Prospects for Using Metagenomic Analysis As a Tool for The Accurate Diagnosis of Capripoxvirus Infections in Farm Animals

Infectious diseases of small domestic ruminants caused by viruses belonging to the Capripoxvirus genus are a serious economic threat. However, the diagnostic tools currently available for these pathogens do not provide sufficient strain information for effective disease control. This can be solved by sequencing and analysis of the full virus genome, which is currently achievable by the use of next generation sequencing technologies followed by metagenomic analysis. This review discusses the biology of Capripoxvirus pathogens, and the diagnostic and disease control tools in the context of introducing metagenomic analysis as the primary tool for pathogen identification.