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Sarkar BK, Bhattacharya M, Agoramoorthy G, Dhama K, Chakraborty C. Entropy-Driven, Integrative Bioinformatics Approaches Reveal the Recent Transmission of the Monkeypox Virus from Nigeria to Multiple Non-African Countries. Mol Biotechnol 2023:10.1007/s12033-023-00889-7. [PMID: 37798393 DOI: 10.1007/s12033-023-00889-7] [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: 01/09/2023] [Accepted: 09/06/2023] [Indexed: 10/07/2023]
Abstract
Monkeypox virus (mpox) has currently affected multiple countries around the globe. This study aims to analyze how the virus spread globally. The study uses entropy-driven bioinformatics in five directions to analyze the 60 full-length complete genomes of mpox. We analyzed the topological entropy distribution of the genomes, principal component analysis (PCA), the dissimilarity matrix, entropy-driven phylogenetics, and genome clustering. The topological entropy distribution showed genome positional entropy. We found five clusters of the mpox genomes through the two PCA, while the three PCA elucidated the clustering events in 3D space. The clustering of genomes was further confirmed through the dissimilarity matrix and phylogenetic analysis which showed the bigger size of Cluster 1 and size similarity between Clusters 2 and 4 as well as Clusters 3 and 5. It corroborated with the phylogenetics of the genomes, where Cluster 1 showed clear segregation from the other four clusters. Finally, the study concluded that the spreading of the mpox is likely to have originated from African countries to the rest of the non-African countries. Overall, the spreading and distribution of the mpox will shed light on its evolution and pathogenicity of the mpox and help to adopt preventive measures to stop the spreading of the virus.
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Pal S, Bhattacharya M, Lee SS, Chakraborty C. Correction to: Quantum Computing in the Next-Generation Computational Biology Landscape: from Protein Folding to Molecular Dynamics. Mol Biotechnol 2023:10.1007/s12033-023-00881-1. [PMID: 37768504 DOI: 10.1007/s12033-023-00881-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2023] [Indexed: 09/29/2023]
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Pal S, Bhattacharya M, Dash S, Lee SS, Chakraborty C. Future Potential of Quantum Computing and Simulations in Biological Science. Mol Biotechnol 2023:10.1007/s12033-023-00863-3. [PMID: 37717248 DOI: 10.1007/s12033-023-00863-3] [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: 06/14/2023] [Accepted: 08/16/2023] [Indexed: 09/19/2023]
Abstract
The review article presents the recent progress in quantum computing and simulation within the field of biological sciences. The article is designed mainly into two portions: quantum computing and quantum simulation. In the first part, significant aspects of quantum computing was illustrated, such as quantum hardware, quantum RAM and big data, modern quantum processors, qubit, superposition effect in quantum computation, quantum interference, quantum entanglement, and quantum logic gates. Simultaneously, in the second part, vital features of the quantum simulation was illustrated, such as the quantum simulator, algorithms used in quantum simulations, and the use of quantum simulation in biological science. Finally, the review provides exceptional views to future researchers about different aspects of quantum simulation in biological science.
