key: cord-0823746-z4l3pk23
authors: Liu, Rui; Han, Huan; Liu, Fang; Lv, Zhihua; Wu, Kailang; Liu, Yingle; Feng, Yong; Zhu, Chengliang
title: 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
date: 2020-03-07
journal: Clin Chim Acta
DOI: 10.1016/j.cca.2020.03.009
sha: a044d99ce4fd194fe5d572aada61a4a83c4a274f
doc_id: 823746
cord_uid: z4l3pk23

BACKGROUND: There’s an outbreak of a novel coronavirus (SARS-CoV-2) infection since December 2019, first in China, and currently with more than 80 thousand confirmed infection globally in 29 countries till March 2, 2020. 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. The RT-PCR detection of viral nucleic acid test (NAT) was one of the most quickly established laboratory diagnosis method in a novel viral pandemic, just as in this COVID-19 outbreak. METHODS: 4880 cases that had respiratory infection symptoms or close contact with COVID-19 patients in hospital in Wuhan, China, were tested for SARS-CoV-2 infection by use of quantitative RT-PCR (qRT-PCR) on samples from the respiratory tract. Positive rates were calculated in groups divided by genders or ages. RESULTS: The positive rate was about 38% for the total 4880 specimens. Male and older population had a significant higher positive rates. However, 57% was positive among the specimens from the Fever Clinics. Binary logistic regression analysis showed that age, not gender, was the risk factor for SARS-CoV-2 infection in fever clinics. CONCLUSIONS: Therefore, we concluded that viral NAT played an important role in identifying SARS-CoV-2 infection.

There's an outbreak of a novel coronavirus (SARS-CoV-2) infection since December 2019, first in China, and currently with more than 80 thousand confirmed infection globally in 29 countries till March 2, 2020. 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. The RT-PCR detection of viral nucleic acid test (NAT) was one of the most quickly established laboratory diagnosis method in a novel viral pandemic, just as in this COVID-19 outbreak.

patients in hospital in Wuhan, China, were tested for SARS-CoV-2 infection by use of quantitative RT-PCR (qRT-PCR) on samples from the respiratory tract. Positive rates were calculated in groups divided by genders or ages.

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 groundglass opacities in both lungs even the RT-PCR results were negative [1, 2] . 

Data collection 4880 cases from Jan 22 to Feb 14 were tested for SARS-CoV-2 infection in Renmin Hospital of Wuhan University, who were suspected or at high risk of infection because of, 1) typical respiratory infection symptoms such as fever, cough and hard breath , or 2) close contact with a SARS-CoV-2 patients. Among these cases, 2251 were man (46.13%), 2629 were women (53.87%). The Median Age was 50 years (IQR=27).

Groups based on age: 18-29 (n=482), 30-39 (n=1097), 40-49 (n=841), 50-59 (n=1011), 60-69 (n=886), >70 (n=563). This study was approved by the Ethics Committee of the Renmin Hospital of Wuhan University (WDRM2020-K066) and the need for informed consent was waived.

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.

Statistical analyses were done by using the SPSS25.0 software. Chi-square test was used to compare inter-group differences, and binary logistic regression analysis was performed to analyze the risk factors for SARS-CoV-2 prevalence. Statistical significance was defined as P<0.05.

1875 out of 4880 (38.42%) were positive by RT-PCR-based NAT test with their respiratory specimens. Among this, 39.80% were positive for SARS-CoV-2-NP and 40.98% for SARS-CoV-2-ORF1ab (Table 1 ). We could see that the bronchoalveolar lavage fluid (BLF), exhibited the most highest positive rate of 100% for SARS-CoV-2

ORF1ab gene (n=5). The nasal and pharyngeal swabs (NPS) samples (n=4818) showed a poor positive rate of 38.25%. The Sputum exhibited a 49.12% positive rate.

The male patients are 2251, female are 2629. There is no obvious gender difference during sample collection. But for male, 40.43% were positive while for female, 36.71% were positive ( Table 2 ). The Positive Rate were significantly higher in Male than in Female cases (p<0.01).

When we analyzed the positive rate according to age (Table 3) , and we could see that positive rate increased from 24.90% (age 18-30) to 61.81% (age >70).

Binary logistic regression analysis showed that gender and age were two risk factor for SARS-CoV-2 infection (Table 4 ). Male and older people were more sensitive to the this novel virus infection (p<0.05).

Why the positive rate in this 4880 cases were this low? Or did the viral NAT test fail to serve for the diagnosis in this pneumonia epidemic? Since the 4880 specimens conclude all cases during the period in the hospital, such as fever, cough and hard breath, or close contact with COVID-19 patient, we further analyzed data from adult fever clinics (n=1707 , Table 5 ). Notably, the positive rate of patients in fever clinics (57.00%) was significant higher than the rate of the total (38.42%).

When we analyzed the positive rate between Male and Female cases from Fever Clinics, we did not observed significant difference. There were 499 positive male (57.69%) and 474 female (56.29%) from 1707 total Fever Clinics specimens.

When we analyzed data in age-based groups in Fever Clinics, we could see the older had higher positive rate ( Table 6 ). Positive rate in each group were 38.83%, 48.96%, 53.77%, 56.88%, 57.33% and 76.69%, which were significantly higher than the rate in the total 4880 cases.

Binary logistic regression analysis showed that the age, not the gender, was the risk factor for SARS-CoV-2 infection in Fever Clinics.

There was a quite special period that a large amount of patients rushed to health 

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.

Tables. Table 1 

Sensitivity of Chest CT for COVID-19: Comparison to RT-PCR

Chest CT for Typical 2019-nCoV Pneumonia: Relationship to Negative RT-PCR Testing

Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus-Infected Pneumonia

Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China

A Novel Coronavirus from Patients with Pneumonia in China

Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China

Time Course of Lung Changes On Chest CT During Recovery From

Novel Coronavirus (COVID-19) Pneumonia

Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study

The SARS-CoV-2 NAT positive rate was about 38% for the total 4880 specimens

Age, not gender, was the risk factor for SARS-CoV-2 infection in fever clinics

Viral NAT played an important role in identifying SARS-CoV-2 infection