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Sari H, Putri HH, Paksi PW, Hidayat G, Amelia SR, Sundari CDD, Rachmawati H, Ivansyah AL, Muttaqien F, Iskandar F. Theoretical Investigation of the Green-Synthesized Carbon-Based Nanomaterial Potential as Inhibitors of ACE2 for Blocking SARS-CoV-2 Binding. ACS OMEGA 2024; 9:16701-16715. [PMID: 38617634 PMCID: PMC11007854 DOI: 10.1021/acsomega.4c00759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/01/2024] [Accepted: 03/12/2024] [Indexed: 04/16/2024]
Abstract
Since the emergence of SARS-CoV-2 in 2020, the world has faced a global pandemic, emphasizing the urgent need for effective treatments to combat COVID-19. This study explores the use of green-synthesized carbon-based nanomaterials as potential inhibitors of ACE2, a critical receptor for SARS-CoV-2 entry into host cells. Specifically, the study examines four carbon-based nanomaterials, namely, CD1, CD2, CD3, and CD4 in amino, graphitic, pyridinic, and pyrrolic forms, respectively, synthesized from curcumin, to investigate their binding affinity with ACE2. Molecular docking studies revealed that CD3 (pyridinic form) exhibited the highest binding affinity with ACE2, surpassing that of the control compound, curcumin. Notably, CD3 formed hydrophobic interactions and hydrogen bonds with key ACE2 residues, suggesting its potential to block the binding of SARS-CoV-2 to human cells. Moreover, molecular dynamics simulations demonstrated the stability of these ligand-ACE2 complexes, further supporting the promise of CD3 as an inhibitor. Quantum chemical analyses, including frontier molecular orbitals, natural bond orbital analysis, and the quantum theory of atoms in molecules, unveiled valuable insights into the reactivity and interaction strengths of these ligands. CD3 exhibited desirable chemical properties, signifying its suitability for therapeutic development. The study's findings suggest that green-synthesized carbon-based nanomaterials, particularly CD3, have the potential to serve as effective inhibitors of ACE2, offering a promising avenue for the development of treatments against COVID-19. Further experimental validation is warranted to advance these findings and establish new therapies for the ongoing global pandemic.
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Affiliation(s)
- Harsiwi
Candra Sari
- Master
Program in Computational Science, Faculty of Mathematics and Natural
Sciences, Institut Teknologi Bandung, Jalan Ganesha 10, Bandung, West Java 40132, Indonesia
| | - Haliza Hasnia Putri
- Master
Program in Computational Science, Faculty of Mathematics and Natural
Sciences, Institut Teknologi Bandung, Jalan Ganesha 10, Bandung, West Java 40132, Indonesia
| | - Pinantun Wiguna
Kusuma Paksi
- Master
Program in Computational Science, Faculty of Mathematics and Natural
Sciences, Institut Teknologi Bandung, Jalan Ganesha 10, Bandung, West Java 40132, Indonesia
| | - Gabriel Hidayat
- Master
Program in Computational Science, Faculty of Mathematics and Natural
Sciences, Institut Teknologi Bandung, Jalan Ganesha 10, Bandung, West Java 40132, Indonesia
| | - Silmi Rahma Amelia
- Master
Program in Computational Science, Faculty of Mathematics and Natural
Sciences, Institut Teknologi Bandung, Jalan Ganesha 10, Bandung, West Java 40132, Indonesia
| | - Citra Deliana Dewi Sundari
- Department
of Chemistry, Institut Teknologi Bandung, Jalan Ganesha 10, Bandung, West Java 40132, Indonesia
- Chemistry
Education, Universitas Islam Negeri Sunan
Gunung Djati Bandung, Jl. A. H. Nasution No. 105, Bandung, West Java 40614, Indonesia
| | - Heni Rachmawati
- School
of Pharmacy, Institut Teknologi Bandung, Jalan Ganesha 10, Bandung, West Java 40132, Indonesia
- Research
Center for Nanosciences and Nanotechnology, Institut Teknologi Bandung, Jalan Ganesha 10, Bandung, West Java 40132, Indonesia
| | - Atthar Luqman Ivansyah
- Master
Program in Computational Science, Faculty of Mathematics and Natural
Sciences, Institut Teknologi Bandung, Jalan Ganesha 10, Bandung, West Java 40132, Indonesia
- Department
of Physics, Institut Teknologi Bandung, Jalan Ganesha 10, Bandung, West Java 40132, Indonesia
| | - Fahdzi Muttaqien
- Master
Program in Computational Science, Faculty of Mathematics and Natural
Sciences, Institut Teknologi Bandung, Jalan Ganesha 10, Bandung, West Java 40132, Indonesia
- Department
of Physics, Institut Teknologi Bandung, Jalan Ganesha 10, Bandung, West Java 40132, Indonesia
| | - Ferry Iskandar
- Research
Center for Nanosciences and Nanotechnology, Institut Teknologi Bandung, Jalan Ganesha 10, Bandung, West Java 40132, Indonesia
- Department
of Physics, Institut Teknologi Bandung, Jalan Ganesha 10, Bandung, West Java 40132, Indonesia
- Collaboration
Research Center for Advanced Energy Materials, National Research and Innovation Agency - Institut Teknologi Bandung, Jl. Ganesha 10∇, Bandung 40132, Indonesia
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2
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Winiger RR, Perez L. Therapeutic antibodies and alternative formats against SARS-CoV-2. Antiviral Res 2024; 223:105820. [PMID: 38307147 DOI: 10.1016/j.antiviral.2024.105820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/04/2024]
Abstract
The COVID-19 pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) heavily burdened the entire world. Despite a prompt generation of vaccines and therapeutics to confront infection, the virus remains a threat. The ancestor viral strain has evolved into several variants of concern, with the Omicron variant now having many distinct sublineages. Consequently, most available antibodies targeting the spike went obsolete and thus new therapies or therapeutic formats are needed. In this review we focus on antibody targets, provide an overview of the therapeutic progress made so far, describe novel formats being explored, and lessons learned from therapeutic antibodies that can enhance pandemic preparedness.
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Affiliation(s)
- Rahel R Winiger
- University of Lausanne (UNIL), Lausanne University Hospital (CHUV), Service of Immunology and Allergy, and Center for Human Immunology Lausanne (CHIL), Switzerland.
| | - Laurent Perez
- University of Lausanne (UNIL), Lausanne University Hospital (CHUV), Service of Immunology and Allergy, and Center for Human Immunology Lausanne (CHIL), Switzerland.
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Tchoupou Saha OLF, Dubourg G, Yacouba A, Tola R, Raoult D, Lagier JC. Description of nasopharyngeal bacterial pathogens associated with different SARS-CoV-2 variants. Microb Pathog 2024; 188:106561. [PMID: 38307371 DOI: 10.1016/j.micpath.2024.106561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/16/2024] [Accepted: 01/25/2024] [Indexed: 02/04/2024]
Abstract
The emergence of the coronavirus pandemic facilitated the acquisition of mutations in the SARS-CoV-2 genome, resulting in the appearance of new variants over the past three years. We previously identified several taxa associated with the clinical outcome of COVID-19 disease in a retrospective study involving 120 patients (infected patients and negative subjects). However, little is known about whether the different variants could influence variations in the composition of the nasopharyngeal microbiota. In this study, we used multiplex pathogen-specific PCR to analyse the presence of nasopharyngeal bacterial pathogens from 400 SARS-CoV-2 positive patients (equally distributed in the four SARS-CoV-2 variants studied: B.1.1.7 (Alpha), B.1 0.617.2 (Delta), B.1.160 (Marseille-4), and B.1.1.529 (omicron)). We then compared them to 400 patients who tested negative for all respiratory viruses tested in this study, including SARS-CoV-2. We first observed an enrichment of Staphylococcus aureus (P ≤ .05) and Corynebacterium propinquum (P ≤ .05) in COVID-19-positive patients, regardless of the variant, compared to negative subjects. We specifically highlighted a significantly higher frequency of S. aureus (P ≤ .0001), C. propinquum (P ≤ .0001), and Klebsiella pneumoniae (P ≤ .0001), in patients infected with the omicron variant, whereas that of Haemophilus influenzae was higher in patients infected with Marseille-4 (P ≤ .001) and Alpha (P ≤ .01) variants. Our results suggest that the nasopharyngeal bacterial pathogens have their own specificity according to the SARS-CoV-2 variant and independently of the season. Additional studies are needed to determine the role of these pathogens in the evolution of the clinical outcome of patients.
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Affiliation(s)
- Ornella La Fortune Tchoupou Saha
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), AP-HM, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France
| | - Grégory Dubourg
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), AP-HM, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France.
| | - Abdourahamane Yacouba
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), AP-HM, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France
| | | | - Didier Raoult
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), AP-HM, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France
| | - Jean-Christophe Lagier
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), AP-HM, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France.
