The yield and consistency of the detection of SARS-CoV-2 in multiple respiratory specimens

Zhang, Haixia; Chen, Meiling; Zhang, Yanhua; Wen, Jing; Wang, Yajie; Wang, Liming; Guo, Jinjin; Liu, Chen; Li, Daijing; Wang, Ying; Bai, Jing; Gao, Guiju; Wang, Sa; Yang, Di; Yu, Fengting; Yan, Liting; Wan, Gang; Zhang, Fujie

BACKGROUND: Few studies compared the yield of the RT-PCR assay in nasopharyngeal swabs, oropharyngeal swabs, and sputum for SARS-CoV-2 detection. METHOD: We conducted an observational study in Beijing Ditan Hospital, China. Specimens including nasopharyngeal swabs, oropharyngeal swabs and sputum from confirmed COVID-19 patients were collected for RT-PCR testing. Disease duration was calculated from the date of symptom onset to the date of specimens’ collection and divided into three groups: ≤14days, 14-21days, and >21days. We compared positive rates across three specimens collected in different disease duration. The kappa coefficient (KC) was used to evaluate consistency of RT-PCR results between different specimens. RESULTS: A total of 291 specimens were collected and tested from 43 confirmed patients. Among specimens collected in disease duration of ≤ 14days, the positive rate was highest in sputum (79.2%), and significantly higher than that in nasopharyngeal swabs (37.5%, p=0.003) and oropharyngeal swabs (20.8%, p&0.001). Similar findings were observed in disease duration of 14-21days and >21days. The consistency of testing results between nasopharyngeal swabs and oropharyngeal swabs was low in disease duration of ≤14days and >21days. The consistency between the sputum and oropharyngeal swabs, and between the sputum and nasopharyngeal swabs were very low across all three disease durations with statistical significance. CONCLUSION: Compared to nasopharyngeal swabs and oropharyngeal swabs, sputum had the highest yield of SARS-CoV-2 detection. Nasopharyngeal swabs and oropharyngeal swabs had a similar yield. If sputum was not feasible, a nasopharyngeal swab could be recommended for the detection of SARS-CoV-2 and early testing is needed.