Detection of a novel coronavirus (SARS-CoV-2) by real-time reverse transcription-polymerase chain reaction, China, 2020 (preprint)

ABSTRACT

Background: During the outbreak of unexplained pneumonia in the city of Wuhan in the late December, 2019, a novel coronavirus named SARS-CoV-2 was identified as the cause of this outbreak.Methods: A real-time polymerase chain reaction, which targets the orf1ab gene of viral genome, was established to detect and identify the SARS-CoV-2. We used this assay to screen 309 samples from persons with suspected SARS-CoV-2 infection in Wuhan. Then 6 close-phylogenic coronaviruses and 7 viruses which could cause pneumonia were detected. Moreover, 57 clinical samples infected with other viruses and 77 healthy samples were also tested.Results: The limit of detection of the assay was 6.25 copies per reaction in the detection of cRNA transcribed in vitro. The results of detection of throat and fecal swabs from persons with suspected SARS-CoV-2 infection showed throat swabs were more sensitive than fecal swabs during the first 15 days after onset of symptoms (throat 56.80%, fecal 30.43%), while the situation was reversed after 15 days (throat 20.83%, fecal 27.58%). And matched pair tests suggested the sputum samples had higher virus loads than throat swabs in the patients (P < 0.05). There was no cross-reaction when we detected the inactive culture of six other coronaviruses (human coronavirus 229E, NL63, OC43, HKU1, SARS-CoV, MERS-CoV) and seven other viruses (influenza virus A H1N1, influenza virus A H3N2, influenza virus B, parainfluenza viruses 1, 2, and 3; and respiratory syncytial virus). Besides, 27 BALF samples from pneumonia patients infected with human coronavirus 229E, OC43, HKU1 or human adenovirus 7, 30 throat swabs from patients infected with H1N1 and 77 throat swabs from healthy people tested negative by this assay.Conclusions: The results indicated that the assay specifically and sensitively detected the SARS-CoV-2.