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4
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de Souza AS, Amorim VMDF, de Souza RF, Guzzo CR. Molecular dynamics simulations of the spike trimeric ectodomain of the SARS-CoV-2 Omicron variant: structural relationships with infectivity, evasion to immune system and transmissibility. J Biomol Struct Dyn 2023; 41:9326-9343. [PMID: 36345794 DOI: 10.1080/07391102.2022.2142296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 10/24/2022] [Indexed: 11/11/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron is currently the most prevalent SARS-CoV-2 variant worldwide. Herein, we calculated molecular dynamics simulations of the trimeric spikeWT and SpikeBA.1 for 300 ns. Our results show that SpikeBA.1 has more conformational flexibility than SpikeWT. Our principal component analysis (PCA) allowed us to observe a broader spectrum of different conformations for SpikeBA.1, mainly at N-terminal domain (NTD) and receptor-binding domain (RBD). Such increased flexibility could contribute to decreased neutralizing antibody recognition of this variant. Our molecular dynamics data show that the RBDBA.1 easily visits an up-conformational state and the prevalent D614G mutation is pivotal to explain molecular dynamics results for this variant because to lost hydrogen bonding interactions between the residue pairs K854SC/D614SC, Y837MC/D614MC, K835SC/D614SC, T859SC/D614SC. In addition, SpikeBA.1 residues near the furin cleavage site are more flexible than in SpikeWT, probably due to P681H and D614G substitutions. Finally, dynamical cross-correlation matrix (DCCM) analysis reveals that D614G and P681H may allosterically affect the cleavage site S1/S2. Conversely, S2' site may be influenced by residues located between NTD and RBD of a neighboring protomer of the SpikeWT. Such communication may be lost in SpikeBA.1, explaining the changes of the cell tropism in the viral infection. In addition, the movements of the NTDWT and NTDBA.1 may modulate the RBD conformation through allosteric effects. Taken together, our results explain how the structural aspects may explain the observed gains in infectivity, immune system evasion and transmissibility of the Omicron variant.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anacleto Silva de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Robson Francisco de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Cristiane Rodrigues Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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Burgos G, Ambuludí A, Morales-Jadán D, Garcia-Bereguiain MA, Muslin C, Armijos-Jaramillo V. A tool for the cheap and rapid screening of SARS-CoV-2 variants of concern (VoCs) by Sanger sequencing. Microbiol Spectr 2023; 11:e0506422. [PMID: 37676038 PMCID: PMC10586709 DOI: 10.1128/spectrum.05064-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 07/05/2023] [Indexed: 09/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging virus that, since March 2020, has been responsible for a global and ongoing pandemic. Its rapid spread over the past nearly 3 years has caused novel variants to arise. To monitor the circulation and emergence of SARS-CoV-2 variants, surveillance systems based on nucleotide mutations are required. In this regard, we searched in the spike, ORF8, and nucleocapsid genes to detect variable sites among SARS-CoV-2 variants. We describe polymorphic genetic regions that enable us to differentiate between the Alpha, Beta, Gamma, Delta, and Omicron variants of concern (VoCs). We found 21 relevant mutations, 13 of which are unique for Omicron lineages BA.1/BA.1.1, BA.2, BA.3, BA.4, and BA.5. This genetic profile enables the discrimination between VoCs using only four reverse transcription PCR fragments and Sanger sequencing, offering a cheaper and faster alternative to whole-genome sequencing for SARS-CoV-2 surveillance. IMPORTANCE Our work describes a new (Sanger sequencing-based) screening methodology for SARS-CoV-2, performing PCR amplifications of a few target regions to detect diagnostic mutations between virus variants. Using the methodology developed in this work, we were able to discriminate between the following VoCs: Alpha, Beta, Gamma, Delta, and Omicron (BA.1/BA.1.1, BA.2, BA.3, BA.4, and BA.5). This becomes important, especially in low-income countries where current methodologies like next-generation sequencing have prohibitive costs. Furthermore, rapid detection would allow sanitary authorities to take rapid measures to limit the spread of the virus and therefore reduce the probability of new virus dispersion. With this methodological approach, 13 previously unreported diagnostic mutations among several Omicron lineages were found.
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Affiliation(s)
- Germán Burgos
- Facultad de Medicina, Universidad de Las Américas (UDLA), Quito, Ecuador
- One Health Research Group, Faculty of Health Sciences, Universidad de Las Américas (UDLA), Quito, Ecuador
| | - Andrés Ambuludí
- Carrera de Ingeniería en Biotecnología, Facultad de Ingenierías y Ciencias Aplicadas, Universidad de Las Américas (UDLA), Quito, Ecuador
| | - USFQ SARS-CoV-2 Consortium
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales (COCIBA), Universidad San Francisco de Quito (USFQ), Cumbaya, Ecuador
| | - Diana Morales-Jadán
- One Health Research Group, Faculty of Health Sciences, Universidad de Las Américas (UDLA), Quito, Ecuador
| | | | - Claire Muslin
- One Health Research Group, Faculty of Health Sciences, Universidad de Las Américas (UDLA), Quito, Ecuador
| | - Vinicio Armijos-Jaramillo
- Carrera de Ingeniería en Biotecnología, Facultad de Ingenierías y Ciencias Aplicadas, Universidad de Las Américas (UDLA), Quito, Ecuador
- Grupo de Bio-Quimioinformática, Universidad de Las Américas (UDLA), Quito, Ecuador
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6
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Jamir E, Sarma H, Priyadarsinee L, Kiewhuo K, Nagamani S, Sastry GN. Polypharmacology guided drug repositioning approach for SARS-CoV2. PLoS One 2023; 18:e0289890. [PMID: 37556478 PMCID: PMC10411734 DOI: 10.1371/journal.pone.0289890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 07/27/2023] [Indexed: 08/11/2023] Open
Abstract
Drug repurposing has emerged as an important strategy and it has a great potential in identifying therapeutic applications for COVID-19. An extensive virtual screening of 4193 FDA approved drugs has been carried out against 24 proteins of SARS-CoV2 (NSP1-10 and NSP12-16, envelope, membrane, nucleoprotein, spike, ORF3a, ORF6, ORF7a, ORF8, and ORF9b). The drugs were classified into top 10 and bottom 10 drugs based on the docking scores followed by the distribution of their therapeutic indications. As a result, the top 10 drugs were found to have therapeutic indications for cancer, pain, neurological disorders, and viral and bacterial diseases. As drug resistance is one of the major challenges in antiviral drug discovery, polypharmacology and network pharmacology approaches were employed in the study to identify drugs interacting with multiple targets and drugs such as dihydroergotamine, ergotamine, bisdequalinium chloride, midostaurin, temoporfin, tirilazad, and venetoclax were identified among the multi-targeting drugs. Further, a pathway analysis of the genes related to the multi-targeting drugs was carried which provides insight into the mechanism of drugs and identifying targetable genes and biological pathways involved in SARS-CoV2.
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Affiliation(s)
- Esther Jamir
- Advanced Computation and Data Sciences Division, CSIR–North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Himakshi Sarma
- Advanced Computation and Data Sciences Division, CSIR–North East Institute of Science and Technology, Jorhat, Assam, India
| | - Lipsa Priyadarsinee
- Advanced Computation and Data Sciences Division, CSIR–North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Kikrusenuo Kiewhuo
- Advanced Computation and Data Sciences Division, CSIR–North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Selvaraman Nagamani
- Advanced Computation and Data Sciences Division, CSIR–North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - G. Narahari Sastry
- Advanced Computation and Data Sciences Division, CSIR–North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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7
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Senthilazhagan K, Sakthimani S, Kallanja D, Venkataraman S. SARS-CoV-2: analysis of the effects of mutations in non-structural proteins. Arch Virol 2023; 168:186. [PMID: 37344726 DOI: 10.1007/s00705-023-05818-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/10/2023] [Indexed: 06/23/2023]
Abstract
A worldwide pandemic that started in China in late 2019 was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a single-stranded RNA virus belonging to the family Coronaviridae. Due to its structural variability and mutability, this virus continues to evolve and pose a major health threat around the world. Its characteristics, such as transmissibility, antigenicity, and resistance to drugs and vaccines, are continually altered through mutations. Examining mutational hotspots and their structural repercussions can thus aid in the development of more-effective vaccinations and treatment plans. In this study, we used full genome sequences of SARS-CoV-2 variants to predict structural changes in viral proteins. These sequences were obtained from the Global Initiative on Sharing Avian Influenza Data (GISAID), and a set of significant mutations were identified in each of the non-structural proteins (NSP1-16) and structural proteins, including the envelope, nucleocapsid, membrane, and spike proteins. The mutations were characterized as stabilizing or destabilizing based on their effect on protein dynamics and stability, and their impact on structure and function was evaluated. Among all of the proteins, NSP6 stands out as especially variable. The results of this study augment our understanding of how mutational events influence virus pathogenicity and evolution.
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Affiliation(s)
- Kavya Senthilazhagan
- Department of Biotechnology, Anna University, 600025, Guindy, Chennai, Tamil Nādu, India
| | - Seshagiri Sakthimani
- Department of Biotechnology, Anna University, 600025, Guindy, Chennai, Tamil Nādu, India
| | - Deepthi Kallanja
- Department of Biotechnology, Anna University, 600025, Guindy, Chennai, Tamil Nādu, India
| | - Sangita Venkataraman
- Department of Biotechnology, Anna University, 600025, Guindy, Chennai, Tamil Nādu, India.
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8
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Bhattacharya M, Alshammari A, Alharbi M, Dhama K, Lee SS, Chakraborty C. A novel mutation-proof, next-generation vaccine to fight against upcoming SARS-CoV-2 variants and subvariants, designed through AI enabled approaches and tools, along with the machine learning based immune simulation: A vaccine breakthrough. Int J Biol Macromol 2023; 242:124893. [PMID: 37207746 DOI: 10.1016/j.ijbiomac.2023.124893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/27/2023] [Accepted: 05/12/2023] [Indexed: 05/21/2023]
Abstract
Emerging SARS-CoV-2 variants and subvariants are great concerns for their significant mutations, which are also responsible for vaccine escape. Therefore, the study was undertaken to develop a mutation-proof, next-generation vaccine to protect against all upcoming SARS-CoV-2 variants. We used advanced computational and bioinformatics approaches to develop a multi-epitopic vaccine, especially the AI model for mutation selection and machine learning (ML) strategies for immune simulation. AI-enabled and the top-ranked antigenic selection approaches were used to select nine mutations from 835 RBD mutations. We selected twelve common antigenic B cell and T cell epitopes (CTL and HTL) containing the nine RBD mutations and joined them with the adjuvants, PADRE sequence, and suitable linkers. The constructs' binding affinity was confirmed through docking with TLR4/MD2 complex and showed significant binding free energy (-96.67 kcal mol-1) with positive binding affinity. Similarly, the calculated eigenvalue (2.428517e-05) from the NMA of the complex reveals proper molecular motion and superior residues' flexibility. Immune simulation shows that the candidate can induce a robust immune response. The designed mutation-proof, multi-epitopic vaccine could be a remarkable candidate for upcoming SARS-CoV-2 variants and subvariants. The study method might guide researchers in developing AI-ML and immunoinformatics-based vaccines for infectious disease.
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Affiliation(s)
- Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore 756020, Odisha, India
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si 24252, Gangwon-do, Republic of Korea
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal 700126, India.
