florida, Gainesville, FL, 32610, USA
- UF Clinical and Translational Science Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Todd E Golde
- Department of Neuroscience, College of Medicine, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
- Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
- College of Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Benoit I Giasson
- Department of Neuroscience, College of Medicine, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA.
- Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, 32610, USA.
- College of Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA.
| | - Yuxing Xia
- Department of Neuroscience, College of Medicine, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA.
- Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, 32610, USA.
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19
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Chen J, Lu H. New challenges to fighting COVID-19: Virus variants, potential vaccines, and development of antivirals. Biosci Trends 2021; 15:126-128. [PMID: 33746183 DOI: 10.5582/bst.2021.01092] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Despite strict control measures implemented worldwide, the COVID-19 pandemic continues to rage. Several drugs, including lopinavir/ritonavir, hydroxychloroquine, dexamethasone, and remdesivir, have been evaluated for the treatment of COVID-19 during the past year. While most of the drugs failed to display efficacy in treating COVID-19, scientists have encouraged herd immunity to control the pandemic. Immunity generated after natural infection with SARS-CoV-2 is precarious, as indicated by real-world evidence in the form of epidemiological data from Manaus, Brazil. Vaccines using different platforms are therefore the most promising approach to help us return to normality. Although several vaccines have been authorized for emergency use, there are still many concerns regarding their accessibility, the vaccination rate, and most importantly, their efficacy in preventing infection with emerging virus variants. Continued virus surveillance and rapid redesign of new vaccines to counter new variants are crucial to fighting COVID-19. Rapid production and extensive vaccination are also essential to preventing the emergence of new variants. Nevertheless, antivirals including monoclonal antibodies and oral medicines need to be developed in light of uncertainties with regard to vaccination. In the battle between humans and SARS-CoV-2, the speed with which we fight the virus, and especially its emerging variants, is the key to winning.
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Affiliation(s)
- Jun Chen
- Department of Infectious Diseases and Immunology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Hongzhou Lu
- Department of Infectious Diseases and Immunology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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20
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Lin Q, Huang Y, Jiang Z, Wu F, Ma L. Deciphering the Subtype Differentiation History of SARS-CoV-2 Based on a New Breadth-First Searching Optimized Alignment Method Over a Global Data Set of 24,768 Sequences. Front Genet 2021; 11:591833. [PMID: 33505425 PMCID: PMC7831388 DOI: 10.3389/fgene.2020.591833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/04/2020] [Indexed: 11/13/2022] Open
Abstract
SARS-CoV-2 has caused a worldwide pandemic. Existing research on coronavirus mutations is based on small data sets, and multiple sequence alignment using a global-scale data set has yet to be conducted. Statistical analysis of integral mutations and global spread are necessary and could help improve primer design for nucleic acid diagnosis and vaccine development. Here, we optimized multiple sequence alignment using a conserved sequence search algorithm to align 24,768 sequences from the GISAID data set. A phylogenetic tree was constructed using the maximum likelihood (ML) method. Coronavirus subtypes were analyzed via t-SNE clustering. We performed haplotype network analysis and t-SNE clustering to analyze the coronavirus origin and spread. Overall, we identified 33 sense, 17 nonsense, 79 amino acid loss, and 4 amino acid insertion mutations in full-length open reading frames. Phylogenetic trees were successfully constructed and samples clustered into subtypes. The COVID-19 pandemic differed among countries and continents. Samples from the United States and western Europe were more diverse, and those from China and Asia mainly contained specific subtypes. Clades G/GH/GR are more likely to be the origin clades of SARS-CoV-2 compared with clades S/L/V. Conserved sequence searches can be used to segment long sequences, making large-scale multisequence alignment possible, facilitating more comprehensive gene mutation analysis. Mutation analysis of the SARS-CoV-2 can inform primer design for nucleic acid diagnosis to improve virus detection efficiency. In addition, research into the characteristics of viral spread and relationships among geographic regions can help formulate health policies and reduce the increase of imported cases.
