Application and optimization of RT-PCR in diagnosis of SARS-CoV-2 infection

Abstract

syndrome coronavirus 2 (SARS-CoV-2) has become a global threat to public health. Aiming to construct an efficient screening pattern, we comprehensively evaluated the performances of RT-PCR and chest CT in diagnosing COVID-19. Methods:The records including demographics, RT-PCR, and CT from 87 confirmed cases and 481 exclusion cases were collected. The diagnostic accuracy of the pharyngeal swab RT-PCR, CT, combination with the second pharyngeal swab RT-PCR or with CT were evaluated individually.Besides, all the stool RT-PCR results were plotted by time to explore the value of stool RT-PCR. Findings: Combination of RT-PCR and CT has the higher sensitivity (91.9%,79/86) than RT-PCR alone (78.2% ， 68/87) or CT alone (66.7%, 54 of 81) or combination of two RT-PCR tests (86.2%,75/87). There was good agreement between RT-PCR and CT (kappa-value, 0.430). In 34 COVID-19 cases with inconsistent results, 94.1% (n=32) are mild infection, 62.5% of which (20/32) showed positive RT-PCR. 46.7% (35/75) COVID-19 patients had at least one positive stool during the course. Two cases had positive stool earlier than the pharyngeal swabs. Importantly, one patient had consecutive positive stool but negative pharyngeal swabs.Interpretation: Combination of RT-PCR and CT with the highest sensitivity is an optimal pattern to screen COVID-19. RT-PCR is superior to CT in diagnosing mild infections. Stool RT-PCR should be considered as an item for improving discovery rate and hospital discharge. This study shed light for optimizing scheme of screening and monitoring of SARS-CoV-2 infection. : medRxiv preprint person-to-person transmission of SARS-CoV-2 in hospital and family settings 2,6,7 . As of February 17, 2020, more than 71,000 laboratory-confirmed and 1,770 death cases have been documented in China and in other countries worldwide (including the USA, German, japan and South Korea) 8,9 . The mortality rate of SARS-CoV-2 was around 2%. The WHO has recently declared the SARS-CoV-2 a public health emergency of international concern 10 . Thus, diagnostic tests specific for this infection are urgently needed for confirming suspected cases, screening patients and conducting virus surveillance.Identification of pathogens mainly includes virus isolation and viral nucleic acid detection.According to the traditional Koch's postulates, virus isolation is the gold standard for virus diagnosis in the laboratory. Thus, based on SARS-CoV-2 possesses a strong capability to infect humans, CDC recommends that clinical virology laboratories should not attempt viral isolation from specimens collected from COVID-19 patients under investigation. Because SARS-CoV-2 is a newly discovered virus, the spectrum of the available diagnostic tools is tight. In the early stage, SARS-CoV-2 has been detected in human clinical specimens by next-generation sequencing, cell culture, and electron microscopy 11 . Further development of accurate and rapid methods to identify this emergency . CC-BY-ND 4.0 International license It is made available under a author/funder, who has...

Clinical Pathway for Early Diagnosis of COVID-19: Updates from Experience to Evidence-Based Practice

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