Insertion sequence (IS) 6110 is found at multiple sites in the Mycobacterium tuberculosis genome and displays a high degree of polymorphism with respect to copy number and insertion sites. Therefore, IS6110 is considered to be a useful molecular marker for diagnosis and strain typing of M. tuberculosis. Generally IS6110 elements are identified using experimental methods, useful for analysis of a limited number of isolates. Since short read genome sequences generated using next-generation sequencing (NGS) platforms are available for a large number of isolates, a computational pipeline for identification of IS6110 elements from these datasets was developed. This study shows results from analysis of NGS data of 1377 M. tuberculosis isolates. These isolates represent all seven major global lineages of M. tuberculosis. Lineage specific copy number patterns and preferential insertion regions were observed. Intra-lineage differences were further analyzed for identifying spoligotype specific variations. Copy number distribution and preferential locations of IS6110 in different lineages imply independent evolution of IS6110, governed mainly through ancestral insertion, fitness (gene truncation, promoter activity) and recombinational loss of some copies. A phylogenetic tree based on IS6110 insertion data of different isolates was constructed in order to understand genome level variations of different markers across different lineages.

Background: Although the SARS-CoV-2 and dengue viruses seriously endanger human health, there is presently no vaccine that can stop a person from contracting both viruses at the same time. In this study, four antigens from SARS-CoV-2 and dengue virus were tested for immunogenicity, antigenicity, allergenicity, and toxicity and chosen to predict dominant T- and B-cell epitopes.Methods: For designing a multi-epitope vaccine, the sequences were retrieved, and using bioinformatics and immunoinformatics, the physicochemical and immunological properties, as well as secondary structures, of the vaccine were predicted and studied. Additionally, the three-dimensional structure was estimated, improved upon, and confirmed using bioinformatics methods before being docked with TLR-2 and TLR-4. Eight helper T-cell lymphocyte (HTL) epitopes, ten cytotoxic T-cell lymphocyte (CTL) epitopes, nine B-cell epitopes, and TLR agonists were used to create a new multi-epitope vaccine. Furthermore, according to the immunological stimulation hypothesis, the vaccine could stimulate T and B cells to create large quantities of Th1 cytokines and antibodies.Results: The study indicates that the developed vaccine is a favorable vaccine candidate with antigenicity, immunogenicity, non-toxicity, and non-allergenicity properties. The vaccine construct was made up of 460 amino acids, had an MW of 49391.51 Da, a theoretical pI of 9.86, and the formula C₂₂₀₃H₃₄₃₃N₆₄₃O₆₁₈S₁₈, a lipid index of 39.84, a GRAVY of −0.473, an aliphatic index of 63.80, and an instability index of 39.84, which classifies the protein to be stable.Conclusion: The acquired data showed that both vaccine designs had a considerable chance of preventing the co-infection of SARS-CoV-2 and dengue virus and that they demonstrate good results following in-silico testing. Furthermore, the vaccine may be an effective strategy in preventing SARS-CoV-2 and dengue since it can cause noticeably high levels of Th1 cytokines and antibodies.

SARS-CoV-2 is a highly virulent and deadly RNA virus causing the Covid-19 pandemic and several deaths across the world. The pandemic is so fast that any concrete theory of sudden widespread of this disease is still not known. In this work, we studied and analyzed a large number of publicly available SARS-CoV-2 genomes across the world using the multifractal approach. The mutation events in the isolates obey the Markov process and exhibit very high mutational rates, which occur in six specific genes and highest in orf1ab gene, leading to virulent nature. f ( α ) analysis indicated that the isolates are highly asymmetric (left-skewed), revealing the richness of complexity and dominance by large fluctuations in genome structure organization. The values of H _q and D _q are found to be significantly large, showing heterogeneous genome structure self-organization, strong positive correlation in organizing the isolates, and quite sensitive to fluctuations in and around it. We then present multiple-isolates hosts-virus interaction models, and derived Price equation for the model. The phase plane analysis of the model showed asymptotic stability type bifurcation. The competition among the mutant isolates drives the trade-off of the dominant mutant isolates, otherwise confined to the present hosts.