Detection and phylogenetic analysis of lumpy skin disease virus in cattle from selected districts in Uganda

A dissertation submitted to the Directorate of Research and Graduate Training in partial fulfilment of the requirements for the award of the Degree of Master of Science In Biochemistry of Makerere University

Lumpy skin disease (LSD) is a viral disease of significant economic impact for the cattle industry in Africa, including Uganda. It is caused by lumpy skin disease virus (LSDV), which belongs to the genus Capri poxvirus, family Poxviridae and subfamily Chordopoxvirinae. The disease in cattle is characterized by fever, enlarged superficial lymph nodes, granular swellings in the skin dermis, mucous membranes of the digestive and respiratory tracts, with animals exhibiting salivation, lachrymation and nasal discharges. The painful cutaneous and internal lesions, causes losses in milk production, hide quality degradation and in some cases death of the infected animal. There is anecdotal evidence that Lumpy skin disease virus (LSDV) is present and causes disease in Ugandan cattle. This is based on clinical signs observed and reported by the local veterinary officers. However, no molecular epidemiological studies have been undertaken to acertain that the clinical signs for lumpy skin disease observed in Ugandan cattle is indeed caused by the LSDV. This study used RT-PCR, standard PCR and DNA sequence comparison to confirm the presence of the LSDV in the suspected cattle sampled from five districts in Uganda (Kween, Mukono, Kapchorwa, Kiruhura and Kotido) between 2010 and 2013. A total of 36 out of 400 (11%) samples collected were positive for LSDV DNA by RT-PCR; 13 of these were from Mukono and 23 from Kiruhura. The LSDV DNA was not detectable in Samples from Kotido, Kapchorwa, and Kween. Out of the 36 LSDV positive samples, only 8 yielded products of the viral RPO30 gene using standard PCR; 5 from Kiruhura, and 3 from Mukono. When the 8 PCR products were sequenced, a sequence alignment using BioEdit (v7.2) showed that these sequences were 100% identical. A phylogenetic analysis using Mega 6 (v4) showed that all the Ugandan LSDV isolates belonged to the LSDV lineage and were closely related to the Niger, South Africa, Egypt and Sudan LSDV strains. This study has therefore confirmed, for the first time, that Lumpy Skin Disease Virus is present and infects cattle in Uganda. It further confirmed that the viral isolates from the districts of Kiruhura and Mukono (2010-2013) belonged to the same strain whose possible origin could be Kenya, Sudan, Niger, or South Africa. However more studie need to be done to verify this possible origin.