CpG Signature Profiling and Heatmap Visualization of SARS-CoV Genomes: Tracing the Genomic Divergence From SARS-CoV (2003) to SARS-CoV-2 (2019)

ObjectiveThe primary objective of this study was to analyze CpG dinucleotide dynamics in coronaviruses by comparing Wuhan-Hu-1 with its closest and most distant relatives. Heatmaps were generated to visualize CpG counts and O/E ratios across intergenic regions, providing a clear depiction of conserved and divergent CpG patterns.Methods1. Data CollectionSource : The dataset includes CpG counts and O/E ratios for various coronaviruses, extracted from publicly available genomic sequences.Format : Data was compiled into a CSV file containing columns for intergenic regions, CpG counts, and O/E ratios for each virus.2. PreprocessingData Cleaning :Missing values (NaN), infinite values (inf, -inf), and blank entries were handled using Python's pandas library.Missing values were replaced with column means, and infinite values were capped at a large finite value (1e9).Reshaping :The data was reshaped into matrices for CpG counts and O/E ratios using meltpandas[] and pivot[] functions.3. Distance CalculationEuclidean Distance :Pairwise Euclidean distances were calculated between Wuhan-Hu-1 and other viruses using the scipy.spatial.distance.euclidean function.Distances were computed separately for CpG counts and O/E ratios, and the total distance was derived as the sum of both metrics.4. Identification of Closest and Distant RelativesThe virus with the smallest total distance was identified as the closest relative .The virus with the largest total distance was identified as the most distant relative .5. Heatmap GenerationTools :Heatmaps were generated using Python's seaborn library (sns.heatmap) and matplotlib for visualization.Parameters :Heatmaps were annotated with numerical values for clarity.A color gradient (coolwarm) was used to represent varying CpG counts and O/E ratios.Titles and axis labels were added to describe the comparison between Wuhan-Hu-1 and its relatives.ResultsClosest Relative :The closest relative to Wuhan-Hu-1 was identified based on the smallest Euclidean distance.Heatmaps for CpG counts and O/E ratios show high similarity in specific intergenic regions.Most Distant Relative :The most distant relative was identified based on the largest Euclidean distance.Heatmaps reveal significant differences in CpG dynamics compared to Wuhan-Hu-1 .Tools and LibrariesThe following tools and libraries were used in this analysis:Programming Language :Python 3.13Libraries :pandas: For data manipulation and cleaning.numpy: For numerical operations and handling missing/infinite values.scipy.spatial.distance: For calculating Euclidean distances.seaborn: For generating heatmaps.matplotlib: For additional visualization enhancements.File Formats :Input: CSV files containing CpG counts and O/E ratios.Output: PNG images of heatmaps.Files IncludedCSV File :Contains the raw data of CpG counts and O/E ratios for all viruses.Heatmap Images :Heatmaps for CpG counts and O/E ratios comparing Wuhan-Hu-1 with its closest and most distant relatives.Python Script :Full Python code used for data processing, distance calculation, and heatmap generation.Usage NotesResearchers can use this dataset to further explore the evolutionary dynamics of CpG dinucleotides in coronaviruses.The Python script can be adapted to analyze other viral genomes or datasets.Heatmaps provide a visual summary of CpG dynamics, aiding in hypothesis generation and experimental design.AcknowledgmentsSpecial thanks to the open-source community for developing tools like pandas, numpy, seaborn, and matplotlib.This work was conducted as part of an independent research project in molecular biology and bioinformatics.LicenseThis dataset is shared under the CC BY 4.0 License , allowing others to share and adapt the material as long as proper attribution is given.DOI: 10.6084/m9.figshare.28736501<br>