Integrative genomics important to understand host–pathogen interactions.

This article focuses on integrative genomics approaches, particularly RNA sequencing (RNA-seq), to investigate the complex interactions between pathogens, host responses, and co-infecting microbes that influence infectious disease severity and clinical outcomes. It highlights how RNA-seq data can simultaneously characterize pathogen genome architecture, host protein-coding and non-coding RNA expression, alternative splicing events, and transcriptionally active co-infecting microbes from clinical samples. The study emphasizes the importance of considering these interconnected functional domains together to better understand disease progression, immune responses, and microbial dysbiosis, advocating for an expanded definition of genomic surveillance that includes host and microbiome factors alongside pathogen genomics. This integrative strategy aims to enhance insights for disease management and pandemic preparedness.