School Of Basic And Applied Sciences

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    Understanding Mutations in Human SARS-CoV-2 Spike Glycoprotein: A Systematic Review & Meta-Analysis
    (MDPI, 2023-03-28T00:00:00) Kumar, Reetesh; Srivastava, Yogesh; Muthuramalingam, Pandiyan; Singh, Sunil Kumar; Verma, Geetika; Tiwari, Savitri; Tandel, Nikunj; Beura, Samir Kumar; Panigrahi, Abhishek Ramachandra; Maji, Somnath; Sharma, Prakriti; Rai, Pankaj Kumar; Prajapati, Dinesh Kumar; Shin, Hyunsuk; Tyagi, Rajeev K.
    Genetic variant(s) of concern (VoC) of SARS-CoV-2 have been emerging worldwide due to mutations in the gene encoding spike glycoprotein. We performed comprehensive analyses of spike protein mutations in the significant variant clade of SARS-CoV-2, using the data available on the Nextstrain server. We selected various mutations, namely, A222V, N439K, N501Y, L452R, Y453F, E484K, K417N, T478K, L981F, L212I, N856K, T547K, G496S, and Y369C for this study. These mutations were chosen based on their global entropic score, emergence, spread, transmission, and their location in the spike receptor binding domain (RBD). The relative abundance of these mutations was mapped with global mutation D614G as a reference. Our analyses suggest the rapid emergence of newer global mutations alongside D614G, as reported during the recent waves of COVID-19 in various parts of the world. These mutations could be instrumentally imperative for the transmission, infectivity, virulence, and host immune system�s evasion of SARS-CoV-2. The probable impact of these mutations on vaccine effectiveness, antigenic diversity, antibody interactions, protein stability, RBD flexibility, and accessibility to human cell receptor ACE2 was studied in silico. Overall, the present study can help researchers to design the next generation of vaccines and biotherapeutics to combat COVID-19 infection. � 2023 by the authors.
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    Macrophage Activation Syndrome and COVID 19: Impact of MAPK Driven Immune-Epigenetic Programming by SARS-Cov-2
    (Frontiers Media S.A., 2021-10-01T00:00:00) Roy, Roshan Kumar; Sharma, Uttam; Wasson, Mishi Kaushal; Jain, Aklank; Hassan, Md. Imtaiyaz; Prakash, Hridayesh
    [No abstract available]
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    Current Insights and Molecular Docking Studies of the Drugs under Clinical Trial as RdRp Inhibitors in COVID-19 Treatment
    (Bentham Science Publishers, 2022-11-08T00:00:00) Pauly, Irine; Singh, Ankit Kumar; Kumar, Adarsh; Singh, Yogesh; Thareja, Suresh; Kamal, Mohammad A.; Verma, Amita; Kumar, Pradeep
    Study Background & Objective: After the influenza pandemic (1918), COVID-19 was declared a Vth pandemic by the WHO in 2020. SARS-CoV-2 is an RNA-enveloped single-stranded virus. Based on the structure and life cycle, Protease (3CLpro), RdRp, ACE2, IL-6, and TMPRSS2 are the major targets for drug development against COVID-19. Pre-existing several drugs (FDA-approved) are used to inhibit the above targets in different diseases. In coronavirus treatment, these drugs are also in different clinical trial stages. Remdesivir (RdRp inhibitor) is the only FDA-approved medicine for coronavirus treatment. In the present study, by using the drug repurposing strategy, 70 preexisting clinical or under clinical trial molecules were used in scrutiny for RdRp inhibitor potent molecules in coronavirus treatment being surveyed via docking studies. Molecular simulation studies further confirmed the binding mechanism and stability of the most potent compounds. Material and Methods: Docking studies were performed using the Maestro 12.9 module of Schrodinger soft-ware over 70 molecules with RdRp as the target and remdesivir as the standard drug and further confirmed by simulation studies. Results: The docking studies showed that many HIV protease inhibitors demonstrated remarkable binding interactions with the target RdRp. Protease inhibitors such as lopinavir and ritonavir are effective. Along with these, AT-527, ledipasvir, bicalutamide, and cobicistat showed improved docking scores. RMSD and RMSF were further analyzed for potent ledipasvir and ritonavir by simulation studies and were identified as potential candidates for corona disease. Conclusion: The drug repurposing approach provides a new avenue in COVID-19 treatment. � 2022 Bentham Science Publishers.
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    Exploring the COVID-19 vaccine candidates against SARS-CoV-2 and its variants: where do we stand and where do we go?
