Innate immune transcriptomic remodeling across clinical stages of bovine leukemia virus infection

Bovine leukemia virus (BLV) is an oncogenic deltaretrovirus that establishes lifelong infection in cattle and may progress from asymptomatic carriage to persistent lymphocytosis (PL) and lymphoma. Although adaptive immune alterations have been widely studied, the stage-specific transcriptional landscape of innate immunity in BLV infection remains incompletely defined. In this study, we performed a targeted innate immune transcriptomic analysis using RNA-seq data derived from 18 Holstein dairy cows selected from a screened population of 130 animals in Querétaro, Mexico. Animals were classified into three groups based on serology, proviral load, and hematological criteria: BLV-seronegative controls (n = 5), asymptomatic BLV-infected cattle (AL), and BLV-infected cattle with PL. Total peripheral blood leukocytes were subjected to RNA extraction and sequencing on the Illumina NovaSeq platform. Differential gene expression analysis was conducted using DESeq2 with significance defined as adjusted P -value ( padj ) < 0.05 and |log 2 fold change|≥ 1. A curated panel of innate immune-related genes encompassing pattern recognition receptors, interferon signaling, inflammatory mediators, inflammasome components, and cytotoxic effectors was analyzed. Comparison between Control and Asymptomatic cattle identified 8 genes that were significantly altered ( padj < 0.05). Asymptomatic animals demonstrated upregulation of antiviral and immune-regulatory genes, including EIF2AK2 (log 2 FC = 1.10, padj = 0.011), KLRK1 (log 2 FC = 0.98, padj = 0.009), and IL18 (log 2 FC = 0.77, padj = 0.015), indicating activation of interferon-associated and inflammatory pathways. Marked upregulation of TNFRSF13C (log 2 FC = 3.25, padj = 0.046) and TNFAIP3 (log 2 FC = 2.03, padj = 0.049) suggests modulation of B-cell survival signaling and NF-κB regulatory control. In contrast, NCR1 (log 2 FC = − 1.04, padj = 0.044), LMX1B (log 2 FC = − 0.80, padj = 0.030), and TNFSF12 (log 2 FC = − 0.78, padj = 0.044) were downregulated, reflecting selective adjustment of cytotoxic and TNF superfamily pathways. PL animals exhibited broader innate immune transcriptional alterations consistent with sustained inflammatory activation. These findings demonstrate that asymptomatic BLV infection is characterized by controlled activation of antiviral and regulatory innate immune pathways, whereas disease progression toward PL is associated with expanded inflammatory reprogramming. Stage-specific innate immune signatures may therefore contribute to viral persistence and clinical outcome in BLV-infected cattle.