Sheep pox virus is one of the most serious diseases of livestock. The virus causes damage to integuments, spreads rapidly within the herd, and often leads to serious economic losses. The set of sanitary and epidemiological measures during outbreaks of the infection largely depends on identification of the virus strain and unambiguous differentiation of the infectious strain from vaccine ones. The most modern and precise approach to identifying virus strains is the whole metagenome sequencing of samples followed by assembly and analysis of the virome of the sample. We evaluate the applicability of shotgun metagenomic sequencing to accurately confirm the species of the virus and to identify it to the level of the strain using de novo assembly of the virome. It is shown that this approach allows one not only to accurately determine the strain affiliation of an infectious agent, but also to reveal and identify possible coinfections of both viral and bacterial natures.