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9
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Zabidi NZ, Liew HL, Farouk IA, Puniyamurti A, Yip AJW, Wijesinghe VN, Low ZY, Tang JW, Chow VTK, Lal SK. Evolution of SARS-CoV-2 Variants: Implications on Immune Escape, Vaccination, Therapeutic and Diagnostic Strategies. Viruses 2023; 15:v15040944. [PMID: 37112923 PMCID: PMC10145020 DOI: 10.3390/v15040944] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 is associated with a lower fatality rate than its SARS and MERS counterparts. However, the rapid evolution of SARS-CoV-2 has given rise to multiple variants with varying pathogenicity and transmissibility, such as the Delta and Omicron variants. Individuals with advanced age or underlying comorbidities, including hypertension, diabetes and cardiovascular diseases, are at a higher risk of increased disease severity. Hence, this has resulted in an urgent need for the development of better therapeutic and preventive approaches. This review describes the origin and evolution of human coronaviruses, particularly SARS-CoV-2 and its variants as well as sub-variants. Risk factors that contribute to disease severity and the implications of co-infections are also considered. In addition, various antiviral strategies against COVID-19, including novel and repurposed antiviral drugs targeting viral and host proteins, as well as immunotherapeutic strategies, are discussed. We critically evaluate strategies of current and emerging vaccines against SARS-CoV-2 and their efficacy, including immune evasion by new variants and sub-variants. The impact of SARS-CoV-2 evolution on COVID-19 diagnostic testing is also examined. Collectively, global research and public health authorities, along with all sectors of society, need to better prepare against upcoming variants and future coronavirus outbreaks.
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Affiliation(s)
- Nur Zawanah Zabidi
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Hern Liang Liew
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Isra Ahmad Farouk
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Ashwini Puniyamurti
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Ashley Jia Wen Yip
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | | | - Zheng Yao Low
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Julian W Tang
- Department of Respiratory Sciences, University of Leicester, Leicester LE1 7RH, UK
| | - Vincent T K Chow
- Infectious Diseases Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Sunil K Lal
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
- Tropical Medicine & Biology Platform, Monash University, Subang Jaya 47500, Selangor, Malaysia
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10
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Ahmadi K, Shahbazi B, Zakeri AJ, Gouklani H. Characterization of SARS-CoV-2 omicron variants from Iran and evaluation of the effect of mutations on the spike, nucleocapsid, ORF8, and ORF9b proteins function. J Biomol Struct Dyn 2022; 41:11415-11430. [PMID: 36576175 DOI: 10.1080/07391102.2022.2162131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/18/2022] [Indexed: 12/29/2022]
Abstract
The SARS-CoV-2 'Omicron' strain, with 15 mutations in the receptor binding domain (RBD), was detected in South Africa and rapidly spread worldwide. SARS-CoV-2 ORF9b protein by binding to the TOM70 receptor and ORF8 protein by binding to MHC-I, IF3 receptors inhibit the host's immune response. In this study, genomics variations were evaluated for 96 samples isolated from Iran from March to July 2022 using the Nextclade web server and informatics tools. We identified the mutations occurring in the SARS-CoV-2 proteins. We also evaluated the effect of mutations on spike protein interaction with the ACE2 receptor, ORF9b protein interaction with the TOM70 receptor, and structural stability of ORF8 and nucleocapsid proteins using docking and molecular dynamics. Results indicated that during March and April 2022, the BA.2 strain was dominant in the south of Iran, while during June 2022, the BA.5 strain was dominant. BF.5 strain had the most divergence among SARS-CoV-2 strains reported from south of Iran. The binding affinity of BA.5 and BF.5 strains spike protein to ACE2 receptor is similar, and compared to BA.2 strain, was stronger. The BF.5 ORF9b K40R mutation causes a better binding affinity of the protein to the TOM70 receptor. Also, mutations that occurred in the ORF8 protein led to instability in the dimer formation of this protein and improved immune response for mutations that occurred in BA.2 strain, while this mutation did not occur in BF.5 strain. The mutations that were detected in nucleocapsid protein CTD and NTD domains caused the stability of these domains.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Khadijeh Ahmadi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Behzad Shahbazi
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Abdul-Jabbar Zakeri
- Social Determinants in Health Promotion Research Center, Research Institute for Health, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Hamed Gouklani
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
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Singh P, Sharma K, Shaw D, Bhargava A, Negi SS. Mosaic Recombination Inflicted Various SARS-CoV-2 Lineages to Emerge into Novel Virus Variants: a Review Update. Indian J Clin Biochem 2022; 38:1-8. [PMID: 36569378 PMCID: PMC9759274 DOI: 10.1007/s12291-022-01109-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
Human Coronaviruses (hCoVs) belongs to the enormous and dissimilar family of positive-sense, non-segmented, single-stranded RNA viruses. The RNA viruses are prone to high rates of mutational recombination resulting in emergence of evolutionary variant to alter various features including transmissibility and severity. The evolutionary changes affect the immune escape and reduce effectiveness of diagnostic and therapeutic measures by becoming undetectable by the currently available diagnostics and refractory to therapeutics and vaccines. Whole genome sequencing studies from various countries have adequately reported mosaic recombination between different lineage strain of SARS-CoV-2 whereby RNA dependent RNA polymerase (RdRp) gene reconnects with a homologous RNA strand at diverse position. This all lead to evolutionary emergence of new variant/ lineage as evident with the emergence of XBB in India at the time of writing this review. The continuous periodical genomic surveillance is utmost required for understanding the various lineages involved in recombination to emerge into hybrid variant. This may further help in assessing virus transmission dynamics, virulence and severity factor to help health authorities take appropriate timely action for prevention and control of any future COVID-19 outbreak.
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Affiliation(s)
- Pushpendra Singh
- Department of Microbiology, All India Institute of Medical Sciences, Raipur, Chhattisgarh India
| | - Kuldeep Sharma
- Department of Microbiology, All India Institute of Medical Sciences, Raipur, Chhattisgarh India
| | - Dipika Shaw
- Department of Microbiology, All India Institute of Medical Sciences, Raipur, Chhattisgarh India
| | - Anudita Bhargava
- Department of Microbiology, All India Institute of Medical Sciences, Raipur, Chhattisgarh India
| | - Sanjay Singh Negi
- Department of Microbiology, All India Institute of Medical Sciences, Raipur, Chhattisgarh India
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12
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Molecular Docking and Dynamics Simulation of Several Flavonoids Predict Cyanidin as an Effective Drug Candidate against SARS-CoV-2 Spike Protein. Adv Pharmacol Pharm Sci 2022; 2022:3742318. [DOI: 10.1155/2022/3742318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/13/2022] [Accepted: 10/15/2022] [Indexed: 11/10/2022] Open
Abstract
The in silico method has provided a versatile process of developing lead compounds from a large database in a short duration. Therefore, it is imperative to look for vaccinations and medications that can stop the havoc caused by SARS-CoV-2. The spike protein of SARS-CoV-2 is required for the viral entry into the host cells, hence inhibiting the virus from fusing and infecting the host. This study determined the binding interactions of 36 flavonoids along with two FDA-approved drugs against the spike protein receptor-binding domain of SARS-CoV-2 through molecular docking and molecular dynamics (MD) simulations. In addition, the molecular mechanics generalized Born surface area (MM/GBSA) approach was used to calculate the binding-free energy (BFE). Flavonoids were selected based on their in vitro assays on SARS-CoV and SARS-CoV-2. Our pharmacokinetics study revealed that cyanidin showed good drug-likeness, fulfilled Lipinski’s rule of five, and conferred favorable toxicity parameters. Furthermore, MD simulations showed that cyanidin interacts with spike protein and alters the conformation and binding-free energy suited. Finally, an in vitro assay indicated that about 50% reduction in the binding of hACE2 with S1-RBD in the presence of cyanidin-containing red grapes crude extract was achieved at approximately 1.25 mg/mL. Hence, cyanidin may be a promising adjuvant medication for the SARS-CoV-2 spike protein based on in silico and in vitro research.
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13
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Shukla V, Kaushik A, Sachan B, Singh AK, Kumari R, Kandpal SD, Jauhari S. Disparity in Relation to Covid-19 Preventive Behaviour and Associated Myths among Rural and Urban Residents of Lucknow: A Community Based Study. INDIAN JOURNAL OF COMMUNITY HEALTH 2022. [DOI: 10.47203/ijch.2022.v34i03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Introduction: For curbing Covid-19 disease, adequate knowledge, attitude, and practices of both rural and urban population for Covid-19 disease prevention is required along with busting of the associated myths. Objectives: To assess the Knowledge, Attitude and Practices of urban and rural residents of Lucknow district regarding covid-19 preventive behaviour and associated myths. Methodology: A community-based study was conducted among 420 rural and 421 urban residents of Lucknow. Multistage random sampling was done to select the study subjects. A pre-designed pretested semi-structured questionnaire was used to collect the information regarding the Knowledge, Attitude and Practices of the residents for covid-19 disease causes, prevention, and treatment. Further, KAP scoring was done to compare the two groups. Results: The mean age of the rural and urban residents was 31.48 ± 12.05 and 30.93 ± 11.96 years respectively. Only 40.4 % urban and 25.5 % rural people had correct knowledge about social distancing (p<0.0001). Knowledge regarding quarantine for covid-19 disease prevention was less among the urban residents (64.6%) as compared to rural (70.5%) (p=0.035). More than one-third (37.6%) of the rural resident believed in the myth that alcohol can prevent the covid-19 disease (p=0.003). 68.8 and 70.5 percent rural and urban residents had positive attitude towards the Indian government’ efforts in curbing the disease. Majority of the urban (90%) and rural (87.6%) residents wore mask when they went out. Only one-fourth of the urban (24.7%) and rural (22.9%) had correct practices for the duration of hand washing. Conclusion: The knowledge was more among the urban people, attitude and practices were almost similar among both the rural and urban residents while myths were more observed among the rural residents.
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Rana R, Kant R, Huirem RS, Bohra D, Ganguly NK. Omicron variant: Current insights and future directions. Microbiol Res 2022; 265:127204. [PMID: 36152612 PMCID: PMC9482093 DOI: 10.1016/j.micres.2022.127204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/22/2022] [Accepted: 09/13/2022] [Indexed: 01/08/2023]
Abstract
The global COVID-19 outbreak has returned with the identification of the SARS-CoV-2 Omicron variant (B.1.1.529) after appearing to be persistently spreading for the more than past two years. In comparison to prior SARS-CoV-2 variants, this new variant revealed a significant amount of mutation. This novel variety may have a greater rate of transmissibility which might impede the effectiveness of current diagnostic equipment as well as vaccination efficacy and also impede immunotherapies (Antibody / monoclonal antibody based). WHO designated B.1.1.529 as a variant of concern on November 26, 2021, identified as Omicron. The Omicron variant transmission method and severity, on the other hand, are well defined. The global spread of Omicron, which has now seized many nations, has resulted in numerous speculations regarding its origin and degree of infectivity. The following sections will go over its potential for transmission, omicron structure, and impact on COVID-19 vaccines, how it is different from delta variant and diagnostics.
