Genomic and pathological insights into the first identified genotype IIIb chicken anemia virus strain in Bangladesh.

Chicken anemia virus (CAV) is a highly infectious pathogen that causes severe immunosuppression and significant economic losses in poultry, with limited genomic data in Bangladesh hindering effective disease control. This study characterizes a CAV strain from a field outbreak in Bangladesh through clinical, pathological, and molecular analyses, including genome sequencing, genotyping, and assessment of viral protein structure. Clinically suspected chickens exhibiting anemia, depression, pale combs, and cyanotic wings underwent gross and histopathological examinations. Viral DNA was extracted from bone marrow samples and analyzed using PCR, followed by complete genome sequencing with next-generation sequencing. Phylogenetic analysis, genotyping, mutational profiling, and structural predictions of viral proteins (VP1, VP2, and VP3) were performed to assess evolutionary relationships and pathogenic potential. Histopathology confirmed severe lymphoid depletion in the thymus, spleen, and bursa of Fabricius, consistent with CAV-induced immunosuppression. Molecular detection confirmed CAV presence in eight out of ten samples. Whole-genome analysis revealed a 2,330 bp genome with 42% GC content, clustering within genotype IIIb and showing close genetic relatedness to a Chinese strain. Mutational analysis revealed several nucleotide substitutions in the viral genomes, with the highest number of amino acid changes observed in the VP3 protein. Computational modeling revealed minor structural variations in VP1 and VP2, which may affect antigenicity and phosphatase activity. This study provides the complete genome characterization of a Bangladeshi CAV strain, revealing critical genetic variations that may influence viral virulence. The findings underscore the need for enhanced surveillance and targeted vaccine strategies to mitigate CAV-related losses in poultry. IMPORTANCE: This study provides the first complete genomic characterization of a genotype IIIb chicken anemia virus (CAV) strain in Bangladesh. By integrating clinical, pathological, and molecular analyses, the research identifies critical genetic variations that could influence viral virulence, immune evasion, and disease severity. The findings highlight the close genetic relationship between this Bangladeshi strain and a previously reported Chinese strain, suggesting potential epidemiological links. Furthermore, the study underscores the need for enhanced surveillance and targeted vaccine strategies to mitigate CAV-induced immunosuppression and economic losses in poultry farming. The insights gained from this research contribute to a deeper understanding of CAV evolution and could inform future diagnostic and control measures to protect poultry populations.