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Benefiting from the advancement of eukaryotic, prokaryotic (e.g., MATQ\u2010seq and BacDrop), and dual (e.g., PatH\u2010Cap) single\u2010cell sequencing technologies, changes in each side and host\u2010pathogen interactions can be elucidated. Pathogens undergo adaptive evolution in the host microenvironment, exhibiting different transcription profiles (e.g., upregulated HSV\u20101 immediate\u2010early genes during infection), transcription efficiencies, and others. Consequently, they develop distinct replication capacity, virulence, and other phenotypes. For the host, intrinsic differences among cells and variations brought by diverse phenotypic pathogens together determine the heterogeneity of its responses (e.g., the dual roles of interferon\u2010I at different infection stages). Interferon\u2010related pathway alterations (influencing both adaptive and innate immune responses) and cell exhaustion (manifesting as the functional impairment of cells) are observed in various infections, seemingly as a shared approach in host\u2010pathogen interactions. These underlying commonalities provide a basis for the development of broad\u2010spectrum therapeutic targets. Collectively, this work reviewed recent progress of single\u2010cell sequencing technologies and their applications in infectious diseases, aiming to facilitate the development of powerful diagnostic or therapeutic strategies and thus advance precision medicine.<\/jats:p>","DOI":"10.1002\/advs.202415678","type":"journal-article","created":{"date-parts":[[2025,7,4]],"date-time":"2025-07-04T09:25:14Z","timestamp":1751621114000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Advances in Single\u2010Cell Sequencing for Infectious Diseases: Progress and Perspectives"],"prefix":"10.1002","volume":"12","author":[{"given":"Mengyuan","family":"Lyu","sequence":"first","affiliation":[{"name":"Department of Laboratory Medicine West China Hospital Sichuan University  Chengdu Sichuan 610041 P. R. 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