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El-Sayed A, Abdel-Daim MM, Kamel M. Zoonotic and anthropozoonotic potential of COVID-19 and its implications for public health. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:52599-52609. [PMID: 34523089 PMCID: PMC8439532 DOI: 10.1007/s11356-021-16415-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 09/05/2021] [Indexed: 05/07/2023]
Affiliation(s)
- Amr El-Sayed
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Mohamed M Abdel-Daim
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah, 21442, Saudi Arabia
- Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, 41522, Egypt
| | - Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt.
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102
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Günl F, Mecate-Zambrano A, Rehländer S, Hinse S, Ludwig S, Brunotte L. Shooting at a Moving Target-Effectiveness and Emerging Challenges for SARS-CoV-2 Vaccine Development. Vaccines (Basel) 2021; 9:1052. [PMID: 34696160 PMCID: PMC8540924 DOI: 10.3390/vaccines9101052] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 02/06/2023] Open
Abstract
Since late 2019 the newly emerged pandemic SARS-CoV-2, the causative agent of COVID-19, has hit the world with recurring waves of infections necessitating the global implementation of non-pharmaceutical interventions, including strict social distancing rules, the wearing of masks and the isolation of infected individuals in order to restrict virus transmissions and prevent the breakdown of our healthcare systems. These measures are not only challenging on an economic level but also have a strong impact on social lifestyles. Using traditional and novel technologies, highly efficient vaccines against SARS-CoV-2 were developed and underwent rapid clinical evaluation and approval to accelerate the immunization of the world population, aiming to end the pandemic and return to normality. However, the emergence of virus variants with improved transmission, enhanced fitness and partial immune escape from the first generation of vaccines poses new challenges, which are currently being addressed by scientists and pharmaceutical companies all over the world. In this ongoing pandemic, the evaluation of SARS-CoV-2 vaccines underlies diverse unpredictable dynamics, posed by the first broad application of the mRNA vaccine technology and their compliance, the occurrence of unexpected side effects and the rapid emergence of variations in the viral antigen. However, despite these hurdles, we conclude that the available SARS-CoV-2 vaccines are very safe and efficiently protect from severe COVID-19 and are thereby the most powerful tools to prevent further harm to our healthcare systems, economics and individual lives. This review summarizes the unprecedented pathways of vaccine development and approval during the ongoing SARS-CoV-2 pandemic. We focus on the real-world effectiveness and unexpected positive and negative side effects of the available vaccines and summarize the timeline of the applied adaptations to the recommended vaccination strategies in the light of emerging virus variants. Finally, we highlight upcoming strategies to improve the next generations of SARS-CoV-2 vaccines.
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Affiliation(s)
- Franziska Günl
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
| | - Angeles Mecate-Zambrano
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
- Interdisciplinary Centre for Clinical Research (IZKF), Medical Faculty, University of Münster, 48149 Münster, Germany
| | - Selina Rehländer
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
| | - Saskia Hinse
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
| | - Stephan Ludwig
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
- Interdisciplinary Centre for Clinical Research (IZKF), Medical Faculty, University of Münster, 48149 Münster, Germany
| | - Linda Brunotte
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
- Interdisciplinary Centre for Clinical Research (IZKF), Medical Faculty, University of Münster, 48149 Münster, Germany
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103
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Xi B, Chen Z, Li S, Liu W, Jiang D, Bai Y, Qu Y, Lon JR, Huang L, Du H. AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. Comput Struct Biotechnol J 2021; 19:5029-5038. [PMID: 34512928 PMCID: PMC8416686 DOI: 10.1016/j.csbj.2021.09.002] [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: 05/24/2021] [Revised: 08/17/2021] [Accepted: 09/02/2021] [Indexed: 11/14/2022] Open
Abstract
In our previous work, we developed an automated tool, AutoVEM, for real-time monitoring the candidate key mutations and epidemic trends of SARS-CoV-2. In this research, we further developed AutoVEM into AutoVEM2. AutoVEM2 is composed of three modules, including call module, analysis module, and plot module, which can be used modularly or as a whole for any virus, as long as the corresponding reference genome is provided. Therefore, it's much more flexible than AutoVEM. Here, we analyzed three existing viruses by AutoVEM2, including SARS-CoV-2, HBV and HPV-16, to show the functions, effectiveness and flexibility of AutoVEM2. We found that the N501Y locus was almost completely linked to the other 16 loci in SARS-CoV-2 genomes from the UK and Europe. Among the 17 loci, 5 loci were on the S protein and all of the five mutations cause amino acid changes, which may influence the epidemic traits of SARS-CoV-2. And some candidate key mutations of HBV and HPV-16, including T350G of HPV-16 and C659T of HBV, were detected. In brief, we developed a flexible automated tool to analyze candidate key mutations and epidemic trends for any virus, which would become a standard process for virus analysis based on genome sequences in the future.
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Affiliation(s)
| | | | | | - Wei Liu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Dawei Jiang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Yunmeng Bai
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Yimo Qu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Jerome Rumdon Lon
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Lizhen Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Hongli Du
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
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104
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Li X, Zhang L, Chen S, Ji W, Li C, Ren L. Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 93:104971. [PMID: 34146731 PMCID: PMC8213438 DOI: 10.1016/j.meegid.2021.104971] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/09/2021] [Accepted: 06/14/2021] [Indexed: 02/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) infection has caused a global pandemic in the past year, which poses continuing threat to human beings. To date, more than 3561 mutations in the viral spike protein were identified, including 2434 mutations that cause amino acid changes with 343 amino acids located in the viral receptor-binding domain (RBD). Among these mutations, the most representative ones are substitution mutations such as D614G, N501Y, Y453F, N439K/R, P681H, K417N/T, and E484K, and deletion mutations of ΔH69/V70 and Δ242-244, which confer the virus with enhanced infectivity, transmissibility, and resistance to neutralization. In this review, we discussed the recent findings of SARS-CoV-2 for highlighting mutations and variants on virus transmissibility and pathogenicity. Moreover, several suggestions for prevention and controlling the pandemic are also proposed.
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Affiliation(s)
- Xue Li
- College of Animal Sciences, Key Lab for Zoonoses Research, Ministry of Education, Jilin University, 5333 Xi' An Road, Changchun 130062, China
| | - Liying Zhang
- College of Animal Sciences, Key Lab for Zoonoses Research, Ministry of Education, Jilin University, 5333 Xi' An Road, Changchun 130062, China
| | - Si Chen
- College of Animal Sciences, Key Lab for Zoonoses Research, Ministry of Education, Jilin University, 5333 Xi' An Road, Changchun 130062, China
| | - Weilong Ji
- College of Animal Sciences, Key Lab for Zoonoses Research, Ministry of Education, Jilin University, 5333 Xi' An Road, Changchun 130062, China
| | - Chang Li
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Military Veterinary Institute, Academy of Military Medical Sciences, Changchun 130112, China
| | - Linzhu Ren
- College of Animal Sciences, Key Lab for Zoonoses Research, Ministry of Education, Jilin University, 5333 Xi' An Road, Changchun 130062, China.
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105
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Fantini J, Yahi N, Azzaz F, Chahinian H. Structural dynamics of SARS-CoV-2 variants: A health monitoring strategy for anticipating Covid-19 outbreaks. J Infect 2021; 83:197-206. [PMID: 34089757 PMCID: PMC8172274 DOI: 10.1016/j.jinf.2021.06.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 06/01/2021] [Indexed: 02/07/2023]
Abstract
OBJECTIVES the Covid-19 pandemic has been marked by sudden outbreaks of SARS-CoV-2 variants harboring mutations in both the N-terminal (NTD) and receptor binding (RBD) domains of the spike protein. The goal of this study was to predict the transmissibility of SARS-CoV-2 variants from genomic sequence data. METHODS we used a target-based molecular modeling strategy combined with surface potential analysis of the NTD and RBD. RESULTS we observed that both domains act synergistically to ensure optimal virus adhesion, which explains why most variants exhibit concomitant mutations in the RBD and in the NTD. Some mutation patterns affect the affinity of the spike protein for ACE-2. However, other patterns increase the electropositive surface of the spike, with determinant effects on the kinetics of virus adhesion to lipid raft gangliosides. Based on this new view of the structural dynamics of SARS-CoV-2 variants, we defined an index of transmissibility (T-index) calculated from kinetic and affinity parameters of coronavirus binding to host cells. The T-index is characteristic of each variant and predictive of its dissemination in animal and human populations. CONCLUSIONS the T-index can be used as a health monitoring strategy to anticipate future Covid-19 outbreaks due to the emergence of variants of concern.
