Comprehensive transcriptional and epitranscriptomic landscape of African swine fever virus (ASFV) in porcine alveolar macrophages revealed by Oxford Nanopore long-read and Direct RNA sequencing
This study utilized long-read sequencing combined with direct RNA sequencing (DRS) technology from Oxford Nanopore Technologies (ONT) to analyze the transcriptome and epitranscriptome of African swine fever virus (ASFV) in porcine alveolar macrophages (PAMs). At 24 and 36 hours post-infection (MOI 0.5), we generated over 15 million long-read sequences (approximately 16 Gb of total sequencing data), with 7.4% of reads aligning to the ASFV genome. We re-annotated the viral genome, correcting several translation initiation sites. We mapped natural RNA modifications (primarily m6A and m5C) using DRS and found that these modifications were significantly enriched in highly variable terminal regions of the ASFV genome. Correlation analysis further demonstrated a significant positive correlation between mRNA modification levels and gene expression. The original sequencing data and related metadata are publicly available to support research on ASFV gene expression, RNA biology, and the development of novel antiviral strategies and vaccines.