Conditions: Influenza, Human
Keywords: H1N1 Complications PCR Seasonal Influenza Viral Shedding
Allocation: RANDOMIZED | Intervention model: PARALLEL
Enrollment: 716
Healthy volunteers: no

Brief summary:
People who are infected with the influenza virus may develop respiratory illnesses, such as pneumonia, or other life-threatening complications. Currently, there are four antiviral medications that are used to treat influenza. This study will examine one of these medications, oseltamivir, to examine how it affects the shedding of influenza virus in infected people.

Detailed description:
Seasonal influenza is responsible for excess hospitalizations and, despite effective antivirals, causes significant morbidity and mortality (about 24,000 deaths each year in the United States alone). The influenza virus that emerged in 2009 (A/California/07/2009 H1N1) caused fewer deaths (12,000 flu-related deaths in the U.S.) but in contrast to seasonal flu, nearly 90% of the deaths with the 2009 H1N1 occurred among people younger than 65 years of age. Although there are four currently licensed anti-influenza medications (amantadine and rimantadine, oseltamivir, and zanamivir), previous studies have not demonstrated conclusively to what extent these medications affect influenza viral shedding. This study will evaluate whether oseltamivir modifies the viral shedding during the treatment of uncomplicated influenza in an adult population and also assess methods to detect viral replication in the upper respiratory tract.

Subjects who presented with an influenza-like illness without any risk factors for severe disease were screened for the study. Those with a confirmatory test for influenza (rapid antigen or polymerase chain reaction \[PCR\]) were randomized in a 1:1 manner to receive a blinded study treatment consisting of either the oseltamivir or placebo for 5 days. Clinical, virologic, and laboratory assessments on Days 1, 3, 7, and 28 were used for both safety and efficacy analysis.

Arms:
arm 1: None arm 2: None

Interventions: intervention 1: Oseltamivir intervention 2: Placebo
Intervention descriptions: intervention 1: Subjects were prescribed Oseltamivir twice daily for 5 days, and each dose consisted of one capsule of Oseltamivir 75 mg. intervention 2: Subjects were prescribed the matching placebo twice daily for 5 days, and each dose consisted of one capsule of placebo.

Protocol document:
Prot_001.pdf: 
Protocol IRC-004  
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3AUG2016, Version 8 
 
 
Protocol Number: IRC-004 
 
 
 
A Randomized Double-Blind Study Comparing Oseltamivir versus Placebo 
for the Treatment of Influenza in Low Risk Adults 
 
 
 
 
 
 
Sponsored by: 
Office of Clinical Research Policy and Regulatory Operations (OCRPRO) 
Division of Clinical Research (DCR) 
National Institute of Allergy and Infectious Diseases (NIAID) 
5601 Fishers Lane, MSC-9820 
Bethesda, MD 20892-9820 
 
 
 
 
 
A Non-IND Study 
 
 
 
 
 
 
 
 
 
Version: 8  
 
Date: August 3, 2016


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3AUG2016, Version 8 
Précis            
Seasonal influenza is responsible for excess hospitalizations and, despite effective antivirals, 
causes significant morbidity and mortality (about 24,000 deaths each year in the United States 
alone). Although there are four currently licensed anti-influenza medications (amantadine and 
rimantadine, oseltamivir, and zanamivir), previous studies have not demonstrated conclusively to 
what extent these medications affect influenza viral shedding.  This study will evaluate whether 
oseltamivir modifies the viral shedding during the treatment of uncomplicated influenza in an 
adult population and also assess methods to detect viral replication in the upper respiratory tract.  
 
Subjects who present with an influenza-like illness without any risk factors for severe disease 
will be screened for the study. Those with a confirmatory test for influenza (rapid antigen or 
polymerase chain reaction [PCR]) will be randomized in a 1:1 manner to receive a blinded study 
treatment consisting of either the oseltamivir or placebo for 5 days. Clinical, virologic, and 
laboratory assessments on Days 3, 7, and 28 will be used for both safety and efficacy analysis.   


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3AUG2016, Version 8 
LIST OF ABBREVIATIONS 
AE 
Adverse event  
BMI 
Body mass index 
CDC 
The Centers for Disease Control and Prevention 
CFR 
Code of Federal Regulations 
COPD 
Chronic obstructive pulmonary disease 
DCR 
Division of Clinical Research 
DSMB 
Data and Safety Monitoring Board 
eCRF 
electronic Case Report Form 
FDA 
Food and Drug Administration  
GCP 
Guidelines for Good Clinical Practice 
H1N1  
Influenza A H1N1, swine flu 
HA 
Hemagglutination 
HAI 
Hemagglutination inhibition  
HIV 
Human immunodeficiency virus 
ICH 
International Conference on Harmonisation  
IDSA 
Infectious Disease Society of America 
IEC 
Independent Ethics Committee 
IRB 
Institutional Review Board 
ITT 
Intention to treat  
MMWR 
Morbidity and Mortality Weekly Report  
MOP 
Manual of Operations  
NA 
Neuraminidase 
NAI 
Neuraminidase inhibitors 
NIAID 
National Institute of Allergy and Infectious Diseases 
NP(S) 
Nasopharyngeal (swab) 
OCRPRO 
Office of Clinical Research Policy and Regulatory Operations 
OTC 
Over the counter 
PCR 
Polymerase chain reaction 
SAE 
Serious adverse event 
SSS 
Social & Scientific Systems, Inc. 
WHO 
World Health Organization 
 


