Despite intensive vaccination efforts, Chicken Infectious Anemia Virus (CIAV) remains a formidable threat to the Egyptian poultry industry, primarily through the emergence of vaccine-escape variants. While most studies have focused on Northern Egypt, there is a critical knowledge gap regarding the viral landscape in the Southern provinces. This study provides the most extensive surveillance to date, spanning 10 diverse Egyptian governorates with a strategic focus on Upper Egypt (2024–2025). Out of 400 collected samples, TaqMan-based qPCR revealed a high prevalence of 30%(120/400). Five representative isolates were selected for whole-genome sequencing and molecular characterization. The isolates were classified as Genotype II by phylogenetic analysis, showing a notable genetic divergence (85–87% amino acid similarity) from traditional Genotype I vaccine strains. Notably, comprehensive …