Study Patients
Respiratory etiological surveillance monitoring system of Centers for Disease Control (CDC) of Beijing is designed to monitor respiratory pathogens in Beijing. Peking University Third hospital is a sentinel hospital and responsible for routine surveillance of respiratory tract infection. We conduct a retrospective study for the patients in routine surveillance with acute respiratory infections from June 2017 through July 2018 at Fever clinic. The patients were enrolled according to the following criteria.
1. CAP are diagnosed according to the diagnostic criteria of Chinese adult community acquired pneumonia (2016 edition) developed by Chinese society of respiratory medicine: (1) fever (a body temperature > 38.0 °C) or hypothermia (a body temperature < 35.5 °C), (2) leukocytosis (a white blood cell count > 10,000/ml) or leukopenia (a white blood cell count < 4000/ml); (3) had signs/symptoms of cough, sputum ,respiratory symptom aggravation, With or without purulent sputum, chest pain, dyspnea and hemoptysis. (4) chest radiological imaging features are patchy infiltration,leaf segment consolidation shadow, leaf segment consolidation shadow, interstitial inflammation change, with or without pleural effusion (5) Signs of lung consolidation or rales of lung auscultation. CAP can be established when tuberculosis, pulmonary tumor, non-infectious pulmonary interstitial disease, pulmonary edema, pulmonary atelectasis, pulmonary embolism, pulmonary eosinophil infiltration and pulmonary vasculitis are excluded.
2. Acute upper respiratory tract infections (AURTIs) are diagnosed according to following criteria: 1. symptoms of acute infection, defined as fever (a body temperature > 38.0 °C) with sore throat, runny nose, cough, nasal obstruction, rhinorrhea, cough and other upper respiratory symptoms.
Data and specimen collection。
Detailed demographic information was documented, and laboratory data were collected from the patients’ medical files. We collected throat swab from the patients diagnosed with acute upper respiratory tract infections within one week after onset of disease, and sputum diagnosed with CAP, or throat swab if there is no sputum. Specimen were transported to CDC laboratory for pathogen nucleic acid amplification test by reverse transcription-polymerase chain reaction (RT-PCR).
The test includes the following virus: human rhinovirus (HRV), influenza A virus (Flu A),novel influenza A (H1N1) ,seasonal H3 influenza(H3N2), influenza B virus (Flu B),, human coronavirus(HCoV) 229E/HKU1,HCoV OC43/NL63、ADV, RSV, PIV1-4, hMPV and EV.
Statistics
All analyses were performed with the Statistical 18.0 and Microsoft Excel 2007.. General data are presented as a percentage (P), or mean ±SD. Differences in categorical variables between groups were compared by the χ2 test. A single-tailed P value of <0.05 was considered to be statistically significant.
Experimental methods
1. Nucleic Acid Extraction: Total nucleic acids including DNA and RNA were extracted from 200 𝜇L of each specimen using magnetic bead nucleic acid Extraction Kit (Thermo Fisher, American, NO.KFR-805496) by ABI Mag MAX express 96 according to the manufacturer’s instructions.
2. RT-PCR Screening for Respiratory Viruses. For all collected specimens, RT-PCRs were performed to detect infection with ADVs, HBoV, HCoV, hMPV, IFVs,RSV, PIV, EV, and HRV. RT-PCR was performed using a RT-PCR Taq kit (HeChuang, JiangSu, China) by ABI 7500 (real-time PCR) instrument.
3 .Results determination: The following conditions should be simultaneously met the following three standards: 1. sleek S-Curve, 2. CT≤35 3, 3. ΔRn>1×104