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3AUG2016, Version 8 
TABLE OF CONTENTS 
LIST OF ABBREVIATIONS ...................................................................................................... 3 
TABLE OF CONTENTS ............................................................................................................. 4 
PROTOCOL SUMMARY ........................................................................................................... 7 
1 BACKGROUND INFORMATION AND SCIENTIFIC RATIONALE ......................... 10 
1.1 Influenza Infections in Humans ..................................................................................... 10 
1.1.1 Epidemiology ........................................................................................................ 10 
1.1.2 Antiviral Therapy for Influenza ............................................................................ 10 
1.1.3 Antiviral Resistance .............................................................................................. 10 
1.1.4 Treatment of Influenza .......................................................................................... 11 
1.2 Rationale for the Study .................................................................................................. 12 
1.3 Oseltamivir ..................................................................................................................... 12 
1.3.1 Standard Oseltamivir Dosing ................................................................................ 13 
1.3.2 Oseltamivir Therapy for Human Influenza ........................................................... 13 
1.4 Risks and Benefits.......................................................................................................... 14 
1.4.1 Risks of Oseltamivir ............................................................................................. 14 
1.4.2 Risk of Not Treating Influenza ............................................................................. 15 
1.4.3 Risk of Phlebotomy............................................................................................... 15 
1.4.4 Risk of Nasal Swab ............................................................................................... 15 
1.4.5 Benefits ................................................................................................................. 15 
1.4.6 Alternatives ........................................................................................................... 15 
2 STUDY OBJECTIVES ......................................................................................................... 16 
2.1 Primary Objective .......................................................................................................... 16 
2.2 Secondary Objectives ..................................................................................................... 16 
3 INVESTIGATIONAL PLAN .............................................................................................. 17 
3.1 Overview of Study Design ............................................................................................. 17 
3.2 Definitions for the Purpose of this Study ....................................................................... 18 
3.3 Study Endpoints ............................................................................................................. 18 
3.3.1 Primary Endpoint .................................................................................................. 18 
3.3.2 Secondary Endpoints ............................................................................................ 19 
3.3.3 Endpoint Definitions ............................................................................................. 19 
4 STUDY POPULATION ....................................................................................................... 19 
4.1 Rationale for Research Subject Selection ...................................................................... 19 
4.1.1 Justification of Exclusions of Pregnant Women and Children ............................. 19 
4.2 Recruitment .................................................................................................................... 20 
4.3 Inclusion Criteria for Enrollment (Screening) ............................................................... 20 
4.4 Inclusion Criteria for Randomization ............................................................................ 20 
4.5 Exclusion Criteria (for Enrollment or Randomization) ................................................. 20 
4.6 Subject Withdrawal ........................................................................................................ 21 
4.7 Discontinuation of Study Medication ............................................................................ 21 
4.8 Discontinuation of Subject by Investigator.................................................................... 22 
4.9 Discontinuation of Study ............................................................................................... 22 
4.10 Participation in Other Protocols ..................................................................................... 22 


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4.11 Emergency Unblinding .................................................................................................. 23 
5 TREATMENT ....................................................................................................................... 23 
5.1 Method of Assignment to Treatment ............................................................................. 23 
5.2 Study Regimens and Administration ............................................................................. 24 
5.3 Justification of Dose ...................................................................................................... 24 
5.4 Surveillance.................................................................................................................... 24 
5.5 Study Drug Acquisition ................................................................................................. 24 
5.6 Study Drug Accountability ............................................................................................ 24 
5.7 Concomitant Medications .............................................................................................. 25 
6 STUDY PROCEDURES ...................................................................................................... 25 
6.1 Personnel and Location for Study Procedures ............................................................... 26 
6.2 Hospitalization ............................................................................................................... 27 
6.3 Detailed Description of Assessments ............................................................................. 27 
6.3.1 Study Day −1 to 0: Screening ............................................................................... 27 
6.3.2 Determination of Eligibility and Randomization .................................................. 28 
6.3.3 Study Day 0: Baseline Evaluation ........................................................................ 28 
6.3.4 Day 1 ..................................................................................................................... 29 
6.3.5 Day 2 ..................................................................................................................... 29 
6.3.6 Study Day 3........................................................................................................... 29 
6.3.7 Reference Laboratory Tests on Day 3 .................................................................. 30 
6.3.8 Study Day 7 (+/- 1 Day) ....................................................................................... 30 
6.3.9 Study Day 28 (+/- 3 Days) .................................................................................... 30 
7 MEASURES OF SAFETY, EFFICACY, AND COMPLIANCE ..................................... 31 
7.1 Safety Evaluations ......................................................................................................... 31 
7.1.1 Laboratory Evaluations ......................................................................................... 31 
7.1.2 Other Safety Examinations ................................................................................... 31 
7.2 Influenza A Diagnostics ................................................................................................. 31 
7.2.1 Determination of Influenza Infection .................................................................... 31 
7.2.2 Site Influenza Testing ........................................................................................... 31 
7.3 Efficacy Evaluations ...................................................................................................... 32 
7.3.1 Diary Card for Fever, Symptoms, and Functional Assessment ............................ 32 
7.3.2 Assessment for Presence of Complications of Influenza ...................................... 33 
7.3.3 Vital Signs, Including SaO2 ................................................................................. 34 
7.3.4 Virology Measures ................................................................................................ 34 
7.4 Serologic Analysis ......................................................................................................... 36 
7.5 Compliance Measures .................................................................................................... 36 
7.6 Research Assays ............................................................................................................. 36 
8 SAFETY MONITORING AND REPORTING ................................................................. 36 
8.1 Documenting, Recording, and Reporting Adverse Events ............................................ 36 
8.2 Definitions...................................................................................................................... 36 
8.3 Investigator Assessment of Adverse Events .................................................................. 38 
8.3.1 Determination of Adverse Event .......................................................................... 38 
8.3.2 Period of Assessment ............................................................................................ 39 
8.3.3 Assessment of Adverse Event ............................................................................... 39 
8.3.4 Severity ................................................................................................................. 39 


