Molecular Characterization of Lineage IV Peste des Petits Ruminants Viruses in Sudan Isolated from Outbreaks Between 2015 and 2018 Suggests the Existence of the North–East Africa Episystem

Multiple outbreaks with high mortality rates and a pattern of disease occurrence similar to peste des petits ruminants (PPR) were observed in sheep and goats across many states of Sudan between 2015 and 2018. Therefore, this study aimed to investigate and identify the cause of these disease outbreaks. A total of 276 blood and lung tissue samples were collected from infected sheep (n = 223) and goats (n = 53). Sample analysis in an IC-ELISA revealed the presence of the PPRV antigen in 56.9% of sheep and 62.3% of goat samples. Twenty-seven [sheep (18) and goats (9)] PPRV-positive samples from IC-ELISA were subsequently confirmed positive using the PPRV N-gene-based RT-PCR. Two PPR viruses were isolated from infected small ruminant lung tissues in Vero cells. The partial N-gene sequences for five PPRV strains originating from sheep and goats were determined. Phylogenetic tree grouped PPRV strains identified in this study in lineage IV in sub-lineage NEA (North–East Africa), with the highest sequence identity observed with strains circulating in North African countries. This study and earlier published phylogenetic analysis and patterns of animal movements suggest that the transboundary transmission of PPRV lineage IV strains between East and North African countries has been happening since 2008 and established a new North–East Africa episystem that needs to be disrupted for the successful global eradication of PPR.