Abstract: To identify the pathogen of severe acute pneumonia in Chifeng city,Inner Mongolia and to analyze the homeology of pol gene of the pathogen.Methods Reverse transcription PCR(RT-PCR)and multiplex PCR were used to detect nucleic acid of the influenza virus and respiratory viruses from oropharyngeal swabs of infection cases.Onestep RT-PCR was used to amplified the pol gene from the human coronavirus 299E,OC43,NL63,and HKU1 virus and the pol gene was sequenced to analyze the homeology of the positive sample.Results The human coronavirus HKU1 virus was detected from one sample.The pol gene sequence data showed that the virus had high homeology with the reference human coronavirus HKU1.Conclusion The study identified one patient infected with human coronavirus HKU1 virus and other infection cases need to be studied further.