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8.3.5 Causality of Adverse Event to the Intervention .................................................... 39 
8.4 Investigator Reporting Responsibilities to the Sponsor ................................................. 40 
8.4.1 Adverse Events ..................................................................................................... 40 
8.4.2 Serious Adverse Events ........................................................................................ 41 
8.4.3 Unanticipated Problems ........................................................................................ 41 
8.4.4 Pregnancy .............................................................................................................. 42 
8.5 Investigator Reporting Responsibilities to the Site IRB/EC .......................................... 42 
8.5.1 Safety reports ........................................................................................................ 42 
8.5.2 Expedited Reporting to the Site IRB/EC .............................................................. 42 
8.5.3 Annual Reporting to the IRB/EC .......................................................................... 42 
8.6 Follow-up of Adverse Events and Serious Adverse Events .......................................... 42 
8.7 Safety Monitoring .......................................................................................................... 43 
8.7.1 Study Monitoring .................................................................................................. 43 
8.7.2 Investigator Safety Monitoring ............................................................................. 43 
8.7.3 Protocol Team Monitoring .................................................................................... 43 
8.7.4 Medical Monitor ................................................................................................... 44 
8.7.5 Data and Safety Monitoring Plan .......................................................................... 44 
9 STATISTICAL CONSIDERATIONS ................................................................................ 44 
9.1 General Considerations .................................................................................................. 45 
9.2 Sample Size and Power Calculations ............................................................................. 45 
9.2.1 Sample Size Re-estimation ................................................................................... 46 
10 DATA MANAGEMENT AND MONITORING ................................................................ 48 
10.1 Source Documents ......................................................................................................... 48 
10.2 Data Management Plan .................................................................................................. 48 
10.3 Data Capture Methods ................................................................................................... 48 
10.4 Study Record Retention ................................................................................................. 48 
11 HUMAN SUBJECTS ............................................................................................................ 49 
11.1 IRB/IEC Approval ......................................................................................................... 49 
11.2 Compliance with Good Clinical Practices (GCP) .......................................................... 49 
11.3 Informed Consent Process ............................................................................................. 49 
11.4 Anonymity and Confidentiality ..................................................................................... 50 
11.5 Conflict of Interest ......................................................................................................... 50 
11.6 Compensation ................................................................................................................ 50 
12 RESEARCH USE OF STORED HUMAN SAMPLES, SPECIMENS, AND DATA ..... 50 
12.1 Intended Use of the Samples/Specimens/Data .............................................................. 50 
12.2 Storage of Samples/Specimens/Data ............................................................................. 51 
12.3 Storage of Genetic Sample ............................................................................................. 51 
12.4 Tracking Samples/Specimens/Data ............................................................................... 51 
12.5 Use of Samples/Specimens/Data at the Completion of the Protocol ............................. 51 
12.6 Reporting Loss or Destruction of Samples/Specimens/Data ......................................... 51 
13 REFERENCES ...................................................................................................................... 52 
 
 
 


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3AUG2016, Version 8 
PROTOCOL SUMMARY 
 
Full Title:  A Randomized Double-Blind Study Comparing Oseltamivir versus Placebo for the 
Treatment of Influenza in Low Risk Adults 
 
 
Short Title: IRC-004 
 
Sponsor: Office of Clinical Research Policy and Regulatory Operations (OCRPRO), Division of 
Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID) 
 
Conducted by: NIAID Influenza Research Collaboration (NIRC) 
 
Sample Size: N= 560 subjects 
 
Accrual Ceiling: Up to 800 subjects will be screened to randomize 560 subjects 
 
Study Population: Outpatient subjects at low risk for complications and morbidity from 
influenza (using US CDC criteria), and that have a diagnosis of influenza by rapid antigen or 
PCR. 
 
Study Design: This randomized double-blind study will assess evaluate whether oseltamivir 
modifies viral shedding in an ambulatory population with uncomplicated influenza. This study is 
also designed to explore the relationship between virologic effects and clinical effects, effects on 
pro-inflammatory mediators, and to start understanding if improvements to virologic shedding 
correlate with improvements in clinical outcomes.  This is a multicenter international study.  Up 
to approximately 50 sites may participate in this protocol. 
 
Subjects with an influenza-like illness will be screened for the study, and those found positive for 
influenza will be randomized in a 1:1 manner to receive a blinded study treatment consisting of 
either oseltamivir or placebo for 5 days. Subjects will be assessed on Study Day 0 (pre-dose), 
and on Study Days 3, 7, and 28. All subjects will undergo a series of efficacy and safety 
assessments during the study. Subjects will have a NP swab to test for influenza virus on Days 0, 
3, 7, and blood samples will be collected on Days 0, 3, 7, and 28. Subjects will also perform self-
collection of nasal swabs for the detection of influenza virus on Days 0, 1, 2, and 3. 
 
Study Agent: Oseltamivir versus placebo. 
 
Primary Objective:  
The overall objective of the study is to evaluate the antiviral efficacy of oseltamivir compared to 
placebo in the treatment of subjects with confirmed influenza infection (Primary Efficacy 
Population) as measured by percentage of subjects with virus detectable by PCR in NP swab at 
Day 3. 
 
Secondary Objectives:  


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1. Evaluate the antiviral efficacy of treatment with oseltamivir compared with placebo in those 
subjects with confirmed influenza infection (primary efficacy population) and intention to treat 
(ITT) population as assessed by the following parameters: 
 
Virologic: (by PCR in NP swab) 
◦ AUC of viral shedding 
◦ Duration of viral shedding  
◦ Percent cessation of viral shedding on Days 3 and 7 
◦ Frequency of emergence of antiviral resistance 
 
Clinical: 
◦ Time to alleviation of influenza clinical symptoms 
◦ Time to absence of fever  
◦ Time to resolution of all symptoms AND fever 
◦ Time to resumption of normal activity 
◦ Proportion of subjects who require hospitalization 
◦ Proportion of subjects who develop bronchitis, pneumonia, or other complications of 
influenza 
 
2. Evaluate the association of viral shedding (both qualitative and quantitative) to clinical 
symptoms and fever. 
 
3. Evaluate if changes in viral shedding by antiviral treatment predict changes in clinical 
symptoms and fever.  
 
4.  Evaluate subject self-collected nasal samples compared with study team collected samples for 
the determination of viral shedding. 
 
