Selection pressure analysis of dengue virus complete genome and E gene nucleotide sequences from Pakistan

This dataset comprises 43 E gene and 44 complete genome nucleotide sequences of the dengue virus from serotypes DENV-1 to DENV-4, representing all documented sequences in Pakistan to date, sourced from the Virus Pathogen Resource (ViPR) database and NCBI. The E gene is critical as it is involved in serotype changes of the dengue virus, making it a pivotal target for understanding shifts in viral pathogenicity and immune escape mechanisms. The aim of compiling this dataset is to facilitate comprehensive genetic analysis and enhance understanding of the evolutionary dynamics of the dengue virus within the region. To assess the evolutionary pressures acting on these sequences, we conducted a selection pressure analysis utilizing computational methods. These methods include the Single Likelihood Ancestor Counting (SLAC), Fixed Effects Likelihood (FEL), adaptive Branch Site Random Effects Likelihood (aBSREL), Mixed Effects Model of Evolution (MEME), and the Genetic Algorithm for Recombinatio..., Data Collection: The dataset consists of all documented Pakistani dengue virus E gene and complete genome nucleotide sequences available as of the latest update. These sequences were acquired from the Virus Pathogen Resource (ViPR)  and database, which is a comprehensive and freely accessible resource providing sequence data and related information on viral pathogens. The selected sequences span all four serotypes of the dengue virus, specifically DENV-1, DENV-2, DENV-3, and DENV-4, encompassing a total of 43 E gene sequences.
Data Processing and Analysis: Upon collection, the sequences were subjected to several preprocessing steps to ensure data integrity and uniformity. Initially, sequence alignment for the 43 E gene sequences was performed using MEGA-X, a robust tool for aligning nucleotide sequences and conducting phylogenetic analyses. This was followed by further alignment using MUSCLE (Multiple Sequence Comparison by Log-Expectation), which creates high-quality alignments of nucl..., , # Selection pressure analysis of dengue virus complete genome and E gene nucleotide sequences from Pakistan

[https://doi.org/10.5061/dryad.cjsxksnff](https://doi.org/10.5061/dryad.cjsxksnff)

**Dataset Summary:**

This dataset contains 43 E gene and 44 complete genome nucleotide sequences of the dengue virus, encompassing all four serotypes (DENV-1, DENV-2, DENV-3, and DENV-4) identified in Pakistan to date. Additionally, the dataset includes four reference sequences of the dengue virus and six sequences from regions outside Pakistan to provide a broader comparative perspective. All sequences were retrieved from the Virus Pathogen Resource (ViPR) database.

**Experimental Procedures:**

1.      **Data Collection and Sequence Alignment:** Sequences were aligned using MUSCLE for initial processing and MEGA X for detailed phylogenetic analyses. This dual approach ensures robust sequence alignment critical for accurate downstream analysis.

2.      **Phylogenetic Analysis:** After alignmen...