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Abratenko P, Andrade Aldana D, Anthony J, Arellano L, Asaadi J, Ashkenazi A, Balasubramanian S, Baller B, Barr G, Barrow J, Basque V, Bathe-Peters L, Benevides Rodrigues O, Berkman S, Bhanderi A, Bhattacharya M, Bishai M, Blake A, Bogart B, Bolton T, Book JY, Camilleri L, Caratelli D, Caro Terrazas I, Cavanna F, Cerati G, Chen Y, Conrad JM, Convery M, Cooper-Troendle L, Crespo-Anadón JI, Del Tutto M, Dennis SR, Detje P, Devitt A, Diurba R, Dorrill R, Duffy K, Dytman S, Eberly B, Ereditato A, Evans JJ, Fine R, Finnerud OG, Foreman W, Fleming BT, Foppiani N, Franco D, Furmanski AP, Garcia-Gamez D, Gardiner S, Ge G, Gollapinni S, Goodwin O, Gramellini E, Green P, Greenlee H, Gu W, Guenette R, Guzowski P, Hagaman L, Hen O, Hicks R, Hilgenberg C, Horton-Smith GA, Irwin B, Itay R, James C, Ji X, Jiang L, Jo JH, Johnson RA, Jwa YJ, Kalra D, Kamp N, Karagiorgi G, Ketchum W, Kirby M, Kobilarcik T, Kreslo I, Leibovitch MB, Lepetic I, Li JY, Li K, Li Y, Lin K, Littlejohn BR, Louis WC, Luo X, Manivannan K, Mariani C, Marsden D, Marshall J, Martinez N, Martinez Caicedo DA, Mason K, Mastbaum A, McConkey N, Meddage V, Miller K, Mills J, Mogan A, Mohayai T, Mooney M, Moor AF, Moore CD, Mora Lepin L, Mousseau J, Mulleriababu S, Naples D, Navrer-Agasson A, Nayak N, Nebot-Guinot M, Nowak J, Nunes M, Oza N, Palamara O, Pallat N, Paolone V, Papadopoulou A, Papavassiliou V, Parkinson HB, Pate SF, Patel N, Pavlovic Z, Piasetzky E, Ponce-Pinto ID, Pophale I, Prince S, Qian X, Raaf JL, Radeka V, Reggiani-Guzzo M, Ren L, Rochester L, Rodriguez Rondon J, Rosenberg M, Ross-Lonergan M, Rudolf von Rohr C, Scanavini G, Schmitz DW, Schukraft A, Seligman W, Shaevitz MH, Sharankova R, Shi J, Smith A, Snider EL, Soderberg M, Söldner-Rembold S, Spitz J, Stancari M, St John J, Strauss T, Sword-Fehlberg S, Szelc AM, Tang W, Taniuchi N, Terao K, Thorpe C, Torbunov D, Totani D, Toups M, Tsai YT, Tyler J, Uchida MA, Usher T, Viren B, Weber M, Wei H, White AJ, Williams Z, Wolbers S, Wongjirad T, Wospakrik M, Wresilo K, Wright N, Wu W, Yandel E, Yang T, Yates LE, Yu HW, Zeller GP, Zennamo J, Zhang C. First Constraints on Light Sterile Neutrino Oscillations from Combined Appearance and Disappearance Searches with the MicroBooNE Detector. PHYSICAL REVIEW LETTERS 2023; 130:011801. [PMID: 36669216 DOI: 10.1103/physrevlett.130.011801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
We present a search for eV-scale sterile neutrino oscillations in the MicroBooNE liquid argon detector, simultaneously considering all possible appearance and disappearance effects within the 3+1 active-to-sterile neutrino oscillation framework. We analyze the neutrino candidate events for the recent measurements of charged-current ν_{e} and ν_{μ} interactions in the MicroBooNE detector, using data corresponding to an exposure of 6.37×10^{20} protons on target from the Fermilab booster neutrino beam. We observe no evidence of light sterile neutrino oscillations and derive exclusion contours at the 95% confidence level in the plane of the mass-squared splitting Δm_{41}^{2} and the sterile neutrino mixing angles θ_{μe} and θ_{ee}, excluding part of the parameter space allowed by experimental anomalies. Cancellation of ν_{e} appearance and ν_{e} disappearance effects due to the full 3+1 treatment of the analysis leads to a degeneracy when determining the oscillation parameters, which is discussed in this Letter and will be addressed by future analyses.