5. Evaluate the variability in the sample collection. (pilot study only) 
 
 
Endpoints: 
 
Primary Endpoint 
Percentage of subjects shedding virus by PCR in NP swab at day 3.  
 
Secondary Endpoints 
Clinical Endpoints: 
• Time to alleviation of influenza clinical symptoms  
• Time to absence of fever  
• Time to resumption of normal activity 
• Number of premature study treatment discontinuations 
• Proportion of subjects who develop bronchitis, pneumonia, or other complications of 
influenza 
• Proportion of subjects who require hospitalization 
• 28-day mortality  


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Virologic Endpoints: (assessed by PCR in NP swab) 
• Duration of viral shedding 
• Change in viral shedding as a function of time 
• AUC of viral shedding 
• Frequency of emergence of antiviral resistance  
 


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3AUG2016, Version 8 
1 
BACKGROUND INFORMATION AND SCIENTIFIC RATIONALE 
1.1 
Influenza Infections in Humans 
1.1.1 
Epidemiology 
Influenza causes annual epidemics of acute respiratory illness. Most people who get influenza 
will recover in a few days to less than 2 weeks, but some people will develop complications 
(such as pneumonia) as a result of influenza, some of which can be life-threatening and result in 
death. Complications from influenza can happen at any age, but some people are at higher risk of 
developing serious influenza-related complications. People at higher risk include people 65 years 
and older, people of any age with certain chronic medical conditions (including asthma, diabetes, 
immunosuppression, and heart disease), pregnant women, and infants. Despite effective 
antivirals and vaccines, influenza is responsible on average for 226,000 excess hospitalizations 
and about 24,000 deaths each year in the United States alone. [1] The number of deaths is 
estimated to be over 500,000 worldwide. 
 
1.1.2 
Antiviral Therapy for Influenza 
Viral glycoproteins (hemagglutinin [HA] and neuraminidase [NA]) are the main targets of the 
immune response to influenza. Vaccines elicit an immune response to these glycoproteins, 
particularly HA and are the primary means for prevention. However, influenza HA and NA  
antigens vary frequently as a result of antigenic drift and rarely by antigenic shift, many at-risk 
person do not respond adequately to immunization, influenza vaccines are under-utilized, and 
sometimes antigenically matched vaccines are not available in a timely manner.  Antiviral drugs 
are the principal treatment of influenza viruses. [2, 3] There are four currently licensed anti-
influenza medications: 2 oral adamantanes, (amantadine and rimantadine) and 2 neuraminidase 
inhibitors (NAIs) (the oral drug oseltamivir [Tamiflu®] as well as the inhaled medication 
zanamivir [Relenza®]).  
 
1.1.3 
Antiviral Resistance 
Resistance of influenza A viruses to amantadine or rimantadine can occur spontaneously or 
emerge rapidly during treatment. Most (>95%) recent seasonal H3N2 isolates are resistant to 
these compounds [4], though still maintain sensitivity to oseltamivir and zanamivir. Most 
(>98%) of seasonal H1N1 isolates during 2008-9 were resistant to oseltamivir, [5] though still 
sensitive to amantadine, rimantadine, and zanamivir. The pandemic influenza A/H1N1 2009 
isolates are resistant to amantadine and rimantadine, [6] and some isolates have additional 
resistance to oseltamivir and peramivir.[7]  
 
Resistance to the M2 inhibitors is mediated by mutations in the M2 ion channel and results in 
cross-resistance among all drugs in the class. M2 inhibitor resistance appears to be stable and 
resistant variants have circulated globally in the absence of selective drug pressure. [8, 9] These 
features have contributed to the rapid and widespread emergence of influenza A/H3 virus 
resistant to M2 inhibitors which currently limits the effectiveness of this class of drugs.[10] On 
the other hand, NAI resistance can occur as the result of mutations in either the NA gene, HA 
gene, or both, although almost all oseltamivir-resistant clinical isolates have had specific 
mutations in NA. Resistance patterns depend on the particular mutation, virus type and subtype, 


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and NAI.  In seasonal A (H1N1) viruses, high-level resistance to oseltamivir (>300 fold reduced) 
has been conferred by a H275Y mutation in NA that also diminishes susceptibility to peramivir 
but does not affect susceptibility to zanamivir.   
 
1.1.4 
Treatment of Influenza 
The U.S. CDC has recommended the following regarding the treatment of influenza: 
http://www.cdc.gov/h1n1flu/recommendations.htm#3  
Prompt empiric treatment is recommended for persons with suspected or confirmed influenza 
and: 
• Illness requiring hospitalization 
• Progressive, severe, or complicated illness, regardless of previous health status, 
and/or  
• Patients at risk for severe disease 
 
The following medical conditions have been associated with an increased risk of complications 
from influenza: [11] 
• Asthma 
• Neurological and neuro-developmental conditions [including disorders of the brain, 
spinal cord, peripheral nerve, and muscle such as cerebral palsy, epilepsy (seizure 
disorders), stroke, intellectual disability (mental retardation), moderate to severe 
developmental delay, muscular dystrophy, or spinal cord injury].  
• Chronic lung disease (such as chronic obstructive pulmonary disease [COPD] and 
cystic fibrosis) 
• Heart disease (such as congenital heart disease, congestive heart failure and coronary 
artery disease)  
• Blood disorders (such as sickle cell disease) 
• Endocrine disorders (such as diabetes mellitus) 
• Kidney disorders 
• Liver disorders 
• Metabolic disorders (such as inherited metabolic disorders and mitochondrial 
disorders) 
• Weakened immune system due to disease or medication (such as people with 
HIV/AIDS, or cancer, or those on chronic steroids) 
• People younger than 19 years of age who are receiving long-term aspirin therapy 
 
Additionally, for the 2009 H1N1influenza, morbid obesity (body mass index [BMI] ≥40) has 
been suggested as an independent risk factor. [12] 
 
The Infectious Diseases Society of America (IDSA) guidelines for influenza recommended 
treatment for persons who meet the following criteria: 
a. Persons with laboratory-confirmed or highly suspected influenza virus infection at high 
risk of developing complications within 48 hours after symptom onset.  
b. Persons requiring hospitalization for laboratory-confirmed or highly suspected 
influenza illness, regardless of underlying illness or influenza vaccination status, if 
treatment can be initiated within 48 hours after onset of symptoms.  