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Affiliation(s)
- Rashmi Rana
- Department of Research, Sir Ganga Ram Hospital, Delhi, India.
| | - Ravi Kant
- Department of Research, Sir Ganga Ram Hospital, Delhi, India
| | | | - Deepika Bohra
- Department of Research, Sir Ganga Ram Hospital, Delhi, India
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15
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Abstract
BACKGROUND In the context of the novel coronavirus disease 2019 (COVID-19) pandemic, people have had to stay at home more and make fewer trips to the hospital. Furthermore, hospitals give priority to the treatment of COVID-19 patients. These factors are not conducive to the treatment of diabetic foot, and even increase the risk of amputation. Therefore, how to better treat patients with diabetic foot during the COVID-19 epidemic, prevent further aggravation of the disease and reduce the risk of amputation in patients with diabetic foot has become an urgent problem for doctors around the world. METHODS The researchers searched PubMed, the Cochrane Library, and the Embase database. The retrieval time was set from the database establishment to October 2021. All studies on treatment of diabetic foot in the COVID-19 pandemic were included in our study. RESULTS A total of 6 studies were included in this study. In the 6 protocols for treating patients with diabetic foot, the researchers classified patients according to the condition of their diabetic foot. Diabetic foot patients with general conditions received treatment at home, and doctors can guide the wound dressing change and medication treatment of patients through telemedicine. Patients with severe conditions of diabetic foot were admitted to hospital for treatment. Patients were screened for COVID-19 before hospitalization, those infected or suspected of COVID-19 were treated in isolation, and those not infected with COVID-19 were treated in a general ward. CONCLUSION Through this systematic review, we proposed a new protocol for the treatment of patients with diabetic foot in the context of the COVID-19 pandemic. It provided reference for the treatment of diabetic foot in the context of COVID-19 epidemic. However, the global applicability of the treatment protocol for diabetic foot in the context of COVID-19 epidemic proposed in this study needs further clinical testing.
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Affiliation(s)
- Jingui Yan
- Department of Surgery, Huji Hospital, Binzhou, China
| | - Yiqing Xiao
- West Coast New District Community Health Service Center, Qingdao, China
| | - Rui Cao
- Research Center, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yipeng Su
- Department of Plastic Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Dan Wu
- Department of Burn and Plastic Surgery, Zibo Central Hospital, Zibo, China
| | - Yanjin Wang
- Department of Plastic Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
- * Correspondence: Yanjin Wang, Department of Plastic Surgery, Affiliated Hospital of Qingdao University, No. 16 Jiangsu Road, Qingdao 266000, Shandong Province, China (e-mail: , )
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16
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The global response: How cities and provinces around the globe tackled Covid-19 outbreaks in 2021. THE LANCET REGIONAL HEALTH. SOUTHEAST ASIA 2022; 4:100031. [PMID: 35775040 PMCID: PMC9217141 DOI: 10.1016/j.lansea.2022.100031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Background Tackling the spread of COVID-19 remains a crucial part of ending the pandemic. Its highly contagious nature and constant evolution coupled with a relative lack of immunity make the virus difficult to control. For this, various strategies have been proposed and adopted including limiting contact, social isolation, vaccination, contact tracing, etc. However, given the heterogeneity in the enforcement of these strategies and constant fluctuations in the strictness levels of these strategies, it becomes challenging to assess the true impact of these strategies in controlling the spread of COVID-19. Methods In the present study, we evaluated various transmission control measures that were imposed in 10 global urban cities and provinces in 2021- Bangkok, Gauteng, Ho Chi Minh City, Jakarta, London, Manila City, New Delhi, New York City, Singapore, and Tokyo. Findings Based on our analysis, we herein propose the population-level Swiss cheese model for the failures and pitfalls in various strategies that each of these cities and provinces had. Furthermore, whilst all the evaluated cities and provinces took a different personalized approach to managing the pandemic, what remained common was dynamic enforcement and monitoring of breaches of each barrier of protection. The measures taken to reinforce the barriers were adjusted continuously based on the evolving epidemiological situation. Interpretation How an individual city or province handled the pandemic profoundly affected and determined how the entire country handled the pandemic since the chain of transmission needs to be broken at the very grassroot level to achieve nationwide control. Funding The present study did not receive any external funding.
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17
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Confirming Multiplex RT-qPCR Use in COVID-19 with Next-Generation Sequencing: Strategies for Epidemiological Advantage. Glob Health Epidemiol Genom 2022; 2022:2270965. [PMID: 35950011 PMCID: PMC9339135 DOI: 10.1155/2022/2270965] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/13/2022] [Indexed: 12/15/2022] Open
Abstract
Rapid identification and tracking of emerging SARS-CoV-2 variants are critical for understanding the transmission dynamics and developing strategies for interrupting the transmission chain. Next-Generation Sequencing (NGS) is an exceptional tool for whole-genome analysis and deciphering new mutations. The technique has been instrumental in identifying the variants of concern (VOC) and tracking this pandemic. However, NGS is complex and expensive for large-scale adoption, and epidemiological monitoring with NGS alone could be unattainable in limited-resource settings. In this study, we explored the application of RT-qPCR-based detection of the variant identified by NGS. We analyzed a total of 78 deidentified samples that screened positive for SARS-CoV-2 from two timeframes, August 2020 and July 2021. All 78 samples were classified into WHO lineages by whole-genome sequencing and then compared with two commercially available RT-qPCR assays for spike protein mutation(s). The data showed good concordance between RT-qPCR and NGS analysis for specific SARS-CoV-2 lineages and characteristic mutations. RT-qPCR assays are quick and cost-effective and thus can be implemented in synergy with NGS for screening NGS-identified mutations of SARS-CoV-2 for clinical and epidemiological interest. Strategic use of NGS and RT-qPCR can offer several COVID-19 epidemiological advantages.
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18
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Ashoor D, Marzouq M, Trabelsi K, Chlif S, Abotalib N, Khalaf NB, Ramadan AR, Fathallah MD. How concerning is a SARS-CoV-2 variant of concern? Computational predictions and the variants labeling system. Front Cell Infect Microbiol 2022; 12:868205. [PMID: 36034694 PMCID: PMC9399656 DOI: 10.3389/fcimb.2022.868205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 07/04/2022] [Indexed: 11/24/2022] Open
Abstract
In this study, we evaluated the use of a predictive computational approach for SARS-CoV-2 genetic variations analysis in improving the current variant labeling system. First, we reviewed the basis of the system developed by the World Health Organization (WHO) for the labeling of SARS-CoV-2 genetic variants and the derivative adapted by the United States Centers for Disease Control and Prevention (CDC). Both labeling systems are based on the virus’ major attributes. However, we found that the labeling criteria of the SARS-CoV-2 variants derived from these attributes are not accurately defined and are used differently by the two agencies. Consequently, discrepancies exist between the labels given by WHO and the CDC to the same variants. Our observations suggest that giving the variant of concern (VOC) label to a new variant is premature and might not be appropriate. Therefore, we used a comparative computational approach to predict the effects of the mutations on the virus structure and functions of five VOCs. By linking these data to the criteria used by WHO/CDC for variant labeling, we ascertained that a predictive computational comparative approach of the genetic variations is a good way for rapid and more accurate labeling of SARS-CoV-2 variants. We propose to label all emergent variants, variant under monitoring or variant being monitored (VUM/VBM), and to carry out computational predictive studies with thorough comparison to existing variants, upon which more appropriate and informative labels can be attributed. Furthermore, harmonization of the variant labeling system would be globally beneficial to communicate about and fight the COVID-19 pandemic.
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Affiliation(s)
- Dana Ashoor
- Department of Life Sciences, Health Biotechnology Program - King Fahad Chair for Health Biotechnology, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Maryam Marzouq
- Department of Life Sciences, Health Biotechnology Program - King Fahad Chair for Health Biotechnology, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Khaled Trabelsi
- Department of Life Sciences, Health Biotechnology Program - King Fahad Chair for Health Biotechnology, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Sadok Chlif
- Department of Family and Community Medicine, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
| | - Nasser Abotalib
- Department of Life Sciences, Health Biotechnology Program - King Fahad Chair for Health Biotechnology, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Noureddine Ben Khalaf
- Department of Life Sciences, Health Biotechnology Program - King Fahad Chair for Health Biotechnology, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Ahmed R. Ramadan
- Department of Life Sciences, Health Biotechnology Program - King Fahad Chair for Health Biotechnology, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - M-Dahmani Fathallah
- Department of Life Sciences, Health Biotechnology Program - King Fahad Chair for Health Biotechnology, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
- *Correspondence: M-Dahmani Fathallah,
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19
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Appraisal of SARS-CoV-2 mutations and their impact on vaccination efficacy: an overview. J Diabetes Metab Disord 2022; 21:1763-1783. [PMID: 35891981 PMCID: PMC9305048 DOI: 10.1007/s40200-022-01002-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/07/2022] [Indexed: 12/02/2022]
Abstract
With the unexpected emergence of the novel 2019 Wuhan coronavirus, the world was faced with a sudden uproar that quickly shifted into a serious life-threatening pandemic. Affecting the lives of the global population and leaving drastic damage in various sections and systems, several measures have been constantly taken to tackle down this crisis. For instance, numerous vaccines have been developed in the past two years, some of which have been granted emergency use, thus providing sufficient immunity to the vaccinated individuals. However, the appearance of newly emerged SARS-CoV-2 variants with accelerated transmission and fatality has led the world towards another pandemic. Having undergone various mutations in genomic and/or amino acid profiles, some of the emerged variants of concern (VOCs) including Alpha, Beta, Gamma, and Delta have displayed immune evasion and pathogenicity even in the vaccinated population, hence raising concerns regarding the efficacy of current vaccines against new VOCs of COVID-19. Therefore, genomic investigations of SARS-CoV-2 mutations are expected to provide valuable insight into the evolution of SARS-CoV-2, while also determining the impact of different mutations on infection severity. This study was constructed with the aim of shining light on recent advances regarding mutations in major COVID-19 VOCs, as well as vaccination efficacy against those VOCs.
