Prolonged COVID-19 pandemic accelerates the emergence and transmissibility of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants through the accumulation of adaptive mutations. Particularly, adaptive mutations in spike (S) protein of SARS-CoV-2 leads to increased viral infectivity, severe morbidity and mortality, and immune evasion. This study focuses on the phylodynamic distribution of SARS-CoV-2 variants during the year 2021 in India besides analyzing the functional significance of mutations in S-protein of SARS-CoV-2 variants.Whole genome of SARS-CoV-2 sequences (n = 87957) from the various parts of India over the period of January to December 2021 was retrieved from Global Initiative on Sharing All Influenza Data. All the S-protein sequences were subjected to clade analysis, variant calling, protein stability, immune escape potential, structural divergence, Furin cleavage efficiency, and phylogenetic analysis using various in silico tools.Delta variant belonging to 21A, 21I, and 21J clades was found to be predominant throughout the year 2021 though many variants were also present. A total of 4639 amino acid mutations were found in S-protein. D614G was the most predominant mutation in the S-protein followed by P681R, L452R, T19R, T478K, and D950N. The highest number of mutations was found in the N-terminal domain of S-protein. Mutations in the crucial sites of S-protein impacting pathogenicity, immunogenicity, and fusogenicity were identified. Intralineage diversity analysis showed that certain variants of SARS-CoV-2 possess high diversification.The study has disclosed the distribution of various variants including the Delta, the predominant variant, in India throughout the year 2021. The study has identified mutations in S-protein of each SARS-CoV-2 variant that can significantly impact the virulence, immune evasion, increased transmissibility, high morbidity, and mortality. In addition, it is found that mutations acquired during each viral replication cycle introduce new sub-lineages as studied by intralineage diversity analysis.
The emergence of a novel coronavirus in China has turned into a SARS-CoV-2 pandemic with high fatality. As vaccines are developed through various strategies, their immunogenic potential may drastically vary and thus pose several challenges in offering immune responses against the virus.In this study, we adopted an immunoinformatics-aided approach for developing a new multi-epitope vaccine construct (MEVC). In silico approach was taken for the identification of B-cell and T-cell epitopes in the Spike protein, for MEVC various cytotoxic T-lymphocyte, helper T-lymphocyte, and B-cell epitopes with the highest affinity for the respective HLA alleles were assembled and joined by linkers.The computational data suggest that the MEVC is nontoxic, nonallergenic and thermostable and elicit both humoral and cell-mediated immune responses. Subsequently, the biological activity of MEVC was assessed by bioinformatic tools using the interaction between the vaccine candidate and the innate immune system receptors TLR3 and TLR4. The epitopes of the construct were analyzed with that of the strains belonging to various clades including the emerging variants having multiple unique mutations in S protein.Due to the advantageous features, the MEVC can be tested in vitro for more practical validation and the study offers immense scope for developing a potential vaccine candidate against SARS-CoV-2 in view of the public health emergency associated with COVID-19 disease caused by SARS-CoV-2.
Abstract Development of microbial fermentation and scale up processes for the production of value added metabolites including enzymes derives importance in industrial research. Though there are numerous studies on the production of industrial enzymes especially proteases using shake flasks, scale up studies with respect to mass transfer and hydrodynamics of fermentation in bioreactors are limited. The study deals with the production and scale up of an extracellular alkaline protease using Bacillus sp. S2 MTCC 13117 from shake flask level to 300 L fermenter. Glucose, DO, and pH profiles during scale up were studied in detail. Scale up parameters related to oxygen dynamics such as oxygen uptake rate (OUR), oxygen transfer rate (OTR), specific OUR and volumetric oxygen transfer coefficient (k L a) were evaluated. Results showed that yield coefficients with respect to biomass, product and substrate were reproduced at different levels of protease scale up in the batch mode of fermentation. Protease production was subjected to catabolite repression and it was shown to be derepressed at low specific growth rates. It was observed that the bioprocess of protease production was an aerobic one and was highly influenced by hydrodynamic conditions in the bioreactors. Use of bioreactor systems enabled effective oxygen transfer and the duration for achieving optimal protease production was reached earlier (t = 36 h in 19 L and t = 24 h in 300 L) when compared to shake flask experiments (t = 44 h). Besides, improvement in the productivity of the fermentation was substantiated by several other scale up parameters such as aeration rate, impeller tip speed, gas hold up and superficial gas velocity for effective mixing and rheological properties of the broth during fermentation in 19 and 300 L fermenters.