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They further state, treatment should be considered for both adults and children with influenza 
virus infection who meet the following criteria:  
a. Outpatients at high risk of complications (with illness that is not improving and who 
have a positive influenza test result from a specimen obtained >48 hours after onset of 
symptoms. 
b. Outpatients with laboratory-confirmed or highly suspected influenza virus infection 
who are not at increased risk of complications, whose onset of symptoms is <48 hours 
before presentation, and who wish to shorten the duration of illness. 
 
1.2 
Rationale for the Study 
The overall objective of the study is to evaluate the virologic efficacy of oseltamivir compared 
with placebo using PCR, and to determine the association between virologic improvement and 
clinical improvement. 
 
1.3 
Oseltamivir  
The neuraminidase inhibitors currently available include zanamivir (Relenza®) and oseltamivir 
(Tamiflu®).  Both are sialic acid analogues that potently and specifically inhibit the viral 
neuraminidase by competitively and reversibly interacting with the active enzyme site of 
influenza A and B viruses. [13] Influenza neuraminidase cleaves terminal sialic acid residues and 
destroys the receptors recognized by viral hemagglutinin. This action is essential for release of 
virus from infected cells, prevention of viral aggregates, and spread within the respiratory tract. 
[14] 
 
Oral oseltamivir phosphate is cleaved by esterases in the liver, gastrointestinal (GI) tract, and 
blood to the active oseltamivir carboxylate with good bioavailability estimated ~80%. [15] The 
time to maximum plasma concentrations of the active form is about 3 to 4 hours.  Administration 
with food may delay absorption slightly but does not decrease overall bioavailability. Following 
oral administration of oseltamivir, the plasma half-life (t1/2) of oseltamivir carboxylate averages 7 
to 9 hours. Both the prodrug and parent are eliminated primarily unchanged through the kidney. 
Distribution is not well characterized in humans, but peak bronchoalveolar lavage levels are 
similar to plasma levels in animals. [16] In humans, concentrations in sinus and middle ear fluid 
aspirates are similar to those in plasma. [17] 
 
No clinically significant drug interactions have been recognized for either drug.  Neither 
oseltamivir or oseltamivir carboxylate interact with human cytochrome P450 enzymes, which 
suggests that drug interactions as a result of competition with this pathway are unlikely. 
Oseltamivir elimination is inhibited by administration of probenecid, a finding that indicates that 
the carboxylate is excreted in part by tubular secretion. [17]   
 
Oral oseltamivir is generally well tolerated and no serious end-organ toxicity has been found. 
Oral oseltamivir is associated with nausea, abdominal discomfort and, less often, emesis in a 
minority of influenza-infected patients. Gastrointestinal (GI) complaints are usually mild to 
moderate in intensity, often diminished despite continued dosing, and ameliorated by 


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administration with food. Additional rare side effects include severe rash, hepatic dysfunction, 
low platelet count, and allergic reactions/anaphylaxis. 
 
1.3.1 
Standard Oseltamivir Dosing  
The standard dose (US FDA approved dose) of oseltamivir is 75 mg bid for 5 days for treatment 
of influenza A or B for adults and children ≥13 years old. [18]  
 
1.3.2 
Oseltamivir Therapy for Human Influenza 
Prospective, placebo-controlled data supporting the use of oseltamivir in the treatment of human 
influenza comes from five published studies. [19-23] Three of these evaluated acute 
uncomplicated community influenza in ambulatory persons (2 adult trials [19, 20] and one 
pediatric [21]), and the other two studies evaluated experimentally induced influenza. [22, 23] 
No prospective, placebo controlled studies of oseltamivir treatment have been reported in 
hospitalized patients, those with more severe illness, or in patients with treatment initiation after 
2 days from illness onset. 
 
In the adult acute treatment trials, both studied adults who presented within 36 hours of 
developing fever, respiratory symptoms, and constitutional symptoms.  Both trials randomized 
patients to placebo, oseltamivir 75 mg bid, or oseltamivir 150 mg bid.  Using syndromic 
inclusion criteria and documentation of local influenza activity, influenza infection was 
documented in 58-69% of all study groups.  Treatment with oseltamivir was associated with 
decreased duration (decreased by 29 hours at 75 mg bid and 35 hours at 150 mg bid in one study, 
and 31 hours and 33 hours, respectively, in the other) and severity of illness.  Oseltamivir 
treatment resulted in decreased nose and throat swab (combined) viral titers in both studies. In 
only one study was this demonstrated to be statistically significant. [20] In this study, the viral 
shedding AUC for placebo was 130 TCID50*h/mL, the viral shedding AUC for the oseltamivir 
75 mg bid arm was 78 TCID50*h/mL (p=0.03) and the oseltamivir 150 mg bid arm was 94 
TCID50*h/mL (p=0.003).  The concern in the analysis is the difference in viral shedding AUC of 
36 TCID50*h/mL (oseltamivir 150 bid vs placebo) gave a p=0.003, while a 44% larger difference 
in viral shedding AUC (52 TCID50*h/mL difference between oseltamivir 75 mg bid and placebo) 
gave a larger (less significant) p=0.03. 
 