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Affiliation(s)
- Qianyu Lin
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, China
| | | | - Ziyi Jiang
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Feng Wu
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Lan Ma
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, China.,Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China.,Shenzhen Bay Laboratory, Shenzhen, China
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21
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Dhama K, Natesan S, Iqbal Yatoo M, Patel SK, Tiwari R, Saxena SK, Harapan H. Plant-based vaccines and antibodies to combat COVID-19: current status and prospects. Hum Vaccin Immunother 2020; 16:2913-2920. [PMID: 33270484 PMCID: PMC7754927 DOI: 10.1080/21645515.2020.1842034] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 12/19/2022] Open
Abstract
Globally, researchers are undertaking significant efforts to design and develop effective vaccines, therapeutics, and antiviral drugs to curb the spread of coronavirus disease 2019 (COVID-19). Plants have been used for the production of vaccines, monoclonal antibodies, immunomodulatory proteins, drugs, and pharmaceuticals via molecular farming/transient expression system and are considered as bioreactors or factories for their bulk production. These biological products are stable, safe, effective, easily available, and affordable. Plant molecular farming could facilitate rapid production of biologics on an industrial scale, and has the potential to fulfill emergency demands, such as in the present situation of the COVID-19 pandemic. This article aims to describe the methodology and basics of plant biopharming, in addition to its prospective applications for developing effective vaccines and antibodies to counter COVID-19.
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Affiliation(s)
- Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Senthilkumar Natesan
- Division of Biological & Life Sciences, Indian Institute of Public Health Gandhinagar, Ganghinagar, India
| | - Mohd. Iqbal Yatoo
- Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Alusteng Srinagar, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Shailesh Kumar Patel
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, Uttar Pradesh Pandit Deen Dayal Upadhyaya Pashu Chikitsa Vigyan Vishwavidyalaya Evam Go Anusandhan Sansthan (DUVASU), Mathura, India
| | - Shailendra K Saxena
- Centre for Advanced Research (CFAR), Faculty of Medicine, King George’s Medical University (KGMU), Lucknow, India
| | - Harapan Harapan
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia
- Tropical Disease Centre, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia
- Department of Microbiology, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia
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22
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Mutiawati E, Syahrul S, Fahriani M, Fajar JK, Mamada SS, Maliga HA, Samsu N, Ilmawan M, Purnamasari Y, Asmiragani AA, Ichsan I, Emran TB, Rabaan AA, Masyeni S, Nainu F, Harapan H. Global prevalence and pathogenesis of headache in COVID-19: A systematic review and meta-analysis. F1000Res 2020; 9:1316. [PMID: 33953911 PMCID: PMC8063523 DOI: 10.12688/f1000research.27334.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/30/2020] [Indexed: 09/01/2023] Open
Abstract
Background: This study was conducted to determine the prevalence of headache in coronavirus disease 2019 (COVID-19) and to assess its association as a predictor for COVID-19. This study also aimed to discuss the possible pathogenesis of headache in COVID-19. Methods: Available articles from PubMed, Scopus, and Web of Science were searched as of September 2 nd, 2020. Data on characteristics of the study, headache and COVID-19 were extracted following the PRISMA guidelines. Biases were assessed using the Newcastle-Ottawa scale. The cumulative prevalence of headache was calculated for the general population (i.e. adults and children). The pooled odd ratio (OR) with 95% confidence intervals (95%CI) was calculated using the Z test to assess the association between headache and the presence of COVID-19 cases. Results: We included 104,751 COVID-19 cases from 78 eligible studies to calculate the global prevalence of headache in COVID-19 and 17 studies were included to calculate the association of headache and COVID-19. The cumulative prevalence of headache in COVID-19 was 25.2% (26,464 out of 104,751 cases). Headache was found to be more prevalent, approximately by two-fold, in COVID-19 patients than in non-COVID-19 patients with symptoms of other respiratory viral infections, OR: 1.73; 95% CI: 1.94, 2.5 with p=0.04. Conclusion: Headache is common among COVID-19 patients and seems to be more common in COVID-19 patients compared to those with the non-COVID-19 viral infection. No definitive mechanisms on how headache emerges in COVID-19 patients but several possible hypotheses have been proposed. However, extensive studies are warranted to elucidate the mechanisms. PROSPERO registration: CRD42020210332 (28/09/2020).
