Background Since 2018, atrophy of the bursa has been found among vaccinated chickens with high antibody titres against infectious bursal disease virus (IBDV) in Fujian, China, suggesting poor vaccine efficacy against circulating IBDV strains. Methods Novel IBDV strains were isolated, and vp2 and vp1 genes were sequenced and used to carry out phylogenetic analysis. Pathogenicity was investigated using 21‐day‐old specific pathogen‐free (SPF) chickens. In addition, the effectiveness of current commercial vaccines used in China was evaluated against the isolated novel IBDV strains. Results Six IBDV isolates were successfully obtained, which formed an independent cluster and belonged to genotype A2dB1, based on phylogenetic analysis of the vp2 and vp1 genes. The pathogenicity of the novel IBDV FJ2019‐01 isolate in 21‐day‐old SPF chickens was characterised by severe atrophy of the bursa and a largely decreased number of lymphocytes, atrophy of the follicle and broadening of mesenchyme in the bursa 3–23 days after infection. Unfortunately, all vaccinated chickens with high antibody titres against IBDV also developed atrophy and largely decreased lymphocytes in the bursa, as in the unvaccinated birds challenged with FJ2019‐01. Furthermore, high viral loads of FJ2019‐01 were detected in the bursa of all vaccinated chickens. Conclusions These findings suggest that current commercial IBDV vaccines used in China did not provide protection against novel IBDV variants.

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