Molecular characterization of peste des petits ruminants virus in small ruminants from the Savannah District, Northern Ivory Coast.

Objectives: Peste des petits ruminants (PPR) is a highly contagious viral disease affecting sheep and goats, with significant socio-economic consequences. The disease is endemic in the Ivory Coast; molecular data on circulating strains, particularly in the northern Savannah district, remain limited. This study aimed to characterize the PPR virus (PPRV) strains circulating among sheep and goats in this area. Materials and Methods: A total of 355 nasal swabs were collected from unvaccinated small ruminants, regardless of clinical status, across three regions of the Savannah district (Poro, Tchologo, and Bagoué). Viral ribonucleic acid (RNA) was extracted and screened using real-time reverse transcription polymerase chain reaction (RT-qPCR) targeting the nucleoprotein (N) gene of PPRV, followed by conventional RT-PCR (RT-cPCR). Positive amplicons were sequenced using the Sanger method, and phylogenetic analysis was performed with PhyML and edited in MEGA X software. Results: Out of 355 samples analyzed, 25 (7%) tested positive by RT-qPCR, and 17 of these were amplified by RT-cPCR for nucleotide sequencing. Ten sequences were of sufficient quality for phylogenetic analysis. All sequences described in this study clustered within lineage IV of PPRV and shared high nucleotide identity (96-98%) with previously described West African PPRV strains. Phylogenetic reconstruction revealed two distinct sub-clusters, suggesting possible multiple viral introductions, likely facilitated by uncontrolled transboundary livestock movements. Conclusions: This study provides the first molecular evidence of PPRV circulation in the Savannah district, confirming the dominance of lineage IV. The findings underscore the need for enhanced molecular surveillance and cross-border collaboration to inform regional vaccination and eradication efforts.