Research Article A New Informatics Framework for Evaluating the Codon Usage Metrics, Evolutionary Models and Phylogeographic Reconstruction of Tomato Yellow Leaf Curl Virus (TYLCV) in Different Regions of Asian Countries

Not AvailableTomato yellow leaf curl virus (TYLCV) is a major devastating viral disease, majorly affecting the tomato production globally. The disease is majorly transmitted by the Whitefly. The Begomovirus (TYLCV) having a six major protein coding genes, among them the C1/AC1 is evidently associated with viral replication. Owing to immense role of C1/AC1 gene, the present study is an initial effort to elucidate the factors shaping the codon usage bias and evolutionary pattern of TYLCV-C1/AC1 gene in five major Asian countries. Based on publicly available nucleotide sequence data the Codon usage pattern, Evolutionary and Phylogeographic reconstruction was carried out. The study revealed the presence of significant variation between the codon bias indices in all the selected regions. Implying that the codon usage pattern indices (eNC, CAI, RCDI, GRAVY, Aromo) are seriously affected by selection and mutational pressure, taking a supremacy in shaping the codon usage bias of viral gene. Further, the tMRCA age was 1853, 1939, 1855, 1944, 1828 for China, India, Iran, Oman and South Korea, respectively for TYLCV-C1/AC1 gene. The integrated analysis of Codon usage bias, Evolutionary rate and Phylogeography analysis in viruses signifies the positive role of selection and mutational pressure among the selected regions for TYLCV (C1/AC1) gene.Not Availabl

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Not AvailableAfrican swine fever virus (ASFV) belongs to the family of Asfarviridae to the genus Asfivirus. ASF virus causes hemorrhage illness with a high mortality rate and hence, commercial loss in the swine community. The ASFV has been categorized by variation in codon usage that is caused by high mutation rates and natural selection. The evolution is caused mainly due to the mutation pressure and regulating the protein gene expression. Based on publicly accessible nucleotide sequences of the ASFV and its host (pig & tick), codon usage bias analysis was performed since an approved effective vaccination is not available to date, it is very important to analyze the codon usage bias of the p30, p54, and p72 proteins of ASFV to produce an effective and efficient vaccine to control the disease. Even though the codon usage bias analyses have been evaluated earlier, the evaluation of the codon usage pattern specific to p30, p54, and p72 of ASFV is inadequate. In all the protein-coding sequences, nucleotide base and codons terminating with base T were most frequent and the mean effective number of codons (Nc) was high, indicating the presence of codon usage bias. The GC contents and dinucleotide frequencies also indicated the codon usage bias of the ASFV pig and tick. The Nc plot, parity plot, neutrality plot analysis, revealed natural selection, as well as mutation pressure, were the major constraints in altering the codon bias of ASF virus. codon usage bias analysis was performed with no substantial differences in codon usage of the ASFV in pig and tickNot Availabl

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Not AvailableBackground and Aim: Classical swine fever (CSF), caused by CSF virus (CSFV), is a highly contagious disease in pigs causing 100% mortality in susceptible adult pigs and piglets. High mortality rate in pigs causes huge economic loss to pig farmers. CSFV has a positive-sense RNA genome of 12.3 kb in length flanked by untranslated regions at 5’ and 3’ end. The genome codes for a large polyprotein of 3900 amino acids coding for 11 viral proteins. The 1300 codons in the polyprotein are coded by different combinations of three nucleotides which help the infectious agent to evolve itself and adapt to the host environment.  This study performed and employed various methods/techniques to estimate the changes occurring in the process of CSFV evolution by analyzing the codon usage pattern. Materials and Methods: The evolution of viruses is widely studied by analyzing their nucleotides and coding regions/ codons using various methods. A total of 115 complete coding regions of CSFVs including one complete genome from our laboratory (MH734359) were included in this study and analysis was carried out using various methods in estimating codon usage bias and evolution. This study elaborates on the factors that influence the codon usage pattern. Results: The effective number of codons (ENC) and relative synonymous codon usage showed the presence of codon usage bias. The mononucleotide (A) has a higher frequency compared to the other mononucleotides (G, C, and T). The dinucleotides CG and CC are underrepresented and overrepresented. The codons CGT was underrepresented and AGG was overrepresented. The codon adaptation index value of 0.71 was obtained indicating that there is a similarity in the codon usage bias. The principal component analysis, ENC-plot, Neutrality plot, and Parity Rule 2 plot produced in this article indicate that the CSFV is influenced by the codon usage bias. The mutational pressure and natural selection are the important factors that influence the codon usage bias. Conclusion: The study provides useful information on the codon usage analysis of CSFV and may be utilized to understand the host adaptation to virus environment and its evolution. Further, such findings help in new gene discovery, design of primers/probes, design of transgenes, determination of the origin of species, prediction of gene expression level, and gene function of CSFV. To the best of our knowledge, this is the first study on codon usage bias involving such a large number of complete CSFVs including one sequence of CSFV from India.Not Availabl