In the other adult licensing study the difference in viral shedding was not statistically significant 
between any of the arms, though the decrease in viral shedding was suggested (but not 
statistically shown) to be dose dependent. [19] Notably, the duration of upper respiratory viral 
shedding was reduced to a median of 0 after day 1.   
 
The mortality was nil in all treatment groups including placebo of both studies, and the all-cause 
hospitalization rate very low.  Of note, the tolerability of the higher oseltamivir dose was 
generally comparable to the currently approved one; both were associated with 10-15% 
frequencies of GI side effects (nausea, emesis) but no serious end-organ toxicity.  
 
In the pediatric study of acute influenza treatment with oseltamivir, 2 mg/kg/dose bid was 
associated with a reduction of the duration of illness by approximately 36 hours, and decreased viral 


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titers in nasal washes. [21] Further analysis of the prospectively collected data from controlled 
studies determined that oseltamivir treatment was associated with significant reductions in lower 
respiratory complications of influenza, antibiotic use, and all-cause hospitalizations in the month 
after influenza diagnosis. [24] Subsequent retrospective studies have found similar benefits in 
ambulatory children and adults and in elderly nursing home residents treated early, but not later 
than 2 days after illness onset. [25] However retrospective studies in hospitalized patients with 
seasonal influenza, H5N1, and recently pandemic H1N1 infections have found evidence for reduced 
mortality even with treatment delayed beyond 2 days after illness onset. 
 
In experimental models of influenza, treatment with placebo or oseltamivir 20 mg bid, 100 mg bid, 
200 mg bid, or 200 mg qd was started 28 hours after inoculation with influenza A. [23] Treatment 
with oseltamivir (all doses) was associated with decreased symptom score, nasal viral titers, and 
viral shedding duration.  No clear dose response was appreciated, though the number enrolled was 
only 16 per group.  Antiviral effects were found in experimental influenza B. [22] 
 
1.4 
Risks and Benefits 
1.4.1 
Risks of Oseltamivir  
In published data (Table 1) from the manufacturer reflecting 7642 subjects who received 
oseltamivir in 17 clinical protocols for the prophylaxis of influenza, the most common side 
effects were headache, fatigue, and nausea. [26] Upper respiratory infection was also a reported 
side effect but likely represented the course of influenza rather than a side effect of oseltamivir. 
 
Table 1: Number of subjects (%) experiencing adverse events (AEs) in all oseltamivir 
prophylaxis studies in naturally acquired influenza (only events occurring in ≥2% of 
patients in placebo or oseltamivir groups are included) [26] 
 
 
 
Other AEs, such as rash, swelling of the face, toxic epidermal necrolysis, hepatitis, liver function 
test abnormalities, arrhythmias, seizures, confusion, and aggravation of diabetes have been 
reported during post-marketing use of oseltamivir, though causation could not be definitively 
established. There have been postmarketing reports (mostly from Japan) of self-injury and 
delirium with the use of oseltamivir in patients with influenza. The reports were primarily among 
pediatric patients.  
 
There is no evidence of carcinogenesis, mutagenesis, or impaired fertility associated with 
oseltamivir use. A 26-week dermal carcinogenicity study in mice was negative. In an escalating 


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and high-dose (up to 100 × area under the curve [AUC]) fertility and embryonic development 
study in rats, there were no effects on fertility, or early embryonic development. 
 
See the package insert for oseltamivir for additional details. 
 
1.4.2 
Risk of Not Treating Influenza 
Most influenza in low risk ambulatory patients is not diagnosed and not treated with antivirals. It 
has been shown that early treatment with antiviral medications may reduce the severity and 
duration of symptoms and may reduce the use of outpatient services and antibiotics. However, 
neither the U.S. CDC nor IDSA recommend that all ambulatory patients with influenza are 
treated with antivirals. 
 
The risks of not treating influenza are primarily a longer duration of illness and higher severity of 
symptoms. 
 
1.4.3 
Risk of Phlebotomy  
The primary risks of phlebotomy include local discomfort, occasional bleeding or bruising of the 
skin at the site of needle puncture, and rarely hematoma, infection, or fainting. At the time of 
enrollment and during study visits, each subject will be asked about participation in other 
research studies to ensure that blood draws do not exceed the following amounts for all research 
protocols combined: 10.5 mL/kg or 550 mL, whichever is smaller, over any 8-week period for 
adults (though as mandated by restrictions within this protocol the total blood volume will be 
significantly less).  
 
1.4.4 
Risk of Nasal Swab  
The primary risk of a nasal swab is local discomfort. Rarely, there can be local bleeding from the 
nasal mucosa, which is controlled with local measures such as pressure or packing with gauze. 
 
1.4.5 
Benefits 
There may be no benefits to individual subjects for participation in this study, but the 
information may lead to generalizable knowledge about influenza.  There may be earlier 
resolution of symptoms or fewer complications from influenza in those who are randomized to 
the active treatment arm, but benefit is not guaranteed. 
 
1.4.6 
Alternatives 
The alternative to participation in this study is routine standard care. For uncomplicated 
influenza this may be no therapy or may be an antiviral (likely oseltamivir or zanamivir based 
largely on availability and susceptibility). 
 


