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Background  We report a rare case of  Mammalian orthoreovirus  (MRV) infection in a child with a primary immunodeficiency (PID). Infections with Mammalian orthoreovirus are very rare and probably of zoonotic origin. Only a few cases have been described so far, including one with similar pathogenesis as in our case.    Case presentation  The patient, age 11, presented with flu-like symptoms and persistent severe diarrhea.  Enterovirus  has been detected over several months, however, exact typing of a positive cell culture remained inconclusive. Unbiased metagenomic sequencing then detected MRV in stool samples from several time points. The sequencing approach further revealed co-infection with a recombinant  Coxsackievirus  and  Adenovirus . MRV-specific antibodies detected by immunofluorescence proved that the patient seroconverted.    Conclusion  This case highlights the potential of unbiased metagenomic sequencing in supplementing routine diagnostic methods, especially in situations of chronic infection with multiple viruses as seen here in an immunocompromised host. The origin, transmission routes and implications of MRV infection in humans merit further investigation.    Electronic supplementary material  The online version of this article (10.1186/s12879-018-2946-7) contains supplementary material, which is available to authorized users.

bmc infectious diseases

Persistent mammalian orthoreovirus, coxsackievirus and adenovirus co-infection in a child with a primary immunodeficiency detected by metagenomic sequencing: a case report