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. 2020 Mar 21;6(3):e03595.
doi: 10.1016/j.heliyon.2020.e03595. eCollection 2020 Mar.

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

Abdelmalik Ibrahim Khalafalla  1   2 , Ahmed Eisa Elhag  3   4 , Hassan Zackaria Ali Ishag  2   5
Affiliations

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

Abdelmalik Ibrahim Khalafalla et al. Heliyon. .

Abstract

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.

Keywords: Dromedary camels; East Sudan; Field investigation; Infectious disease; Microbiology; Microbiology epidemiology; Parapoxviruses; Phylogenetic characterization; Small ruminants; Veterinary medicine; Virology.

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Figures

Figure 1
Figure 1
Map of the Sudan showing the study location; Showak area in Gedarif State of eastern Sudan, June to September 2016 (Blue color).
Figure 2
Figure 2
Gross lesion caused by Parpoxvirus infection in sheep, goats and camels in eastern Sudan, 2016
Figure 3
Figure 3
Epidemiology of Contagious Ecthyma in Eastern Sudan in 2016. Distribution of studied animals by number, species, season, deaths, treatment and zoonotic transmission of the disease.
Figure 4
Figure 4
Morbidity and case fatality rates due to PPV infection in small ruminants and camels in eastern Sudan, 2016
Figure 5
Figure 5
Phylogenetic analysis of 38 PPV nucleotide sequences based on B2L gene. The evolutionary history was inferred using the Neighbor-Joining method. The optimal tree with the sum of branch length = 0.92508009 is shown. The evolutionary distances were computed using the Maximum Composite Likelihood method and are in the units of the number of base substitutions per site. The significance of all deduced phylogenetic trees was verified by bootstrap analysis of 1000 replicates Evolutionary analyses were conducted in MEGA7 (Kumar et al., 2016). Black circles = PPV isolates from this study in eastern Sudan.
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