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2 
 STUDY OBJECTIVES 
2.1 
Primary Objective 
The overall objective of the study is to evaluate the antiviral efficacy of oseltamivir compared to 
placebo in the treatment of subjects with confirmed influenza infection (Primary Efficacy 
Population) as measured by percentage of subjects with virus detectable by PCR in NP swab at 
Day 3. 
2.2 
Secondary Objectives 
1. Evaluate the antiviral efficacy of treatment with oseltamivir compared with placebo in 
those subjects with confirmed influenza infection (primary efficacy population) and intention 
to treat (ITT) population as assessed by the following parameters: 
 
Virologic: (by PCR in NP swab) 
◦ 
AUC of viral shedding 
◦ 
Duration of viral shedding  
◦ 
Percent cessation of viral shedding on Days 3 and 7 
◦ 
Frequency of emergence of antiviral resistance 
 
Clinical: 
◦ 
Time to alleviation of influenza clinical symptoms 
◦ 
Time to absence of fever  
◦ 
Time to resolution of all symptoms AND fever 
◦ 
Time to resumption of normal activity 
◦ 
Proportion of subjects who require hospitalization 
◦ 
Proportion of subjects who develop bronchitis, pneumonia, or other complications of 
influenza 
 
2. Evaluate the association of viral shedding (both qualitative and quantitative) to clinical 
symptoms and fever. 
 
3. Evaluate if changes in viral shedding by antiviral treatment predict changes in clinical 
symptoms and fever.  
 
4.  Evaluate subject self-collected nasal samples compared with study team collected samples 
for the determination of viral shedding. 
 
5. Evaluate the variability in the sample collection. (pilot study only) 
 
6. Evaluate the association of viral shedding as assessed by TCID50 to viral shedding as 
assessed by qualitative PCR.  (pilot study only) 
 


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3 
INVESTIGATIONAL PLAN 
3.1 
Overview of Study Design 
The purpose of this randomized blinded study is to evaluate whether oseltamivir modifies viral 
shedding in an ambulatory population with uncomplicated influenza. This study is also designed 
to explore the relationship between virologic effects and clinical effects, effects on pro-
inflammatory mediators, and to start understanding if improvements to virologic shedding 
correlate with improvements in clinical outcomes. For this reason, the study is powered to show 
an anticipated difference in virologic shedding. This is a multicenter international study.  Up to 
approximately 50 sites may participate in this protocol. 
 
It is anticipated that about 800 subjects may be enrolled to allow 560 eligible subjects to be 
randomized in this study. The anticipated study duration is 7 years.  The original sample size of 
the study was powered to show a difference in virologic shedding as detected by TCID50 (as 
detailed in Section 9.2).  With new virologic techniques such as PCR, it is anticipated that the 
objectives of this study may be achievable with smaller numbers of subjects; therefore the 
sample size has been reduced. 
 
Subjects with an influenza-like illness will be screened for the study, and those found positive for 
influenza will be randomized in a 1:1 manner to receive a blinded study treatment consisting of 
either oseltamivir or placebo for 5 days. The study arms are as follows (Table 2): 
 
 Table 2: Treatment Allocation 
Arm 
Drug 
Allocation Ratio 
Capsule 
1 
Oseltamivir 
1 
Oseltamivir 
2 
Oseltamivir placebo 
1 
Placebo 
    
 
Subjects will be assessed on Study Day 0 (pre-dose), and on Study Days 3, 7, and 28. All 
subjects will undergo a series of efficacy and safety assessments during the study. Blood samples 
will be collected on Days 0, 3, 7, and 28.  
 
Table 4 in Section 6 presents the schedule of assessments.  A detailed presentation of 
assessments to be conducted at each visit is presented in Section 6.3.    
 
The first 50 subjects randomized were part of a pilot study to help determine the optimal 
virologic endpoint to be used in the efficacy analysis. These subjects had duplicate virologic 
samples on Day 0 to determine reproducibility. Additionally, all virologic samples from these 
subjects were tested by both PCR and culture (TCID50), and the results were analyzed by several 
different methods as outlined in a separate virology sample analysis plan. This allowed 
determination of the reproducibility of the virologic assays, and measure the distribution, 
variance, and presence and impact of missing data (see Section 9.5 for more details on the 
statistical considerations of the pilot study).  
 


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From this pilot study the primary endpoint was determined to be the percentage of subjects with 
virus detectable by PCR in NP swab at Day 3.  
 
The data collected in this study are essentially identical as for IRC-003.  Therefore, the 
cumulative database will encompass the spectrum of ambulatory influenza (those at risk and 
those not at risk, as well as placebo, monotherapy, and combination therapy treated). 
 
Additionally, this study will explore the utility of subject self-collected samples.  If self-collected 
samples provide the same quantitative information as study team-collected samples, self-
collected samples could be utilized in future studies for more frequent assessment of viral 
shedding with fewer clinic visits.  For this study, a subject self-collected sample will be obtained 
once daily on Study Days 0, 1, 2, and 3. 
3.2 
Definitions for the Purpose of this Study  
Enrolled 
For the purpose of collecting data and samples, and reporting AEs, a subject will be 
considered enrolled beginning from the time the informed consent form is signed until the 
subject is considered “screen failure,” “discontinued,” or “completed.” 
 
Randomized 
Subjects are considered randomized when they meet all of the following criteria: 
◦ 
Confirmation that the inclusion and exclusion criteria are met 
◦ 
Consent is given and signed by the subject for the study 
◦ 
Randomization number is assigned 
 
Screen Failures 
Subjects are considered screen failures when they meet one of the following criteria after 
signing consent: 
◦ 
Screening tests reveal that the subject is ineligible 
◦ 
Subject withdraws consent before being randomized 
 
Discontinued 
Subjects are considered discontinued when they meet one or more of the following criteria: 
◦ 
Subject withdraws consent after being randomized (see Section 4.6) 
◦ 
Subject is withdrawn after enrollment by investigator (see Section 4.8) including lost 
to follow-up 
 
Completed 
Subjects are considered completed when they are followed through Study Day 28 and 
complete the final study follow-up visit (Study Day 28) or die prior to this study visit. 
 
