IBDV-SSA, a novel molecular approach for the recovery of infectious bursal disease virus whole genomes from FTA cards.

Infectious bursal disease (IBD), a highly contagious viral disease in young chickens, poses significant economic losses due to high mortality and immunosuppression. While IBD virus (IBDV) virulence is influenced by multiple genes, whole-genome sequencing (WGS) of IBDV is crucial for defining the strain pathotype and clinical profile. Flinders Technology Associates (FTA) cards are convenient for field sample collection, but their filter paper matrix can hinder nucleic acid recovery, impacting sequencing efficiency. This study evaluated two enrichment strategies, single primer amplification (SPA) and IBDV segment-specific amplification (SSA), coupled with short-read (Illumina) and long-read (Oxford Nanopore Technologies, ONT) sequencing platforms, to optimize IBDV whole-genome recovery from FTA cards. Illumina sequencing produced comparable raw read counts for both methods, yet IBDV-SSA samples achieved significantly higher genome mapping rates (76%) than IBDV-SPA (12%). Genome coverage analysis revealed that IBDV-SSA provided uniform read distribution across both genomic segments, ensuring complete coverage, while IBDV-SPA exhibited significant bias, with most reads mapping to segment B, and limited coverage of segment A. Importantly, IBDV-SSA also proved compatible with ONT long-read sequencing, providing complete genome coverage. Notably, IBDV-SSA coupled with short-read sequencing successfully characterized coinfections in two samples. This optimized approach using IBDV-SSA enables efficient and comprehensive WGS of IBDV from FTA cards, facilitating strain characterization, virulence prediction, and epidemiological investigations.IMPORTANCEThis research tackles a significant problem for poultry farmers: a virus called infectious bursal disease virus (IBDV) that harms young chickens, causing high death rates and economic losses. To fight it effectively, scientists need to analyze its complete genetic makeup. Traditionally, collecting and preserving IBDV field samples was challenging. Flinders Technology Associates (FTA) cards have simplified this process, but getting usable genetic material from them has been difficult. This study introduces a new genome enrichment method, IBDV segment-specific amplification (IBDV-SSA), which successfully allows for IBDV complete genome recovery from FTA cards. By using this improved approach, scientists can accurately identify virus strains, assess how harmful they are, and monitor their spread. This, in turn, helps to improve vaccines and protect flocks. IBDV-SSA is a powerful tool for outbreak surveillance, supporting the poultry industry and ensuring a stable food supply.