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Chakraborty C, Bhattacharya M, Dhama K, Lee SS. Quantum computing on nucleic acid research: Approaching towards next-generation computing. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:53-56. [PMID: 37449046 PMCID: PMC10336077 DOI: 10.1016/j.omtn.2023.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
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Chakraborty C, Bhattacharya M, Lee SS. Artificial intelligence enabled ChatGPT and large language models in drug target discovery, drug discovery, and development. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:866-868. [PMID: 37680991 PMCID: PMC10481150 DOI: 10.1016/j.omtn.2023.08.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
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Chatterjee S, Bhattacharya M, Dhama K, Lee SS, Chakraborty C. Molnupiravir's mechanism of action drives "error catastrophe" in SARS-CoV-2: A therapeutic strategy that leads to lethal mutagenesis of the virus. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:49-52. [PMID: 37397276 PMCID: PMC10300273 DOI: 10.1016/j.omtn.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
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Chakraborty C, Bhattacharya M. The current landscape of long COVID clinical trials: NIH's RECOVER to Stanford Medicine's STOP-PASC initiative. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:887-889. [PMID: 37680987 PMCID: PMC10481149 DOI: 10.1016/j.omtn.2023.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
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Chatterjee S, Bhattacharya M, Lee SS, Chakraborty C. Can artificial intelligence-strengthened ChatGPT or other large language models transform nucleic acid research? MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:205-207. [PMID: 37727444 PMCID: PMC10505907 DOI: 10.1016/j.omtn.2023.06.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
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Abratenko P, Alterkait O, Andrade Aldana D, Anthony J, Arellano L, Asaadi J, Ashkenazi A, Balasubramanian S, Baller B, Barr G, Barrow J, Basque V, 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, Cohen EO, Conrad JM, Convery M, Cooper-Troendle L, Crespo-Anadón JI, Del Tutto M, Dennis SR, Detje P, Devitt A, Diurba R, Djurcic Z, 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, 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, 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, Rafique A, 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, Snider EL, Soderberg M, Söldner-Rembold S, Spitz J, Stancari M, John JS, 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 Double-Differential Measurement of Kinematic Imbalance in Neutrino Interactions with the MicroBooNE Detector. PHYSICAL REVIEW LETTERS 2023; 131:101802. [PMID: 37739352 DOI: 10.1103/physrevlett.131.101802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 05/09/2023] [Accepted: 07/14/2023] [Indexed: 09/24/2023]
Abstract
We report the first measurement of flux-integrated double-differential quasielasticlike neutrino-argon cross sections, which have been made using the Booster Neutrino Beam and the MicroBooNE detector at Fermi National Accelerator Laboratory. The data are presented as a function of kinematic imbalance variables which are sensitive to nuclear ground-state distributions and hadronic reinteraction processes. We find that the measured cross sections in different phase-space regions are sensitive to different nuclear effects. Therefore, they enable the impact of specific nuclear effects on the neutrino-nucleus interaction to be isolated more completely than was possible using previous single-differential cross section measurements. Our results provide precision data to help test and improve neutrino-nucleus interaction models. They further support ongoing neutrino-oscillation studies by establishing phase-space regions where precise reaction modeling has already been achieved.
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Chatterjee S, Bhattacharya M, Dhama K, Lee SS, Chakraborty C. Can the RBD mutation R346X provide an additional fitness to the "variant soup," including offspring of BQ and XBB of SARS-CoV-2 Omicron for the antibody resistance? MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 32:61-63. [PMID: 36938362 PMCID: PMC10015894 DOI: 10.1016/j.omtn.2023.02.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
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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, 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, Djurcic Z, 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, 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, Rafique A, 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, Snider EL, Soderberg M, Söldner-Rembold S, Spitz J, Stancari M, John JS, 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 Measurement of Quasielastic Λ Baryon Production in Muon Antineutrino Interactions in the MicroBooNE Detector. PHYSICAL REVIEW LETTERS 2023; 130:231802. [PMID: 37354393 DOI: 10.1103/physrevlett.130.231802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/07/2023] [Accepted: 04/28/2023] [Indexed: 06/26/2023]
Abstract
We present the first measurement of the cross section of Cabibbo-suppressed Λ baryon production, using data collected with the MicroBooNE detector when exposed to the neutrinos from the main injector beam at the Fermi National Accelerator Laboratory. The data analyzed correspond to 2.2×10^{20} protons on target running in neutrino mode, and 4.9×10^{20} protons on target running in anti-neutrino mode. An automated selection is combined with hand scanning, with the former identifying five candidate Λ production events when the signal was unblinded, consistent with the GENIE prediction of 5.3±1.1 events. Several scanners were employed, selecting between three and five events, compared with a prediction from a blinded Monte Carlo simulation study of 3.7±1.0 events. Restricting the phase space to only include Λ baryons that decay above MicroBooNE's detection thresholds, we obtain a flux averaged cross section of 2.0_{-1.7}^{+2.2}×10^{-40} cm^{2}/Ar, where statistical and systematic uncertainties are combined.