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Affiliation(s)
- Jacques Fantini
- INSERM UMR_S 1072, 13015 Marseille, France; Aix-Marseille Université, 13015 Marseille, France.
| | - Nouara Yahi
- INSERM UMR_S 1072, 13015 Marseille, France; Aix-Marseille Université, 13015 Marseille, France
| | - Fodil Azzaz
- INSERM UMR_S 1072, 13015 Marseille, France; Aix-Marseille Université, 13015 Marseille, France
| | - Henri Chahinian
- INSERM UMR_S 1072, 13015 Marseille, France; Aix-Marseille Université, 13015 Marseille, France
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106
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D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. mBio 2021; 12:e0058721. [PMID: 34311586 PMCID: PMC8406174 DOI: 10.1128/mbio.00587-21] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Since the D614G substitution in the spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged, the variant strain has undergone a rapid expansion to become the most abundant strain worldwide. Therefore, this substitution may provide an advantage for viral spreading. To explore the mechanism, we analyzed 18 viral isolates containing S proteins with either G614 or D614 (S-G614 and S-D614, respectively). The plaque assay showed a significantly higher virus titer in S-G614 than in S-D614 isolates. We further found increased cleavage of the S protein at the furin substrate site, a key event that promotes syncytium formation, in S-G614 isolates. The enhancement of the D614G substitution in the cleavage of the S protein and in syncytium formation has been validated in cells expressing S protein. The effect on the syncytium was abolished by furin inhibitor treatment and mutation of the furin cleavage site, suggesting its dependence on cleavage by furin. Our study pointed to the impact of the D614G substitution on syncytium formation through enhanced furin-mediated S cleavage, which might increase the transmissibility and infectivity of SARS-CoV-2 strains containing S-G614.
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107
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Gan HH, Twaddle A, Marchand B, Gunsalus KC. Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. J Mol Biol 2021; 433:167051. [PMID: 33992693 PMCID: PMC8118711 DOI: 10.1016/j.jmb.2021.167051] [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: 03/10/2021] [Revised: 05/06/2021] [Accepted: 05/08/2021] [Indexed: 12/16/2022]
Abstract
The COVID-19 pandemic has triggered concerns about the emergence of more infectious and pathogenic viral strains. As a public health measure, efficient screening methods are needed to determine the functional effects of new sequence variants. Here we show that structural modeling of SARS-CoV-2 Spike protein binding to the human ACE2 receptor, the first step in host-cell entry, predicts many novel variant combinations with enhanced binding affinities. By focusing on natural variants at the Spike-hACE2 interface and assessing over 700 mutant complexes, our analysis reveals that high-affinity Spike mutations (including N440K, S443A, G476S, E484R, G502P) tend to cluster near known human ACE2 recognition sites (K31 and K353). These Spike regions are structurally flexible, allowing certain mutations to optimize interface interaction energies. Although most human ACE2 variants tend to weaken binding affinity, they can interact with Spike mutations to generate high-affinity double mutant complexes, suggesting variation in individual susceptibility to infection. Applying structural analysis to highly transmissible variants, we find that circulating point mutations S477N, E484K and N501Y form high-affinity complexes (~40% more than wild-type). By combining predicted affinities and available antibody escape data, we show that fast-spreading viral variants exploit combinatorial mutations possessing both enhanced affinity and antibody resistance, including S477N/E484K, E484K/N501Y and K417T/E484K/N501Y. Thus, three-dimensional modeling of the Spike/hACE2 complex predicts changes in structure and binding affinity that correlate with transmissibility and therefore can help inform future intervention strategies.
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Affiliation(s)
- Hin Hark Gan
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, United States,Corresponding authors at: Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, United States (K.C. Gunsalus)
| | - Alan Twaddle
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, United States,NYU Abu Dhabi Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Benoit Marchand
- High-Performance Computing, Center for Research Computing, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Kristin C. Gunsalus
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, United States,NYU Abu Dhabi Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates,Corresponding authors at: Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, United States (K.C. Gunsalus)
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108
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Wang C, Zheng Y, Niu Z, Jiang X, Sun Q. The virological impacts of SARS-CoV-2 D614G mutation. J Mol Cell Biol 2021; 13:712-720. [PMID: 34289053 PMCID: PMC8344946 DOI: 10.1093/jmcb/mjab045] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/18/2021] [Accepted: 05/26/2021] [Indexed: 11/12/2022] Open
Abstract
The coronavirus diseases 2019 (COVID-19) caused by the infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in December 2019 has caused more than 140 million infections worldwide by the end of April 2021. As an enveloped single-stranded positive-sense RNA virus, SARS-CoV-2 underwent constant evolution that produced novel variants carrying mutation conferring fitness advantages. The current prevalent D614G variant, with glycine substituted for aspartic acid at position 614 in the spike glycoprotein, is one of such variants that became the main circulating strain worldwide in a short period of time. Over the past year, intensive studies from all over the world had defined the epidemiological characteristics of this highly contagious variant and revealed the underlying mechanisms. This review aims at presenting an overall picture of the impacts of D614G mutation on virus transmission, elucidating the underlying mechanisms of D614G in virus pathogenicity, and providing insights into the development of effective therapeutics.
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Affiliation(s)
- Chenxi Wang
- Laboratory of Cell Engineering, Institute of Biotechnology, Research Unit of Cell Death Mechanism, Chinese Academy of Medical Science, 2020RU009, Beijing 100071, China
| | - You Zheng
- Laboratory of Cell Engineering, Institute of Biotechnology, Research Unit of Cell Death Mechanism, Chinese Academy of Medical Science, 2020RU009, Beijing 100071, China
| | - Zubiao Niu
- Laboratory of Cell Engineering, Institute of Biotechnology, Research Unit of Cell Death Mechanism, Chinese Academy of Medical Science, 2020RU009, Beijing 100071, China
| | - Xiaoyi Jiang
- Laboratory of Cell Engineering, Institute of Biotechnology, Research Unit of Cell Death Mechanism, Chinese Academy of Medical Science, 2020RU009, Beijing 100071, China
| | - Qiang Sun
- Laboratory of Cell Engineering, Institute of Biotechnology, Research Unit of Cell Death Mechanism, Chinese Academy of Medical Science, 2020RU009, Beijing 100071, China
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109
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Wang W, Li Q, Wu J, Hu Y, Wu G, Yu C, Xu K, Liu X, Wang Q, Huang W, Wang L, Wang Y. Lentil lectin derived from Lens culinaris exhibit broad antiviral activities against SARS-CoV-2 variants. Emerg Microbes Infect 2021; 10:1519-1529. [PMID: 34278967 PMCID: PMC8330776 DOI: 10.1080/22221751.2021.1957720] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutated continuously and newly emerging variants escape from antibody-mediated neutralization raised great concern. S protein is heavily glycosylated and the glycosylation sites are relatively conserved, thus glycans on S protein surface could be a target for the development of anti-SARS-CoV-2 strategies against variants. Here, we collected 12 plant-derived lectins with different carbohydrate specificity and evaluated their anti-SARS-CoV-2 activity against mutant strains and epidemic variants using a pseudovirus-based neutralization assay. The Lens culinaris-derived lentil lectin which specifically bind to oligomannose-type glycans and GlcNAc at the non-reducing end terminus showed most potent and broad antiviral activity against a panel of mutant strains and variants, including the artificial mutants at N-/O-linked glycosylation site, natural existed amino acid mutants, as well as the epidemic variants B.1.1.7, B.1.351, and P.1. Lentil lectin also showed antiviral activity against SARS-CoV and MERS-CoV. We found lentil lectin could block the binding of ACE2 to S trimer and inhibit SARS-CoV-2 at the early steps of infection. Using structural information and determined N-glycan profile of S trimer, taking together with the carbohydrate specificity of lentil lectin, we provide a basis for the observed broad spectrum anti-SARS-CoV-2 activity. Lentil lectin showed weak haemagglutination activity at 1 mg/mL and no cytotoxicity activity, and no weight loss was found in single injection mouse experiment. This report provides the first evidence that lentil lectin strongly inhibit infection of SARS-COV-2 variants, which should provide valuable insights for developing future anti-SARS-CoV-2 strategies.
