Genetic Characterisation and Risk Factors Associated With Capripoxvirus Outbreaks Among Small Ruminants in Uganda, 2021-2022.

Abstract

Background: Sheeppox and goatpox are systemic, contagious viral diseases of small ruminants caused by sheep and goat pox viruses of the genus capripoxvirus. These diseases cause fever, generalised skin lesions and negatively affect health, economics and welfare. Between 2011 and 2020, an average of four clinically suspected Capripox outbreaks were reported annually in Uganda through passive surveillance. However, information on the genetic characteristics of circulating capripoxviruses affecting remains limited. We conducted this study to (i) genetically characterise capripoxvirus strains associated with outbreaks in small ruminants and (ii) identify farm-level risk factors associated with the infections. Samples comprising skin scabs, nasal, ocular swabs and whole blood from were collected from clinically affected goats and sheep during suspected outbreaks reported between September 2021 to September 2022 in Nakaseke, Gomba and Kiryandongo districts. Samples were screened using conventional polymerase chain reaction [PCR] targeting the 30 kDa RNA polymerase subunit (RPO30) gene, followed by dideoxy Sanger sequencing and phylogenetic analysis based on RP030, GPCR and P32 gene Farm level risk and factors were documented and assessed during the study.

Results: Capripoxvirus DNA was detected by PCR in 30 out of 107 samples, reflecting a true positivity rate of 28.7%. All positive samples were from goats, while none of the sheep samples tested positive. Phylogenetic analysis based on all three genes (RPO30, GPCR and P32) classified the isolates as goatpox virus and separated it from other capripoxvirus reference strains. Goatpox virus strains detected across the four outbreaks were 100% identical to each other based on phylogenetic analysis, indicating circulation of a closely related strain within the affected districts. Phylogeny showed that Uganda goatpox virus isolates clustered closely [96%-100% with i reference strains from Kenya, Ghana, Sudan, Oman, Yemen, Burkina Faso and Chad. Low farm level biosecurity characterised by poor carcass disposal methods, human traffic and co-mingling of infected and apparently healthy] as well as uncontrolled animal and animal product movement, were identified at field level as probable exposure factors. The genetic relationship between GTPV strains from outbreaks and regional reference strains underpins the transboundary nature of goat pox virus disease.

Conclusion: Our study confirmed goatpox virus as the causative agent of outbreaks investigated between 2021-2022. Multi-gene phylogenetic analysis showed a close relationship between Uganda GTPV isolates and strains in parts of Africa and Middle East. The findings provide a basis for sustained surveillance to determine diversity of GTPV strains, increased adoption of good biosecurity practices, as well as improvement in animal movement control as key measures to reduce future outbreaks.