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Chatterjee S, Bhattacharya M, Nag S, Dhama K, Chakraborty C. A Detailed Overview of SARS-CoV-2 Omicron: Its Sub-Variants, Mutations and Pathophysiology, Clinical Characteristics, Immunological Landscape, Immune Escape, and Therapies. Viruses 2023; 15:167. [PMID: 36680207 PMCID: PMC9866114 DOI: 10.3390/v15010167] [Citation(s) in RCA: 80] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
The COVID-19 pandemic has created significant concern for everyone. Recent data from many worldwide reports suggest that most infections are caused by the Omicron variant and its sub-lineages, dominating all the previously emerged variants. The numerous mutations in Omicron's viral genome and its sub-lineages attribute it a larger amount of viral fitness, owing to the alteration of the transmission and pathophysiology of the virus. With a rapid change to the viral structure, Omicron and its sub-variants, namely BA.1, BA.2, BA.3, BA.4, and BA.5, dominate the community with an ability to escape the neutralization efficiency induced by prior vaccination or infections. Similarly, several recombinant sub-variants of Omicron, namely XBB, XBD, and XBF, etc., have emerged, which a better understanding. This review mainly entails the changes to Omicron and its sub-lineages due to it having a higher number of mutations. The binding affinity, cellular entry, disease severity, infection rates, and most importantly, the immune evading potential of them are discussed in this review. A comparative analysis of the Delta variant and the other dominating variants that evolved before Omicron gives the readers an in-depth understanding of the landscape of Omicron's transmission and infection. Furthermore, this review discusses the range of neutralization abilities possessed by several approved antiviral therapeutic molecules and neutralizing antibodies which are functional against Omicron and its sub-variants. The rapid evolution of the sub-variants is causing infections, but the broader aspect of their transmission and neutralization has not been explored. Thus, the scientific community should adopt an elucidative approach to obtain a clear idea about the recently emerged sub-variants, including the recombinant variants, so that effective neutralization with vaccines and drugs can be achieved. This, in turn, will lead to a drop in the number of cases and, finally, an end to the pandemic.
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Behera JK, Mishra P, Jena AK, Bhattacharya M, Behera B. Understanding of environmental pollution and its anthropogenic impacts on biological resources during the COVID-19 period. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022:10.1007/s11356-022-24789-6. [PMID: 36580239 PMCID: PMC9797902 DOI: 10.1007/s11356-022-24789-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
The global outbreak of the COVID-19 pandemic has given rise to a significant health emergency to adverse impact on environment, and human society. The COVID-19 post-pandemic not only affects human beings but also creates pollution crisis in environment. The post-pandemic situation has shown a drastic change in nature due to biomedical waste load and other components. The inadequate segregation of untreated healthcare wastes, chemical disinfectants, and single-use plastics leads to contamination of the water, air, and agricultural fields. These materials allow the growth of disease-causing agents and transmission. Particularly, the COVID-19 outbreak has posed a severe environmental and health concern in many developing countries for infectious waste. In 2030, plastic enhances a transboundary menace to natural ecological communities and public health. This review provides a complete overview of the COVID-19 pandemic on environmental pollution and its anthropogenic impacts to public health and natural ecosystem considering short- and long-term scenarios. The review thoroughly assesses the impacts on ecosystem in the terrestrial, marine, and atmospheric realms. The information from this evaluation can be utilized to assess the short-term and long-term solutions for minimizing any unfavorable effects. Especially, this topic focuses on the excessive use of plastics and their products, subsequently with the involvement of the scientific community, and policymakers will develop the proper management plan for the upcoming generation. This article also provides crucial research gap knowledge to boost national disaster preparedness in future perspectives.
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Chakraborty C, Bhattacharya M, Chatterjee S, Sharma AR, Saha RP, Dhama K, Agoramoorthy G. Integrative Bioinformatics Approaches Indicate a Particular Pattern of Some SARS-CoV-2 and Non-SARS-CoV-2 Proteins. Vaccines (Basel) 2022; 11:vaccines11010038. [PMID: 36679883 PMCID: PMC9864461 DOI: 10.3390/vaccines11010038] [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: 11/08/2022] [Revised: 12/12/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
Pattern recognition plays a critical role in integrative bioinformatics to determine the structural patterns of proteins of viruses such as SARS-CoV-2. This study identifies the pattern of SARS-CoV-2 proteins to depict the structure-function relationships of the protein alphabets of SARS-CoV-2 and COVID-19. The assembly enumeration algorithm, Anisotropic Network Model, Gaussian Network Model, Markovian Stochastic Model, and image comparison protein-like alphabets were used. The distance score was the lowest with 22 for "I" and highest with 40 for "9". For post-processing and decision, two protein alphabets "C" (PDB ID: 6XC3) and "S" (PDB ID: 7OYG) were evaluated to understand the structural, functional, and evolutionary relationships, and we found uniqueness in the functionality of proteins. Here, models were constructed using "SARS-CoV-2 proteins" (12 numbers) and "non-SARS-CoV-2 proteins" (14 numbers) to create two words, "SARS-CoV-2" and "COVID-19". Similarly, we developed two slogans: "Vaccinate the world against COVID-19" and "Say no to SARS-CoV-2", which were made with the proteins structure. It might generate vaccine-related interest to broad reader categories. Finally, the evolutionary process appears to enhance the protein structure smoothly to provide suitable functionality shaped by natural selection.