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Affiliation(s)
- Wenbo Wang
- Division of Monoclonal Antibody Products, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Qianqian Li
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China.,Graduate School of Peking Union Medical College, Beijing, People's Republic of China
| | - Jiajing Wu
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China.,Wuhan Institute of Biological Products, Hubei, People's Republic of China
| | - Yu Hu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, People's Republic of China.,School of Life Sciences, University of Science and Technology of China, Hefei, People's Republic of China
| | - Gang Wu
- Division of Monoclonal Antibody Products, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Chuanfei Yu
- Division of Monoclonal Antibody Products, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Kangwei Xu
- Division of Respiratory Virus Vaccines, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Xumei Liu
- Division of Monoclonal Antibody Products, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China.,School of Pharmacy, Yantai University, Yantai, People's Republic of China
| | - Qihui Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, People's Republic of China
| | - Weijin Huang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Lan Wang
- Division of Monoclonal Antibody Products, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Youchun Wang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
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110
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Aljindan RY, Al-Subaie AM, Al-Ohali AI, Kumar D T, Doss C GP, Kamaraj B. Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Comput Biol Med 2021; 135:104654. [PMID: 34346317 PMCID: PMC8282961 DOI: 10.1016/j.compbiomed.2021.104654] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 12/22/2022]
Abstract
COVID-19 is an infectious and pathogenic viral disease caused by SARS-CoV-2 that leads to septic shock, coagulation dysfunction, and acute respiratory distress syndrome. The spreading rate of SARS-CoV-2 is higher than MERS-CoV and SARS-CoV. The receptor-binding domain (RBD) of the Spike-protein (S-protein) interacts with the human cells through the host angiotensin-converting enzyme 2 (ACE2) receptor. However, the molecular mechanism of pathological mutations of S-protein is still unclear. In this perspective, we investigated the impact of mutations in the S-protein and their interaction with the ACE2 receptor for SAR-CoV-2 viral infection. We examined the stability of pathological nonsynonymous mutations in the S-protein, and the binding behavior of the ACE2 receptor with the S-protein upon nonsynonymous mutations using the molecular docking and MM_GBSA approaches. Using the extensive bioinformatics pipeline, we screened the destabilizing (L8V, L8W, L18F, Y145H, M153T, F157S, G476S, L611F, A879S, C1247F, and C1254F) and stabilizing (H49Y, S50L, N501Y, D614G, A845V, and P1143L) nonsynonymous mutations in the S-protein. The docking and binding free energy (ddG) scores revealed that the stabilizing nonsynonymous mutations show increased interaction between the S-protein and the ACE2 receptor compared to native and destabilizing S-proteins and that they may have been responsible for the virulent high level. Further, the molecular dynamics simulation (MDS) approach reveals the structural transition of mutants (N501Y and D614G) S-protein. These insights might help researchers to understand the pathological mechanisms of the S-protein and provide clues regarding mutations in viral infection and disease propagation. Further, it helps researchers to develop an efficient treatment approach against this SARS-CoV-2 pandemic.
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Affiliation(s)
- Reem Y Aljindan
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
| | - Abeer M Al-Subaie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
| | - Ahoud I Al-Ohali
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
| | - Thirumal Kumar D
- Meenakshi Academy of Higher Education and Research, Chennai, Tamil Nadu, 600078, India.
| | - George Priya Doss C
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
| | - Balu Kamaraj
- Department of Neuroscience Technology, College of Applied Medical Sciences in Jubail, Imam Abdulrahman Bin Faisal University, Jubail, Saudi Arabia.
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111
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Zahan MN, Habibi H, Pencil A, Abdul-Ghafar J, Ahmadi SA, Juyena NS, Rahman MT, Parvej MS. Diagnosis of COVID-19 in symptomatic patients: An updated review. ACTA ACUST UNITED AC 2021; 23:55-61. [PMID: 34276268 PMCID: PMC8275488 DOI: 10.1016/j.vacun.2021.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/17/2021] [Indexed: 12/21/2022]
Abstract
A group of pneumonia patients was detected in Hubei Province, in China in December 2019. The etiology of the disease was unknown. Later, the researchers diagnosed the novel Coronavirus as the causal agent of this respiratory disease. On February 12th 2020, the World Health Organization (WHO) officially named this disease Coronavirus disease 2019 (COVID-19). Consequently, the disease spread globally and became a pandemic. As there is no specific treatment for the symptomatic patients and several vaccines are approved by WHO, the efficacy and effectiveness of these vaccines are not fully understood yet and the availability of these vaccines are very limited. In addition, new variants and mutants of SARS-CoV-2 are thought to be able to evade the immune system of the host. So, diagnosis and isolation of infected individuals is advised. Currently, real-time reverse transcription-polymerase chain reaction (RT-PCR) is considered the gold standard method to detect novel Coronavirus, however, there are few limitations associated with RT-PCR such as false-negative results. This demanded another diagnostic tool to detect and isolate COVID-19 early and accurately. Chest computed tomography (CT) became another option to diagnose COVID-19 patients accurately (about 98% sensitivity). However, it did not apply to the asymptomatic carriers and sometimes the results were misinterpreted as from other groups of Coronavirus infection. The combination of RT-PCR and chest CT might be the best option in detecting novel Coronavirus infection early and accurately thereby allowing adaptation of measures for the prevention and control of the COVID-19.
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Affiliation(s)
- M N Zahan
- Department of Surgery and Theriogenology, Sher-e-Bangla Agricultural University, 1207 Dhaka, Bangladesh
| | - H Habibi
- Department of Orthopedic Surgery, Osaka City University, Japan
| | - A Pencil
- Graduate School of Human Life Science, Osaka City University, Japan
| | - J Abdul-Ghafar
- Department of Pathology and Clinical Laboratory, French Medical Institute for Mothers and Children (FMIC), Kabul, Afghanistan
| | - S A Ahmadi
- Department of Orthopedic Surgery, Wazir Akbar khan Hospital, Kabul, Afghanistan
| | - N S Juyena
- Department of Surgery & Obstetrics, Bangladesh Agricultural University, 2202 Mymensingh, Bangladesh
| | - M T Rahman
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, 2202 Mymensingh, Bangladesh
| | - M S Parvej
- Department of Para-clinical Courses, Faculty of Veterinary and Animal Sciences, Gono University, Savar, 1344 Dhaka, Bangladesh
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112
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Wu T, Kang S, Peng W, Zuo C, Zhu Y, Pan L, Fu K, You Y, Yang X, Luo X, Jiang L, Deng M. Original Hosts, Clinical Features, Transmission Routes, and Vaccine Development for Coronavirus Disease (COVID-19). Front Med (Lausanne) 2021; 8:702066. [PMID: 34295915 PMCID: PMC8291337 DOI: 10.3389/fmed.2021.702066] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 05/31/2021] [Indexed: 01/08/2023] Open
Abstract
The pandemic of coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to public concern worldwide. Although a variety of hypotheses about the hosts of SARS-CoV-2 have been proposed, an exact conclusion has not yet been reached. Initial clinical manifestations associated with COVID-19 are similar to those of other acute respiratory infections, leading to misdiagnoses and resulting in the outbreak at the early stage. SARS-CoV-2 is predominantly spread by droplet transmission and close contact; the possibilities of fecal-oral, vertical, and aerosol transmission have not yet been fully confirmed or rejected. Besides, COVID-19 cases have been reported within communities, households, and nosocomial settings through contact with confirmed COVID-19 patients or asymptomatic individuals. Environmental contamination is also a major driver for the COVID-19 pandemic. Considering the absence of specific treatment for COVID-19, it is urgent to decrease the risk of transmission and take preventive measures to control the spread of the virus. In this review, we summarize the latest available data on the potential hosts, entry receptors, clinical features, and risk factors of COVID-19 and transmission routes of SARS-CoV-2, and we present the data about development of vaccines.
