Respiratory Virus Infections in Acutely Hospitalized Adult Patients With Pulmonary and Extrapulmonary Complications
Conditions: Respiratory Virus Infection, Stroke, Lung Disease, Acute Coronary Syndrome
Sponsor: The University of Hong Kong

1 
 
 
 
 
 
 
 
 
 
Protocol Title 
 
Respiratory virus infections in acutely hospitalized 
adult patients with pulmonary and extrapulmonary 
complications 
 
Principal Investigator 
Dr. Kelvin To 
MBBS, FRCPath, FHKCPath, FRCP (Edin), MD 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Date: 4th January 2019 
Version: 20190104 

2 
 
Table of content 
 
Section 
Content 
Page number 
1 
Protocol synopsis 
3 
2 
Background and rationale 
4 
2.1 
Background of respiratory virus infection 
4 
2.2 
Study rationale 
4 
3 
Study Design 
5 
3.1 
Study objectives 
5 
3.2 
Study design and organization 
5 
3.2.1 
Overall study design 
5 
3.3 
Outcome measurements 
6 
3.3.1 
Primary outcome measurement 
6 
3.3.2 
Secondary outcome measurements 
6 
3.4 
Informed consent 
6 
3.5 
Confidentiality of data 
6 
3.6  
Archive of data 
7 
4 
Selection and enrollment of participants 
7 
4.1 
Selection of study population at in-patient 
7 
4.11 
Inclusion criteria 
7 
4.12 
Exclusion criteria 
7 
4.2 
Selection of study population at out-patient 
7 
4.2.1 
Inclusion criteria 
7 
4.2.2 
Exclusion criteria 
7 
4.3 
Study enrollment procedures 
8 
5 
Study procedures 
8 
5.1 
Schedule of evaluations 
8 
5.1.1 
Participants at acute medical ward (in-
patients) 
8 
5.1.2 
Participants at the out-patient clinic 
8 
5.2 
Assessment and clinical data collection 
8 
5.3 
Detection of respiratory viruses 
9 
5.3.1 
Specimen collection 
9 
5.3.2 
Molecular testing of respiratory viruses 
9 
5.4 
Healthcare utilization of respiratory virus 
infection 
9 
6 
Statistical methods 
10 
6.1 
Sample size 
10 
6.2 
Analysis of study 
10 
7 
Study team and study site 
11 
7.1 
Study team 
11 
7.2 
Study site 
11 
8 
References 
11 
 
 

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1. PROTOCOL SYNOPSIS: 
 
Protocol title 
Respiratory virus infections in acutely hospitalized adult patients with 
pulmonary and extrapulmonary complications 
 
Hypothesis 
The incidence of respiratory virus infection were underestimated 
 
Primary 
objective 
To determine the incidence and adjusted population attributable fraction of 
respiratory virus infection among patients with pulmonary and extrapulmonary 
complications 
 
Study 
participants 
1. Adult hospitalized patients admitted to the acute medical ward of Queen 
Mary Hospital 
2. Adult out-patients of Queen Mary Hospital 
 
Study design 
 
This is a prospective cohort study involving hospitalized adult patients 
admitted to the acute medical ward of Queen Mary Hospital, an acute care 
university-affiliated hospital with 1,700 beds in Hong Kong. Consecutive 
patients will be screened for eligibility based on inclusion and exclusion 
criteria. Written informed consent will be obtained from all study participants. 
Saliva specimens will be collected from study participants, and will be tested 
for respiratory viruses by a multiplex PCR panel. Patients’ demographics, 
underlying diseases, and outcome measures will be collected. The crude 
incidence will be assessed. Adjusted population attributable fraction will be 
calculated by adjusting the crude incidence of acutely hospitalized adult 
patients with the background rate among adult out-patients.  
 
