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The animal health monitoring is required to issue health certificates. The viral hepatitis virus is one of the most important infectious agents in mice breeding colonies. This research used RT-PCR to identify contaminations to mouse hepatitis virus. 18 out of 29 specimens were found to be infected, a prevalence of 62%. PCR product was purified and sequenced. Phylogenetic analysis revealed that the identified strain in this study was closely related to a strain reported from France. In the conventional system, contamination with different infectious agents is inevitable, thus it is better to replace the contaminated colonies with clean animals.