Intracellular microbial shifts during COVID-19 infection and longitudinal recovery revealed by single-cell RNA sequencing

Host-microbe dynamics during SARS-CoV-2 Omicron variant infection and recovery remain poorly understood, particularly regarding intracellular microbial communities in immune cells. We performed single-cell RNA sequencing of 191,417 peripheral blood mononuclear cells (PBMCs) from 57 individuals (9 healthy, 24 Omicron-infected, 16 recently recovered, 8 long-recovered) using the BD Rhapsody platform. Microbial signatures identified with PathogenTrack revealed elevated alpha diversity in acutely infected and recently recovered groups, driven by opportunistic pathogens such as Escherichia coli and Providentia stuartii. In contrast, healthy and long-recovered individuals displayed commensal-dominated profiles, notably Streptomyces sviceus , indicative of restored balance. Functional analysis showed persistent microbial signatures, including Clostridium botulinum's rpoB in B cells of long-recovered individuals, broad expression of E. coli stress gene sgrR , and Mycoplasma hyopneumoniae's rpsO across 12 immune subsets. Notably, S. sviceus dnaK was exclusive to healthy monocytes. These results suggest enduring intracellular microbial influences, implicating them in long-COVID pathophysiology with potential therapeutic relevance.