Primary 
outcome 
Incidence of respiratory viruses 
Secondary 
outcome 
1. Length of hospital stay 
2. Length of stay in general medical ward 
3. Length of stay in high dependency unit 
4. Length of stay in intensive care unit 
5. Proportion of patients requiring oxygen supplementation 
6. Proportion of patients requiring positive pressure ventilation 
7. Proportion of patients requiring intubation 
8. Proportion of patients admitted to intensive care unit 
9. Proportion of patients admitted to coronary care unit 
10. Proportion of patients admitted to high dependency unit 
11. Proportion of patients who die during hospitalization 
12. Initial blood test results on admission 
13. Radiological investigation results 
14. Microbiological investigations results 
 
Data analysis 
The fraction of hospitalization that can be attributed by a particular respiratory 
pathogen will be calculated using adjusted population attributable fraction. 

4 
 
Continuous variables and categorical variables will be compared using Mann 
Whitney U test and Fisher’s exact test, respectively. A P value of <0.05 with 
two sided testing will be considered statistically significant. Statistical test will 
be performed using SPSS 23.0.0. 
 
 
2. BACKGROUND AND RATIONALE 
 
2.1. 
Background and study rationale 
Respiratory viruses cause severe infections, and contribute to a substantial number of 
hospitalizations, admission to intensive care units and deaths (1). Many hospitalizations due to 
respiratory virus infection are related to pneumonia or exacerbation of chronic lung disease. In 
addition, many hospitalizations are related to extrapulmonary complications, such as acute 
coronary syndrome or stroke (2).  
 
Previous studies have reported the incidence of respiratory viruses among patients with 
pulmonary complications (3), or the association of respiratory viruses with acute coronary 
syndrome or stroke (4). However, there are several problems associated with these studies. First, 
many of these studies are retrospective in nature, and therefore testing was only performed in 
selected patients with respiratory symptoms. Hence, many patients without respiratory symptoms 
were not recruited. Second, respiratory virus can be detected in some asymptomatic individuals. 
Therefore, the presence of respiratory virus may be an incidental finding rather than the cause of 
the complication. Third, many studies only focus on a few respiratory viruses, especially on 
influenza virus.  
 
This study aims to address these issues. We propose to conduct a prospective cohort study. We 
will recruit hospitalized adult patients with exacerbation of underlying lung disease, acute 
coronary syndrome or stroke. As controls, we will recruit outpatients follow-up for chronic heart 
disease, chronic lung disease or neurological conditions. We will collect saliva from study 
participants and perform respiratory virus testing using a multiplex PCR panel. Our previous 
studies have shown that there is a high concordance between results from respiratory virus 
testing on saliva and nasopharyngeal specimens (5, 6). 
Our study will provide accurate data on the epidemiology of respiratory viruses in pulmonary 
and extrapulmonary complications. These data are important for clinicians, public health 
practitioners and scientists. 
  
3. STUDY DESIGN 
 
3.1. 
Study objectives 
1. To determine the crude incidence of respiratory virus infection among patients with 
exacerbation of chronic lung disease, acute coronary syndrome or stroke 
2. To determine the adjusted population attributable fraction of respiratory virus infection among 
patients with exacerbation of chronic lung disease, acute coronary syndrome or stroke 
 
3.2 
Study design and organization 
 

5 
 
3.2.1 Overall study design 
 
This is a prospective cohort study involving hospitalized adult patients admitted to the 
acute medical ward of Queen Mary Hospital, an acute care university-affiliated hospital with 
1,700 beds in Hong Kong. Patients will be screened for eligibility based on inclusion and 
exclusion criteria. Written informed consent will be obtained from all study participants. Saliva 
specimens will be collected from study participants, and will be tested for respiratory viruses 
using a multiplex PCR panel. Patients’ demographics, underlying diseases, and outcome 
measures will be collected.   
Since respiratory viruses can be detected in asymptomatic adults, we will also recruit 
outpatients followed up for a chronic condition to determine the frequency of respiratory viruses 
among these patients without any acute symptoms requiring hospitalization. We will adjust the 
crude incidence from this background rate. 
 
