Immunological interpretation of infectious bronchitis virus detection in vaccinated broiler flocks: distinguishing vaccine virus replication from early field challenge

Background: Infectious bronchitis virus (IBV) remains one of the most challenging pathogens affecting poultry health worldwide, particularly in regions where multiple genotypes co-circulate. In Egypt, the emergence and persistence of Variant 2–like strains (GI-23 lineage) alongside intensive vaccination programs have raised important immunological and epidemiological questions regarding vaccine virus circulation, field virus challenge, and the timing of protective immunity. Understanding the interaction between vaccine-derived immunity and circulating field strains is critical for optimizing immunization strategies and improving flock health outcomes.

Methods: This study evaluated IBV dynamics in commercial broiler flocks vaccinated at day one with different infectious bronchitis vaccination programs, including combinations of Ma5 and 4/91 vaccines, as well as flocks primed with IB classical vaccines. Cloacal swab samples were collected from broilers aged 16, 19, and 23 days showing respiratory and systemic clinical signs. Molecular detection of IBV was performed using real-time RT-PCR, followed by partial S1 gene sequencing for genotypic characterization. Comparative nucleotide and amino acid analyses were conducted against known vaccine and reference field strains. In parallel, a structured immunological follow-up protocol incorporating serology (ELISA and HI), PCR screening, and zootechnical performance monitoring was applied to assess vaccine take and immune development over the production cycle.

Results: High quantities of IBV RNA were detected across multiple flocks, with cycle threshold (Ct) values ranging from 18.1 to 25.2, indicating active viral replication. In 16-day-old broilers, sequencing confirmed 100% nucleotide and amino acid homology with the 4/91 vaccine strain, strongly suggesting vaccine virus detection rather than field virus infection. In contrast, samples collected at 19 and 23 days of age revealed the presence of Egypt/benisuef/05 field virus (GI-23 lineage), showing 99% homology with the reference strain and limited amino acid substitutions within the S1 protein. Epitope prediction analysis demonstrated minimal changes in hydrophilicity, indicating largely conserved immunologically relevant regions. These findings suggest that early field exposure may
have occurred before full development of vaccine-induced protective immunity, particularly under conditions of high infection pressure or suboptimal vaccine application.

Conclusions: The study highlights the importance of integrating molecular diagnostics with immunological monitoring to accurately interpret IBV detection in vaccinated flocks. Detection of vaccine virus should not be misinterpreted as vaccine failure, while early circulation of GI-23 field strains underscores the need for precise vaccine administration and timing. Comprehensive immunological follow-up protocols can support informed decision-making, improve vaccine performance assessment, and enhance control strategies against evolving IBV variants in endemic regions.

To be updated shortly..