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Affiliation(s)
- Ting Wu
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, China
- Department of Cardiovascular Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Shuntong Kang
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Wenyao Peng
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Chenzhe Zuo
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Yuhao Zhu
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Liangyu Pan
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, China
| | - Keyun Fu
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Yaxian You
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, China
| | - Xinyuan Yang
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Xuan Luo
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, China
- Hunan Yuanpin Cell Biotechnology Co., Ltd, Changsha, China
| | - Liping Jiang
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Meichun Deng
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
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113
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Hashemi SA, Bahrani S, Mousavi SM, Omidifar N, Arjmand M, Behbahan NGG, Ramakrishna S, Lankarani KB, Moghadami M, Firoozsani M. Ultrasensitive Biomolecule‐Less Nanosensor Based on β‐Cyclodextrin/Quinoline Decorated Graphene Oxide toward Prompt and Differentiable Detection of Corona and Influenza Viruses. ADVANCED MATERIALS TECHNOLOGIES 2021. [DOI: 10.1002/admt.202100341] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Seyyed Alireza Hashemi
- Nanomaterials and Polymer Nanocomposites Laboratory School of Engineering University of British Columbia Kelowna BC V1V 1V7 Canada
| | - Sonia Bahrani
- Health Policy Research Center Health Institute Shiraz University of Medica Sciences Shiraz 71348‐45794 Iran
| | - Seyyed Mojtaba Mousavi
- Department of Chemical Engineering National Taiwan University of Science and Technology Taipei 10607 Taiwan
| | - Navid Omidifar
- Clinical Education Research Center Shiraz University of Medical Sciences Shiraz 71348‐14336 Iran
- Department of Pathology Medical School Shiraz University of Medical Sciences Shiraz 71348‐14336 Iran
| | - Mohammad Arjmand
- Nanomaterials and Polymer Nanocomposites Laboratory School of Engineering University of British Columbia Kelowna BC V1V 1V7 Canada
| | - Nader Ghaleh Golab Behbahan
- Razi Vaccine and Serum Research Institute Agricultural Research Education and Extension Organization (AREEO) Shiraz Branch Shiraz 71888‐43568 Iran
| | - Seeram Ramakrishna
- Department of Mechanical Engineering Center for Nanofibers and Nanotechnology National University of Singapore Singapore 117575 Singapore
| | - Kamran Bagheri Lankarani
- Health Policy Research Center Health Institute Shiraz University of Medica Sciences Shiraz 71348‐45794 Iran
| | - Mohsen Moghadami
- Health Policy Research Center Health Institute Shiraz University of Medica Sciences Shiraz 71348‐45794 Iran
| | - Mohammad Firoozsani
- Member of the Board of Trustees Zand Institute of Higher Education Shiraz 71887‐73489 Iran
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114
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Ilmjärv S, Abdul F, Acosta-Gutiérrez S, Estarellas C, Galdadas I, Casimir M, Alessandrini M, Gervasio FL, Krause KH. Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. Sci Rep 2021; 11:13705. [PMID: 34210996 PMCID: PMC8249556 DOI: 10.1038/s41598-021-91662-w] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 05/25/2021] [Indexed: 01/18/2023] Open
Abstract
The D614G mutation in the Spike protein of the SARS-CoV-2 has effectively replaced the early pandemic-causing variant. Using pseudotyped lentivectors, we confirmed that the aspartate replacement by glycine in position 614 is markedly more infectious. Molecular modelling suggests that the G614 mutation facilitates transition towards an open state of the Spike protein. To explain the epidemiological success of D614G, we analysed the evolution of 27,086 high-quality SARS-CoV-2 genome sequences from GISAID. We observed striking coevolution of D614G with the P323L mutation in the viral polymerase. Importantly, the exclusive presence of G614 or L323 did not become epidemiologically relevant. In contrast, the combination of the two mutations gave rise to a viral G/L variant that has all but replaced the initial D/P variant. Our results suggest that the P323L mutation, located in the interface domain of the RNA-dependent RNA polymerase, is a necessary alteration that led to the epidemiological success of the present variant of SARS-CoV-2. However, we did not observe a significant correlation between reported COVID-19 mortality in different countries and the prevalence of the Wuhan versus G/L variant. Nevertheless, when comparing the speed of emergence and the ultimate predominance in individual countries, it is clear that the G/L variant displays major epidemiological supremacy over the original variant.
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Affiliation(s)
- Sten Ilmjärv
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Fabien Abdul
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Silvia Acosta-Gutiérrez
- Department of Chemistry, University College London, London, UK.,Institute for the Physics of Living Systems, University College London, London, UK.,Institute of Structural and Molecular Biology, University College London, London, UK
| | | | | | | | - Marco Alessandrini
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Francesco Luigi Gervasio
- Department of Chemistry, University College London, London, UK.,Institute of Structural and Molecular Biology, University College London, London, UK.,School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Karl-Heinz Krause
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland. .,Division of Infectious Disease and Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland.
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115
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Lv J, Tu S, Xu L. Detection of Phenotype-Related Mutations of COVID-19 via the Whole Genomic Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:1242-1249. [PMID: 33417561 PMCID: PMC8769011 DOI: 10.1109/tcbb.2021.3049836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 11/30/2020] [Accepted: 01/03/2021] [Indexed: 06/12/2023]
Abstract
The coronavirus disease 2019 (COVID-19) epidemic continues to spread rapidly around the world and nearly 20 millions people are infected. This paper utilises both single-locus analysis and joint-SNPs analysis for detection of significant single nucleotide polymorphisms (SNPs) in the phenotypes of symptomatic versus asymptomatic, the early collection time versus the late collection time, the old versus the young, and the male versus the female. Also, this paper analyses the relationship between any two SNPs via linkage disequilibrium analysis, and visualises the patterns of cumulative mutations of SNPs over collection time. The results are in three folds. First, the SNP which locates at the nucleotide position 4321 is found to be an independent significant locus associated with all the first three phenotypes. Moreover, 12 significant SNPs are found in the first two studies. Second, gene orf1ab containing SNP-4321 is detected to be significantly associated with the first three phenotypes, and the three genes S, ORF3a, and N, are detected to be significant in the first two phenotypes. Third, some of the detected genes or SNPs are related to the SARS-COV-2 as supported by literature survey, which indicates that the results here may be helpful for further investigation.
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Affiliation(s)
- Jinxiong Lv
- Center for Cognitive Machines and Computational Health (CMaCH)Department of Computer Science and EngineeringShanghai Jiao Tong UniversityShanghai200240China
| | - Shikui Tu
- Center for Cognitive Machines and Computational Health (CMaCH)Department of Computer Science and EngineeringShanghai Jiao Tong UniversityShanghai200240China
| | - Lei Xu
- Center for Cognitive Machines and Computational Health (CMaCH)Department of Computer Science and EngineeringShanghai Jiao Tong UniversityShanghai200240China
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116
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Tada T, Dcosta BM, Samanovic MI, Herati RS, Cornelius A, Zhou H, Vaill A, Kazmierski W, Mulligan MJ, Landau NR. Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. mBio 2021; 12:e0069621. [PMID: 34060334 PMCID: PMC8262901 DOI: 10.1128/mbio.00696-21] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/28/2021] [Indexed: 12/21/2022] Open
Abstract
The increasing prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with spike protein mutations raises concerns that antibodies elicited by natural infection or vaccination and therapeutic monoclonal antibodies will become less effective. We show that convalescent-phase sera neutralize pseudotyped viruses with the B.1.1.7, B.1.351, B.1.1.248, COH.20G/677H, 20A.EU2, and mink cluster 5 spike proteins with only a minor loss in titer. Similarly, antibodies elicited by Pfizer BNT162b2 vaccination neutralized B.1.351 and B.1.1.248 with only a 3-fold decrease in titer, an effect attributable to E484K. Analysis of the Regeneron monoclonal antibodies REGN10933 and REGN10987 showed that REGN10933 has lost neutralizing activity against the B.1.351 and B.1.1.248 pseudotyped viruses, and the cocktail is 9- to 15-fold decreased in titer. These findings suggest that antibodies elicited by natural infection and by the Pfizer vaccine will maintain protection against the B.1.1.7, B.1.351, and B.1.1.248 variants but that monoclonal antibody therapy may be less effective for patients infected with B.1.351 or B.1.1.248 SARS-CoV-2. IMPORTANCE The rapid evolution of SARS-CoV-2 variants has raised concerns with regard to their potential to escape from vaccine-elicited antibodies and anti-spike protein monoclonal antibodies. We report here on an analysis of sera from recovered patients and vaccinated individuals and on neutralization by Regeneron therapeutic monoclonal antibodies. Overall, the variants were neutralized nearly as well as the wild-type pseudotyped virus. The B.1.351 variant was somewhat resistant to vaccine-elicited antibodies but was still readily neutralized. One of the two Regeneron therapeutic monoclonal antibodies seems to have lost most of its activity against the B.1.351 variant, raising concerns that the combination therapy might be less effective for some patients. The findings should alleviate concerns that vaccines will become ineffective but suggest the importance of continued surveillance for potential new variants.