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Chakraborty C, Bhattacharya M, Sharma AR, Dhama K. Evolution, epidemiology, geographical distribution, and mutational landscape of newly emerging monkeypox virus. GeroScience 2022; 44:2895-2911. [PMID: 36094771 PMCID: PMC9466330 DOI: 10.1007/s11357-022-00659-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/05/2022] [Indexed: 01/18/2023] Open
Abstract
Recent monkeypox (MPX) outbreaks are major ones in non-endemic countries. The present study analyzed molecular phylogenetics, divergence, epidemiology, the geographical distribution, entropy diversity of genome, mutational landscape, and evolution of the monkeypox virus (MPXV) genome and the current MPXV is entitled "hMPXV1." We used different in-silico and statistical methods to study our objectives. The developed phylogram from molecular phylogenetics describes the origin and evolution of hMPXV1 of A, A.1, A.1.1, A.2, and B.1 lineages. The microevolution of B.1 lineage shows its evolution from May to August 2022. B.1 lineage is further adapting and showing more mutation and sub-lineages. The scatter plot of all lineages shows the clustering pattern of lineages and the divergence. We also developed two statistical models of confirmed cases and a diagram of the age-related pattern of infected cases to illustrate the epidemiology of the MPX outbreaks. The entropy diversity and mutational landscape of the hMPXV1 genome were analyzed in nucleotide and codon contexts. Our study has shown the in-depth evolution pattern of different lineages of the hMPXV1. We found B.1 lineage is associated with the current outbreaks. The mutational landscape informs about the slow mutation of the virus. Finally, the study might assists the new therapeutic development considering all the above points and would help the researcher to set up their future research directions.
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Chatterjee S, Bhattacharya M, Agoramoorthy G, Chakraborty C. Current status in clinical advancement of RNA therapeutics - Correspondence. Int J Surg 2022; 108:106996. [PMID: 36368421 DOI: 10.1016/j.ijsu.2022.106996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/06/2022] [Indexed: 11/10/2022]
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Sharma AR, Lee YH, Bat-Ulzii A, Bhattacharya M, Chakraborty C, Lee SS. Recent advances of metal-based nanoparticles in nucleic acid delivery for therapeutic applications. J Nanobiotechnology 2022; 20:501. [PMID: 36434667 PMCID: PMC9700905 DOI: 10.1186/s12951-022-01650-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/27/2022] [Indexed: 11/26/2022] Open
Abstract
Recent efforts in designing nanomaterials to deliver potential therapeutics to the targeted site are overwhelming and palpable. Engineering nanomaterials to deliver biological molecules to exert desirable physiological changes, with minimized side effects and optimal dose, has revolutionized the next-generation therapy for several diseases. The rapid progress of nucleic acids as biopharmaceutics is going to alter the traditional pharmaceutics practices in modern medicine. However, enzymatic instability, large size, dense negative charge (hydrophilic for cell uptake), and unintentional adverse biological responses-such as prolongation of the blood coagulation and immune system activation-hamper the potential use of nucleic acids for therapeutic purposes. Moreover, the safe delivery of nucleic acids into the clinical setting is an uphill task, and several efforts are being put forward to deliver them to targeted cells. Advances in Metal-based NanoParticles (MNPs) are drawing attention due to the unique properties offered by them for drug delivery, such as large surface-area-to-volume ratio for surface modification, increased therapeutic index of drugs through site-specific delivery, increased stability, enhanced half-life of the drug in circulation, and efficient biodistribution to the desired targeted site. Here, the potential of nanoparticles delivery systems for the delivery of nucleic acids, specially MNPs, and their ability and advantages over other nano delivery systems are reviewed.