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Chatterjee S, Bhattacharya M, Dhama K, Lee SS, Chakraborty C. Resistance to nirmatrelvir due to mutations in the Mpro in the subvariants of SARS-CoV-2 Omicron: Another concern? MOLECULAR THERAPY - NUCLEIC ACIDS 2023; 32:263-266. [PMID: 37041859 PMCID: PMC10078092 DOI: 10.1016/j.omtn.2023.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
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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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Chakraborty C, Bhattacharya M, Saha A, Alshammari A, Alharbi M, Saikumar G, Pal S, Dhama K, Lee SS. Revealing the structural and molecular interaction landscape of the favipiravir-RTP and SARS-CoV-2 RdRp complex through integrative bioinformatics: Insights for developing potent drugs targeting SARS-CoV-2 and other viruses. J Infect Public Health 2023; 16:1048-1056. [PMID: 37196368 DOI: 10.1016/j.jiph.2023.05.010] [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: 02/01/2023] [Revised: 05/04/2023] [Accepted: 05/08/2023] [Indexed: 05/19/2023] Open
Abstract
BACKGROUND The global research community has made considerable progress in therapeutic and vaccine research during the COVID-19 pandemic. Several therapeutics have been repurposed for the treatment of COVID-19. One such compound is, favipiravir, which was approved for the treatment of influenza viruses, including drug-resistant influenza. Despite the limited information on its molecular activity, clinical trials have attempted to determine the effectiveness of favipiravir in patients with mild to moderate COVID-19. Here, we report the structural and molecular interaction landscape of the macromolecular complex of favipiravir-RTP and SARS-CoV-2 RdRp with the RNA chain. METHODS Integrative bioinformatics was used to reveal the structural and molecular interaction landscapes of two macromolecular complexes retrieved from RCSB PDB. RESULTS We analyzed the interactive residues, H-bonds, and interaction interfaces to evaluate the structural and molecular interaction landscapes of the two macromolecular complexes. We found seven and six H-bonds in the first and second interaction landscapes, respectively. The maximum bond length is 3.79 Å. In the hydrophobic interactions, five residues (Asp618, Asp760, Thr687, Asp623, and Val557) were associated with the first complex and two residues (Lys73 and Tyr217) were associated with the second complex. The mobilities, collective motion, and B-factor of the two macromolecular complexes were analyzed. Finally, we developed different models, including trees, clusters, and heat maps of antiviral molecules, to evaluate the therapeutic status of favipiravir as an antiviral drug. CONCLUSIONS The results revealed the structural and molecular interaction landscape of the binding mode of favipiravir with the nsp7-nsp8-nsp12-RNA SARS-CoV-2 RdRp complex. Our findings can help future researchers in understanding the mechanism underlying viral action and guide the design of nucleotide analogs that mimic favipiravir and exhibit greater potency as antiviral drugs against SARS-CoV-2 and other infectious viruses. Thus, our work can help in preparing for future epidemics and pandemics.
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Chakraborty C, Bhattacharya M, Dhama K, Agoramoorthy G. Artificial intelligence-enabled clinical trials might be a faster way to perform rapid clinical trials and counter future pandemics: lessons learned from the COVID-19 period. Int J Surg 2023; 109:1535-1538. [PMID: 36906740 PMCID: PMC10389411 DOI: 10.1097/js9.0000000000000088] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/20/2022] [Indexed: 03/13/2023]
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Chakraborty C, Bhattacharya M, Saikumar G, Alshammari A, Alharbi M, Lee SS, Dhama K. A European perspective of phylogenomics, sublineages, geographical distribution, epidemiology, and mutational landscape of mpox virus: Emergence pattern may help to fight the next public health emergency in Europe. J Infect Public Health 2023; 16:1004-1014. [PMID: 37172461 PMCID: PMC10147450 DOI: 10.1016/j.jiph.2023.04.017] [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: 02/09/2023] [Revised: 04/09/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND The 2022 outbreak of the mpox virus (previously monkeypox virus, MPXV) in non-epidemic regions has created a global issue. The emergence of MPXV was first reported in Europe, which was described as the MPXV epicenter, however, no reports are available to illustrate its outbreak patterns in Europe. METHODS The study used numerous in silico and statistical methods to analyze hMPXV1 in European countries. Here, we used different bioinformatics servers and software to evaluate the spread of hMPXV1 in European countries. For analysis, we use various advanced servers like Nextstrain, Taxonium, MpoxSpectrum, etc. Similarly, for the statistical model, we used PAST software. RESULTS The phylogenetic tree was depicted to illustrate the origin and evolution of hMPXV1 using vas number of genome sequences (n = 675). We found several sublineages in Europe, indicating microevolution. The scatter plot reveals the clustering patterns of the newly developed lineages in Europe. We developed statistical models for the monthly total relative frequency counts of these sublineages. The epidemiology of MPX in Europe was examined in an attempt to capture the epidemiological pattern, total cases, and deaths. Our Study noted the highest number of cases was in Spain (7500 cases) and the second-highest in France (4114 cases). The third highest number of cases was in the UK (3730 cases), which was very similar to Germany (3677 cases). Finally, we noted the mutational landscape throughout European genomes. Significant mutations were observed at the nucleotide and protein levels. We identified several unique homoplastic mutations in Europe. CONCLUSION This study reveals several essential aspects of the European outbreak. It might help to eradicate the virus in Europe, assist in strategy formation to fight against the virus, and support working against the next public health emergency in Europe.