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Affiliation(s)
- Takuya Tada
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USA
| | - Belinda M. Dcosta
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USA
| | - Marie I. Samanovic
- NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, New York, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Ramin S. Herati
- NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, New York, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Amber Cornelius
- NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, New York, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Hao Zhou
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USA
| | - Ada Vaill
- Biohaven Pharmaceuticals, Inc., New Haven, Connecticut, USA
| | - Wes Kazmierski
- Biohaven Pharmaceuticals, Inc., New Haven, Connecticut, USA
| | - Mark J. Mulligan
- NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, New York, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Nathaniel R. Landau
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USA
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117
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Spratt AN, Kannan SR, Woods LT, Weisman GA, Quinn TP, Lorson CL, Sönnerborg A, Byrareddy SN, Singh K. Evolution, correlation, structural impact and dynamics of emerging SARS-CoV-2 variants. Comput Struct Biotechnol J 2021; 19:3799-3809. [PMID: 34188776 PMCID: PMC8225291 DOI: 10.1016/j.csbj.2021.06.037] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/22/2021] [Accepted: 06/22/2021] [Indexed: 01/07/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infections remain unmanageable in some parts of the world. As with other RNA viruses, mutations in the SARS-CoV-2 gene have been continuously evolving. Recently, four variants have been identified, B.1.1.7, B.1.351, P.1 and CAL.20C. These variants appear to be more infectious and transmissible than the original Wuhan-Hu-1 virus. Using a combination of bioinformatics and structural analyses, we show that the new SARS-CoV-2 variants emerged in the background of an already known Spike protein mutation D614G together with another mutation P323L in the RNA polymerase of SARS-CoV-2. The phylogenetic analysis showed that the CAL.20C and B.1.351 shared one common ancestor, whereas the B.1.1.7 and P.1 shared a different ancestor. Structural comparisons did not show any significant difference between the wild-type and mutant ACE2/Spike complexes. Structural analysis indicated that the N501Y mutation may increase hydrophobic interactions at the ACE2/Spike interface. However, reported greater binding affinity of N501Y Spike with ACE2 does not seem to be entirely due to increased hydrophobic interactions, given that Spike mutation R417T in P.1 or K417N in B.1.351 results in the loss of a salt-bridge interaction between ACE2 and S-RBD. The calculated change in free energy did not provide a clear trend of S protein stability of mutations in the variants. As expected, we show that the CAL.20C generally migrated from the west coast to the east coast of the USA. Taken together, the analyses suggest that the evolution of variants and their infectivity is complex and may depend upon many factors.
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Affiliation(s)
- Austin N Spratt
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Saathvik R Kannan
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Lucas T Woods
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.,Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Gary A Weisman
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.,Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Thomas P Quinn
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Christian L Lorson
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.,Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Anders Sönnerborg
- Division of Infectious Diseases, Department of Medicine, Karolinska Institute, Huddinge 14186, Stockholm, Sweden.,Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Huddinge 14186, Stockholm, Sweden
| | - Siddappa N Byrareddy
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Huddinge 14186, Stockholm, Sweden.,Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Kamal Singh
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.,Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA.,Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Huddinge 14186, Stockholm, Sweden.,Sanctum Therapeutics Corporation, Sunnyvale, CA 94087, USA
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118
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Nag K, Chandra Baray J, Rahman Khan M, Mahmud A, Islam J, Myti S, Ali R, Haq Sarker E, Kumar S, Hossain Chowdhury M, Roy R, Islam F, Barman U, Khan H, Chakraborty S, Badsha A, Hossain M, Ahammad S, Rahman Chowdhury M, Ghosh P, Islam Shimul R, Ahmmed R, Hussain Bhuiya E, Kumar Biswas B, Mohiuddin M, Sultana N. An mRNA-based vaccine candidate against SARS-CoV-2 elicits stable immuno-response with single dose. Vaccine 2021; 39:3745-3755. [PMID: 34039497 PMCID: PMC8130517 DOI: 10.1016/j.vaccine.2021.05.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 05/01/2021] [Accepted: 05/12/2021] [Indexed: 12/24/2022]
Abstract
D614G genotype of SARS-CoV-2 virus is highly infectious and responsible for almost all infection for 2nd wave. However, there are currently no reports with D614G as vaccine candidate. Here we report the development of an mRNA-LNP vaccine with D614G variant and characterization in animal model. We have used special mRNA-architecture and formulation that provides suitable response of the product. The surface plasmon resonance (SPR) data with spike protein (S) revealed that immunization generated specific antibody pools against the whole extracellular domain (RBD and S2) of the spike protein. The anti-sera and purified IgGs from immunized mice neutralized SARS-CoV-2-pseudoviruses in ACE2-expressing HEK293 cells in a dose dependent manner. Importantly, single-dose immunization protected mice-lungs from homotypic-pseudovirus entry and cytopathy. The immunologic responses have been implicated by a balanced and stable population of CD4+ cells with a Th1 bias. The data suggested great promise for immediate translation of the technology to the clinic.
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Affiliation(s)
- Kakon Nag
- Globe Biotech Limited, 3/Ka (New), Tejgaon I/A, Dhaka 1208, Bangladesh.
| | | | | | - Asif Mahmud
- Globe Biotech Limited, 3/Ka (New), Tejgaon I/A, Dhaka 1208, Bangladesh
| | - Jikrul Islam
- Globe Biotech Limited, 3/Ka (New), Tejgaon I/A, Dhaka 1208, Bangladesh
| | - Sanat Myti
- Globe Biotech Limited, 3/Ka (New), Tejgaon I/A, Dhaka 1208, Bangladesh
| | - Rostum Ali
- Globe Biotech Limited, 3/Ka (New), Tejgaon I/A, Dhaka 1208, Bangladesh
| | - Enamul Haq Sarker
- Globe Biotech Limited, 3/Ka (New), Tejgaon I/A, Dhaka 1208, Bangladesh
| | - Samir Kumar
- Globe Biotech Limited, 3/Ka (New), Tejgaon I/A, Dhaka 1208, Bangladesh
| | | | - Rony Roy
- Globe Biotech Limited, 3/Ka (New), Tejgaon I/A, Dhaka 1208, Bangladesh
| | - Faqrul Islam
- Globe Biotech Limited, 3/Ka (New), Tejgaon I/A, Dhaka 1208, Bangladesh
| | - Uttam Barman
- Globe Biotech Limited, 3/Ka (New), Tejgaon I/A, Dhaka 1208, Bangladesh
| | - Habiba Khan
- Globe Biotech Limited, 3/Ka (New), Tejgaon I/A, Dhaka 1208, Bangladesh
| | | | - Alam Badsha
- Globe Biotech Limited, 3/Ka (New), Tejgaon I/A, Dhaka 1208, Bangladesh
| | - Manik Hossain
- Globe Biotech Limited, 3/Ka (New), Tejgaon I/A, Dhaka 1208, Bangladesh
| | - Shamim Ahammad
- Globe Biotech Limited, 3/Ka (New), Tejgaon I/A, Dhaka 1208, Bangladesh
| | | | - Polash Ghosh
- Globe Biotech Limited, 3/Ka (New), Tejgaon I/A, Dhaka 1208, Bangladesh
| | | | - Ronzu Ahmmed
- Globe Biotech Limited, 3/Ka (New), Tejgaon I/A, Dhaka 1208, Bangladesh
| | | | | | | | - Naznin Sultana
- Globe Biotech Limited, 3/Ka (New), Tejgaon I/A, Dhaka 1208, Bangladesh.