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Bhattacharya M, Dhama K, Chakraborty C. A call for a novel and next-generation vaccine against monkeypox disease. Ann Med Surg (Lond) 2022; 84:104968. [DOI: 10.1016/j.amsu.2022.104968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 11/12/2022] [Indexed: 11/18/2022] Open
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Chakraborty C, Bhattacharya M, Sharma AR, Dhama K, Lee SS. The rapid emergence of multiple sublineages of Omicron (B.1.1.529) variant: Dynamic profiling via molecular phylogenetics and mutational landscape studies. J Infect Public Health 2022; 15:1234-1258. [PMID: 36270226 DOI: 10.1016/j.jiph.2022.10.004] [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: 08/29/2022] [Revised: 09/27/2022] [Accepted: 10/05/2022] [Indexed: 11/28/2022] Open
Abstract
PURPOSE The recent Omicron (B.1.1.529) variant poses a significant threat to global health. This variant has spread worldwide, and several sublineages have rapidly emerged. Study tried to analyze the microevolution of this variant. METHODS We studied the molecular phylogenetics, divergence, geographical distributions, frequencies, risk mutations for antibody affinity, and mutational landscape for Omicron sublineages using in silico analysis and statistical models. The risk mutation of spike for nAb affinity was analyzed and illustrated by statistical plots. Finally, the mutational properties of the spike mutations and their stability were predicted and demonstrated. RESULTS First, we studied the microevolutionary Omicron sublineages using molecular phylogenetics. Simultaneously, we revealed divergence events of the Omicron sublineages and observed the lowest minimum divergence of 51 in clade 21K and the highest maximum divergence of 90 in clade 21L. We have demonstrated cluster analyses, geographical distributions, frequencies of Omicron and its sublineages. Finally, we evaluated the mutational landscape of the Omicron sublineages. In this mutational study, we performed a genome-wide analysis of general mutations, mutations in the non-spike genome, and spike mutations of Omicron sublineages. The risk mutation of S-glycoprotein for nAb affinity has been analyzed for Omicron sublineages. Here, we found that some sublineages have all four significant highly destabilizing mutations. Such sublineages are BA.1 (G446S, E484A, T95I, and D614G), BA.2 (H655Y, Q493R, G493S, and D614G), BA.4 (N501Y, Y505H, N969K, and D614G), and BA.2.75 (Q454H, T547K, N764K, D614G and G446S). Finally, from the mutation stability prediction through ΔΔG, we observed that BA.1 and BA.4 had two destabilizing and two stabilizing mutations. Similarly, BA.2, BA.5, and BA.2.12.1 have one destabilizing and three stabilizing mutations. However, all four mutations in BA.2.75 are stabilizing mutations. CONCLUSIONS Our molecular phylogenetic studies provided a deeper understanding of the microevolution of sublineages and the creation of Omicron. Similarly, this study might help scientists develop pan-coronavirus vaccines that consider their mutational properties.
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Chakraborty C, Bhattacharya M, Sharma AR, Dhama K, Agoramoorthy G. A comprehensive analysis of the mutational landscape of the newly emerging Omicron (B.1.1.529) variant and comparison of mutations with VOCs and VOIs. GeroScience 2022; 44:2393-2425. [PMID: 35989365 PMCID: PMC9393103 DOI: 10.1007/s11357-022-00631-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 07/20/2022] [Indexed: 01/18/2023] Open
Abstract
The Omicron variant is spreading rapidly throughout several countries. Thus, we comprehensively analyzed Omicron's mutational landscape and compared mutations with VOC/VOI. We analyzed SNVs throughout the genome, and AA variants (NSP and SP) in VOC/VOI, including Omicron. We generated heat maps to illustrate the AA variants with high mutation prevalence (> 75% frequency) of Omicron, which demonstrated eight mutations with > 90% prevalence in ORF1a and 29 mutations with > 75% prevalence in S-glycoprotein. A scatter plot for Omicron and VOC/VOI's cluster evaluation was computed. We performed a risk analysis of the antibody-binding risk among four mutations (L452, F490, P681, D614) and observed three mutations (L452R, F490S, D614G) destabilized antibody interactions. Our comparative study evaluated the properties of 28 emerging mutations of the S-glycoprotein of Omicron, and the ΔΔG values. Our results showed K417N with minimum and Q954H with maximum ΔΔG value. Furthermore, six important RBD mutations (G339D, S371L, N440K, G446S, T478K, Q498R) were chosen for comprehensive analysis for stabilizing/destabilizing properties and molecular flexibility. The G339D, S371L, N440K, and T478K were noted as stable mutations with 0.019 kcal/mol, 0.127 kcal/mol, 0.064 kcal/mol, and 1.009 kcal/mol. While, G446S and Q498R mutations showed destabilizing results. Simultaneously, among six RBD mutations, G339D, G446S, and Q498R mutations increased the molecular flexibility of S-glycoprotein. This study depicts the comparative mutational pattern of Omicron and other VOC/VOI, which will help researchers to design and deploy novel vaccines and therapeutic antibodies to fight against VOC/VOI, including Omicron.