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Islam MA, Kaifa FH, Chandran D, Bhattacharya M, Chakraborty C, Bhattacharya P, Dhama K. XBB.1.5: A new threatening SARS-CoV-2 Omicron subvariant. Front Microbiol 2023; 14:1154296. [PMID: 37143546 PMCID: PMC10152970 DOI: 10.3389/fmicb.2023.1154296] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/28/2023] [Indexed: 05/06/2023] Open
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Chatterjee S, Bhattacharya M, Agoramoorthy G, Chakraborty C. Calling for continuous surgical support in Ukraine. Int J Surg 2023; 110:01279778-990000000-00245. [PMID: 37026787 PMCID: PMC10389569 DOI: 10.1097/js9.0000000000000040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/18/2022] [Indexed: 04/08/2023]
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Chakraborty C, Bhattacharya M, Chopra H, Bhattacharya P, Islam MA, Dhama K. Recently emerged omicron subvariant BF.7 and its R346T mutation in the RBD region reveal increased transmissibility and higher resistance to neutralization antibodies: need to understand more under the current scenario of rising cases in China and fears of driving a new wave of the COVID-19 pandemic. Int J Surg 2023; 109:1037-1040. [PMID: 37097619 PMCID: PMC10132299 DOI: 10.1097/js9.0000000000000219] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 01/06/2023] [Indexed: 04/26/2023]
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Chakraborty C, Bhattacharya M, Chopra H, Islam MA, Saikumar G, Dhama K. The SARS-CoV-2 Omicron recombinant subvariants XBB, XBB.1, and XBB.1.5 are expanding rapidly with unique mutations, antibody evasion, and immune escape properties - an alarming global threat of a surge in COVID-19 cases again? Int J Surg 2023; 109:1041-1043. [PMID: 36917125 PMCID: PMC10132296 DOI: 10.1097/js9.0000000000000246] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 03/16/2023]
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Chakraborty C, Saha A, Bhattacharya M, Dhama K, Agoramoorthy G. Natural selection of the D614G mutation in SARS-CoV-2 Omicron (B.1.1.529) variant and its subvariants. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 31:437-439. [PMID: 36817724 PMCID: PMC9923361 DOI: 10.1016/j.omtn.2023.01.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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Chakraborty C, Bhattacharya M, Dhama K, Lee SS. Evaluation of differentially expressed genes during replication using gene expression landscape of monkeypox-infected MK2 cells: A bioinformatics and systems biology approach to understanding the genomic pattern of viral replication. J Infect Public Health 2023; 16:399-409. [PMID: 36724696 PMCID: PMC9874307 DOI: 10.1016/j.jiph.2023.01.015] [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: 10/31/2022] [Revised: 01/12/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
PURPOSE The current outbreak of monkeypox (MPX) has created colossal concerns. However, immense research gaps have been noted in our understanding of the replication process, machinery, and genomic landscape during host cell infection. To fill this gap, differentially expressed genes (DEGs) were comprehensively analyzed during viral replication in host (MK2) cells. METHODS We used a microarray GEO dataset which was divided into three groups: control, MPXV-infected MK2 cells at 3 h, and MPXV-infected MK2 cells at 7 h. Using the dataset, DEG analysis, PPI network analysis, co-expression, and pathway analysis were conducted using bioinformatics, systems biology, and statistical approaches. RESULTS We identified 250 DEGs and 24 top-ranked genes. During the DEG analysis, we identified eight up-regulated genes (LOC695323, TMEM107, LOC695427, HIST1H2AD, LOC705469, PMAIP1, HIST1H2BJ, and HIST1H3D) and 16 down-regulated genes (HOXA9, BAMBI, LMO4, PAX6, AJUBA, CREBRF, CD24, JADE1, SLC7A11, EID2, SOX4, B4GALT5, PPARGC1A, BUB3, SOS2, and CDK19). We also developed PPI networks and performed co-expression analyses using the top-ranked genes. Furthermore, five genes were listed for co-expression pattern analysis. CONCLUSIONS This study will help in better understanding the replication process, machinery, and genomic landscape of the virus. This will further aid the discovery and development of therapeutics against viruses.
