Abstract: OBJECTIVE To analyze the clinical application value of respiratory detection by metagenomic next generation sequencing(mNGS). METHODS The random amplification, DNA nanoball, BGI-500 sequencing platform, and BWA analysis were used to do mNGS of viral nucleic acid extracts from respiratory tract sputums. The number of virus sequences in sputum samples＞100 was included in the study, and indexes of virus types, virus reads number, and abundance were observed. RESULTS Our result showed that 9 cases were included in our evaluation, and 77.78%(7/9) were immunocompromise patients, such as cardiac surgery, hormone therapy, malignant tumor, HIV infection and so on. The nucleic acid positive results of different viruses were detected as follows: 4 Epstein Barr virus(EBV), 2 Herpes Simplex Virus-I(HSV1), 1 Cytomegalovirus(CMV), 1 Human bocavirus and 1 adenovirus D, and Torque teno virus and Pig endogenous virus E were combinedly detected in some specimens. Pearson correlation analysis showed that in the sequencing parameters, the RPKM parameters (reads per kb million) were linearly related to PO2 of the patients. CONCLUSION Respiratory tract virus infection occurs mostly in host with immunosuppressive factors, of the virus are EBV, HSV1 and CMV, and Torque teno virus and Pig endogenous virus are mostly co-detected. In addition, RPKM may be correlated with severity of pneumonia, which suggests that RPKM may be useful in predicting the severity of lung lesions which is clinically meaningful.