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Behera JK, Bhattacharya M, Mishra P, Mishra A, Dash AA, Kar NB, Behera B, Patra BC. Regulatory role of miRNAs in Wnt signaling pathway linked with cardiovascular diseases. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2022; 3:100133. [PMID: 36568258 PMCID: PMC9780067 DOI: 10.1016/j.crphar.2022.100133] [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: 07/01/2022] [Revised: 09/15/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022] Open
Abstract
MicroRNAs (miRNAs) are discovered in science about 23 years ago. These are short, a series of non-coding, single-stranded and evolutionary conserved RNA molecules found in eukaryotic cells. It involved post-transcriptional fine-tune protein expression and repressing the target of mRNA in different biological processes. These miRNAs binds with the 3'-UTR region of specific mRNAs to phosphorylate the mRNA degradation and inhibit the translation process in various tissues. Therefore, aberrant expression in miRNAs induces numerous cardiovascular diseases and developmental defects. Subsequently, the miRNAs and Wnt singling pathway are regulating a cellular process in cardiac development and regeneration, maintain the homeostasis and associated heart diseases. In Wnt signaling pathway majority of the signaling components are expressed and regulated by miRNAs, whereas the inhibition or dysfunction of the Wnt signaling pathway induces cardiovascular diseases. Moreover, inadequate studies about the important role of miRNAs in heart development and diseases through Wnt signaling pathway has been exist still now. For this reason in present review we summarize and update the involvement of miRNAs and the role of Wnt signaling in cardiovascular diseases. We have discussed the mechanism of miRNA functions which regulates the Wnt components in cellular signaling pathway. The fundamental understanding of Wnt signaling regulation and mechanisms of miRNAs is quite essential for study of heart development and related diseases. This approach definitely enlighten the future research to provide a new strategy for formulation of novel therapeutic approaches against cardiovascular diseases.
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Bhattacharya M, Chatterjee S, Mallik B, Sharma AR, Chakraborty C. Therapeutic Role of Neutralizing Antibody for the Treatment against SARS-CoV-2 and Its Emerging Variants: A Clinical and Pre-Clinical Perspective. Vaccines (Basel) 2022; 10:vaccines10101612. [PMID: 36298477 PMCID: PMC9606861 DOI: 10.3390/vaccines10101612] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/09/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
Since early 2020, the entire world has been facing a disastrous outbreak of the SARS-CoV-2 virus, with massive reporting of death and infections per day. Medical practitioners adopted certain measures such as convalescent plasma therapy, antibody treatment, and injecting vaccines to eradicate the pandemic. In this review, we have primarily focused on the neutralizing antibodies presently under pre-clinical and clinical trials, focusing on their structures, binding affinity, mechanism of neutralization, and advantages over other therapeutics. We have also enlisted all the nAbs against SARS-CoV-2 and its emerging variants in different phases of clinical trials (phase-1, phase-II, and phase-III). The efficacy of administering antibody cocktails over the normal antibodies and their efficacy for the mutant variants of the SARS-CoV-2 virus in minimizing viral virulence is discussed. The potent neutralizing antibodies have eliminated many of the common problems posed by several other therapeutics. A common mechanism of the antibodies and their relevant sources have also been listed in this review.