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.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.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.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.
Abstract Development of microbial fermentation and scale up processes for the production of value added metabolites including enzymes derives importance in industrial research. Though there are numerous studies on the production of industrial enzymes especially proteases using shake flasks, scale up studies with respect to mass transfer and hydrodynamics of fermentation in bioreactors are limited. The study deals with the production and scale up of an extracellular alkaline protease using Bacillus sp. S2 MTCC 13117 from shake flask level to 300 L fermenter. Glucose, DO, and pH profiles during scale up were studied in detail. Scale up parameters related to oxygen dynamics such as oxygen uptake rate (OUR), oxygen transfer rate (OTR), specific OUR and volumetric oxygen transfer coefficient (k L a) were evaluated. Results showed that yield coefficients with respect to biomass, product and substrate were reproduced at different levels of protease scale up in the batch mode of fermentation. Protease production was subjected to catabolite repression and it was shown to be derepressed at low specific growth rates. It was observed that the bioprocess of protease production was an aerobic one and was highly influenced by hydrodynamic conditions in the bioreactors. Use of bioreactor systems enabled effective oxygen transfer and the duration for achieving optimal protease production was reached earlier (t = 36 h in 19 L and t = 24 h in 300 L) when compared to shake flask experiments (t = 44 h). Besides, improvement in the productivity of the fermentation was substantiated by several other scale up parameters such as aeration rate, impeller tip speed, gas hold up and superficial gas velocity for effective mixing and rheological properties of the broth during fermentation in 19 and 300 L fermenters.
Monkeypox, now named mpox, has emerged as a significant public threat, as evidenced by the 2022 outbreak affecting over seventy countries globally. This infectious disease presents debilitating symptoms, including painful skin rashes, mucosal lesions, enlarged lymph nodes, and fever. The situation intensifies with concerns about a novel transmission route, specifically through sexual contact, and the evolution of more transmissible strains. Complicating matters further is the documented spillback of mpox from humans to animals, raising the potential for new animal reservoirs. This study utilized a systematic approach to gather, analyse, and interpret data regarding global mpox outbreaks, phylogenomics, human APOBEC3 enzyme activity, antiviral resistance issues, and the application of the One Health intervention. Emphasizing a One Health approach covers various aspects, including zoonotic origins, pathogenesis, changing epidemiological landscapes, phylogenomic diversity, and clade dynamics. The review underscores the crucial role of global collaboration in understanding and combatting mpox and making it a valuable resource for shaping effective prevention and control measures on a global scale.
Abstract The emergence of a novel coronavirus in China in late 2019 has turned into a SARS-CoV-2 pandemic affecting several millions of people worldwide in a short span of time with high fatality. The crisis is further aggravated by the emergence and evolution of new variant SARS-CoV-2 strains in UK during December, 2020 followed by their transmission to other countries. A major concern is that prophylaxis and therapeutics are not available yet to control and prevent the virus which is spreading at an alarming rate, though several vaccine trials are in the final stage. As vaccines are developed through various strategies, their immunogenic potential may drastically vary and thus pose several challenges in offering both arms of immunity such as humoral and cell-mediated immune responses against the virus. In this study, we adopted an immunoinformatics-aided identification of B cell and T cell epitopes in the Spike protein, which is a surface glycoprotein of SARS-CoV-2, for developing a new Multiepitope vaccine construct (MEVC). MEVC has 575 amino acids and comprises adjuvants and various cytotoxic T-lymphocyte (CTL), helper T-lymphocyte (HTL), and B-cell epitopes that possess the highest affinity for the respective HLA alleles, assembled and joined by linkers. The computational data suggest that the MEVC is non-toxic, non-allergenic and thermostable with the capability to elicit both humoral and cell-mediated immune responses. The population coverage of various countries affected by COVID-19 with respect to the selected B and T cell epitopes in MEVC was also investigated. Subsequently, the biological activity of MEVC was assessed by bioinformatic tools using the interaction between the vaccine candidate and the innate immune system receptors TLR3 and TLR4. The epitopes of the construct were analyzed with that of the strains belonging to various clades including the new variant UK strain having multiple unique mutations in S protein. Due to the advantageous features, the MEVC can be tested in vitro for more practical validation and the study offers immense scope for developing a potential vaccine candidate against SARS-CoV-2 in view of the public health emergency associated with COVID-19 disease caused by SARS-CoV-2.
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