We performed a retrospective study at the CSMUH, which is a 1100-bed Medical Centre in Central Taiwan.
We recruited consecutive patients admitted from the emergency department with suspected pneumonia after an evaluation based on standard practice including clinical evaluation, routine blood tests, and CXR. We included all participants with fever ≧38℃ with or without ARIs initially presented at our out-patient or emergency department during the period of January 21 to March 27, 2020 and who underwent the rRT-PCR test of SARS-CoV-2 and had sufficient follow-up data. We excluded the patients did not have the rRT-PCR test of SARS- CoV-2 and they did not have any follow-up visit (Fig.1). Presence of an acute infiltrate was interpreted by the physician in charge of the patient. The diagnosis of pneumonia on the CXR examination would be presented by the expert radiologist on duty at the same time. We noted the clinical characteristics, fever, respiratory symptoms, CXR, and laboratory and microbiological findings of patients suspected with SARS-CoV-2-infection. In present study, the data was collected from electronic medical records by retrospective review.
Framework followed by the government to identify SARS-CoV-2 (COVID-19) Cases
Individuals with respiratory syndrome who sought medical attention at clinics were given the notice of mandatory home quarantine, or self-home quarantine, or self-health management and were informed to report to the physician of their medical history (T.O.C.C.), residence history, and whether anyone else has similar symptoms(Fig. 2 and Supplementary Table 1 and 2).17,27 The other scenario was when the patients had ARI and sought medical attention, physician took medical history of T.O.C.C. and used risk assessment for patients having the possibility of COVID-19 (Fig. 2 and Supplementary Table 2). 17,27 Those who met the criteria of definition of confirmed COVID-19 case were reported to the Communicable Diseases Network Taiwan CDC to be presumed a COVID-19 case. Subsequently, we used rRT-PCR assay to survey coronavirus in the nasopharynx, oropharynx, or sputum specimens (Fig. 2 and 3).17,27,31
Definition of Confirmed Coronavirus Disease 2019 (COVID-19) Case
We obtained the clinical information based on the guidelines of WHO and Taiwan CDC.13,32 Then, we established the urgent countermeasures of SARS-CoV-2 related COVID-19 at the Centre of Infection control of CSMUH in February 2020. (Fig. 2 and 3)17, 27, 28 For confirmation of SARS-CoV-2 infections, Taiwan CDC recommends fitting in the case definition and diagnostic testing of patients who meet the clinical, or laboratory, or epidemiologic criteria for a SARS-CoV-2 person under investigation.
Case definition for reporting SARS-CoV-2 infection:28
A. Clinical criteria is a patient with at least one of the following symptoms:
1. Fever (≧38℃) or patients with acute respiratory infection (sudden onset of cough, sore throat, shortness of breath)
2. Patients with pneumonia diagnosed by clinical signs and symptoms, or by radiological or histopathologic means
3. Patients with community-acquired-pneumonia with unknown pathogens
B. Laboratory Criteria at least one of the following:
Collected specimens from lower or upper respiratory tracts, including expectorated sputum, bronchoalveolar lavage, endotracheal aspirate, nasopharyngeal swab or oropharyngeal swab.
1. Isolation and confirmed SARS-CoV-2
2. Positive testing by SARS-CoV-2 rRT-PCR assay
C. Epidemiologic criteria
In the 14 days prior to the onset of symptoms, met at least one of the following:
1. Had a history of live in or travel to warning level 3 destinations or were in close contact with a symptomatic person with presumed ongoing community transmission of SARS-CoV-2.
2. Had a history of close contact with a symptomatic probable case or confirmed case having had face-to-face contact or without airway protection
3. Health-care-workers
4. A familial cluster or a hospital cluster
D. Reported illnesses, meets at least one of the following:
1. Meets at least one of the clinical criteria plus epidemiologic criteria (1) or (3)
2. Clinical criteria (2) plus epidemiologic criteria (2)
3. Meets the clinical criteria (3)
4. Meets at least one of the laboratory Criteria
E. Classification of the disease
1. Presumed case
A presumed case meets clinical criteria, but SARS-CoV-2 for testing is inconclusive (the result of the test reported by the laboratory) or a suspected case had close contact with a symptomatic confirmed case of SARS-CoV-2 infection in the 14 days prior to onset of symptoms.
2. Confirmed case:
Patients with laboratory confirmation of SARS-CoV-2 infection, irrespective of clinical signs and symptom
Real-Time Reverse-transcription Polymerase Chain Reaction
We obtained the respiratory samples including nasopharyngeal or oropharyngeal swabs, or sputum specimens in the negative pressure room from hospitalized patients or patients who sought medical attention at the emergency department and it was stored in viral- transport medium. The physicians wore PPE, including gloves, face shield or goggles, water resistant gown, and N95 mask or respirator, when they collected the specimens (Fig. 2). All samples were processed at the central laboratory of the CSMUH for diagnostic detection of SARS-CoV-2 and influenza by rRT-PCR. The protocol was performed according to the guidelines of WHO and Taiwan CDC as described in detail in other researches.25,31 We detected of respiratory pathogens using FilmArray™ Respiratory Panel (BioFire Diagnostics, bioMérieux, Utah, USA) from the nasopharyngeal specimens collected from the presumed COVID-19 patients.33
Statistical analysis
We used SPSS for Windows Version 22.0 (SPSS Inc., Chicago, IL, USA) to analyse the data. Continuous variables were expressed as mean and standard deviation; categorical variables were expressed as number (%) and Chi-square test was used to compare between pneumonia and presumed infection groups. Statistical significance was defined as a p-value less than 0.05 and all tests were two-tailed.