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Sah R, Hada V, Mohanty A, Alshahrani NZ, Chakraborty S, Bhattacharya M, Chakraborty C, Dhama K. Recent first report of human-to-dog transmission of Monkeypox virus emphasizes an urgent need of enhancing surveillance and strengthen further explorative research to reveal its real magnitude of reverse zoonosis from other animals including pets as like that happened with SARS-CoV-2 / COVID-19 pandemic - Correspondence. Int J Surg 2022; 106:106949. [PMID: 36174830 PMCID: PMC9534089 DOI: 10.1016/j.ijsu.2022.106949] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 09/22/2022] [Indexed: 11/28/2022]
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Dhama K, Chandran D, Chakraborty S, Yatoo MI, Islam MA, Bhattacharya M, Chakraborty C, Harapan H, Chaicumpa W. Zoonotic concerns of Marburg virus: Current knowledge and counteracting strategies including One Health approach to limit animal-human interface: An update. Int J Surg 2022; 106:106941. [PMID: 36162729 DOI: 10.1016/j.ijsu.2022.106941] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 09/18/2022] [Indexed: 11/15/2022]
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Mohapatra RK, Sarangi AK, Chakraborty S, Tuli HS, Bhattacharya M, Chakraborty C, Chaicumpa W, Dhama K. NeoCoronavirus (NeoCoV) and its possible future global health threats - Current knowledge and counteracting prospects - Correspondence. Int J Surg 2022; 106:106922. [PMID: 36150652 DOI: 10.1016/j.ijsu.2022.106922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/12/2022] [Indexed: 10/14/2022]
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Chakraborty C, Bhattacharya M, Pandya P, Dhama K. Monkeypox in South-East Asia: Is an alarming bell for this region? - Correspondence. Int J Surg 2022; 106:106917. [PMID: 36115529 PMCID: PMC9628891 DOI: 10.1016/j.ijsu.2022.106917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 09/10/2022] [Indexed: 11/25/2022]
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Chakraborty C, Bhattacharya M, Sharma AR, Mohapatra RK, Chakraborty S, Pal S, Dhama K. Immediate need for next-generation and mutation-proof vaccine to protect against current emerging Omicron sublineages and future SARS-CoV-2 variants: An urgent call for researchers and vaccine companies - Correspondence. Int J Surg 2022; 106:106903. [PMID: 36108909 PMCID: PMC9467924 DOI: 10.1016/j.ijsu.2022.106903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 08/28/2022] [Indexed: 12/03/2022]
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Bhattacharya M, Dhama K, Chakraborty C. Recently spreading human monkeypox virus infection and its transmission during COVID-19 pandemic period: A travelers' prospective. Travel Med Infect Dis 2022; 49:102398. [PMID: 35779853 PMCID: PMC9239924 DOI: 10.1016/j.tmaid.2022.102398] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 12/04/2022]
Abstract
Presently, monkeypox has emerged in multiple countries with many confirmed cases, posing a global public health threat. A link has been found between air travel and the international spread of infectious diseases including the previous spread of monkeypox. This article highlights the spread of COVID-19 through air travel, and then monkeypox spread from one country to another. Scientists are trying to establish the air travel and monkeypox spread. Any travel link from an endemic country has not been proven yet to describe the rising number of current monkeypox cases in non-endemic countries. Due to the quantification method, the direct link of the diseases with air travel might be difficult to establish. However, we have also developed different statistical models of the confirmed cases and the number of air travelers per year (noted in countries where monkeypox has spread). As there is no direct link, these models might show a probability of an indirect association of air travel. However, more strong evidence is needed in this direction. Although, the sudden appearance of monkeypox cases in multiple countries in a few days demands comprehensive epidemiological investigations, genome sequencing, and phylogenetic analysis of viral isolates to prove the travel link from an endemic country. At the same time, it is also necessary to know the real cause while also exploring any direct and/or indirect travel links between different countries. Similarly, the possibility of any zoonotic event should find out to understand the more about natural animal reservoir(s) for the monkeypox virus, which is unknown until now. However, this report will help researchers for conducting further explorative research and investigations for understanding transmission patterns and guide policymakers to make proactive policies to limit the spread of monkeypox.
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Chakraborty C, Bhattacharya M, Sharma AR, Roy SS, Islam MA, Chakraborty S, Nandi SS, Dhama K. Deep learning research should be encouraged for diagnosis and treatment of antibiotic resistance of microbial infections in treatment associated emergencies in hospitals. Int J Surg 2022; 105:106857. [PMID: 36028138 DOI: 10.1016/j.ijsu.2022.106857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 08/19/2022] [Indexed: 10/15/2022]
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Bhattacharya M, Sharma AR, Mallick B, Lee SS, Seo EM, Chakraborty C. B.1.1.7 (Alpha) variant is the most antigenic compared to Wuhan strain, B.1.351, B.1.1.28/triple mutant and B.1.429 variants. Front Microbiol 2022; 13:895695. [PMID: 36033846 PMCID: PMC9411949 DOI: 10.3389/fmicb.2022.895695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
The rapid spread of the SARS-CoV-2 virus and its variants has created a catastrophic impact worldwide. Several variants have emerged, including B.1.351 (Beta), B.1.1.28/triple mutant (P.1), B.1.1.7 (Alpha), and B.1.429 (Epsilon). We performed comparative and comprehensive antigenicity mapping of the total S-glycoprotein using the Wuhan strain and the other variants and identified 9-mer, 15-mer, and 20-mer CTL epitopes through in silico analysis. The study found that 9-mer CTL epitope regions in the B.1.1.7 variant had the highest antigenicity and an average of the three epitope types. Cluster analysis of the 9-mer CTL epitopes depicted one significant cluster at the 70% level with two nodes (KGFNCYFPL and EGFNCYFPL). The phage-displayed peptides showed mimic 9-mer CTL epitopes with three clusters. CD spectra analysis showed the same band pattern of S-glycoprotein of Wuhan strain and all variants other than B.1.429. The developed 3D model of the superantigen (SAg)-like regions found an interaction pattern with the human TCR, indicating that the SAg-like component might interact with the TCR beta chain. The present study identified another partial SAg-like region (ANQFNSAIGKI) from the S-glycoprotein. Future research should examine the molecular mechanism of antigen processing for CD8+ T cells, especially all the variants’ antigens of S-glycoprotein.