    (Taylor and Francis Ltd., 2021-12-03T00:00:00) Joshi, Gaurav; Borah, Pobitra; Thakur, Shweta; Sharma, Praveen; Mayank; Poduri, Ramarao
    As of September 2021, 117 COVID-19 vaccines are in clinical development, and 194 are in preclinical development as per the World Health Organization (WHO) published draft landscape. Among the 117 vaccines undergoing clinical trials, the major platforms include protein subunit; RNA; inactivated virus; viral vector, among others. So far, USFDA recognized to approve the Pfizer-BioNTech (Comirnaty) COVID-19 vaccine for its full use in individuals of 16�years of age and older. Though the approved vaccines are being manufactured at a tremendous pace, the wealthiest countries have about 28% of total vaccines despite possessing only 10.8% of the total world population, suggesting an inequity of vaccine distribution. The review comprehensively summarizes the history of vaccines, mainly focusing on vaccines for SARS-CoV-2. The review also connects relevant topics, including measurement of vaccines efficacy against SARS-CoV-2 and its variants, associated challenges, and limitations, as hurdles in global vaccination are also kept forth. � 2021 Taylor & Francis Group, LLC.
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    Selection of active antiviral compounds against COVID-19 disease targeting coronavirus endoribonuclease nendou/NSP15 via ligand-based virtual screening and molecular docking
    (Bentham Science Publishers, 2020-12-15T00:00:00) Joshi, Gaurav; Poduri, Ramarao
    Background: The rapid spread of SARS-CoV-2 has caused havoc and panic among individuals, which has further worsened due to the unavailability of a proven drug(s) regime. Objective: The current work involves drug repurposing from the pool of USFDA approved drugs involving in silico virtual screening technique against COVID-19. Materials and Methods: Methodology involves virtual screening of 8548 FDA approved drugs against target protein endoribonuclease NendoU (Nsp15) (PDB ID: 6VWW). Result: Virtual screening-based analysis enabled us to identify four drugs, Eprosartan, Inarigivir soproxil, Foretinib, and DB01813 that could plausibly target Nsp15 against COVID-19 disease. Conclusion: The work offers the scope to corroborate the findings via in vitro and in vivo techniques to identify the potential of selected leads against COVID-19. The outcome may also help in tracing their molecular mechanism(s) in addition to their development at the clinical level in the future. � 2021 Bentham Science Publishers.
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    Prediction studies of the epidemic peak of coronavirus disease in Japan: From Caputo derivatives to Atangana-Baleanu derivatives
    (World Scientific, 2021-09-30T00:00:00) Kumar, Pushpendra; Rangaig, Norodin A.; Abboubakar, Hamadjam; Kumar, Anoop; Manickam, A.
    New atypical pneumonia caused by a virus called Coronavirus (COVID-19) appeared in Wuhan, China in December 2019. Unlike previous epidemics due to the severe acute respiratory syndrome (SARS) and the Middle East respiratory syndrome coronavirus (MERS-CoV), COVID-19 has the particularity that it is more contagious than the other previous ones. In this paper, we try to predict the COVID-19 epidemic peak in Japan with the help of real-time data from January 15 to February 29, 2020 with the uses of fractional derivatives, namely, Caputo derivatives, the Caputo-Fabrizio derivatives, and Atangana-Baleanu derivatives in the Caputo sense. The fixed point theory and Picard-Lindel of approach used in this study provide the proof for the existence and uniqueness analysis of the solutions to the noninteger-order models under the investigations. For each fractional model, we propose a numerical scheme as well as prove its stability. Using parameter values estimated from the Japan COVID-19 epidemic real data, we perform numerical simulations to confirm the effectiveness of used approximation methods by numerical simulations for different values of the fractional-order ?, and to give the predictions of COVID-19 epidemic peaks in Japan in a specific range of time intervals. � 2022 World Scientific Publishing Company.
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    A case study of 2019-nCOV cases in Argentina with the real data based on daily cases from March 03, 2020 to March 29, 2021 using classical and fractional derivatives
    (Springer Science and Business Media Deutschland GmbH, 2021-07-20T00:00:00) Kumar, Pushpendra; Erturk, Vedat Suat; Murillo-Arcila, Marina; Banerjee, Ramashis; Manickam, A.