3.3 
Outcome measurements 
 
3.3.1 Primary outcome measurement 
1. Incidence of respiratory viruses 
 
3.3.2 Secondary outcome measurements 
1. Length of hospital stay 
2. Length of stay in general medical ward 
3. Length of stay in high dependency unit 
4. Length of stay in intensive care unit 
5. Proportion of patients requiring oxygen supplementation 
6. Proportion of patients requiring positive pressure ventilation 
7. Proportion of patients requiring intubation 
8. Proportion of patients admitted to intensive care unit 
9. Proportion of patients admitted to coronary care unit 
10. Proportion of patients admitted to high dependency unit 
11. Proportion of patients who die during hospitalization 
12. Initial blood test results on admission 
13. Radiological investigation results 
14. Microbiological investigations results 
 
3.4. 
Informed consent 
The investigator or his/her representative will explain the nature of the study to the subjects, and 
answer all questions by the subjects regarding this study. Prior to any study-related screening 
procedures being performed on the subject, the informed consent statement will be reviewed and 
signed and dated by the subjects and the person who administered the informed consent.  
 
3.5 
Confidentiality of data 
Permission for direct access to a subject's data will be sought in writing by the investigator and from 
the subject as part of the informed consent procedure. This gives permission to examine, analyse, 
verify and reproduce any records and reports that are important to the evaluation of the study. Any 
party (e.g., domestic and foreign regulatory authorities, monitors and auditors) with direct access 
must take all reasonable precautions within the constraints of the applicable regulatory requirements 
to maintain the confidentiality of the subjects’ identities and the Hospital Authority’s proprietary 

6 
 
information. It is the monitor’s responsibility to verify that each subject has consented, in writing, to 
direct access.  
 
3.6 
Archive of data 
The investigator must retain all study documentation pertaining to the conduct of the study at the 
study site for a period of at least 5 years.  
 
3.7 
Ethical and administrative endorsement 
The study was approved by the Institutional Review Board (IRB) of the University of Hong Kong 
and Hospital Authority (IRB reference number: to be added when approved)  
 
 
4.  
SELECTION AND ENROLLMENT OF PARTICIPANTS 
 
4.1 
Selection of study population at in-patient 
 
4.1.1. Inclusion criteria 
1. Admitted to the acute medical ward of Queen Mary Hospital via the accident and emergency 
department  
2. Aged 18 years or above 
3. Hospitalized for less than 24 hours at the time of recruitment 
4. Presented with exacerbation of underlying lung disease, acute coronary syndrome or stroke 
5. Competent and agree to provide written informed consent 
 
4.1.2 Exclusion criteria 
1. Admitted to any hospitals in the past 14 days  
2. Respiratory virus testing performed in the past 14 days  
3. Antiviral against respiratory virus given within the past 14 days 
4. Not sufficient saliva 
 
4.2 
Selection of study population at out-patient 
 
4.2.1 Inclusion criteria 
1. Aged 18 years or above  
2. Follow-up at out-patient clinic or at the physiotherapy department of Queen Mary Hospital 
3. Competent and agree to provide written informed consent 
 
4.2.2 Exclusion criteria 
1. Admitted to any hospitals in the past 14 days 
2. Respiratory virus testing performed in the past 14 days 
3. Antiviral against respiratory virus given within the past 14 days 
4. Onset of new respiratory or non-respiratory symptoms within the past 14 days 
5. Not sufficient saliva 
 
4.3 
Study enrollment procedures 

7 
 
Patients will be screened for eligibility by a research nurse. Reasons for ineligibility or non-
participation of eligible candidates will be documented. A written informed consent will be 
signed by the patient.   
 