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20
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Contrasting Epidemiology and Population Genetics of COVID-19 Infections Defined by Multilocus Genotypes in SARS-CoV-2 Genomes Sampled Globally. Viruses 2022; 14:v14071434. [PMID: 35891414 PMCID: PMC9316073 DOI: 10.3390/v14071434] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 12/28/2022] Open
Abstract
Since its emergence in 2019, SARS-CoV-2 has spread and evolved globally, with newly emerged variants of concern (VOCs) accounting for more than 500 million COVID-19 cases and 6 million deaths. Continuous surveillance utilizing simple genetic tools is needed to measure the viral epidemiological diversity, risk of infection, and distribution among different demographics in different geographical regions. To help address this need, we developed a proof-of-concept multilocus genotyping tool and demonstrated its utility to monitor viral populations sampled in 2020 and 2021 across six continents. We sampled globally 22,164 SARS-CoV-2 genomes from GISAID (inclusion criteria: available clinical and demographic data). They comprised two study populations, “2020 genomes” (N = 5959) sampled from December 2019 to September 2020 and “2021 genomes” (N = 16,205) sampled from 15 January to 15 March 2021. All genomes were aligned to the SARS-CoV-2 reference genome and amino acid polymorphisms were called with quality filtering. Thereafter, 74 codons (loci) in 14 genes including orf1ab polygene (N = 9), orf3a, orf8, nucleocapsid (N), matrix (M), and spike (S) met the 0.01 minimum allele frequency criteria and were selected to construct multilocus genotypes (MLGs) for the genomes. At these loci, 137 mutant/variant amino acids (alleles) were detected with eight VOC-defining variant alleles, including N KR203&204, orf1ab (I265, F3606, and L4715), orf3a H57, orf8 S84, and S G614, being predominant globally with > 35% prevalence. Their persistence and selection were associated with peaks in the viral transmission and COVID-19 incidence between 2020 and 2021. Epidemiologically, older patients (≥20 years) compared to younger patients (<20 years) had a higher risk of being infected with these variants, but this association was dependent on the continent of origin. In the global population, the discriminant analysis of principal components (DAPC) showed contrasting patterns of genetic clustering with three (Africa, Asia, and North America) and two (North and South America) continental clusters being observed for the 2020 and 2021 global populations, respectively. Within each continent, the MLG repertoires (range 40−199) sampled in 2020 and 2021 were genetically differentiated, with ≤4 MLGs per repertoire accounting for the majority of genomes sampled. These data suggested that the majority of SARS-CoV-2 infections in 2020 and 2021 were caused by genetically distinct variants that likely adapted to local populations. Indeed, four GISAID clade-defined VOCs - GRY (Alpha), GH (Beta), GR (Gamma), and G/GK (Delta variant) were differentiated by their MLG signatures, demonstrating the versatility of the MLG tool for variant identification. Results from this proof-of-concept multilocus genotyping demonstrates its utility for SARS-CoV-2 genomic surveillance and for monitoring its spatiotemporal epidemiology and evolution, particularly in response to control interventions including COVID-19 vaccines and chemotherapies.
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21
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Kumar DGS, Vadgaonkar D, Purunaik DS, Shelatkar R, Vaidya VG, Ganu DG, Vadgaonkar DA, Joshi S. Efficacy and Safety of Aspirin, Promethazine, and Micronutrients for Rapid Clinical Recovery in Mild to Moderate COVID-19 Patients: A Randomized Controlled Clinical Trial. Cureus 2022; 14:e25467. [PMID: 35783877 PMCID: PMC9240808 DOI: 10.7759/cureus.25467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2022] [Indexed: 11/21/2022] Open
Abstract
Introduction In the present study, the combination of two tablets, one with Aspirin and Promethazine and the other with vitamin D3, C, and B3 along with zinc and selenium supplementation was proposed as an intervention (APMV2020). The ingredients in the formulation represent a precise, tailored therapy for the symptoms of COVID-19, combined with natural constituents to help the body itself build immunity to recover from infection. The present study was conducted to clinically validate the safety and efficacy of the APMV2020 tablets. Trial design The present trial is a randomized, multicentric, controlled clinical trial involving 260 mild to moderate COVID-19 patients. The treatment duration was of 10 days. Methodology The subjects were randomized to receive either the control intervention (clinical management protocol for COVID-19 advocated by the Indian Council of Medical Research (ICMR) or the test intervention (treatment with APMV2020 tablets along with the standard control treatment. The assessment days were baseline, days five and 10. Results APMV2020 significantly (<0.05) improved symptoms of COVID-19 like cough, myalgia, headache, and anosmia as compared to the control group. APMV2020 treatment also reduced inflammatory markers like lactate dehydrogenase (LDH), ferritin, and C-reactive protein (CRP). Conclusion APMV2020 can prove as a good candidate to be integrated into the COVID-19 management protocol. As it can offer speedy clinical recovery to reduce the burden on healthcare infrastructure, second, the combination shows significant anti-inflammatory potential to improve prognosis, and lastly, the immunomodulatory properties offer long-term protection that can help in combating long COVID symptoms and complications.
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22
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Jamison DA, Anand Narayanan S, Trovão NS, Guarnieri JW, Topper MJ, Moraes-Vieira PM, Zaksas V, Singh KK, Wurtele ES, Beheshti A. A comprehensive SARS-CoV-2 and COVID-19 review, Part 1: Intracellular overdrive for SARS-CoV-2 infection. Eur J Hum Genet 2022; 30:889-898. [PMID: 35577935 PMCID: PMC9108708 DOI: 10.1038/s41431-022-01108-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/20/2022] [Accepted: 04/12/2022] [Indexed: 12/15/2022] Open
Abstract
COVID-19, the disease caused by SARS-CoV-2, has claimed approximately 5 million lives and 257 million cases reported globally. This virus and disease have significantly affected people worldwide, whether directly and/or indirectly, with a virulent pathogen that continues to evolve as we race to learn how to prevent, control, or cure COVID-19. The focus of this review is on the SARS-CoV-2 virus' mechanism of infection and its proclivity at adapting and restructuring the intracellular environment to support viral replication. We highlight current knowledge and how scientific communities with expertize in viral, cellular, and clinical biology have contributed to increase our understanding of SARS-CoV-2, and how these findings may help explain the widely varied clinical observations of COVID-19 patients.
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Affiliation(s)
| | - S Anand Narayanan
- COVID-19 International Research Team, Medford, MA, USA. .,Department of Nutrition & Integrative Physiology, Florida State University, Tallahassee, FL, USA.
| | - Nídia S Trovão
- COVID-19 International Research Team, Medford, MA, USA.,Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Joseph W Guarnieri
- COVID-19 International Research Team, Medford, MA, USA.,Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michael J Topper
- COVID-19 International Research Team, Medford, MA, USA.,Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Pedro M Moraes-Vieira
- COVID-19 International Research Team, Medford, MA, USA.,Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, SP, Brazil.,Obesity and Comorbidities research Center (OCRC), University of Campinas, Campinas, SP, Brazil.,Experimental Medicine Research Cluster, University of Campinas, Campinas, Brazil
| | - Viktorija Zaksas
- COVID-19 International Research Team, Medford, MA, USA.,Center for Translational Data Science, University of Chicago, Chicago, IL, USA
| | - Keshav K Singh
- COVID-19 International Research Team, Medford, MA, USA.,Department of Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Eve Syrkin Wurtele
- COVID-19 International Research Team, Medford, MA, USA.,Center for Metabolic Biology, Bioinformatics and Computational Biology, and Genetics Development, and Cell Biology, Iowa State University, Ames, IA, USA
| | - Afshin Beheshti
- COVID-19 International Research Team, Medford, MA, USA. .,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA.
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Degarege A, Naveed Z, Kabayundo J, Brett-Major D. Heterogeneity and Risk of Bias in Studies Examining Risk Factors for Severe Illness and Death in COVID-19: A Systematic Review and Meta-Analysis. Pathogens 2022; 11:563. [PMID: 35631084 PMCID: PMC9147100 DOI: 10.3390/pathogens11050563] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/02/2022] [Accepted: 05/05/2022] [Indexed: 02/07/2023] Open
Abstract
This systematic review and meta-analysis synthesized the evidence on the impacts of demographics and comorbidities on the clinical outcomes of COVID-19, as well as the sources of the heterogeneity and publication bias of the relevant studies. Two authors independently searched the literature from PubMed, Embase, Cochrane library, and CINAHL on 18 May 2021; removed duplicates; screened the titles, abstracts, and full texts by using criteria; and extracted data from the eligible articles. The variations among the studies were examined by using Cochrane, Q.; I2, and meta-regression. Out of 11,975 articles that were obtained from the databases and screened, 559 studies were abstracted, and then, where appropriate, were analyzed by meta-analysis (n = 542). COVID-19-related severe illness, admission to the ICU, and death were significantly correlated with comorbidities, male sex, and an age older than 60 or 65 years, although high heterogeneity was present in the pooled estimates. The study design, the study country, the sample size, and the year of publication contributed to this. There was publication bias among the studies that compared the odds of COVID-19-related deaths, severe illness, and admission to the ICU on the basis of the comorbidity status. While an older age and chronic diseases were shown to increase the risk of developing severe illness, admission to the ICU, and death among the COVID-19 patients in our analysis, a marked heterogeneity was present when linking the specific risks with the outcomes.
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Affiliation(s)
- Abraham Degarege
- Department of Epidemiology, College of Public Health, University of Nebraska Medical Center, Omaha, NE 68198, USA; (Z.N.); (J.K.); (D.B.-M.)