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Affiliation(s)
- Endang Mutiawati
- Department of Neurology, Universitas Syiah Kuala, Banda Aceh, Aceh, 23111, Indonesia
- Department of Neurology, Dr. Zainoel Abidin Hospital, Banda Aceh, Aceh, 23126, Indonesia
| | - Syahrul Syahrul
- Department of Neurology, Universitas Syiah Kuala, Banda Aceh, Aceh, 23111, Indonesia
- Department of Neurology, Dr. Zainoel Abidin Hospital, Banda Aceh, Aceh, 23126, Indonesia
| | - Marhami Fahriani
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, 23111, Indonesia
| | - Jonny Karunia Fajar
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, 23111, Indonesia
- Brawijaya Internal Medicine Research Center, Department of Internal Medicine, Faculty of Medicine, Universitas Brawijaya, Malang, East Java, 65145, Indonesia
| | - Sukamto S. Mamada
- Faculty of Pharmacy, Hasanuddin University, Makassar, South Sulawesi, 90245, Indonesia
| | | | - Nur Samsu
- Brawijaya Internal Medicine Research Center, Department of Internal Medicine, Faculty of Medicine, Universitas Brawijaya, Malang, East Java, 65145, Indonesia
| | - Muhammad Ilmawan
- Faculty of Medicine, Universitas Brawijaya, Malang, East Java, 65117, Indonesia
| | - Yeni Purnamasari
- Faculty of Medicine, Universitas Brawijaya, Malang, East Java, 65117, Indonesia
| | | | - Ichsan Ichsan
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, 23111, Indonesia
- Department of Microbiology, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh, 23111, Indonesia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh
| | - Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, 31311, Saudi Arabia
| | - Sri Masyeni
- Department of Internal Medicine, Faculty of Medicine and Health Sciences, Universitas Warmadewa, Denpasar, Bali, 80235, Indonesia
- Department of Internal Medicine, Sanjiwani Hospital, Denpasar, Bali, 80235, Indonesia
| | - Firzan Nainu
- Faculty of Pharmacy, Hasanuddin University, Makassar, South Sulawesi, 90245, Indonesia
| | - Harapan Harapan
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, 23111, Indonesia
- Department of Microbiology, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh, 23111, Indonesia
- Tropical Disease Centre, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh, 23111, Indonesia
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23
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Mutiawati E, Syahrul S, Fahriani M, Fajar JK, Mamada SS, Maliga HA, Samsu N, Ilmawan M, Purnamasari Y, Asmiragani AA, Ichsan I, Emran TB, Rabaan AA, Masyeni S, Nainu F, Harapan H. Global prevalence and pathogenesis of headache in COVID-19: A systematic review and meta-analysis. F1000Res 2020; 9:1316. [PMID: 33953911 PMCID: PMC8063523 DOI: 10.12688/f1000research.27334.2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/01/2021] [Indexed: 01/19/2023] Open
Abstract
Background: This study was conducted to determine the prevalence of headache in coronavirus disease 2019 (COVID-19) and to assess its association as a predictor for COVID-19. This study also aimed to discuss the possible pathogenesis of headache in COVID-19. Methods: Available articles from PubMed, Scopus, and Web of Science were searched as of September 2 nd, 2020. Data on characteristics of the study, headache and COVID-19 were extracted following the PRISMA guidelines. Biases were assessed using the Newcastle-Ottawa scale. The cumulative prevalence of headache was calculated for the general population (i.e. adults and children). The pooled odd ratio (OR) with 95% confidence intervals (95%CI) was calculated using the Z test to assess the association between headache and the presence of COVID-19 cases. Results: We included 104,751 COVID-19 cases from 78 eligible studies to calculate the global prevalence of headache in COVID-19 and 17 studies were included to calculate the association of headache and COVID-19. The cumulative prevalence of headache in COVID-19 was 25.2% (26,464 out of 104,751 cases). Headache was found to be more prevalent, approximately by two-fold, in COVID-19 patients than in non-COVID-19 patients (other respiratory viral infections), OR: 1.73; 95% CI: 1.94, 2.5 with p=0.04. Conclusion: Headache is common among COVID-19 patients and seems to be more common in COVID-19 patients compared to those with the non-COVID-19 viral infection. No definitive mechanisms on how headache emerges in COVID-19 patients but several possible hypotheses have been proposed. However, extensive studies are warranted to elucidate the mechanisms. PROSPERO registration: CRD42020210332 (28/09/2020).