5. 
STUDY PROCEDURES 
 
5.1 
Schedule of evaluations 
 
5.1.1 Participants at the acute medical ward (in-patients) 
On the day of enrollment: 
- Inclusion and exclusion criteria 
- Written informed consent  
- Demographic information 
- Questionnaire on vaccine history and symptoms  
- Collection of saliva specimen  
 
Follow-up after patient discharge 
- Hospitalization data (length of stay, laboratory and radiological tests, treatment) 
 
5.1.2 Participants at the out-patient clinic 
On the day of enrollment: 
- Inclusion and exclusion criteria 
- Written informed consent  
- Demographic information 
- Questionnaire on vaccine history and symptoms  
- Collection of saliva specimen 
 
5.2 
Assessment and clinical data collection 
Initial symptom assessment will be performed by trained research nurses at the medical or at 
outpatient clinics. At the time of enrollment, the following information will be collected from the 
patient by the research staff using a standard questionnaire: 
- Symptoms and date of symptom onset 
- Prior use of oseltamivir or zanamivir within 14 days 
- Prior use of antibiotics within 14 days 
- Attended out-patient clinic for the same illness 
- Close contacts with respiratory symptoms in the past 7 days 
- Receive influenza vaccine in the past season 
- Receive pneumococcal vaccine 
 
The following data will be extracted from the clinical management system: 
- Age, sex, comorbidities 
- National Early Warning Score (NEWS) at A&E (20) (respiration rate, oxygen saturation, need 
for supplemental oxygen, temperature, systolic blood pressure, heart rate, level of consciousness) 
- Time of hospital admission and discharge 
- Clinical findings 
 Underlying disease 

8 
 
 Clinical symptoms and signs during hospitalization 
 Hematological, biochemical, microbiological, immunological, and radiological 
investigation results on admission 
 Need for supplementary oxygen, positive pressure ventilation, intubation, admission to 
intensive care unit, coronary care unit or high dependency unit during the hospital stay 
 Final diagnosis 
 
 
5.3 
Detection of respiratory viruses 
 
5.3.1 Specimen collection 
Patients will be asked to spit out saliva (~1 ml) into a sterile container and viral transport 
medium (VTM) will be added as we described previously (5, 6). The specimens will be 
transported to the laboratory and stored at -80C until testing.  
 
5.3.2  Molecular testing of respiratory virus  
Saliva will be tested for respiratory viruses using a commercially available multiplex PCR panel.  
 
6.  
STATISTICAL METHODS 
 
6.1. 
Sample size 
The sample size is based on the feasibility of the budget. A total of 100 hospitalized patients and 
100 out-patients will be recruited. 
 
6.2 
Analysis of the study 
Crude incidence of each respiratory virus and overall respiratory virus infection among 
hospitalized patients and out-patients will be estimated. To adjust for the background rate of 
respiratory virus detection among out-patients, we will calculate adjusted population attributable 
fraction (aPAF) as described previously (22). Conceptually, aPAF represents the fraction of 
hospitalization that can be attributed to a particular pathogen. Death rate of each detected 
respiratory virus and overall respiratory virus infection among patients in the acute medical 
wards will be estimated. 
 
For symptomatology of respiratory viruses, frequencies and proportions of respiratory and non-
respiratory symptoms for each respiratory virus and overall respiratory virus infection will be 
calculated.  
 
Statistical test will be performed using SPSS version 23.0. A P value of <0.05 with two-sided 
testing will be considered statistically significant.  
 
7. STUDY TEAM and STUDY SITE 
 
7.1  
Study team 
Principal investigator 
- Design of study, coordination and assessment of subjects for study enrollment, analysis of data, 
writing up 

9 
 
 
Co-investigators 
- Coordination and assessment of subjects for study enrollment 
Study nurse 
- Subject enrollment, collection of clinical specimens, data collection 
 
7.2 
Study site 
Queen Mary Hospital, Pokfulam Road, Pokfulam, Hong Kong Special Administrative Region, 
China 
 
 
8. 
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