Deciphering viral infections at single-cell resolution: From immune dynamics to host-pathogen interactions

Area of Science:

• Virology
• Immunology
• Genomics

Background:

• Single-cell RNA sequencing (scRNA-seq) is a powerful tool for studying viral infections at high resolution.
• It reveals cellular heterogeneity, immune responses, and host-pathogen interactions.
• Applications span various viruses like SARS-CoV-2, HBV, HIV, influenza, and RSV.

Purpose of the Study:

• To review recent advances in scRNA-seq applications for viral infection research.
• To highlight insights into immune regulation, host-pathogen co-transcriptomics, and signaling pathways.
• To discuss limitations, computational strategies, and future integration with other omics platforms.

Main Methods:

• Analysis of viral transcripts within single infected cells.
• Characterization of immune cell heterogeneity and landscape remodeling.
• Integrated T-cell receptor (TCR) and B-cell receptor (BCR) sequencing for adaptive immunity.

Main Results:

• scRNA-seq identifies distinct cellular states and distinguishes infected from bystander cells.
• It reveals virus-induced transcriptional reprogramming and intra-host viral diversity.
• Comparative studies show shared antiviral programs and virus-specific adaptations in acute and chronic infections.

Conclusions:

• scRNA-seq provides critical insights into viral pathogenesis and immune responses.
• It facilitates biomarker discovery and understanding of viral evolution.
• Future integration with spatial transcriptomics and multi-omics will enhance mechanistic understanding and therapeutic strategies for viral diseases.