Results
Out of 30 samples screened for ORFV, 20 were positive giving a rate of 67%. Animals <2 years had higher prevalence (76.5%) of ORF compared to older ages 2-3 years and >3 years with 50% and 66.7%, respectively. More females than males (80% versus 64%) were infected with ORFV despite having five-fold more of the later in our study. Logistic analysis showed rate of occurrence of Orf did not differ significantly with animals’ ages and sexes (P>0.05). Goat with 71.4% prevalence demonstrated higher susceptibility to ORFV compared to sheep (55.6%). Hundred percent attack rate was observed among the Uda and WAD breeds followed by a decreasing susceptibility in Niger (71.4%), Kano Brown (66.7%), Yankasa (25%) and Balami (0%) breeds(Table 1). A differential distribution of Orf was observed in relation to sources of livestock sampled from the market. Animals sourced from Niger State (100%) were more infected followed by Kano State (80%), Yobe State (75%), Niger republic (71%) and Katsina State (40%). Though, current study did not observe any significant influence of source on the occurrence of ORFV infection (p>0.05).
The ML phylogenetic treeshowed a distinct diversification of the isolates analyzed into 2 lineages, African and Asian lineage, with majority of the Nigerian strains clusteringwithin the African lineage, a few Nigerian stains also clustered within the Asian lineage along with some South African strains and reference strains from China (Fig. 2).
Time scaled MCC phylogeny of the ORFV sequences indicates that the MRCA of the African strains was around 2002. The African Viruses clustered into 2 major clades with both clades containing West African (Nigerian) and South African viruses (Fig. 3a). There was also a strain from Botswana which clustered very closely with Nigerian isolates and shared same TMRCA of around 2014 highest posterior density interval (HPD 2012-2017), while the TMRCA for the entire African sequences was around 2004 (HPD 2000-2006).. The evolutionary rate of the African ORFV B2L genes was 7.45 × 10-4, 95% HPD (3.46 × 10-4 to 1.17 × 10-3) substitutions/ site/year. The demographic history of the African ORFV B2L genes showed a constant viral population expansion from 2005 to 2016, with a slight rise in population expansion between 2018 to 2020 (Fig. 3b). Amino acid alignment of the complete B2L protein coding sequence also showed some non-synonymous mutations (Suppl. Figure 1) which are summarized in Table 2. The sampling dates and Genbank accession numbers of the study sequences can be assessed in Suppl. Table 1.