Positive rate of RT-PCR detection of SARS-CoV-2 infection in 4880 cases from one hospital in Wuhan, China, from Jan to Feb 2020

1. Introduction

Since December 2019, an epidemic Coronavirus disease (COVID-19) caused by novel coronavirus (SARS-CoV-2) infection has occurred unexpectedly in China. Till March 2, 2020, more than 80 thousand confirmed cases have been reported in China. Of these cases, 49 thousand were identified in Wuhan City. Identification, isolation and caring for patients early are essential to limit human-to-human transmission including reducing secondary infections among close contacts and health care workers, preventing transmission amplification events. Following the national recommendations for diagnosis and treatment of pneumonia caused by 2019-nCoV (the 5th edition) and current status of clinical practice in Hubei Province, RT-PCR analysis was used to detect the causative virus from respiratory secretions. However, some investigators and clinical doctors argued that CT imaging should be served to identify the SARS-CoV-2 infection instead, since quite a bit cases showed progressive multiple peripheral ground-glass opacities in both lungs even the RT-PCR results were negative [1], [2].

Since RT-PCR was one of the most quickly established laboratory diagnosis method in a novel viral pandemic, just as this COVID-19, it served efficiently to confirm a viral infection within 2 h. During the early Feb, the need of detect increased dramatically up to 10 thousands of samples per day in Wuhan City. But to what extend was this RT-PCR based viral nucleic acid test (NAT) could reflect the real SARS-CoV-2 infection?

Therefore in this study, we retrospectively analysed NAT test of 4880 cases from Jan 22 to Feb 14, 2020 in Renmin Hospital of Wuhan University. All the cases were suspected of SARS-CoV-2 infection because of, (1) typical respiratory infection symptoms such as fever, cough and dyspnoea, or (2) close contact with a COVID-19 patient. RT-PCR were performed to detect ORF1ab and NP genes fragments from respiratory specimens, including nasal and pharyngeal swabs (NPS), bronchoalveolar lavage fluid (BLF) and sputum.

2. Materials and methods

3. RT-PCR detection

The presence of SARS-CoV-2 in respiratory specimens was detected by real-time RT-PCR amplification of SARS-CoV-2 open reading frame 1ab (ORF1ab), nucleocapsid protein (NP) genes fragments using kits provided by Shanghai Huirui Biotechnology Co., Ltd. Conditions for amplifications were 50 °C for 15 min, 95 °C for 3 min, followed by 45 cycles of 95 °C for 15 s and 60 °C for 30 s. As previously described [3], when two targets (ORF1ab, NP) tested positive by specific real-time RT-PCR, the case would be considered to be laboratory-confirmed. A cycle threshold value (Ct-value) less than 37 was defined as a positive test, and a Ct-value of 40 or more was defined as a negative test. A medium load, defined as a Ct-value of 37 to less than 40, required confirmation by retesting.

4. Results

5. Discussion

For the 2019 novel coronavirus disease (COVID-19), patients can be afebrile in the early stages of infection, with only chills and respiratory symptoms, but not always high temperature [4], [5], [6]. Elevated C-reactive protein (CRP) and lymphopenia are important factors. More and more evidence had shown distinct and complicated performance of COVID-19 as compared to SARS or MERS, which provided typical clinical symptoms for diagnosis [5]. Therefore, diagnosis of suspected SARS-CoV-2 caused pneumonia in Wuhan was based on clinical characteristics, chest imaging [1], [7], and the ruling out of common bacterial and viral pathogens that cause pneumonia as suggested by the latest National recommendations for diagnosis and treatment of pneumonia caused by 2019-nCoV (the 6th edition).

Here in this study, we analyzed recent 4880 cases by laboratory diagnosis of suspect SARS-CoV-2 infection in one hospital in Wuhan City, showing 38.42% positive percentage for total, but 57.00% positive in Fever Clinics. Relatively increased positive percentage in Fever Clinics suggested that the fever associated clinical symptoms were linked with viral NAT, at some degree. Interestingly, total positive percentage were associated with gender and age, while positive percentage in Fever Clinics was only associated with age, not gender. Therefore, consistent with other reports, we could conclude that for suspect SARS-CoV-2 infection, positive percentage would be higher in Male and Old, but in Fever Clinics, gender was not a risk factor.

The epidemic seems to be spreading rapidly worldwide, especially in Korea, Italy and Iran. Based on the reasons mentioned above, we suggest that viral NAT is a rapid, easy conducted, and widely used laboratory diagnosis for SARS-CoV-2 infection, especially for Fever Clinics. Clinical characteristics, chest imaging and etiology testing based on viral genes RT-PCR should be combined to tell a confirmation [4], [8]. Since there exists infection with atypical symptoms, RT-PCR should be taken for several times just in case of fake negative results.

For those countries who are facing an increased number of SARS-CoV-2 infection, we strongly suggest to prepare more reagents for SARS-CoV-2 NAT. Also, more laboratories and facilities should be trained and prepared for RT-PCR detection under a Biological Safety Protection 3-Level, just in case the horrible increasing requirements for detection that happened in early Feb in Wuhan, China.