Field investigation and phylogenetic characterization of orf virus (ORFV) circulating in small ruminants and Pseudocowpoxvirus (PCPV) in dromedary camels of eastern Sudan.

In this study, livestock herders in eastern Sudan were interviewed through structured questionnaire involved 14046 animals in 151 herds (87 camel herds, 51 sheep and 13 goats) from June to September of 2016 in Showak area of Gadarif State to get some epidemiological information on contagious ecthyma (CE) infection. 102 suspected cases of CE were investigated (38 sheep, 22 goats and 42 camels) by a second questionnaire focusing on age and sex of affected animals beside number and localization of the lesions. Representative tissue samples of scab lesion scrapings were collected from a total of 36 suspected sheep, goats and camels for DNA extraction to identify PPV by quantitative real-time PCR and gel-based PCR, then a PCR protocol was used to obtain DNA fragment of B2L gene from six DNAs (2 from each animal species) for sequencing. Phylogenetic tree based on nucleotide sequences was constructed and all data were analyzed statistically. Obtained result has shown morbidity rate of 23.8% and a case fatality rate of 4.7 % in overall investigated animals resulting in a significant economic loss. Within individual herd, the morbidity rate varied from 5.6 to 42.8%, while the case fatality rate ranged between 0 and 33.3%. Camels accounted for the highest case fatality rate with 6.5% compared to sheep and goats which their rates were 2.8% and 1.3%, respectively. 93% of the affected animals were young less than one-year-old. The prevalence of CE was high in the rainy season compared to winter and summer. Out of 36 scab materials collected from sheep, goats, and camels, 24 gave positive specific amplification in real-time PCR and 21 in the gel-based PCR. DNA sequencing confirmed the PCR results. All sequences had a high G + C content of 62.6-63.9%. A BLAST search also revealed that the studied sheep PPV (SPPV) isolates shared 99.08% nucleotide sequence intragroup identity, 96.88-97.27% identity with the goat PPV (GPPV) isolates and together they belong to the Orf virus (ORFV) species, while the camel PPV (CPPV) isolates are close to the Pseudocowpoxvirus (PCPV) species of the PPV genus and share 92.51-93.62 % identity with the GPPV isolates. In conclusion the present study demonstrated that the gross lesion produced by PPV in sheep, goats and camels is generally similar, yet the PPVs circulating in eastern Sudan in camels (PCPV) are genetically distinct from those affecting sheep and goats (ORFV). Contagious ecthyma in eastern Sudan causes significant morbidities and mortalities and control measures, guided by the results of this investigation ought to be implemented.