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Probing the Immune System Dynamics of the COVID-19 Disease for Vaccine Designing and Drug Repurposing Using Bioinformatics Tools. IMMUNO 2022. [DOI: 10.3390/immuno2020022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The pathogenesis of COVID-19 is complicated by immune dysfunction. The impact of immune-based therapy in COVID-19 patients has been well documented, with some notable studies on the use of anti-cytokine medicines. However, the complexity of disease phenotypes, patient heterogeneity and the varying quality of evidence from immunotherapy studies provide problems in clinical decision-making. This review seeks to aid therapeutic decision-making by giving an overview of the immunological responses against COVID-19 disease that may contribute to the severity of the disease. We have extensively discussed theranostic methods for COVID-19 detection. With advancements in technology, bioinformatics has taken studies to a higher level. The paper also discusses the application of bioinformatics and machine learning tools for the diagnosis, vaccine design and drug repurposing against SARS-CoV-2.
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Dumache R, Enache A, Macasoi I, Dehelean CA, Dumitrascu V, Mihailescu A, Popescu R, Vlad D, Vlad CS, Muresan C. SARS-CoV-2: An Overview of the Genetic Profile and Vaccine Effectiveness of the Five Variants of Concern. Pathogens 2022; 11:pathogens11050516. [PMID: 35631037 PMCID: PMC9144800 DOI: 10.3390/pathogens11050516] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 12/13/2022] Open
Abstract
With the onset of the COVID-19 pandemic, enormous efforts have been made to understand the genus SARS-CoV-2. Due to the high rate of global transmission, mutations in the viral genome were inevitable. A full understanding of the viral genome and its possible changes represents one of the crucial aspects of pandemic management. Structural protein S plays an important role in the pathogenicity of SARS-CoV-2, mutations occurring at this level leading to viral forms with increased affinity for ACE2 receptors, higher transmissibility and infectivity, resistance to neutralizing antibodies and immune escape, increasing the risk of infection and disease severity. Thus, five variants of concern are currently being discussed, Alpha, Beta, Gamma, Delta and Omicron. In the present review, a comprehensive summary of the following critical aspects regarding SARS-CoV-2 has been made: (i) the genomic characteristics of SARS-CoV-2; (ii) the pathological mechanism of transmission, penetration into the cell and action on specific receptors; (iii) mutations in the SARS-CoV-2 genome; and (iv) possible implications of mutations in diagnosis, treatment, and vaccination.
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Affiliation(s)
- Raluca Dumache
- Ethics and Human Identification Research Center, Department of Neurosciences, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (R.D.); (A.E.); (A.M.); (C.M.)
| | - Alexandra Enache
- Ethics and Human Identification Research Center, Department of Neurosciences, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (R.D.); (A.E.); (A.M.); (C.M.)
| | - Ioana Macasoi
- Departament of Toxicology and Drug Industry, Faculty of Pharmacy, “Victor Babeş” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timişoara, Romania
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
- Correspondence: (I.M.); (C.A.D.)
| | - Cristina Adriana Dehelean
- Departament of Toxicology and Drug Industry, Faculty of Pharmacy, “Victor Babeş” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timişoara, Romania
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
- Correspondence: (I.M.); (C.A.D.)
| | - Victor Dumitrascu
- Department of Pharmacology and Biochemistry, Discipline of Pharmacology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (V.D.); (D.V.); (C.S.V.)
| | - Alexandra Mihailescu
- Ethics and Human Identification Research Center, Department of Neurosciences, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (R.D.); (A.E.); (A.M.); (C.M.)
- Genetics, Genomic Medicine Research Center, Department of Microscopic Morphology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania
| | - Roxana Popescu
- Department of Microscopic Morphology, Discipline of Molecular and Cell Biology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania;
| | - Daliborca Vlad
- Department of Pharmacology and Biochemistry, Discipline of Pharmacology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (V.D.); (D.V.); (C.S.V.)
| | - Cristian Sebastian Vlad
- Department of Pharmacology and Biochemistry, Discipline of Pharmacology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (V.D.); (D.V.); (C.S.V.)
| | - Camelia Muresan
- Ethics and Human Identification Research Center, Department of Neurosciences, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (R.D.); (A.E.); (A.M.); (C.M.)
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de Souza AS, de Freitas Amorim VM, Guardia GDA, dos Santos FF, Ulrich H, Galante PAF, de Souza RF, Guzzo CR. Severe Acute Respiratory Syndrome Coronavirus 2 Variants of Concern: A Perspective for Emerging More Transmissible and Vaccine-Resistant Strains. Viruses 2022; 14:827. [PMID: 35458557 PMCID: PMC9029021 DOI: 10.3390/v14040827] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/29/2022] [Accepted: 04/01/2022] [Indexed: 02/06/2023] Open
Abstract
Novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) are constantly threatening global public health. With no end date, the pandemic persists with the emergence of novel variants that threaten the effectiveness of diagnostic tests and vaccines. Mutations in the Spike surface protein of the virus are regularly observed in the new variants, potentializing the emergence of novel viruses with different tropism from the current ones, which may change the severity and symptoms of the disease. Growing evidence has shown that mutations are being selected in favor of variants that are more capable of evading the action of neutralizing antibodies. In this context, the most important factor guiding the evolution of SARS-CoV-2 is its interaction with the host's immune system. Thus, as current vaccines cannot block the transmission of the virus, measures complementary to vaccination, such as the use of masks, hand hygiene, and keeping environments ventilated remain essential to delay the emergence of new variants. Importantly, in addition to the involvement of the immune system in the evolution of the virus, we highlight several chemical parameters that influence the molecular interactions between viruses and host cells during invasion and are also critical tools making novel variants more transmissible. In this review, we dissect the impacts of the Spike mutations on biological parameters such as (1) the increase in Spike binding affinity to hACE2; (2) bound time for the receptor to be cleaved by the proteases; (3) how mutations associate with the increase in RBD up-conformation state in the Spike ectodomain; (4) expansion of uncleaved Spike protein in the virion particles; (5) increment in Spike concentration per virion particles; and (6) evasion of the immune system. These factors play key roles in the fast spreading of SARS-CoV-2 variants of concern, including the Omicron.
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Affiliation(s)
- Anacleto Silva de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
| | - Vitor Martins de Freitas Amorim
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
| | - Gabriela D. A. Guardia
- Centro de Oncologia Molecular, Hospital Sírio Libanes, São Paulo 01308-060, Brazil; (G.D.A.G.); (F.F.d.S.); (P.A.F.G.)
| | - Filipe F. dos Santos
- Centro de Oncologia Molecular, Hospital Sírio Libanes, São Paulo 01308-060, Brazil; (G.D.A.G.); (F.F.d.S.); (P.A.F.G.)
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil;
| | - Henning Ulrich
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil;
| | - Pedro A. F. Galante
- Centro de Oncologia Molecular, Hospital Sírio Libanes, São Paulo 01308-060, Brazil; (G.D.A.G.); (F.F.d.S.); (P.A.F.G.)
| | - Robson Francisco de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
| | - Cristiane Rodrigues Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
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Tastan Bishop Ö, Mutemi Musyoka T, Barozi V. Allostery and missense mutations as intermittently linked promising aspects of modern computational drug discovery. J Mol Biol 2022; 434:167610. [DOI: 10.1016/j.jmb.2022.167610] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 12/15/2022]
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Chakraborty C, Sharma AR, Bhattacharya M, Lee SS. A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. Front Immunol 2022; 13:801522. [PMID: 35222380 PMCID: PMC8863680 DOI: 10.3389/fimmu.2022.801522] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/05/2022] [Indexed: 01/08/2023] Open
Abstract
The infective SARS-CoV-2 is more prone to immune escape. Presently, the significant variants of SARS-CoV-2 are emerging in due course of time with substantial mutations, having the immune escape property. Simultaneously, the vaccination drive against this virus is in progress worldwide. However, vaccine evasion has been noted by some of the newly emerging variants. Our review provides an overview of the emerging variants' immune escape and vaccine escape ability. We have illustrated a broad view related to viral evolution, variants, and immune escape ability. Subsequently, different immune escape approaches of SARS-CoV-2 have been discussed. Different innate immune escape strategies adopted by the SARS-CoV-2 has been discussed like, IFN-I production dysregulation, cytokines related immune escape, immune escape associated with dendritic cell function and macrophages, natural killer cells and neutrophils related immune escape, PRRs associated immune evasion, and NLRP3 inflammasome associated immune evasion. Simultaneously we have discussed the significant mutations related to emerging variants and immune escape, such as mutations in the RBD region (N439K, L452R, E484K, N501Y, K444R) and other parts (D614G, P681R) of the S-glycoprotein. Mutations in other locations such as NSP1, NSP3, NSP6, ORF3, and ORF8 have also been discussed. Finally, we have illustrated the emerging variants' partial vaccine (BioNTech/Pfizer mRNA/Oxford-AstraZeneca/BBIBP-CorV/ZF2001/Moderna mRNA/Johnson & Johnson vaccine) escape ability. This review will help gain in-depth knowledge related to immune escape, antibody escape, and partial vaccine escape ability of the virus and assist in controlling the current pandemic and prepare for the next.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging and Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, South Korea
| | | | - Sang-Soo Lee
- Institute for Skeletal Aging and Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, South Korea
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29
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Epistatic models predict mutable sites in SARS-CoV-2 proteins and epitopes. Proc Natl Acad Sci U S A 2022; 119:2113118119. [PMID: 35022216 PMCID: PMC8795541 DOI: 10.1073/pnas.2113118119] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2021] [Indexed: 12/21/2022] Open
Abstract
During the COVID pandemic, new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants emerge and spread, some being of major concern due to their increased infectivity or capacity to reduce vaccine efficiency. Anticipating mutations, which might give rise to new variants, would be of great interest. We construct sequence models predicting how mutable SARS-CoV-2 positions are, using a single SARS-CoV-2 sequence and databases of other coronaviruses. Predictions are tested against available mutagenesis data and the observed variability of SARS-CoV-2 proteins. Interestingly, predictions agree increasingly with observations, as more SARS-CoV-2 sequences become available. Combining predictions with immunological data, we find an overrepresentation of mutations in current variants of concern. The approach may become relevant for potential outbreaks of future viral diseases. The emergence of new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major concern given their potential impact on the transmissibility and pathogenicity of the virus as well as the efficacy of therapeutic interventions. Here, we predict the mutability of all positions in SARS-CoV-2 protein domains to forecast the appearance of unseen variants. Using sequence data from other coronaviruses, preexisting to SARS-CoV-2, we build statistical models that not only capture amino acid conservation but also more complex patterns resulting from epistasis. We show that these models are notably superior to conservation profiles in estimating the already observable SARS-CoV-2 variability. In the receptor binding domain of the spike protein, we observe that the predicted mutability correlates well with experimental measures of protein stability and that both are reliable mutability predictors (receiver operating characteristic areas under the curve ∼0.8). Most interestingly, we observe an increasing agreement between our model and the observed variability as more data become available over time, proving the anticipatory capacity of our model. When combined with data concerning the immune response, our approach identifies positions where current variants of concern are highly overrepresented. These results could assist studies on viral evolution and future viral outbreaks and, in particular, guide the exploration and anticipation of potentially harmful future SARS-CoV-2 variants.
