Integrated Environmental and Genetic Data Analysis for Detection and Prediction of Pathogen Mutations: Influenza virus, Plasmodium falciparum, Dengue virus, and Vibrio cholerae in Yemen

Abstract

Hussein Dedy

This study investigates the integration of genetic and environmental data to detect and predict mutations in key infectious disease agents namely Influenza virus, Dengue virus, Plasmodium falciparum (malaria), and Vibrio cholerae (cholera) in Yemen, particularly in the climate-affected region of Al-Hodeidah. By analyzing original and integrated genetic sequences alongside 50 years of climate data ( 2023 - 2047 ) , specific deletion mutations were identified and their probable timelines estimated: Influenza (10–15 years), Dengue (15–20 years), Malaria (20–25 years), and Cholera (25–30 years). Tools such as FastQC, MultiQC, MAFFT, GATK, and SnpEff were used to assess data quality, perform sequence alignment, and annotate mutations. The findings reveal a strong correlation between climatic variations and the emergence of mutations that influence pathogen virulence, transmissibility, and drug resistance. For example, deletions of nucleotides (such as AUG and AGC) altered amino acid sequences, potentially impacting protein functionality. Mutations were also detected in key genes such as PfCRT in Plasmodium and beta-lactamase genes in Vibrio cholerae, both associated with increased resistance to antimalarial and antibiotic therapies.

Additionally, variations in GC content and structural RNA elements (e.g., stem-loops) among viral genomes were linked to greater adaptability and transmission potential. This integrative approach highlights the importance of including environmental data in genomic surveillance systems to improve early detection and epidemic preparedness. The study recommends the adoption of machine learning models, real-time mutation databases, and stronger collaboration between blood banks and genomic laboratories to develop predictive tools for pathogen evolution. This approach offers critical insights for public health strategies, especially in regions vulnerable to climate change and disease outbreaks.

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