Sujit Mohanty, USDA-ARS

Islam Nour, Sonsiray Álvarez-Narváez, Arun Kulkarni, and Sujit K. Mohanty

Epidemiology, Evolution, and Diversity

Infectious bursal disease (IBD) is a devastating viral illness affecting young chickens, causing substantial economic losses due to high mortality rates/immunosuppression, necessitating comprehensive genomic characterization. Although FTA cards are suitable for field sampling, their paper matrix hinders nucleic acid recovery and lowers sequencing efficiency. This study evaluated two IBDV genomic amplification-based enrichment strategies, a single primer (SPAE) or dual sets each is segment specific (SSAE). Moreover, two sequencing platforms, involving Illumina and Oxford Nanopore Technologies, were used to test the suitability of the candidate enrichment method for both platforms. Whereas both methods yielded close raw read counts with Illumina, SSAE demonstrated significantly higher mapping rates to the IBDV genome (76% vs. 12% for SPAE) and more consistent coverage across the entire genome (X94 minimum depth). SPAE exhibited a strong bias towards segment B. Prominently, the molecular approach SSAE proved effective for long-read sequencing, resulting in entire genome coverage and X211 average depth. Importantly, we successfully detected cross-contamination and genuine coinfection in 24-84D and 24-33D isolates, respectively using SSAE coupled with Illumina sequencing. Phylogenetic analysis of IBDV strains indicated three different clusters among the Peruvian strains. Two isolates (24-26B and 24-85A) might have emerged from the classical vaccine strain (2512-Winterfield). Whereas 24-33D and 24-84D isolates were closely related to the USA variant (VarE). The remaining isolates exhibited a distinct cluster. This novel molecular strategy, SSAE, provides a robust and efficient method for comprehensive IBDV whole-genome sequencing, facilitating precise strain characterization, pathogenesis studies, and enhanced epidemiological surveillance.