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<p>Avian infectious bronchitis virus (IBV) remains a persistent threat to poultry health and production, particularly in Pakistan, where frequent outbreaks occur despite routine vaccination. To investigate suspected vaccine breakthrough events, one hundred clinical samples (oropharyngeal/tracheal swabs and kidney, lung, and liver tissues) were collected between January and May 2025 from ten commercial chicken farms experiencing IBV-like outbreaks. Postmortem findings revealed classic IBV-associated lesions, including hemorrhagic tracheitis, severe airsacculitis, nephritis with urate deposits, and fluid-filled abdominal cysts in layer birds. Nested RT-PCR confirmed IBV RNA in 26% of samples (26/100), representing 70% of the investigated farms (7/10). Phylogenetic characterization of three representative S1 gene sequences (GenBank PV818074–PV818076) demonstrated clustering within the GI-1 lineage, showing 99.7–100% nucleotide identity with Massachusetts-type vaccine strains (H120, H52, Ma5, M41). The detection of such highly conserved vaccine-like sequences in recently vaccinated flocks suggests that current outbreaks are more likely associated with re-isolation, persistence, or circulation of vaccine-derived strains rather than novel divergent field variants. These findings highlight the potential role of vaccine-related viruses in field outbreaks, emphasize the need for incorporating vaccination history into molecular surveillance, and call for periodic reassessment of vaccination programs to maintain protective efficacy. Overall, this study underscores the importance of continuous genomic monitoring to better understand IBV evolution under vaccine pressure and to support evidence-based strategies for improving disease control and ensuring poultry industry sustainability.</p>

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Molecular Detection and Phylogenetic Characterization of Avian Infectious Bronchitis Virus (IBV) in Vaccinated Commercial Chicken Flocks Experiencing Outbreaks in Faisalabad, Pakistan

  • 期刊论文

  • 发表日期：

    2026年2月19日

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  • Muhammad Mubeen Ahmad,
  • Muhammad Wasif Gulzar,
  • Muhammad Wasif Azeem,
  • Muhammad Musa Mubashar,
  • Rida Fatima,
  • Muhammad Tayyab Naveed,
  • Muhammad Taha,
  • Sana Riaz,
  • Asad Javed,
  • Mudasser Habib,
  • Rizwan Aslam

摘要

Avian infectious bronchitis virus (IBV) remains a persistent threat to poultry health and production, particularly in Pakistan, where frequent outbreaks occur despite routine vaccination. To investigate suspected vaccine breakthrough events, one hundred clinical samples (oropharyngeal/tracheal swabs and kidney, lung, and liver tissues) were collected between January and May 2025 from ten commercial chicken farms experiencing IBV-like outbreaks. Postmortem findings revealed classic IBV-associated lesions, including hemorrhagic tracheitis, severe airsacculitis, nephritis with urate deposits, and fluid-filled abdominal cysts in layer birds. Nested RT-PCR confirmed IBV RNA in 26% of samples (26/100), representing 70% of the investigated farms (7/10). Phylogenetic characterization of three representative S1 gene sequences (GenBank PV818074–PV818076) demonstrated clustering within the GI-1 lineage, showing 99.7–100% nucleotide identity with Massachusetts-type vaccine strains (H120, H52, Ma5, M41). The detection of such highly conserved vaccine-like sequences in recently vaccinated flocks suggests that current outbreaks are more likely associated with re-isolation, persistence, or circulation of vaccine-derived strains rather than novel divergent field variants. These findings highlight the potential role of vaccine-related viruses in field outbreaks, emphasize the need for incorporating vaccination history into molecular surveillance, and call for periodic reassessment of vaccination programs to maintain protective efficacy. Overall, this study underscores the importance of continuous genomic monitoring to better understand IBV evolution under vaccine pressure and to support evidence-based strategies for improving disease control and ensuring poultry industry sustainability.