RESULTS
A total of 73 out of 268 animal sampled (27%) were identified as PPRV positive by RT-PCR (Table 1 and S1). At least one sample was positive for PPRV diagnosis for 17 states: Plateau, Benue, Kwara, Bauchi, Adamawa, Taraba, Katsina, Kebbi, Enugu, Abia, Anambra, Oyo, Ondo, Osun, Rivers, Cross Rivers and Akwa-Ibom. No positive samples out of the twenty (20) tested samples were found for Kano state. Partial N gene sequence was obtained from all samples. A total of 23 different sequences were obtained (Table 1, Gen-bank accession numbers: MT193234 - MT193256). Phylogenetic analyses showed that the sequence of 72 PPR positive samples belonged to lineage IV. One single sequence from the state of Oyo belonged to lineage II (Figures 1, 2 and S1).
Additional phylogenetic analysis using more extensive lineage II dataset showed the lineage II sequenced obtained clustered with poor node support (< 50%) with sequences from Senegal and Mauritania (Figure 2). Another lineage II sequence obtained in Oyo state in 2012 was included in a better-supported cluster (68%) with samples from Ghana. The phylogenetic analysis concentrating on lineage IV showed the presence of multiple well-supported clusters in Nigeria (Figure 4). The two sub-lineages described by Woma and Mantip in 2016 (IV-NigA and IV-NigB) were identified with relatively good support (70-71%). Phylogenetic relationships were not further resolve for most Nigerian Lineage IV sequences. Still, four clusters were observed within Group IV-NigB, each including 3-5 sequences from multiple states, called here IV-NigB1, IV-NigB2, IV-NigB3 and IV-NigB4 (Figures 1 and 3). Clade IV-NigB1 presented sequences from Ondo, Akwa-Ibom and Enugu. Clade IV-NigB2 brought together sequences of strains harvested in Akwa-Ibom, Benue, Taraba and Cross-River (Figure 3). Clade IV-NigB3 grouped strains from Rivers, Plateau, Benue and Osun with lower support (60%). Finally clade IV-NigB4 included sequences obtained from Plateau, Kwara, Katsina and Kebbi (support = 62%). Only two sequences from Kebbi belonged to sub-lineage IV-NigA. They were closely related to a sample from Niger (Figure 4). Two samples, one from Kebbi in 2018 and one from Osun in 2013 were placed out of sub-lineages IV-NigA and NigB in the tree (Figure 3).