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119
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Müller NF, Wagner C, Frazar CD, Roychoudhury P, Lee J, Moncla LH, Pelle B, Richardson M, Ryke E, Xie H, Shrestha L, Addetia A, Rachleff VM, Lieberman NAP, Huang ML, Gautom R, Melly G, Hiatt B, Dykema P, Adler A, Brandstetter E, Han PD, Fay K, Ilcisin M, Lacombe K, Sibley TR, Truong M, Wolf CR, Boeckh M, Englund JA, Famulare M, Lutz BR, Rieder MJ, Thompson M, Duchin JS, Starita LM, Chu HY, Shendure J, Jerome KR, Lindquist S, Greninger AL, Nickerson DA, Bedford T. Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. Sci Transl Med 2021; 13:eabf0202. [PMID: 33941621 PMCID: PMC8158963 DOI: 10.1126/scitranslmed.abf0202] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/23/2021] [Accepted: 04/25/2021] [Indexed: 12/16/2022]
Abstract
The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has gravely affected societies around the world. Outbreaks in different parts of the globe have been shaped by repeated introductions of new viral lineages and subsequent local transmission of those lineages. Here, we sequenced 3940 SARS-CoV-2 viral genomes from Washington State (USA) to characterize how the spread of SARS-CoV-2 in Washington State in early 2020 was shaped by differences in timing of mitigation strategies across counties and by repeated introductions of viral lineages into the state. In addition, we show that the increase in frequency of a potentially more transmissible viral variant (614G) over time can potentially be explained by regional mobility differences and multiple introductions of 614G but not the other variant (614D) into the state. At an individual level, we observed evidence of higher viral loads in patients infected with the 614G variant. However, using clinical records data, we did not find any evidence that the 614G variant affects clinical severity or patient outcomes. Overall, this suggests that with regard to D614G, the behavior of individuals has been more important in shaping the course of the pandemic in Washington State than this variant of the virus.
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Affiliation(s)
- Nicola F Müller
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Cassia Wagner
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Chris D Frazar
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Jover Lee
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Louise H Moncla
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Benjamin Pelle
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Matthew Richardson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Erica Ryke
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Lasata Shrestha
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Amin Addetia
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Victoria M Rachleff
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Nicole A P Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Romesh Gautom
- Washington State Department of Health, Shoreline, WA 98155, USA
| | - Geoff Melly
- Washington State Department of Health, Shoreline, WA 98155, USA
| | - Brian Hiatt
- Washington State Department of Health, Shoreline, WA 98155, USA
| | - Philip Dykema
- Washington State Department of Health, Shoreline, WA 98155, USA
| | - Amanda Adler
- Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Elisabeth Brandstetter
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Peter D Han
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Kairsten Fay
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Misja Ilcisin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kirsten Lacombe
- Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Thomas R Sibley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Melissa Truong
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Caitlin R Wolf
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Michael Boeckh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Janet A Englund
- Seattle Children's Research Institute, Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA 98105, USA
| | | | - Barry R Lutz
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
| | - Mark J Rieder
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Matthew Thompson
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Jeffrey S Duchin
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
- Public Health - Seattle & King County, Seattle, WA98121, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Helen Y Chu
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Scott Lindquist
- Washington State Department of Health, Shoreline, WA 98155, USA
| | - Alexander L Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
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120
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Akkiz H. Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. Front Med (Lausanne) 2021; 8:636532. [PMID: 34026780 PMCID: PMC8137987 DOI: 10.3389/fmed.2021.636532] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/25/2021] [Indexed: 12/15/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative virus of the coronavirus disease 2019 (COVID-19), has been identified in China in late December 2019. SARS-CoV-2 is an enveloped, positive-sense, single-stranded RNA betacoronavirus of the Coronaviridae family. Coronaviruses have genetic proofreading mechanism that corrects copying mistakes and thus SARS-CoV-2 genetic diversity is extremely low. Despite lower mutation rate of the virus, researchers have detected a total of 12,706 mutations in the SARS-CoV-2 genome, the majority of which were single nucleotide polymorphisms. Sequencing data revealed that the SARS-CoV-2 accumulates two-single nucleotide mutations per month in its genome. Recently, an amino acid aspartate (D) to glycine (G) (D614G) mutation due to an adenine to guanine nucleotide change at position 23,403 at the 614th amino-acid position of the spike protein in the original reference genotype has been identified. The SARS-CoV-2 viruses that carry the spike protein D614G mutation have become dominant variant around the world. The D614G mutation has been found to be associated with 3 other mutations in the spike protein. Clinical and pseudovirus experimental studies have demonstrated that the spike protein D614G mutation alters the virus phenotype. However, the impact of the mutation on the rate of transmission between people, disease severity and the vaccine and therapeutic development remains unclear. Three variants of SARS-CoV-2 have recently been identified. They are B.1.1.7 (UK) variant, B.1.351 (N501Y.V2, South African) variant and B.1.1.28 (Brazilian) variant. Epidemiological data suggest that they have a higher transmissibility than the original variant. There are reports that some vaccines are less efficacious against the B.1.351 variant. This review article discusses the effects of novel mutations in the SARS-CoV-2 genome on transmission, clinical outcomes and vaccine development.
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Affiliation(s)
- Hikmet Akkiz
- Department of Gastroenterology and Hepatology, The University of Çukurova, Adana, Turkey
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121
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The SARS-CoV-2 and other human coronavirus spike proteins are fine-tuned towards temperature and proteases of the human airways. PLoS Pathog 2021; 17:e1009500. [PMID: 33886690 PMCID: PMC8061995 DOI: 10.1371/journal.ppat.1009500] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/24/2021] [Indexed: 12/13/2022] Open
Abstract
The high transmissibility of SARS-CoV-2 is related to abundant replication in the upper airways, which is not observed for the other highly pathogenic coronaviruses SARS-CoV and MERS-CoV. We here reveal features of the coronavirus spike (S) protein, which optimize the virus towards the human respiratory tract. First, the S proteins exhibit an intrinsic temperature preference, corresponding with the temperature of the upper or lower airways. Pseudoviruses bearing the SARS-CoV-2 spike (SARS-2-S) were more infectious when produced at 33°C instead of 37°C, a property shared with the S protein of HCoV-229E, a common cold coronavirus. In contrast, the S proteins of SARS-CoV and MERS-CoV favored 37°C, in accordance with virus preference for the lower airways. Next, SARS-2-S-driven entry was efficiently activated by not only TMPRSS2, but also the TMPRSS13 protease, thus broadening the cell tropism of SARS-CoV-2. Both proteases proved relevant in the context of authentic virus replication. TMPRSS13 appeared an effective spike activator for the virulent coronaviruses but not the low pathogenic HCoV-229E virus. Activation of SARS-2-S by these surface proteases requires processing of the S1/S2 cleavage loop, in which both the furin recognition motif and extended loop length proved critical. Conversely, entry of loop deletion mutants is significantly increased in cathepsin-rich cells. Finally, we demonstrate that the D614G mutation increases SARS-CoV-2 stability, particularly at 37°C, and, enhances its use of the cathepsin L pathway. This indicates a link between S protein stability and usage of this alternative route for virus entry. Since these spike properties may promote virus spread, they potentially explain why the spike-G614 variant has replaced the early D614 variant to become globally predominant. Collectively, our findings reveal adaptive mechanisms whereby the coronavirus spike protein is adjusted to match the temperature and protease conditions of the airways, to enhance virus transmission and pathology. The devastating COVID-19 pandemic is caused by SARS-CoV-2, a novel virus that despite recent zoonotic introduction is already very well adapted to its human host. Its rapid spread is related to abundant replication in the upper airways, which is not observed for other highly pathogenic human coronaviruses. To understand the role of the viral spike protein in this airway adaptation, we constructed pseudoviruses of SARS-CoV-2 and other coronaviruses that cause severe pneumonia or, on the contrary, a mild common cold. The key findings were verified with authentic virus. We reveal features of the spike proteins, which optimize the coronavirus towards specific parts of the respiratory tract. Namely, we show that the spike proteins exhibit intrinsic temperature preference to precisely match the upper (~33°C) or lower (37°C) airways. We recognized which proteases of human airways activate the spike for virus entry, in particular one protease that may mediate coronavirus virulence. Finally, a link was perceived between spike stability and entry via endosomal proteases. We propose that these mechanisms of spike fine-tuning may have contributed to a global shift in SARS-CoV-2 epidemiology, from the early spike-D614 to the currently predominating G614 variant.