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Affiliation(s)
- Endang Mutiawati
- Department of Neurology, Universitas Syiah Kuala, Banda Aceh, Aceh, 23111, Indonesia
- Department of Neurology, Dr. Zainoel Abidin Hospital, Banda Aceh, Aceh, 23126, Indonesia
| | - Syahrul Syahrul
- Department of Neurology, Universitas Syiah Kuala, Banda Aceh, Aceh, 23111, Indonesia
- Department of Neurology, Dr. Zainoel Abidin Hospital, Banda Aceh, Aceh, 23126, Indonesia
| | - Marhami Fahriani
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, 23111, Indonesia
| | - Jonny Karunia Fajar
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, 23111, Indonesia
- Brawijaya Internal Medicine Research Center, Department of Internal Medicine, Faculty of Medicine, Universitas Brawijaya, Malang, East Java, 65145, Indonesia
| | - Sukamto S. Mamada
- Faculty of Pharmacy, Hasanuddin University, Makassar, South Sulawesi, 90245, Indonesia
| | | | - Nur Samsu
- Brawijaya Internal Medicine Research Center, Department of Internal Medicine, Faculty of Medicine, Universitas Brawijaya, Malang, East Java, 65145, Indonesia
| | - Muhammad Ilmawan
- Faculty of Medicine, Universitas Brawijaya, Malang, East Java, 65117, Indonesia
| | - Yeni Purnamasari
- Faculty of Medicine, Universitas Brawijaya, Malang, East Java, 65117, Indonesia
| | | | - Ichsan Ichsan
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, 23111, Indonesia
- Department of Microbiology, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh, 23111, Indonesia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh
| | - Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, 31311, Saudi Arabia
| | - Sri Masyeni
- Department of Internal Medicine, Faculty of Medicine and Health Sciences, Universitas Warmadewa, Denpasar, Bali, 80235, Indonesia
- Department of Internal Medicine, Sanjiwani Hospital, Denpasar, Bali, 80235, Indonesia
| | - Firzan Nainu
- Faculty of Pharmacy, Hasanuddin University, Makassar, South Sulawesi, 90245, Indonesia
| | - Harapan Harapan
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, 23111, Indonesia
- Department of Microbiology, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh, 23111, Indonesia
- Tropical Disease Centre, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh, 23111, Indonesia
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24
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Duan L, Zheng Q, Zhang H, Niu Y, Lou Y, Wang H. The SARS-CoV-2 Spike Glycoprotein Biosynthesis, Structure, Function, and Antigenicity: Implications for the Design of Spike-Based Vaccine Immunogens. Front Immunol 2020; 11:576622. [PMID: 33117378 PMCID: PMC7575906 DOI: 10.3389/fimmu.2020.576622] [Citation(s) in RCA: 241] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/16/2020] [Indexed: 12/20/2022] Open
Abstract
The ongoing pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), poses a grave threat to global public health and imposes a severe burden on the entire human society. Like other coronaviruses, the SARS-CoV-2 genome encodes spike (S) glycoproteins, which protrude from the surface of mature virions. The S glycoprotein plays essential roles in virus attachment, fusion and entry into the host cell. Surface location of the S glycoprotein renders it a direct target for host immune responses, making it the main target of neutralizing antibodies. In the light of its crucial roles in viral infection and adaptive immunity, the S protein is the focus of most vaccine strategies as well as therapeutic interventions. In this review, we highlight and describe the recent progress that has been made in the biosynthesis, structure, function, and antigenicity of the SARS-CoV-2 S glycoprotein, aiming to provide valuable insights into the design and development of the S protein-based vaccines as well as therapeutics.