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Carpenter RE, Tamrakar VK, Almas S, Brown E, Sharma R. COVIDSeq as Laboratory Developed Test (LDT) for Diagnosis of SARS-CoV-2 Variants of Concern (VOC). ARCHIVES OF CLINICAL AND BIOMEDICAL RESEARCH 2022; 6:954-970. [PMID: 36588916 PMCID: PMC9802674 DOI: 10.26502/acbr.50170309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Rapid classification and detection of SARS-CoV-2 variants have been critical in comprehending the virus's transmission dynamics. Clinical manifestation of the infection is influenced by comorbidities such as age, immune status, diabetes, and the infecting variant. Thus, clinical management may differ for new variants. For example, some monoclonal antibody treatments are variant-specific. Yet, a U.S. Food and Drug Administration (FDA)-approved test for detecting the SARS-CoV-2 variant is unavailable. A laboratory-developed test (LDT) remains a viable option for reporting the infecting variant for clinical intervention or epidemiological purposes. Accordingly, we have validated the Illumina COVIDSeq assay as an LDT according to the guidelines prescribed by the College of American Pathologists (CAP) and Clinical Laboratory Improvement Amendments (CLIA). The limit of detection (LOD) of this test is Ct<30 (~15 viral copies) and >200X genomic coverage, and the test is 100% specific in the detection of existing variants. The test demonstrated 100% precision in inter-day, intra-day, and intra-laboratory reproducibility studies. It is also 100% accurate, defined by reference strain testing and split sample testing with other CLIA laboratories. Advanta Genetics LDT COVIDSeq has been reviewed by CAP inspectors and is under review by FDA for Emergency Use Authorization.
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Affiliation(s)
- Rob E Carpenter
- Advanta Genetics, 10935 CR 159, Tyler, Texas 75703, USA
- University of Texas at Tyler, 3900 University Boulevard, Tyler, Texas 75799, USA
- Scienetix, 10935 CR 159, Tyler, Texas 75703, USA
| | - Vaibhav K Tamrakar
- ICMR-National Institute of Research in Tribal Health, Jabalpur, MP 482003, INDIA
- RetroBioTech LLC, 838 Dalmalley Ln, Coppell, TX 75019, USA
| | - Sadia Almas
- Advanta Genetics, 10935 CR 159, Tyler, Texas 75703, USA
| | - Emily Brown
- Advanta Genetics, 10935 CR 159, Tyler, Texas 75703, USA
| | - Rahul Sharma
- Advanta Genetics, 10935 CR 159, Tyler, Texas 75703, USA
- RetroBioTech LLC, 838 Dalmalley Ln, Coppell, TX 75019, USA
- Scienetix, 10935 CR 159, Tyler, Texas 75703, USA
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Mohamed NM, Eltelbany RFA. Synthetic Coumarin Derivatives as SARS‐CoV‐2 Major Protease Inhibitors: Design, Synthesis, Bioevaluation and Molecular Docking. ChemistrySelect 2021. [DOI: 10.1002/slct.202103658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Nada M. Mohamed
- Pharmaceutical Chemistry Department Faculty of Pharmacy Modern University for Technology and Information (MTI) Cairo 11585 Egypt
| | - Rania F. A. Eltelbany
- Biochemistry Department Faculty of Pharmacy Modern University for Technology and Information (MTI) Cairo 11585 Egypt
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Moghaddar M, Radman R, Macreadie I. Severity, Pathogenicity and Transmissibility of Delta and Lambda Variants of SARS-CoV-2, Toxicity of Spike Protein and Possibilities for Future Prevention of COVID-19. Microorganisms 2021; 9:2167. [PMID: 34683488 PMCID: PMC8540532 DOI: 10.3390/microorganisms9102167] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/13/2021] [Accepted: 10/13/2021] [Indexed: 12/16/2022] Open
Abstract
The World Health Organization reports that SARS-CoV-2 has infected over 220 million people and claimed over 4.7 million lives globally. While there are new effective vaccines, the differences in behavior of variants are causing challenges in vaccine development or treatment. Here, we discuss Delta, a variant of concern, and Lambda, a variant of interest. They demonstrate high infectivity and are less responsive to the immune response in vaccinated individuals. In this review, we briefly summarize the reason for infectivity and the severity of the novel variants. Delta and Lambda variants exhibit more changes in NSPs proteins and the S protein, compared to the original Wuhan strain. Lambda also has numerous amino acid substitutions in NSPs and S proteins, plus a deletion in the NTD of S protein, leading to partial escape from neutralizing antibodies (NAbs) in vaccinated individuals. We discuss the role of furin protease and the ACE2 receptor in virus infection, hotspot mutations in the S protein, the toxicity of the S protein and the increased pathogenicity of Delta and Lambda variants. We discuss future therapeutic strategies, including those based on high stability of epitopes, conservation of the N protein and the novel intracellular antibody receptor, tripartite-motif protein 21 (TRIM21) recognized by antibodies against the N protein.
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Affiliation(s)
- Mehrnoosh Moghaddar
- School of Science, RMIT University, Bundoora, VIC 3083, Australia; (M.M.); (R.R.)
| | - Ramtin Radman
- School of Science, RMIT University, Bundoora, VIC 3083, Australia; (M.M.); (R.R.)
- School of Health and Medicine, Monash University, Clayton, VIC 3800, Australia
| | - Ian Macreadie
- School of Science, RMIT University, Bundoora, VIC 3083, Australia; (M.M.); (R.R.)
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Abtahi SH, Nouri H, Moradian S, Yazdani S, Ahmadieh H. Eye Disorders in the Post-COVID Era. J Ophthalmic Vis Res 2021; 16:527-530. [PMID: 34840673 PMCID: PMC8593548 DOI: 10.18502/jovr.v16i4.9740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
This is an Editorial and does not have an abstract. Please download the PDF or view the article HTML.
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Affiliation(s)
- Seyed-Hossein Abtahi
- Ophthalmic Research Center, Research Institute for Ophthalmology and Vision Science, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hosein Nouri
- Ophthalmic Research Center, Research Institute for Ophthalmology and Vision Science, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Siamak Moradian
- Ophthalmic Epidemiology Research Center, Research Institute for Ophthalmology and Vision Science, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shahin Yazdani
- Ophthalmic Research Center, Research Institute for Ophthalmology and Vision Science, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Ahmadieh
- Ophthalmic Research Center, Research Institute for Ophthalmology and Vision Science, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Sivasubramanian S, Gopalan V, Ramesh K, Padmanabhan P, Mone K, Govindan K, Velladurai S, Dhandapani P, Krishnasamy K, Kitambi SS. Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. J Glob Infect Dis 2021; 13:164-171. [PMID: 35017872 PMCID: PMC8697821 DOI: 10.4103/jgid.jgid_97_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 09/22/2021] [Accepted: 10/04/2021] [Indexed: 11/18/2022] Open
Abstract
Introduction: The COVID-19 pandemic is associated with high morbidity and mortality, with the emergence of numerous variants. The dynamics of SARS-CoV-2 with respect to clade distribution is uneven, unpredictable and fast changing. Methods: Retrieving the complete genomes of SARS-CoV-2 from India and subjecting them to analysis on phylogenetic clade diversity, Spike (S) protein mutations and their functional consequences such as immune escape features and impact on infectivity. Whole genome of SARS-CoV-2 isolates (n = 4,326) deposited from India during the period from January 2020 to December 2020 is retrieved from Global Initiative on Sharing All Influenza Data (GISAID) and various analyses performed using in silico tools. Results: Notable clade dynamicity is observed indicating the emergence of diverse SARS-CoV-2 variants across the country. GR clade is predominant over the other clades and the distribution pattern of clades is uneven. D614G is the commonest and predominant mutation found among the S-protein followed by L54F. Mutation score prediction analyses reveal that there are several mutations in S-protein including the RBD and NTD regions that can influence the virulence of virus. Besides, mutations having immune escape features as well as impacting the immunogenicity and virulence through changes in the glycosylation patterns are identified. Conclusions: The study has revealed emergence of variants with shifting of clade dynamics within a year in India. It is shown uneven distribution of clades across the nation requiring timely deposition of SARS-CoV-2 sequences. Functional evaluation of mutations in S-protein reveals their significance in virulence, immune escape features and disease severity besides impacting therapeutics and prophylaxis.