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Not AvailableAnthrax is an ancient and acuteillness that affects alarge quantity of animal species and is caused by a bacterium Bacillus anthracis, which is a rod-shaped, gram-positive and spore-forming bacterium. Virulent forms of B.anthracishas two large pathogenicity related plasmids pXO1 and pXO2. pXO1 has the different anthrax toxin genes cya, lef, and pagA where as pXO2 has the genes accountable for capsule synthesis and degradation, capA, capB, capC, and capD. B. anthracis express its pathogenic activity mostly over the capsule and the manufacture of a toxic compound involving three proteins known as edema factor (EF), lethal factor (LF) and protective antigen (PA). These two enormous plasmids of B.anthracisare crucial for full pathogenicity, exclusion of either of the plasmids extremely weakens the malignity of B. anthracis. In the current study we conducted the relative analysis of the codon usage and nucleotide bias of virulent genes subsist in pXO1 plasmid of B.anthracis. Codon usage bias not only plays a substantial role at the extent of gene expression, but also supports to improve the efficacy and accurateness of translation. Codon usage pattern analysis of B. anthracisgenome is essential for understanding the evolutionary characteristicsin the different species. To examine the codon usage arrangement of theB.anthracisgenome, Nucleotide sequences of the virulent genes viz cya, lef and pag were collected from National Center for Biotechnology Information (NCBI). The correlations between GC3s, whole GC content, Effective No. of Codons (ENC), Codon Adaptation Index (CAI), Codon Bias Index (CBI), Frequency of Optimal Codons (FOP), General average hydropathicity (Gravy) and Aromaticity (Aroma), of the selected genes were determined. The ENC-plot i.e., ENc values vs GC3s, Pr2 plot i.e., relationship between A3 / (A3 +T3) and G3 / (G3 +C3), Neutrality plot i.e., GC12 versus GC3s, and the RSCU of the genes, all shows codon usage bias existence in all the virulent genes subsists in pXO1 plasmid of B.anthracis genome. These results expresses the codon usage bias existing in the pXO1 plasmid’s virulent genes of B.anthracis genome could be utilized for further exploration on their evolutionary analysis as in design of primers, design of transgenes, determine of origin of species as well as prediction of gene expression level and gene functionNot Availabl

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Not AvailableBacillus anthracis is a Gram-positive spore-forming bacterium that causes the zoonotic disease: anthrax, an abrupt illness that disproportionately impacts grazing livestock and wild ruminants. The anthrax’s geographical reach despite years of research on anthrax epizootic and epidemics behaviour, till date remains to be elucidated. Existing therapeutics, however, are ineffective in combating this infectious disease, necessitating the development of a better vaccine to halt the pandemic using immunoinformatics approaches, this study intended to predict an efficient epitope for vaccine against the anthrax in animals and humans of the toxin genes such as cya, lef and pagA of B. anthracis against anthrax. The B-cell and T-cell epitopes were predicted utilizing various bioinformatics tools/software and docking analysis was performed. Consequently, it was found that the evaluated epitopes had no allegenicity, no toxicity and had high antigenicity that provides an effectual and most rapid technique to estimate peptide synthetic vaccines to impede the anthrax.Not Availabl

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Not AvailableOutbreaks of very high pathogenic avian influenza (H5N1) viruses are being reported in poultry in almost all countries including Asia. It has been reported that the spread is very fast and found that this virus is spreading in avian species since several years. In this study, the evidence of positive selection prominent to mutations was analyzed for the Hemagglutinin (HA) and Neuraminidase (NA) nucleotide sequences of H5N1 avian influenza from chicken, duck and goose across Asia. H5N1 avian influenza viruses are being a severe risk to the public health. Detection of positive selection sites in Hemagglutinin (HA) and Neuraminidase (NA) genes will help to trace the evolutionary path of these viruses from different poultry hosts. The positive/ diversifying selection (dN/dS (w) >1) was found to be showing significant signals in mutation of HA and NA genes and is evolving rapidly. The cumulative dN/dS (w) ratio was found ranging from 0.21 to 0.23 in HA gene and 0.16 to 0.25 in NA gene of Avian Influenza Virus from chicken, duck and goose. Furthermore, statistical Bayesian model methods were applied to interpret the genetic diversity of H5N1 strain, the evolutionary rates were ranging from 2.36x10-3 to 5.19x10-3 in HA gene and 2.28x10-3 to 6.25x10-3 in NA gene from chicken, duck and goose respectively, which revealed a rapid evolution in these viruses with respect to their genetic ancestor. Substitution rates and selection pressure in these three different hosts indicate that their dynamics of mutation and replication remain similar among the species studied and are important for evolution.Not Availabl