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122
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Bian L, Gao F, Zhang J, He Q, Mao Q, Xu M, Liang Z. Effects of SARS-CoV-2 variants on vaccine efficacy and response strategies. Expert Rev Vaccines 2021; 20:365-373. [PMID: 33851875 PMCID: PMC8054487 DOI: 10.1080/14760584.2021.1903879] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 03/12/2021] [Indexed: 12/26/2022]
Abstract
INTRODUCTION As the global severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic continues to spread, several variants have emerged. Variants B.1.1.7 and B.1.351 have attracted significant attention owing to their widespread transmission and possible immune evasion. A total of 19 SARS-CoV-2 vaccines based on original strains have entered clinical studies, including nine vaccines that have obtained emergency use or conditional marketing authorizations. However, newly emerging variants may affect their protective efficacy. Decreased efficacy of the Novartis, Johnson & Johnson, and AstraZeneca vaccines against B.1.351 has been reported. The spread of variants creates a tremendous challenge for the prevention and control of the SARS-CoV-2 pandemic via vaccination. Several response strategies, including accelerating massive rollouts of current vaccines, increasing vaccine immunogenicity by increasing vaccination doses, and accelerating next-generation vaccines against variants, have been suggested. AREAS COVERED SARS-CoV-2 vaccine efficacy against variants and response strategies for emerging variants. EXPERT OPINION Current SARS-CoV-2 vaccines authorized for emergency use or under clinical trials have shown certain advantages in providing adequate protection against new variants. We analyzed the effects of reported variants on neutralizing antibodies and the protective efficacy of different vaccines and propose strategies for applying current vaccines against variants and developing next-generation vaccines.
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Affiliation(s)
- Lianlian Bian
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Fan Gao
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Jialu Zhang
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Qian He
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Qunying Mao
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Miao Xu
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Zhenglun Liang
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
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123
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Peacock TP, Penrice-Randal R, Hiscox JA, Barclay WS. SARS-CoV-2 one year on: evidence for ongoing viral adaptation. J Gen Virol 2021; 102:001584. [PMID: 33855951 PMCID: PMC8290271 DOI: 10.1099/jgv.0.001584] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/16/2021] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 is thought to have originated in the human population from a zoonotic spillover event. Infection in humans results in a variety of outcomes ranging from asymptomatic cases to the disease COVID-19, which can have significant morbidity and mortality, with over two million confirmed deaths worldwide as of January 2021. Over a year into the pandemic, sequencing analysis has shown that variants of SARS-CoV-2 are being selected as the virus continues to circulate widely within the human population. The predominant drivers of genetic variation within SARS-CoV-2 are single nucleotide polymorphisms (SNPs) caused by polymerase error, potential host factor driven RNA modification, and insertion/deletions (indels) resulting from the discontinuous nature of viral RNA synthesis. While many mutations represent neutral 'genetic drift' or have quickly died out, a subset may be affecting viral traits such as transmissibility, pathogenicity, host range, and antigenicity of the virus. In this review, we summarise the current extent of genetic change in SARS-CoV-2, particularly recently emerging variants of concern, and consider the phenotypic consequences of this viral evolution that may impact the future trajectory of the pandemic.
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Affiliation(s)
- Thomas P. Peacock
- Department of Infectious Diseases, St Marys Medical School, Imperial College London, UK
| | | | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, UK
- A*STAR Infectious Diseases Laboratories (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Wendy S. Barclay
- Department of Infectious Diseases, St Marys Medical School, Imperial College London, UK
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Kumar A, Singh R, Kaur J, Pandey S, Sharma V, Thakur L, Sati S, Mani S, Asthana S, Sharma TK, Chaudhuri S, Bhattacharyya S, Kumar N. Wuhan to World: The COVID-19 Pandemic. Front Cell Infect Microbiol 2021; 11:596201. [PMID: 33859951 PMCID: PMC8042280 DOI: 10.3389/fcimb.2021.596201] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 03/09/2021] [Indexed: 12/24/2022] Open
Abstract
COVID-19 is a Severe Acute Respiratory Syndrome (SARS), caused by SARS-CoV-2, a novel virus which belongs to the family Coronaviridae. It was first reported in December 2019 in the Wuhan city of China and soon after, the virus and hence the disease got spread to the entire world. As of February 26, 2021, SARS-CoV-2 has infected ~112.20 million people and caused ~2.49 million deaths across the globe. Although the case fatality rate among SARS-CoV-2 patient is lower (~2.15%) than its earlier relatives, SARS-CoV (~9.5%) and MERS-CoV (~34.4%), the SARS-CoV-2 has been observed to be more infectious and caused higher morbidity and mortality worldwide. As of now, only the knowledge regarding potential transmission routes and the rapidly developed diagnostics has been guiding the world for managing the disease indicating an immediate need for a detailed understanding of the pathogen and the disease-biology. Over a very short period of time, researchers have generated a lot of information in unprecedented ways in the key areas, including viral entry into the host, dominant mutation, potential transmission routes, diagnostic targets and their detection assays, potential therapeutic targets and drug molecules for inhibiting viral entry and/or its replication in the host including cross-neutralizing antibodies and vaccine candidates that could help us to combat the ongoing COVID-19 pandemic. In the current review, we have summarized the available knowledge about the pathogen and the disease, COVID-19. We believe that this readily available knowledge base would serve as a valuable resource to the scientific and clinical community and may help in faster development of the solution to combat the disease.
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Affiliation(s)
- Ashok Kumar
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
- Manipal Academy of Higher Education, Manipal, India
| | - Rita Singh
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Jaskaran Kaur
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Sweta Pandey
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Vinita Sharma
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
- Central University of Haryana, Mahendragarh, India
| | - Lovnish Thakur
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Sangeeta Sati
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Shailendra Mani
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Shailendra Asthana
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Tarun Kumar Sharma
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Susmita Chaudhuri
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | | | - Niraj Kumar
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
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Liu L, Zeng F, Rao J, Yuan S, Ji M, Lei X, Xiao X, Li Z, Li X, Du W, Liu Y, Tan H, Li J, Zhu J, Yang J, Liu Z. Comparison of Clinical Features and Outcomes of Medically Attended COVID-19 and Influenza Patients in a Defined Population in the 2020 Respiratory Virus Season. Front Public Health 2021; 9:587425. [PMID: 33834012 PMCID: PMC8021703 DOI: 10.3389/fpubh.2021.587425] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/22/2021] [Indexed: 01/10/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-COV-2), which is causing the coronavirus disease-2019 (COVID-19) pandemic, poses a global health threat. However, it is easy to confuse COVID-19 with seasonal influenza in preliminary clinical diagnosis. In this study, the differences between influenza and COVID-19 in epidemiological features, clinical manifestations, comorbidities and pathogen biology were comprehensively compared and analyzed. SARS-CoV-2 causes a higher proportion of pneumonia (90.67 vs. 17.07%) and acute respiratory distress syndrome (12.00 vs. 0%) than influenza A virus. The proportion of leukopenia for influenza patients was 31.71% compared with 12.00% for COVID-19 patients (P = 0.0096). The creatinine and creatine kinase were significantly elevated when there were COVID-19 patients. The basic reproductive number (R0) for SARS-CoV-2 is 2.38 compared with 1.28 for seasonal influenza A virus. The mutation rate of SARS-CoV-2 ranges from 1.12 × 10-3 to 6.25 × 10-3, while seasonal influenza virus has a lower evolutionary rate (0.60-2.00 × 10-6). Overall, this study compared the clinical features and outcomes of medically attended COVID-19 and influenza patients. In addition, the S477N and N439K mutations on spike may affect the affinity with receptor ACE2. This study will contribute to COVID-19 control and epidemic surveillance in the future.