    In this study, our aim is to explore the dynamics of COVID-19 or 2019-nCOV in Argentina considering the parameter values based on the real data of this virus from March�03, 2020 to March�29, 2021 which is a data range of more than one complete year. We propose a Atangana�Baleanu type fractional-order model and simulate it by using predictor�corrector (P-C) method. First we introduce the biological nature of this virus in theoretical way and then formulate a mathematical model to define its dynamics. We use a well-known effective optimization scheme based on the renowned trust-region-reflective (TRR) method to perform the model calibration. We have plotted the real cases of COVID-19 and compared our integer-order model with the simulated data along with the calculation of basic reproductive number. Concerning fractional-order simulations, first we prove the existence and uniqueness of solution and then write the solution along with the stability of the given P-C method. A�number of graphs at various fractional-order values are simulated to predict the future dynamics of the virus in Argentina which is the main contribution of this paper. � 2021, The Author(s).
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    Short-term forecasting of the COVID-19 outbreak in India
    (Oxford University Press, 2021-05-28T00:00:00) Mangla, Sherry; Pathak, Ashok Kumar; Arshad, Mohd; Haque, Ubydul
    As the outbreak of coronavirus disease 2019 (COVID-19) is rapidly spreading in different parts of India, a reliable forecast for the cumulative confirmed cases and the number of deaths can be helpful for policymakers in making the decisions for utilizing available resources in the country. Recently, various mathematical models have been used to predict the outbreak of COVID-19 worldwide and also in India. In this article we use exponential, logistic, Gompertz growth and autoregressive integrated moving average (ARIMA) models to predict the spread of COVID-19 in India after the announcement of various unlock phases. The mean absolute percentage error and root mean square error comparative measures were used to check the goodness-of-fit of the growth models and Akaike information criterion for ARIMA model selection. Using COVID-19 pandemic data up to 20 December 2020 from India and its five most affected states (Maharashtra, Karnataka, Andhra Pradesh, Tamil Nadu and Kerala), we report 15-days-ahead forecasts for cumulative confirmed cases and the number of deaths. Based on available data, we found that the ARIMA model is the best-fitting model for COVID-19 cases in India and its most affected states. � 2021 The Author(s) 2021.
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    A new fractional mathematical modelling of COVID-19 with the availability of vaccine
    (Elsevier B.V., 2021-04-21T00:00:00) Kumar, Pushpendra; Erturk, Vedat Suat; Murillo-Arcila, Marina
    The most dangerous disease of this decade novel coronavirus or COVID-19 is yet not over. The whole world is facing this threat and trying to stand together to defeat this pandemic. Many countries have defeated this virus by their strong control strategies and many are still trying to do so. To date, some countries have prepared a vaccine against this virus but not in an enough amount. In this research article, we proposed a new SEIRS dynamical model by including the vaccine rate. First we formulate the model with integer order and after that we generalize it in Atangana�Baleanu derivative sense. The high motivation to apply Atangana�Baleanu fractional derivative on our model is to explore the dynamics of the model more clearly. We provide the analysis of the existence of solution for the given fractional SEIRS model. We use the famous Predictor�Corrector algorithm to derive the solution of the model. Also, the analysis for the stability of the given algorithm is established. We simulate number of graphs to see the role of vaccine on the dynamics of the population. For practical simulations, we use the parameter values which are based on real data of Spain. The main motivation or aim of this research study is to justify the role of vaccine in this tough time of COVID-19. A clear role of vaccine at this crucial time can be realized by this study. � 2021 The Authors
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    Projections and fractional dynamics of COVID-19 with optimal control strategies
    (Elsevier Ltd, 2021-01-28T00:00:00) Nabi, Khondoker Nazmoon; Kumar, Pushpendra; Erturk, Vedat Suat
    When the entire world is eagerly waiting for a safe, effective and widely available COVID-19 vaccine, unprecedented spikes of new cases are evident in numerous countries. To gain a deeper understanding about the future dynamics of COVID-19, a compartmental mathematical model has been proposed in this paper incorporating all possible non-pharmaceutical intervention strategies. Model parameters have been calibrated using sophisticated trust-region-reflective algorithm and short-term projection results have been illustrated for Bangladesh and India. Control reproduction numbers (Rc) have been calculated in order to get insights about the current epidemic scenario in the above-mentioned countries. Forecasting results depict that the aforesaid countries are having downward trends in daily COVID-19 cases. Nevertheless, as the pandemic is not over in any country, it is highly recommended to use efficacious face coverings and maintain strict physical distancing in public gatherings. All necessary graphical simulations have been performed with the help of Caputo�Fabrizio fractional derivatives. In addition, optimal control strategies for fractional system have been designed and the existence of unique solution has also been showed using Picard�Lindelof technique. Finally, unconditional stability of the fractional numerical technique has been proved. � 2021