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Affiliation(s)
- Liangwei Duan
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Qianqian Zheng
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Hongxia Zhang
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Yuna Niu
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Yunwei Lou
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Hui Wang
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
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25
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Almahboub SA, Algaissi A, Alfaleh MA, ElAssouli MZ, Hashem AM. Evaluation of Neutralizing Antibodies Against Highly Pathogenic Coronaviruses: A Detailed Protocol for a Rapid Evaluation of Neutralizing Antibodies Using Vesicular Stomatitis Virus Pseudovirus-Based Assay. Front Microbiol 2020; 11:2020. [PMID: 33013745 PMCID: PMC7498578 DOI: 10.3389/fmicb.2020.02020] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 07/30/2020] [Indexed: 12/13/2022] Open
Abstract
Emerging highly pathogenic human coronaviruses (CoVs) represent a serious ongoing threat to the public health worldwide. The spike (S) proteins of CoVs are surface glycoproteins that facilitate viral entry into host cells via attachment to their respective cellular receptors. The S protein is believed to be a major immunogenic component of CoVs and a target for neutralizing antibodies (nAbs) and most candidate vaccines. Development of a safe and convenient assay is thus urgently needed to determine the prevalence of CoVs nAbs in the population, to study immune response in infected individuals, and to aid in vaccines and viral entry inhibitor evaluation. While live virus-based neutralization assays are used as gold standard serological methods to detect and measure nAbs, handling of highly pathogenic live CoVs requires strict bio-containment conditions in biosafety level-3 (BSL-3) laboratories. On the other hand, use of replication-incompetent pseudoviruses bearing CoVs S proteins could represent a safe and useful method to detect nAbs in serum samples under biosafety level-2 (BSL-2) conditions. Here, we describe a detailed protocol of a safe and convenient assay to generate vesicular stomatitis virus (VSV)-based pseudoviruses to evaluate and measure nAbs against highly pathogenic CoVs. The protocol covers methods to produce VSV pseudovirus bearing the S protein of the Middle East respiratory syndrome-CoV (MERS-CoV) and the severe acute respiratory syndrome-CoV-2 (SARS-CoV-2), pseudovirus titration, and pseudovirus neutralization assay. Such assay could be adapted by different laboratories and researchers working on highly pathogenic CoVs without the need to handle live viruses in the BSL-3 environment.
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Affiliation(s)
- Sarah A. Almahboub
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdullah Algaissi
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
- Medical Research Center, Jazan University, Jazan, Saudi Arabia
| | - Mohamed A. Alfaleh
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - M-Zaki ElAssouli
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Anwar M. Hashem
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
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26
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Abstract
Alors qu’au début de l’année 2020, l’épidémie de Covid-19 se propageait à toute vitesse, de très nombreuses équipes scientifiques se sont mises au travail à travers le monde. La prise en charge des infections au severe acute respiratory syndrome coronavirus 2 repose sur des traitements non spécifiques (symptomatiques) ou spécifiques (curatifs) expérimentaux. Le vaccin sera la clé d’une immunisation sur le long terme.
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27
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Abstract
In this review, we address issues that relate to the rapid "Warp Speed" development of vaccines to counter the COVID-19 pandemic. We review the antibody response that is triggered by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection of humans and how it may inform vaccine research. The isolation and properties of neutralizing monoclonal antibodies from COVID-19 patients provide additional information on what vaccines should try to elicit. The nature and longevity of the antibody response to coronaviruses are relevant to the potency and duration of vaccine-induced immunity. We summarize the immunogenicity of leading vaccine candidates tested to date in animals and humans and discuss the outcome and interpretation of virus challenge experiments in animals. By far the most immunogenic vaccine candidates for antibody responses are recombinant proteins, which were not included in the initial wave of Warp Speed immunogens. A substantial concern for SARS-CoV-2 vaccines is adverse events, which we review by considering what was seen in studies of SARS-CoV-1 and Middle East respiratory syndrome coronavirus (MERS-CoV) vaccines. We conclude by outlining the possible outcomes of the Warp Speed vaccine program, which range from the hoped-for rapid success to a catastrophic adverse influence on vaccine uptake generally.
