Single-Cell RNA Sequencing Reveals Hemocyte Heterogeneity, Differentiation Trajectories, and Viral Tropism in Shrimp (Macrobrachium rosenbergii) Infected with Decapod Iridescent Virus 1

Abstract

Decapod Iridescent Virus 1 (DIV1) is a highly pathogenic virus threatening crustacean aquaculture. Hemocytes, the primary immune cells in shrimp, play crucial roles in host defense, yet their transcriptional heterogeneity and differentiation dynamics under viral infection remain poorly understood. Here, we characterize hemocyte subpopulations in Macrobrachium rosenbergii before and after DIV1 infection at single-cell resolution. We identified 12 distinct hemocyte clusters with unique molecular signatures. DIV1 infection induced significant shifts in hemocyte composition, with clusters 0, 5, 6, and 8 expanding, while clusters 9 and 10 exhibited resistance. Clusters 0, 5, and 8 were highly susceptible, showing elevated viral gene expression. Pseudo-time analysis revealed that DIV1 accelerates hemocyte differentiation, driving prohemocytes and semi-granulocytes toward terminally differentiated granulocytes and hyalinocytes, particularly the immune-active HC4 subpopulation. Functional enrichment analysis showed that susceptible hemocytes were associated with viral processes, oxidative stress, and phagocytosis, while resistant clusters exhibited distinct immune signatures. Furthermore, knockdown experiments confirmed the antiviral roles of PPO2, RAB11B, LAMP1, and Dorsal, as their silencing led to increased viral loads, higher MCP protein levels, and reduced shrimp survival. Taken together, our study provides the first single-cell resolution atlas of shrimp hemocytes under DIV1 infection, revealing their transcriptional heterogeneity, differentiation trajectories, and immune responses. These findings offer novel insights into shrimp antiviral immunity and lay the foundation for disease-resistant breeding and immunostimulatory strategies in aquaculture. ImportancesDecapod Iridescent Virus 1 (DIV1) is a highly pathogenic virus threatening crustacean aquaculture, causing severe economic losses. Hemocytes, the primary immune cells in shrimp, play crucial roles in antiviral defense, yet their diversity, differentiation, and responses to viral infection remain poorly understood. In this study, we employed single-cell RNA sequencing (scRNA-seq) to comprehensively characterize hemocyte subpopulations in Macrobrachium rosenbergii before and after DIV1 infection. We identified 12 transcriptionally distinct hemocyte clusters and revealed significant changes in hemocyte composition following infection. Notably, we discovered that specific clusters (0, 5 and 8) were highly susceptible to DIV1, while others (9 and 10) exhibited resistance. Additionally, we reconstructed hemocyte differentiation trajectories and found that DIV1 infection drives hematopoiesis, accelerating the transition of progenitor cells into terminally differentiated immune-active hemocytes. Functional analysis highlighted key antiviral effectors, including PPO2, RAB11B, LAMP1, and Dorsal, which were significantly upregulated in response to infection. These findings provide novel insights into shrimp antiviral immunity and viral pathogenesis, offering potential targets for disease-resistant breeding and immunostimulatory interventions.