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Chakraborty C, Bhattacharya M, Sharma AR, Mallik B. Omicron (B.1.1.529) - A new heavily mutated variant: Mapped location and probable properties of its mutations with an emphasis on S-glycoprotein. Int J Biol Macromol 2022; 219:980-997. [PMID: 35952818 PMCID: PMC9359758 DOI: 10.1016/j.ijbiomac.2022.07.254] [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: 02/08/2022] [Revised: 05/23/2022] [Accepted: 07/31/2022] [Indexed: 12/17/2022]
Abstract
Omicron, another SARS-CoV-2 variant, has been recorded and reported as a VoC. It has already spread across >30 countries and is a highly mutated variant. We tried to understand the role of mutations in the investigated variants by comparison with previous characterized VoC. We have mapped the mutations in Omicron S-glycoprotein's secondary and tertiary structure landscape using bioinformatics tools and statistical software and developed different models. In addition, we analyzed the effect of diverse mutations in antibody binding regions of the S-glycoprotein on the binding affinity of the investigated antibodies. This study has chosen eight significant mutations in Omicron (D614G, E484A, N501Y, Q493K, K417N, S477N, Y505H G496S), and seven of them are located in the RBD region. We also performed a comparative analysis of the ΔΔG score of these mutations to understand the stabilizing or destabilizing properties of the investigated mutations. The analysis outcome shows that D614G, Q493K, and S477N mutations are stable mutations with ΔΔG scores of 0.351 kcal/mol, 0.470 kcal/mol, and 0.628 kcal/mol, respectively, according to DynaMut estimations. While other mutations (E484A, N501Y, K417N, Y505H, G496S) showed destabilizing results. The D614G, E484A, N501Y, K417N, Y505H, and G496S mutations increased the molecular flexibility of S-glycoprotein to interact with the ACE2 receptor, increasing the variant's infectivity. Our study will contribute to research on the SARS-CoV-2 variant, Omicron, by providing information on the mutational pattern and exciting properties of these eight significant mutations, such as antibody escape and infectivity quotient (stabilizing or destabilizing; increased or decreased molecular flexibility of S-glycoprotein to interact with the human ACE2 receptor).
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Chatterjee S, Sharma AR, Bhattacharya M, Dhama K, Lee SS, Chakraborty C. Relooking the monkeypox virus during this present outbreak: epidemiology to therapeutics and vaccines. EUROPEAN REVIEW FOR MEDICAL AND PHARMACOLOGICAL SCIENCES 2022; 26:5991-6003. [PMID: 36066177 DOI: 10.26355/eurrev_202208_29541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
OBJECTIVE The recent monkeypox disease outbreak is another significant threat during the ongoing COVID-19 pandemic. This viral disease is zoonotic and contagious. The viral disease outbreak is considered the substantial infection possessed by the Orthopoxvirus family species after the smallpox virus' obliteration, a representative of the same family. It has potentially threatened the Republic of Congo's regions and certain African subcontinent zones. Although repeated outbreaks have been reported in several parts of the world, as conferred from the epidemiological data, very little is explored about the disease landscape. Thus, here we have reviewed the current status of the monkeypox virus along with therapeutic options available to humanity. MATERIALS AND METHODS We have accessed and reviewed the available literature on the monkeypox virus to highlight its epidemiology, pathogenicity, virulence, and therapeutic options available. For the review, we have searched different literature and database such as PubMed, PubMed Central, Google Scholar, Web of Science, Scopus, etc., using different keywords such as "monkeypox", "Orthopox", "smallpox", "recent monkeypox outbreak", "therapeutic strategies", "monkeypox vaccines", etc. This review has included most of the significant references from 1983 to 2022. RESULTS It has been reported that the monkeypox virus shows a remarkable similarity with smallpox during the ongoing outbreak. Sometimes, it creates considerable confusion due to misdiagnosis and similarity with smallpox. The misdiagnosis of the disease should be immediately corrected by rendering some cutting-edge techniques especially intended to isolate the monkeypox virus. The pathophysiology and the histopathological data imply the immediate need to design effective therapeutics to confer resistance against the monkeypox virus. Most importantly, the potential implications of the disease are not given importance due to the lack of awareness programs. Moreover, specific evolutionary evidence is crucial for designing effective therapeutic strategies that confer high resistance, particularly against this species. CONCLUSIONS The review focuses on a brief overview of the recent monkeypox virus outbreak, infection biology, epidemiology, transmission, clinical symptoms, and therapeutic aspects. Such an attempt will support researchers, policymakers, and healthcare professionals for better treatment and containment of the infection caused by the monkeypox virus.
