Optimized Primer for Partial N and F Gene Sequencing of PPRV

Despite global efforts to eradicate Peste des petits ruminants (PPR), this disease remains one of the most devastating viral infections affecting small domestic ruminants. Sensitive and specific molecular diagnostic tools are essential components of successful eradication strategies. Molecular diagnostics and genetic characterization of Peste des petits ruminants virus (PPRV) are commonly based on partial sequencing of the PPRV fusion (F) and nucleocapsid (N) genes, but the primers currently in use were developed several decades ago. In this study, we have developed and validated new primer sets for partial amplification of the PPRV F- and N-genes. PPRV isolates representing more recently circulating representatives of all four viral lineages were included. A total of 16 primer pairs, including previously published primers, were evaluated for their performance in partial amplification of the PPRV F and N genes. The primer pairs PPRV-F-K9 (460 bp) and PPRV-N-K15 (408 bp) demonstrated the highest sensitivity across all four lineages. Additionally, two alternative primer pairs, PPRV-F-K6 (399 bp) and PPRV-N-K3 (366 bp), exhibited comparable sensitivity, making them reliable alternatives for partial F and N gene sequencing. Overall, the newly developed primer pairs exhibited improved sensitivity compared with previously published primers, supporting their suitability for enhanced molecular diagnostics and genetic characterisation of PPRV.