Background: This study aims to find out whether patients admitted to hospitals for influenza symptoms were potentially infected with novel coronavirus [SARS-CoV-2] prior to nucleic acid testing in Wuhan and Taiyuan, China, considering that it broke out during the influenza season and its symptoms mimic influenza. Methods:A total of 685 nucleic acid samples of respiratory pathogenic  microorganisms were obtained from patients with flu-like symptoms  admitted to Renmin Hospital of Wuhan University and Shanxi Provincial People’s Hospital, from 1 November 2019 to 20 January 2020. Samples were respectively detected by 13 Respiratory Pathogen Multiplex Detection Kit and Novel Coronavirus (2019-nCoV) Nucleic Acid Diagnostic Kit. Results: In Wuhan, human rhinovirus was the most frequent infectious pathogen in November (31.5%), and human respiratory syncytial virus appeared the most in December and January (37.1%, 8.6%, respectively). Generally, 115 patients of 616 patients (18.7%) from Wuhan were recognized as COVID-19, and only two patients were co-infected with other respiratory pathogens. In Taiyuan, influenza A virus was detected the most frequently in December and January (30.3%, 12%, respectively) without infection of SARS-COV-2 during study period. Conclusions: Some cases confirmed as influenza before routine nucleic acid testing of SARS-CoV-2 were attributed to COVID-19.