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Chakraborty C, Bhattacharya M, Sharma AR, Dhama K, Lee SS. Continent-wide evolutionary trends of emerging SARS-CoV-2 variants: dynamic profiles from Alpha to Omicron. GeroScience 2022; 44:2371-2392. [PMID: 35831773 PMCID: PMC9281186 DOI: 10.1007/s11357-022-00619-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/27/2022] [Indexed: 01/06/2023] Open
Abstract
The ongoing SARS-CoV-2 evolution process has generated several variants due to its continuous mutations, making pandemics more critical. The present study illustrates SARS-CoV-2 evolution and its emerging mutations in five directions. First, the significant mutations in the genome and S-glycoprotein were analyzed in different variants. Three linear models were developed with the regression line to depict the mutational load for S-glycoprotein, total genome excluding S-glycoprotein, and whole genome. Second, the continent-wide evolution of SARS-CoV-2 and its variants with their clades and divergence were evaluated. It showed the region-wise evolution of the SARS-CoV-2 variants and their clustering event. The major clades for each variant were identified. One example is clade 21K, a major clade of the Omicron variant. Third, lineage dynamics and comparison between SARS-CoV-2 lineages across different countries are also illustrated, demonstrating dominant variants in various countries over time. Fourth, gene-wise mutation patterns and genetic variability of SARS-CoV-2 variants across various countries are illustrated. High mutation patterns were found in the ORF10, ORF6, S, and low mutation pattern E genes. Finally, emerging AA point mutations (T478K, L452R, N501Y, S477N, E484A, Q498R, and Y505H), their frequencies, and country-wise occurrence were identified, and the highest event of two mutations (T478K and L452R) was observed.
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Chakraborty C, Sharma AR, Bhattacharya M, Dhama K, Lee SS. Altered gut microbiota patterns in COVID-19: Markers for inflammation and disease severity. World J Gastroenterol 2022; 28:2802-2822. [PMID: 35978881 PMCID: PMC9280735 DOI: 10.3748/wjg.v28.i25.2802] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/19/2022] [Accepted: 05/14/2022] [Indexed: 02/06/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection leads to a severe respiratory illness and alters the gut microbiota, which dynamically interacts with the human immune system. Microbiota alterations include decreased levels of beneficial bacteria and augmentation of opportunistic pathogens. Here, we describe critical factors affecting the microbiota in coronavirus disease 2019 (COVID-19) patients. These include, such as gut microbiota imbalance and gastrointestinal symptoms, the pattern of altered gut microbiota composition in COVID-19 patients, and crosstalk between the microbiome and the gut-lung axis/gut-brain-lung axis. Moreover, we have illustrated the hypoxia state in COVID-19 associated gut microbiota alteration. The role of ACE2 in the digestive system, and control of its expression using the gut microbiota is discussed, highlighting the interactions between the lungs, the gut, and the brain during COVID-19 infection. Similarly, we address the gut microbiota in elderly or co-morbid patients as well as gut microbiota dysbiosis of in severe COVID-19. Several clinical trials to understand the role of probiotics in COVID-19 patients are listed in this review. Augmented inflammation is one of the major driving forces for COVID-19 symptoms and gut microbiome disruption and is associated with disease severity. However, understanding the role of the gut microbiota in immune modulation during SARS-CoV-2 infection may help improve therapeutic strategies for COVID-19 treatment.
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Chakraborty C, Bhattacharya M, Dhama K, Roy SS, Sharma AR, Mohapatra RK, Lee SS. Deep learning research should be encouraged more and more in different domains of surgery: An open call - Correspondence. Int J Surg 2022; 104:106749. [PMID: 35803516 DOI: 10.1016/j.ijsu.2022.106749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 07/01/2022] [Indexed: 12/21/2022]
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