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Background  Chinese woodchucks ( M. himalayana ) were recently found to be susceptible to woodchuck hepatitis virus (WHV) infection. In this study, we aimed to determine the susceptibility to WHV infection of  M. himalayana  from different areas and their association with the animal genetic background exemplified by cytochrome B and MHC-DRB molecules.    Methods  Animals from four different areas in Qinghai province were inoculated with WHV59 strains. The virological markers including WHV surface antigen (WHsAg), WHV core antibody (WHcAb), and WHV DNA in serum were measured by ELISA and Real-time PCR, respectively. The sequences of cytochrome B gene and MHC-DRB molecules were obtained and sorted with Clustalx software. The nucleotide variation sites were identified using MEGA5 software.    Results  The animals from four different areas had different susceptibility to WHV infection. Animals from TR and TD areas had a high level of long-lasting viremia, while those from GD and WL areas had a low level of transient viremia after WHV inoculation. All of the animals belong to the same subspecies  M. himalayana robusta  identified by cytochrome B gene sequences. Based on their nucleotide variation pattern, 8 alleles of cytochrome B gene were identified, and 7 MHC-DRB alleles were identified. Allele A of cytochrome B and Allele  Mamo-DRB1*02  of MHC-DRB was found to be frequent in animals from TR and TD areas, while Allele H of cytochrome B and Allele  Mamo-DRB1*07  of MHC-DRB was predominant in animals from GD and WL areas.    Conclusion  Chinese woodchucks from different areas differed in their susceptibility to WHV infection, though they belong to the same subspecies  M. himalayana robusta . The genetic background exemplified by cytochrome B and MHC-DRB differed in Chinese woodchucks with different susceptibility to WHV infection.    Electronic supplementary material  The online version of this article (10.1186/s12985-018-1010-y) contains supplementary material, which is available to authorized users.

Chinese woodchucks with different susceptibility to WHV infection differ in their genetic background exemplified by cytochrome B and MHC-DRB molecules