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Affiliation(s)
- Long Liu
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Department of Respiratory, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Feng Zeng
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Department of Respiratory, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Jingjing Rao
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Department of Respiratory, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Shengren Yuan
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Department of Respiratory, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Manshan Ji
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Department of Respiratory, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Xu Lei
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Department of Respiratory, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Xiao Xiao
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Department of Respiratory, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Zhijun Li
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Department of Respiratory, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Xiaohua Li
- Department of Emergency, Dongfeng Maojian Hospital, Sinopharm Group Corporation, Shiyan, China
| | - Weixing Du
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Department of Respiratory, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Yanqing Liu
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Department of Respiratory, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Huabing Tan
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Department of Respiratory, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Junmin Li
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Department of Respiratory, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Jianyong Zhu
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Department of Respiratory, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Jing Yang
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Department of Respiratory, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Zhixin Liu
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Department of Respiratory, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
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Hasan MM, Das R, Rasheduzzaman M, Hussain MH, Muzahid NH, Salauddin A, Rumi MH, Mahbubur Rashid SM, Siddiki AZ, Mannan A. Global and local mutations in Bangladeshi SARS-CoV-2 genomes. Virus Res 2021; 297:198390. [PMID: 33737154 PMCID: PMC7959702 DOI: 10.1016/j.virusres.2021.198390] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 03/07/2021] [Accepted: 03/09/2021] [Indexed: 12/11/2022]
Abstract
Coronavirus Disease 2019 (COVID-19) warrants comprehensive investigations of publicly available Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) genomes to gain new insight about their epidemiology, mutations, and pathogenesis. Nearly 0.4 million mutations have been identified so far among the ∼60,000 SARS-CoV-2 genomic sequences. In this study, we compared a total of 371 SARS-CoV-2 published whole genomes reported from different parts of Bangladesh with 467 sequences reported globally to understand the origin of viruses, possible patterns of mutations, and availability of unique mutations. Phylogenetic analyses indicated that SARS-CoV-2 viruses might have transmitted through infected travelers from European countries, and the GR clade was found as predominant in Bangladesh. Our analyses revealed 4604 mutations at the RNA level including 2862 missense mutations, 1192 synonymous mutations, 25 insertions and deletions and 525 other types of mutation. In line with the global trend, D614G mutation in spike glycoprotein was predominantly high (98 %) in Bangladeshi isolates. Interestingly, we found the average number of mutations in ORF1ab, S, ORF3a, M, and N were significantly higher (p < 0.001) for sequences containing the G614 variant compared to those having D614. Previously reported frequent mutations, such as R203K, D614G, G204R, P4715L and I300F at protein levels were also prevalent in Bangladeshi isolates. Additionally, 34 unique amino acid changes were revealed and categorized as originating from different cities. These analyses may increase our understanding of variations in SARS-CoV-2 virus genomes, circulating in Bangladesh and elsewhere.
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Affiliation(s)
- Md Mahbub Hasan
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh; Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Rasel Das
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Foy's Lake, Chattogram 4202, Bangladesh
| | - Md Rasheduzzaman
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh
| | - Md Hamed Hussain
- School of Science, Monash University Malaysia, 47500 Selangor, Malaysia
| | | | - Asma Salauddin
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh
| | - Meheadi Hasan Rumi
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh
| | - S M Mahbubur Rashid
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Ramna, Dhaka 1000, Bangladesh
| | - Amam Zonaed Siddiki
- Genomics Research Group, Faculty of Veterinary Medicine, Chittagong Veterinary and Animal Sciences University, Chattogram 4202, Bangladesh
| | - Adnan Mannan
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh.
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127
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Jackson CB, Zhang L, Farzan M, Choe H. Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. Biochem Biophys Res Commun 2021; 538:108-115. [PMID: 33220921 PMCID: PMC7664360 DOI: 10.1016/j.bbrc.2020.11.026] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 11/09/2020] [Indexed: 12/15/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped virus which binds its cellular receptor angiotensin-converting enzyme 2 (ACE2) and enters hosts cells through the action of its spike (S) glycoprotein displayed on the surface of the virion. Compared to the reference strain of SARS-CoV-2, the majority of currently circulating isolates possess an S protein variant characterized by an aspartic acid-to-glycine substitution at amino acid position 614 (D614G). Residue 614 lies outside the receptor binding domain (RBD) and the mutation does not alter the affinity of monomeric S protein for ACE2. However, S(G614), compared to S(D614), mediates more efficient ACE2-mediated transduction of cells by S-pseudotyped vectors and more efficient infection of cells and animals by live SARS-CoV-2. This review summarizes and synthesizes the epidemiological and functional observations of the D614G spike mutation, with focus on the biochemical and cell-biological impact of this mutation and its consequences for S protein function. We further discuss the significance of these recent findings in the context of the current global pandemic.
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Affiliation(s)
- Cody B Jackson
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA.
| | - Lizhou Zhang
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Michael Farzan
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Hyeryun Choe
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
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128
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Daniloski Z, Jordan TX, Wessels HH, Hoagland DA, Kasela S, Legut M, Maniatis S, Mimitou EP, Lu L, Geller E, Danziger O, Rosenberg BR, Phatnani H, Smibert P, Lappalainen T, tenOever BR, Sanjana NE. Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells. Cell 2021; 184:92-105.e16. [PMID: 33147445 PMCID: PMC7584921 DOI: 10.1016/j.cell.2020.10.030] [Citation(s) in RCA: 380] [Impact Index Per Article: 126.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/25/2020] [Accepted: 10/20/2020] [Indexed: 12/21/2022]
Abstract
To better understand host-virus genetic dependencies and find potential therapeutic targets for COVID-19, we performed a genome-scale CRISPR loss-of-function screen to identify host factors required for SARS-CoV-2 viral infection of human alveolar epithelial cells. Top-ranked genes cluster into distinct pathways, including the vacuolar ATPase proton pump, Retromer, and Commander complexes. We validate these gene targets using several orthogonal methods such as CRISPR knockout, RNA interference knockdown, and small-molecule inhibitors. Using single-cell RNA-sequencing, we identify shared transcriptional changes in cholesterol biosynthesis upon loss of top-ranked genes. In addition, given the key role of the ACE2 receptor in the early stages of viral entry, we show that loss of RAB7A reduces viral entry by sequestering the ACE2 receptor inside cells. Overall, this work provides a genome-scale, quantitative resource of the impact of the loss of each host gene on fitness/response to viral infection.
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Affiliation(s)
- Zharko Daniloski
- New York Genome Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA
| | - Tristan X Jordan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hans-Hermann Wessels
- New York Genome Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA
| | - Daisy A Hoagland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Silva Kasela
- New York Genome Center, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA
| | - Mateusz Legut
- New York Genome Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA
| | | | - Eleni P Mimitou
- Technology Innovation Lab, New York Genome Center, New York, NY, USA
| | - Lu Lu
- New York Genome Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA
| | - Evan Geller
- New York Genome Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA
| | - Oded Danziger
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brad R Rosenberg
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hemali Phatnani
- New York Genome Center, New York, NY, USA; Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Peter Smibert
- Technology Innovation Lab, New York Genome Center, New York, NY, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA
| | - Benjamin R tenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Neville E Sanjana
- New York Genome Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA.
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129
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Teng X, Li Q, Li Z, Zhang Y, Niu G, Xiao J, Yu J, Zhang Z, Song S. Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades. GENOMICS, PROTEOMICS & BIOINFORMATICS 2020; 18:648-663. [PMID: 33581339 PMCID: PMC7875716 DOI: 10.1016/j.gpb.2020.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/18/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023]
Abstract
COVID-19 and its causative pathogen SARS-CoV-2 have rushed the world into a staggering pandemic in a few months, and a global fight against both has been intensifying. Here, we describe an analysis procedure where genome composition and its variables are related, through the genetic code to molecular mechanisms, based on understanding of RNA replication and its feedback loop from mutation to viral proteome sequence fraternity including effective sites on the replicase-transcriptase complex. Our analysis starts with primary sequence information, identity-based phylogeny based on 22,051 SARS-CoV-2 sequences, and evaluation of sequence variation patterns as mutation spectra and its 12 permutations among organized clades. All are tailored to two key mechanisms: strand-biased and function-associated mutations. Our findings are listed as follows: 1) The most dominant mutation is C-to-U permutation, whose abundant second-codon-position counts alter amino acid composition toward higher molecular weight and lower hydrophobicity, albeit assumed most slightly deleterious. 2) The second abundance group includes three negative-strand mutations (U-to-C, A-to-G, and G-to-A) and a positive-strand mutation (G-to-U) due to DNA repair mechanisms after cellular abasic events. 3) A clade-associated biased mutation trend is found attributable to elevated level of negative-sense strand synthesis. 4) Within-clade permutation variation is very informative for associating non-synonymous mutations and viral proteome changes. These findings demand a platform where emerging mutations are mapped onto mostly subtle but fast-adjusting viral proteomes and transcriptomes, to provide biological and clinical information after logical convergence for effective pharmaceutical and diagnostic applications. Such actions are in desperate need, especially in the middle of the War against COVID-19.
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Affiliation(s)
- Xufei Teng
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qianpeng Li
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhao Li
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuansheng Zhang
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guangyi Niu
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingfa Xiao
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Yu
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhang Zhang
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Shuhui Song
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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