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Affiliation(s)
- Srinivasan Sivasubramanian
- Department of Virology, State Viral Research and Diagnostic Laboratory (VRDL), King Institute of Preventive Medicine and Research, Chennai, Tamil Nadu, India
| | - Vidya Gopalan
- Department of Virology, State Viral Research and Diagnostic Laboratory (VRDL), King Institute of Preventive Medicine and Research, Chennai, Tamil Nadu, India
| | - Kiruba Ramesh
- Department of Virology, State Viral Research and Diagnostic Laboratory (VRDL), King Institute of Preventive Medicine and Research, Chennai, Tamil Nadu, India
| | - Padmapriya Padmanabhan
- Department of Virology, State Viral Research and Diagnostic Laboratory (VRDL), King Institute of Preventive Medicine and Research, Chennai, Tamil Nadu, India
| | - Kiruthiga Mone
- Department of Virology, State Viral Research and Diagnostic Laboratory (VRDL), King Institute of Preventive Medicine and Research, Chennai, Tamil Nadu, India
| | - Karthikeyan Govindan
- Department of Virology, State Viral Research and Diagnostic Laboratory (VRDL), King Institute of Preventive Medicine and Research, Chennai, Tamil Nadu, India
| | - Selvakumar Velladurai
- Department of Virology, State Viral Research and Diagnostic Laboratory (VRDL), King Institute of Preventive Medicine and Research, Chennai, Tamil Nadu, India
| | - Prabu Dhandapani
- Department of Microbiology, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Chennai, Tamil Nadu, India
| | - Kaveri Krishnasamy
- Department of Virology, State Viral Research and Diagnostic Laboratory (VRDL), King Institute of Preventive Medicine and Research, Chennai, Tamil Nadu, India
| | - Satish Srinivas Kitambi
- Department of Translational Sciences, Institute for Healthcare Education and Translational Sciences, Hyderabad, Telengana, India
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Mann C, Griffin JH, Downard KM. Detection and evolution of SARS-CoV-2 coronavirus variants of concern with mass spectrometry. Anal Bioanal Chem 2021; 413:7241-7249. [PMID: 34532764 PMCID: PMC8445501 DOI: 10.1007/s00216-021-03649-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/25/2021] [Accepted: 09/02/2021] [Indexed: 12/24/2022]
Abstract
Mass mapping using high-resolution mass spectrometry has been applied to identify and rapidly distinguish SARS-CoV-2 coronavirus strains across five major variants of concern. Deletions or mutations within the surface spike protein across these variants, which originated in the UK, South Africa, Brazil and India (known as the alpha, beta, gamma and delta variants respectively), lead to associated mass differences in the mass maps. Peptides of unique mass have thus been determined that can be used to identify and distinguish the variants. The same mass map profiles are also utilized to construct phylogenetic trees, without the need for protein (or gene) sequences or their alignment, in order to chart and study viral evolution. The combined strategy offers advantages over conventional PCR-based gene-based approaches exploiting the ease with which protein mass maps can be generated and the speed and sensitivity of mass spectrometric analysis.
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Affiliation(s)
- Christian Mann
- Infectious Disease Responses Laboratory, Prince of Wales Clinical Research Sciences, Sydney, NSW, Australia
| | - Justin H Griffin
- Infectious Disease Responses Laboratory, Prince of Wales Clinical Research Sciences, Sydney, NSW, Australia
| | - Kevin M Downard
- Infectious Disease Responses Laboratory, Prince of Wales Clinical Research Sciences, Sydney, NSW, Australia.
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Mou K, Abdalla M, Wei DQ, Khan MT, Lodhi MS, Darwish DB, Sharaf M, Tu X. Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. INFORMATICS IN MEDICINE UNLOCKED 2021; 25:100675. [PMID: 34337139 PMCID: PMC8314890 DOI: 10.1016/j.imu.2021.100675] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/11/2021] [Accepted: 07/19/2021] [Indexed: 12/23/2022] Open
Abstract
Structural proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are potential drug targets due to their role in the virus life cycle. The envelope (E) protein is one of the structural proteins; plays a critical role in virulency. However, the emergence of mutations oftenly leads to drug resistance and may also play a vital role in virus stabilization and evolution. In this study, we aimed to identify mutations in E proteins that affect the protein stability. About 0.3 million complete whole genome sequences were analyzed to screen mutations in E protein. All these mutations were subjected to stability prediction using the DynaMut server. The most common mutations that were detected at the C-terminal domain, Ser68Phe, Pro71Ser, and Leu73Phe, were examined through molecular dynamics (MD) simulations for a 100ns period. The sequence analysis shows the existence of 259 mutations in E protein. Interestingly, 16 of them were detected in the DFLV amino acid (aa) motif (aa72-aa75) that binds the host PALS1 protein. The results of root mean square deviation, fluctuations, radius of gyration, and free energy landscape show that Ser68Phe, Pro71Ser, and Leu73Phe are exhibiting a more stabilizing effect. However, a more comprehensive experimental study may be required to see the effect on virus pathogenicity. Potential antiviral drugs, and vaccines may be developed used after screening the genomic variations for better management of SARS-CoV-2 infections.
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Affiliation(s)
- Kejie Mou
- Department of Neurosurgery, Bishan Hospital of Chongqing, Chongqing, China
| | - Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Cultural West Road, Shandong Province, 250012, PR China
| | - Dong Qing Wei
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Research Laboratory of Metabolic & Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, PR China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong, 518055, PR China
| | - Muhammad Tahir Khan
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, KM Defence Road, Lahore, Pakistan, 58810
| | - Madeeha Shahzad Lodhi
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, KM Defence Road, Lahore, Pakistan, 58810
| | - Doaa B Darwish
- Department of Biology, Faculty of Science, University of Tabuk, 71491, Saudi Arabia
| | - Mohamed Sharaf
- Department of Biochemistry and Molecular Biology, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, PR China
- Department of Biochemistry, Faculty of Agriculture, AL-Azhar University, Nasr City, Cairo, 11751, Egypt
| | - Xudong Tu
- Chongqing Medical and Pharmaceutical College, Chongqing, China
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Helle KB, Sadiku A, Zelleke GM, Ibrahim TB, Bouba A, Tsoungui Obama HC, Appiah V, Ngwa GA, Teboh-Ewungkem MI, Schneider KA. Is increased mortality by multiple exposures to COVID-19 an overseen factor when aiming for herd immunity? PLoS One 2021; 16:e0253758. [PMID: 34270576 PMCID: PMC8284653 DOI: 10.1371/journal.pone.0253758] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 06/13/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Governments across the globe responded with different strategies to the COVID-19 pandemic. While some countries adopted measures, which have been perceived controversial, others pursued a strategy aiming for herd immunity. The latter is even more controversial and has been called unethical by the WHO Director-General. Inevitably, without proper control measures, viral diversity increases and multiple infectious exposures become common, when the pandemic reaches its maximum. This harbors not only a potential threat overseen by simplified theoretical arguments in support of herd immunity, but also deserves attention when assessing response measures to increasing numbers of infection. METHODS AND FINDINGS We extend the simulation model underlying the pandemic preparedness web interface CovidSim 1.1 (http://covidsim.eu/) to study the hypothetical effect of increased morbidity and mortality due to 'multi-infections', either acquired at by successive infective contacts during the course of one infection or by a single infective contact with a multi-infected individual. The simulations are adjusted to reflect roughly the situation in the USA. We assume a phase of general contact reduction ("lockdown") at the beginning of the epidemic and additional case-isolation measures. We study the hypothetical effects of varying enhancements in morbidity and mortality, different likelihoods of multi-infected individuals to spread multi-infections and different susceptibility to multi-infections in different disease phases. It is demonstrated that multi-infections lead to a slight reduction in the number of infections, as these are more likely to get isolated due to their higher morbidity. However, the latter substantially increases the number of deaths. Furthermore, simulations indicate that a potential second lockdown can substantially decrease the epidemic peak, the number of multi-infections and deaths. CONCLUSIONS Enhanced morbidity and mortality due to multiple disease exposure is a potential threat in the COVID-19 pandemic that deserves more attention. Particularly it underlines another facet questioning disease management strategies aiming for herd immunity.
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Affiliation(s)
- Kristina Barbara Helle
- Department of Applied Computer- and Biosciences, University of Applied Sciences Mittweida, Mittweida, Germany
| | - Arlinda Sadiku
- Department of Applied Computer- and Biosciences, University of Applied Sciences Mittweida, Mittweida, Germany
| | - Girma Mesfin Zelleke
- African Institute for Mathematical Sciences Cameroon, Limbe, Cameroon
- Department of Mathematics, University of Buea, Buea, Cameroon
| | - Toheeb Babatunde Ibrahim
- Department of Applied Computer- and Biosciences, University of Applied Sciences Mittweida, Mittweida, Germany
- African Institute for Mathematical Sciences Cameroon, Limbe, Cameroon
| | - Aliou Bouba
- Department of Applied Computer- and Biosciences, University of Applied Sciences Mittweida, Mittweida, Germany
- African Institute for Mathematical Sciences Cameroon, Limbe, Cameroon
| | | | - Vincent Appiah
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Gideon Akumah Ngwa
- Department of Applied Computer- and Biosciences, University of Applied Sciences Mittweida, Mittweida, Germany
- Department of Mathematics, University of Buea, Buea, Cameroon
| | | | - Kristan Alexander Schneider
- Department of Applied Computer- and Biosciences, University of Applied Sciences Mittweida, Mittweida, Germany
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Chaqroun A, Hartard C, Schvoerer E. Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. Viruses 2021; 13:1171. [PMID: 34207378 PMCID: PMC8234553 DOI: 10.3390/v13061171] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 12/15/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is genetically variable, allowing it to adapt to various hosts including humans. Indeed, SARS-CoV-2 has accumulated around two mutations per genome each month. The first relevant event in this context was the occurrence of the mutant D614G in the Spike gene. Moreover, several variants have emerged, including the well-characterized 20I/501Y.V1, 20H/501Y.V2, and 20J/501Y.V3 strains, in addition to those that have been detected within clusters, such as 19B/501Y or 20C/655Y in France. Mutants have also emerged in animals, including a variant transmitted to humans, namely, the Mink variant detected in Denmark. The emergence of these variants has affected the transmissibility of the virus (for example, 20I/501Y.V1, which was up to 82% more transmissible than other preexisting variants), its severity, and its ability to escape natural, adaptive, vaccine, and therapeutic immunity. In this respect, we review the literature on variants that have currently emerged, and their effect on vaccines and therapies, and, in particular, monoclonal antibodies (mAbs). The emergence of SARS-CoV-2 variants must be examined to allow effective preventive and curative control strategies to be developed.
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Affiliation(s)
- Ahlam Chaqroun
- CNRS, LCPME, Université de Lorraine, 54100 Nancy, France; (A.C.); (C.H.)
| | - Cédric Hartard
- CNRS, LCPME, Université de Lorraine, 54100 Nancy, France; (A.C.); (C.H.)
- Laboratoire de Virologie, CHRU de Nancy Brabois, 54500 Vandoeuvre-lès-Nancy, France
| | - Evelyne Schvoerer
- CNRS, LCPME, Université de Lorraine, 54100 Nancy, France; (A.C.); (C.H.)
- Laboratoire de Virologie, CHRU de Nancy Brabois, 54500 Vandoeuvre-lès-Nancy, France
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Chaturvedi P, Badwe R. With the emergence of Omicron, SARS-CoV-2 is getting weaker and human species is getting stronger due to our inherent cellular intelligence. CANCER RESEARCH, STATISTICS, AND TREATMENT 2021. [DOI: 10.4103/crst.crst_313_21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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