Genomic Surveillance of Infectious Bursal Disease Virus in Brazil Identifies a Novel Genogroup B6 and Putative Reassortment Events

Infectious bursal disease virus (IBDV) is a major immunosuppressive pathogen of poultry that can compromise immune function and increase susceptibility to secondary infections; however, its segment-level genomic diversity in Brazil remains insufficiently characterized. We conducted an integrated molecular surveillance study combining diagnostic detection, VP2 and VP1 sequencing, phylogenetic and genomic constellation analyses, selection analyses, and recombination screening. IBDV was detected in 88 clinical samples among suspected flocks (85.4%), with detection increasing markedly after 14 days of age. Among 21 samples selected for sequencing, 17 VP2 sequences were classified as A4, while 15 VP1 sequences belonged to B1 or the novel B6 genogroup. Among samples with paired VP2–VP1 data, A4B1 was identified in 10/11 samples and A4B6 in one. Analysis of these sequences together with historical Brazilian sequences with paired segments identified A3B2 and A4B1 as the predominant genomic constellations, with A3B2 detected from 2001 to 2024 and A4B1 from 1983 to 2025. Notably, three VP1 sequences were classified within B6, which occurred in both A3 and A4 backgrounds, generating A3B6 and A4B6 constellations consistent with putative reassortment. VP2 exhibited localized diversification against a background of predominant purifying selection, including sites under episodic diversifying selection within the exposed PBC, PDE, and PHI loops. Together, these findings reveal a more dynamic genomic landscape of Brazilian IBDV than suggested by VP2-based surveillance alone, with novel B6-associated constellations providing evidence of previously unrecognized segment-level diversity and putative reassortment, underscoring the importance of dual-segment genomic surveillance for monitoring IBDV evolution and adapting prevention protocols in Brazil.