A Distinct Defense Strategy: The Molecular Basis of WSSV Tolerance in Macrobrachium nipponense Revealed by Comparative Transcriptomics with Litopenaeus vannamei

White Spot Syndrome Virus (WSSV) remains one of the most devastating pathogens in global shrimp aquaculture, causing massive economic losses annually. This study employed comparative transcriptomics to elucidate the molecular basis of the differential resistance to WSSV between the highly susceptible Pacific white shrimp (<i>Litopenaeus vannamei</i>) and the remarkably resistant oriental river prawn (<i>Macrobrachium nipponense</i>). Our analysis of gill, hepatopancreas, and muscle tissues at 24 h post-infection revealed fundamentally distinct defense strategies. The resistant <i>M. nipponense</i> employs a unique "proactive homeostatic reinforcement" strategy, characterized by significant enrichment of pathways central to cellular homeostasis, including signal transduction, cellular processes, and transport/catabolism. This approach, supported by coordinated up-regulation of heat shock proteins and structural genes, enables effective viral control without triggering excessive immune activation. In contrast, susceptible <i>L. vannamei</i> displays either widespread metabolic dysregulation leading to systemic collapse in moribund individuals or dependency on specific immune pathways (Toll-like receptor signaling and apoptosis) in survivors. Through comparative KEGG analysis, we identified heat shock protein 70 kDa (<i>HSP70</i>, K03283) as a key conserved gene and functionally validated its critical role in antiviral defense using RNA interference. Knockdown of <i>HSP70</i> in <i>M. nipponense</i> significantly increased cumulative mortality and viral load, confirming its essential protective function. These findings provide novel insights into crustacean antiviral immunity and identify promising genetic targets for breeding WSSV-resistant shrimp strains, offering sustainable solutions for disease management in aquaculture.