Methods:: Forty-four COVID-19 patients (severe/critical: N = 8, non-severe: N = 36) were examined by next generation sequencing (NGS) of nasopharyngeal test paper to observe the effect of novel coronavirus infection to the microbial composition in upper airway.
Results: In these nasopharyngeal test paper samples, 38 kinds of bacteria, 10 kinds of viruses except SARS-CoV-2 , nine kinds of fungi and three kinds of atypical pathogens had been found. There was some difference in microbial composition in the upper airway between severe and non-severe cases.
Summary: These results are important for us to study the effect of SARS-CoV-2  on the local microbial composition of upper airway and prevent opportunistic infection in severe patients.
Keywords: SARS-CoV-2 , microbial composition, upper airway, next generation sequencing; NGS