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Bhattacharya M, Chatterjee S, Lee SS, Chakraborty C. Therapeutic applications of nanobodies against SARS-CoV-2 and other viral infections: Current update. Int J Biol Macromol 2023; 229:70-80. [PMID: 36586649 PMCID: PMC9797221 DOI: 10.1016/j.ijbiomac.2022.12.284] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/15/2022] [Accepted: 12/25/2022] [Indexed: 12/30/2022]
Abstract
In the last two years, the world encountered the SARS-CoV-2 virus, which is still dominating the population due to the absence of a viable treatment. To eradicate the global pandemic, scientists, doctors, and researchers took an exceptionally significant initiative towards the development of effective therapeutics to save many lifes. This review discusses about the single-domain antibodies (sdAbs), also called nanobodies, their structure, and their types against the infections of dreadful SARS-CoV-2 virus. A precise description highlights the nanobodies and their therapeutic application against the other selected viruses. It aims to focus on the extraordinary features of these antibodies compared to the conventional therapeutics like mAbs, convalescent plasma therapy, and vaccines. The stable structure of these nanobodies along with the suitable mechanism of action also confers greater resistance to the evolving variants with numerous mutations. The nanobodies developed against SARS-CoV-2 and its mutant variants have shown the greater neutralization potential than the primitive ones. Engineering of these specialized antibodies by modern biotechnological approaches will surely be more beneficial in treating this COVID-19 pandemic along with certain other viral infections.
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Bhattacharya M, Chatterjee S, Sharma AR, Lee SS, Chakraborty C. Delta variant (B.1.617.2) of SARS-CoV-2: current understanding of infection, transmission, immune escape, and mutational landscape. Folia Microbiol (Praha) 2023; 68:17-28. [PMID: 35962276 PMCID: PMC9374302 DOI: 10.1007/s12223-022-01001-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 08/07/2022] [Indexed: 12/01/2022]
Abstract
The Delta variant is one of the alarming variants of the SARS-CoV-2 virus that have been immensely detrimental and a significant cause of the prolonged pandemic (B.1.617.2). During the SARS-CoV-2 pandemic from December 2020 to October 2021, the Delta variant showed global dominance, and afterwards, the Omicron variant showed global dominance. Delta shows high infectivity rate which accounted for nearly 70% of the cases after December 2020. This review discusses the additional attributes that make the Delta variant so infectious and transmissible. The study also focuses on the significant mutations, namely the L452R and T478K present on the receptor-binding domain of spike (S)-glycoprotein, which confers specific alterations to the Delta variant. Considerably, we have also highlighted other notable factors such as the immune escape, infectivity and re-infectivity, vaccine escape, Ro number, S-glycoprotein stability, cleavage pattern, and its binding affinity with the host cell receptor protein. We have also emphasized clinical manifestations, symptomatology, morbidity, and mortality for the Delta variant compared with other significant SARS-CoV-2 variants. This review will help the researchers to get an elucidative view of the Delta variant to adopt some practical strategies to minimize the escalating spread of the SARS-CoV-2 Delta variant.
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Chakraborty C, Chatterjee S, Bhattacharya M, Chopra H, Bhattacharya P, Islam MA, Dhama K. The D614G mutation helps to increase the transmissibility and reduce the virulence of SARS-CoV-2 variants through natural selection. Int J Surg 2023; 109:171-174. [PMID: 36799841 PMCID: PMC10389482 DOI: 10.1097/js9.0000000000000155] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 02/18/2023]
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