<![CDATA[Background: Newcastle disease virus (NDV), also known as avian paramyxovirus 1, is a viral disease that affecs domestic poultry and wild birds. NDV remains one of the most significant and widespread infectious diseases that can cause severe economic losses in poultry, including chickens and ducks. Purpose: Molecular characterization of the matrix protein (M) gene was performed to characterize NDV isolates obtained from unvaccinated ducks in Indonesia, determine their phylogenetic relationships, and predict potential B-cell epitopes relevant for vaccine development. Method: One hundred NDV samples were collected from unvaccinated ducks in West Sumatra and East Java, Indonesia. Viral RNA was extracted, and NDV was detected by reverse transcription polymerase chain reaction (RT-PCR) using three primer sets targeting the M gene. Sequence analysis was conducted using MEGA X software to identify mutations and construct phylogenetic trees. Linear B-cell epitopes and immunological parameters were predicted using the Immune Epitope Database (IEDB). Results: Among the 100 samples examined, 96 tested negative for NDV, whereas four samples were confirmed positive. Phylogenetic analysis revealed that three isolates clustered within genotype VII, while the majority belonged to genotype VI. Detailed characterization of the M gene revealed the genetic features of NDV circulating in ducks in Indonesia. Notably, the peptide TVDKRGRKVTFDKLERKI derived from the M protein was identified as a promising candidate for peptide based vaccine development against NDV. Conclusion: Evidence from molecular and phylogenetic analyses confirms the circulation of NDV among ducks in West Sumatra and East Java, Indonesia. Candidate peptide derived from the M protein was identified as a potential component of a peptide based vaccine against NDV; however, further in vitro and in vivo investigations are required to validate its immunogenicity and protective potential.]]>
