february, 2020

Combination of RT‐qPCR testing and clinical features for diagnosis of COVID‐19 facilitates management of SARS‐CoV‐2 outbreak

Yishan Wang, Hanyujie Kang, Xuefeng Liu, Zhaohui Tong

DOI: 10.1002/jmv.25721

Journal of Medical Virology

Abstract

Quantitative real‐time reverse transcriptase‐polymerase chain reaction (RT‐qPCR) assay has routinely been used for the detection of causative viruses from respiratory secretions and final pathogenic diagnostics of COVID‐19. More than seven types of SARS‐CoV‐2 nucleic acid test kit have been developed and approved rapidly, while a large number of the “suspected” cases with typical clinical COVID‐19 features and identical specific computed tomography (CT) images were not diagnosed. Unfortunately, due to an overwhelming situation in local hospitals, many “suspected” cases and diagnosed cases cannot efficiently be separated or treated. Recently, one patient was not confirmed by RT‐qPCR testing for SARS‐CoV‐2 infection for the first three times within 3 weeks before bronchoalveolar lavage fluid (BALF) was acquired, results from both RT‐qPCR and next‐generation sequencing (NGS) testing were positive for SRAS‐CoV‐2. These largely affected efficiency to control viral spreading and outbreak. Indeed, several factors have been proposed to explain the inconsistency or the high false‐negative rate (FNR). For example, results from RT‐qPCR testing using primers in the ORF1ab gene and N genes can be affected by the variation of viral RNA sequences. In terms of the natural history of the disease and viral load in different anatomic sites of the patients, sampling procedures largely contribute to high FNR. By estimate, FNR from one‐time testing was as high as 30% to 50% in real COVID‐19 cases.