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
Recombination Detection (GARD), all implemented in the HyPhy software
package. Our analysis focused on identifying genomic sites under both
positive and negative selection pressures, providing insights into the
adaptive evolutionary processes affecting the E gene of the dengue virus
in Pakistan. Understanding the molecular evolution of this gene is crucial
for predicting serotype evolution, potentially aiding in the development
of effective vaccines and therapeutic strategies.