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Not AvailableKyasanur Forest Disease was ϐirst evolved in the Kyasanur forest, Karnataka. The transmission of the virus has occurred from the monkey to the human by the tick vector. On the early day of viral spread, the disease was restricted to the surrounded region of Kyasanur forest, Shimoga district. But in the present days, the disease has been spreading to neighboring districts and states as well. So, this study involves estimation of codon bias among the gene C, gene E, gene prM, and gene NS5 of the KFD virus and rate of evolution with phylogenetic analysis. The codon usage analysis has revealed the moderate codon bias among all the selected genes and the role of mutation pressure in genesC and E and natural selection in genes- prM and NS5. Also, the tMRCA age was 1942, 1982, 1975, and 1931 of genes- C, E, prM, and NS5, respectively, of the KFD virus. The integrated analysis of codon usage bias and evolutionary rate analysis signiϐies that both mutational pressure and natural selection among the selected genes of the KFD virusNot Availabl

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Not AvailableFoot and mouth disease (FMD) is a major economically important viral disease of cloven-hoofed livestock globally. The FMD virus (FMDV) spreads widely in confined, cool, and humid climatic conditions. Being an RNA virus, FMDV is genetically unstable, and its genome evolution is highly influenced by mutational pressure. The climatic and environmental conditions have a significant impact on mutational pressure. The present study is a primary effort to establish a comprehensive relationship between climatic factors and the molecular evolutionary pattern of serotypes FMDV circulating in India. In this study, isolates of three serotypes (A, Asia 1, and O) were selected from six major climatic zones of India (Montane, Humid subtropical, Tropical wet and dry, Tropical wet, Semi-arid and Arid). Based on the full genome nucleotide sequence data, the codon usage bias, evolutionary and phylogeographic analysis was carried out. The study revealed that the codon use bias indicators in the FMDV serotypes differed significantly depending on the climatic zones. It implies that the selection and mutational pressure influence the codon usage pattern indices, with mutational pressure taking precedence in determining the codon usage bias of the FMDV genome. The tMRCA was estimated to be 1977, 1956, and 1953 for Indian FMD virus serotype-A, Asia 1, and O respectively which is around 32, 60, and 61 years before its actual identification in the field. Based on the evolutionary rates the serotype O is evolving rapidly compare to other serotypes in India. Virus transmission across the region was evident from the phylogeographic analysis. The integrated analysis of codon usage bias, evolutionary rate, and phylogeography analysis signifies the major role of mutational and selection pressure, implying that the FMD virus co-evolution and adaptations are highly influenced by climatic/environmental factors.Not Availabl

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Not AvailableAfrican swine fever virus (ASFV) belongs to the genus of virus of the Asfaviridae family. ASFV infection causes hemorrhage and high death rate hence increased loss to the swine community. It is a complex infectious disease of swine, which constitutes devastating impacts on animal health and the economy of the pig farmers. It has been confirmed that virus infections has been spreading in swine population for many years. In this study, the evolutionary epidemiology analysis of ASF virus from the geographical regions Africa, Europe, and Asia, respectively were retrieved from GenBank for the analysis. The nucleotide gene sequences of the viral protein p72 encoded by B646L gene published during 1960-2020 was taken in to study. The Bayesian skyline model with uncorrelated randomized clock model was employed to reconstruct the evolutionary history of the virus, to identify virus population demographics. Results of the analysis suggested that ASFV exhibited a high evolutionary rate, as the divergence caused reduction in the population in the recent years. The B646L gene of ASFV had an evolutionary rate of 4.13 X 10-6 substitution/site/year and the tMRCA as 3.15 x 105 with 95 percent HPD range in years (2.4 x 104 to 1.23 x 106) was obtained. In conclusion, the evolutionary study of ASFV with p72 protein from the ASFV of the B646L genes indicated that they evolved at a faster rate and plays a major role in the evolutionary process. Further, this study may help in designing or developing vaccines to control the spread of the disease.Not Availabl

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Not AvailableCrimean-Congo hemorrhagic fever (CCHF) virus is one among the major zoonosis viral diseases that use the Hyalomma ticks as their transmission vector to cause viral infection to the human and mammalian community. The fatality of infectious is high across the world especially in Africa, Asia, Middle East, and Europe. This study regarding codon usage bias of S, M, and L segments of the CCHF virus pertaining to the host Homo sapiens, reveals in-depth information about the evolutionary characteristics of CCHFV. Relative Synonymous Codon Usage (RSCU), Effective number of codons (ENC) were calculated, to determine the codon usage pattern in each segment. Correlation analysis between Codon adaptation index (CAI), GRAVY (Hydrophobicity), AROMO (Aromaticity), and nucleotide composition revealed bias in the codon usage pattern. There was no strong codon bias found among any segments of the CCHF virus, indicating both the factors i.e., natural selection and mutational pressure shapes the codon usage biasNot Availabl