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Affiliation(s)
- John P Moore
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - P J Klasse
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
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28
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TopuzoĞullari M, Acar T, Pelİt Arayici P, UÇar B, UĞurel E, Abamor EŞ, ArasoĞlu T, Turgut-Balik D, Derman S. An insight into the epitope-based peptide vaccine design strategy and studies against COVID-19. Turk J Biol 2020; 44:215-227. [PMID: 32595358 PMCID: PMC7314509 DOI: 10.3906/biy-2006-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
SARS-CoV-2 is a new member of the coronavirus family and caused the pandemic of coronavirus disease 2019 (COVID-19) in 2020. It is crucial to design and produce an effective vaccine for the prevention of rapid transmission and possible deaths wcaused by the disease. Although intensive work and research are being carried out all over the world to develop a vaccine, an effective and approved formulation that can prevent the infection and limit the outbreak has not been announced yet. Among all types of vaccines, epitope-based peptide vaccines outshine with their low-cost production, easy modification in the structure, and safety. In this review, vaccine studies against COVID-19 have been summarized and detailed information about the epitope-based peptide vaccines against COVID-19 has been provided. We have not only compared the peptide vaccine with other types of vaccines but also presented comprehensive literature information about development steps for an effective and protective formulation to give an insight into on-going peptide vaccine studies against SARS-CoV-2.
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Affiliation(s)
- Murat TopuzoĞullari
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yıldız Technical University, İstanbul Turkey
| | - Tayfun Acar
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yıldız Technical University, İstanbul Turkey
| | - Pelin Pelİt Arayici
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yıldız Technical University, İstanbul Turkey
| | - Burcu UÇar
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yıldız Technical University, İstanbul Turkey
| | - Erennur UĞurel
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yıldız Technical University, İstanbul Turkey
| | - Emrah Şefik Abamor
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yıldız Technical University, İstanbul Turkey
| | - Tülin ArasoĞlu
- Department of Molecular Biology and Genetics, Faculty of Arts and Science, Yıldız Technical University, İstanbul Turkey
| | - Dilek Turgut-Balik
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yıldız Technical University, İstanbul Turkey
| | - Serap Derman
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yıldız Technical University, İstanbul Turkey
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29
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Tusé D, Nandi S, McDonald KA, Buyel JF. The Emergency Response Capacity of Plant-Based Biopharmaceutical Manufacturing-What It Is and What It Could Be. FRONTIERS IN PLANT SCIENCE 2020; 11:594019. [PMID: 33193552 PMCID: PMC7606873 DOI: 10.3389/fpls.2020.594019] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 09/24/2020] [Indexed: 05/12/2023]
Abstract
Several epidemic and pandemic diseases have emerged over the last 20 years with increasing reach and severity. The current COVID-19 pandemic has affected most of the world's population, causing millions of infections, hundreds of thousands of deaths, and economic disruption on a vast scale. The increasing number of casualties underlines an urgent need for the rapid delivery of therapeutics, prophylactics such as vaccines, and diagnostic reagents. Here, we review the potential of molecular farming in plants from a manufacturing perspective, focusing on the speed, capacity, safety, and potential costs of transient expression systems. We highlight current limitations in terms of the regulatory framework, as well as future opportunities to establish plant molecular farming as a global, de-centralized emergency response platform for the rapid production of biopharmaceuticals. The implications of public health emergencies on process design and costs, regulatory approval, and production speed and scale compared to conventional manufacturing platforms based on mammalian cell culture are discussed as a forward-looking strategy for future pandemic responses.
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Affiliation(s)
- Daniel Tusé
- DT/Consulting Group and GROW Biomedicine, LLC, Sacramento, CA, United States
| | - Somen Nandi
- Department of Chemical Engineering, University of California, Davis, Davis, CA, United States
- Global HealthShare Initiative, University of California, Davis, Davis, CA, United States
| | - Karen A. McDonald
- Department of Chemical Engineering, University of California, Davis, Davis, CA, United States
- Global HealthShare Initiative, University of California, Davis, Davis, CA, United States
| | - Johannes Felix Buyel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
- Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
- *Correspondence: Johannes Felix Buyel, ; orcid.org/0000-0003-2361-143X
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