Ahmad, U.; De Ming, C.; Choy, C. S.; Yusoff, K.; Veerakumarasivam, A.; Abdullah, S.

Newcastle disease virus (NDV) is a promising oncolytic agent with a non-segmented, negative-sense single-stranded RNA (ssRNA) genome of approximately 15 kb. While NDV selectively replicates in and lyses a wide range of human cancer cells, a subset of these cells develop persistent infections, potentially compromising the therapeutic efficacy of NDV-based treatments. To investigate the molecular basis of persistent infection, we performed transcriptome profiling of TCCSUP bladder cancer cells persistently infected with the NDV AF2240 strain. Deep sequencing using Illumina HiSeq 2000 was conducted in triplicate, and the resulting viral and host reads were separated and analyzed. Using Integrative Genomic Viewer (IGV) software, we identified several nucleotide variants linked to persistence. Specifically, nucleotide alterations included a deletion at 359A[->]C and a substitution at 1653C[->]T within the nucleoprotein (NP) gene, as well as an insertion at 3338C[->]T in the matrix protein (M) gene. Additionally, a GGG base insertion was detected at position 2290 in the phosphoprotein (P) gene. Crucially, we observed truncations in the hemagglutinin-neuraminidase (HN) gene (nt 8263-8390) and the large polymerase (L) gene (nt 6203-6342). These mutations and truncations suggest significant disruptions in viral replication, assembly, and host cell attachment, potentially facilitating viral persistence in bladder cancer cells. Understanding these genomic alterations provides valuable insights into the mechanisms driving viral persistence and could inform strategies to optimize the oncolytic efficacy of NDV in cancer therapy.