3.3 
Study Endpoints 
3.3.1 
Primary Endpoint 
Percentage of subjects shedding virus by PCR in NP swab at day 3.  
 


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3.3.2 
Secondary Endpoints 
Clinical Endpoints: 
◦ 
Time to alleviation of influenza clinical symptoms  
◦ 
Time to absence of fever  
◦ 
Time to resumption of normal activity 
◦ 
Number of premature study treatment discontinuations 
◦ 
Proportion of subjects who develop bronchitis, pneumonia, or other complications of 
influenza 
◦ 
Proportion of subjects who require hospitalization 
◦ 
28-day mortality  
 
Virologic Endpoints: (assessed by PCR in NP swab) 
◦ 
Duration of viral shedding 
◦ 
Change in viral shedding as a function of time 
◦ 
AUC of viral shedding 
◦ 
Frequency of emergence of antiviral resistance  
 
3.3.3 
Endpoint Definitions 
◦ 
Duration of viral shedding as assessed by PCR is defined as time to reduction of 
qPCR to below limit of detection, at the first of two successive measurements. 
◦ 
Development of resistance is defined as the percentage of subjects who develop a 
resistant strain population by day 7, as measured by RNA sequencing of NA for 
recognized oseltamivir resistance mutations (e.g., H275Y or N295S in N1, R292K or 
E119V in N2). 
◦ 
Duration of clinical symptoms is defined as the time to alleviation of all clinical 
symptoms to 0 (absent) or 1(mild) on two successive measurements in absence of 
symptom relief medications. 
◦ 
Absence of fever (temperature <38.0ºC/100.4ºF) for 24 hours without antipyretic. 
◦ 
Time to resumption of normal activity is defined as time to the time to the first “yes” 
answer to the global assessment question “Are you functioning as well as you were 
before you had the flu?” (Section 7.3.1.4). 
4 
STUDY POPULATION 
4.1 
Rationale for Research Subject Selection 
The subject population includes those at low risk for complications and morbidity from influenza 
(as defined by the U.S. CDC), and have a diagnosis by rapid antigen or PCR of influenza. 
Exclusions are primarily to increase subject safety. 
 
4.1.1 
Justification of Exclusions of Pregnant Women and Children  
Pregnant women with influenza are recommended to be treated with oseltamivir or zanamivir, 
therefore, randomization of a pregnant woman to possibly receive placebo could not be justified.  
The protocol does not provide access to any treatment that children cannot currently receive, and 
therefore children are excluded from participation. 
 


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4.2 
Recruitment 
It is anticipated that subjects will primarily be recruited through emergency rooms, medical 
clinics, or other health care settings (e.g., university health clinics) that would be first contact of 
subjects with influenza. Information about this study will be disseminated to health care 
providers in these settings. Additionally, direct-to-subject recruitment (using posters and/or other 
informational items) may occur in these settings.  
 
Any direct-to-subject recruitment will be submitted to the reviewing Institutional Review Board 
(IRB)/Independent Ethics Committee (IEC) for approval. Informational items about the study 
that will be circulated to health care staff only are not required to be reviewed by the IRB/IEC. 
 
4.3 
Inclusion Criteria for Enrollment (Screening) 
1. Signed informed consent prior to initiation of any study procedures  
2. Age ≥18 and < 65 years of age  
      3. One or more respiratory symptoms (cough, sore throat, or nasal symptoms)  
4. Onset of respiratory symptoms no more than 48 hours before enrollment (screening)  
5. Willingness to have samples stored 
 
4.4 
Inclusion Criteria for Randomization 
Positive test for influenza (either rapid antigen or PCR) 
◦ 
Randomization may proceed in cases of discrepant results (one positive and one 
negative) 
NOTE: Results from laboratory tests obtained for clinical indications within 24 hours before 
screening/enrollment may be used if available. 
 
4.5 
Exclusion Criteria (for Enrollment or Randomization) 
1. Hospitalization at the time of enrollment 
2. Presence of a medical condition(s) that has been associated with increased risk of 
complications from influenza 
◦ 
Age 65 years of age or older 
◦ 
Asthma 
◦ 
Neurological and neuro-developmental conditions (including disorders of the brain, 
spinal cord, peripheral nerve, and muscle such as cerebral palsy, epilepsy [seizure 
disorders], stroke, moderate to severe developmental delay, muscular dystrophy, or 
spinal cord injury)  
◦ 
Chronic lung disease (such as COPD and cystic fibrosis) 
◦ 
Heart disease (such as congenital heart disease, congestive heart failure, and coronary 
artery disease).  Hypertension or mild arrhythmia alone would not be considered 
exclusionary   
◦ 
Blood disorders  
◦ 
Endocrine disorders (such as diabetes mellitus) 
◦ 
Kidney disorders 
◦ 
Liver disorders 


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◦ 
Metabolic disorders (such as inherited metabolic disorders and mitochondrial disorders) 
◦ 
Weakened immune system due to disease or medication (such as people with 
HIV/AIDS, or cancer, chronic steroids or other medications causing immune 
suppression) 
◦ 
Pregnant or 4 weeks postpartum 
◦ 
BMI ≥40 
3. Breastfeeding 
4. Inability to take oral medication or a history of GI malabsorption which would preclude 
the use of oral medication.  
5. Received more than one dose of any antiviral influenza medications since onset of 
influenza symptoms 
6. Known end stage renal dysfunction  or creatinine clearance less than 60 mL/min 
7. Known hypersensitivity to oseltamivir, peramivir, or zanamivir 
8. Received live attenuated influenza virus vaccine within 3 weeks prior to study entry 
9. Use of any investigational drug within 30 days or 5 half-lives (whichever is longer) prior 
to study entry  
10. Participation in other research protocols that require more than 100 mL of blood to be 
drawn in any 4-week period that overlaps with this study. 
 
4.6 
Subject Withdrawal 
Subjects (or their legal surrogates if subjects become unable to make informed decisions) can 
terminate study participation at any time without prejudice. If a subject terminates participation 
before completing the study, the reason for this decision will be recorded in the electronic case 
report form (eCRF).  
 
Subjects who indicate interest in withdrawing from the study should also be asked permission to 
be contacted at Day 28 by telephone for vital status (any AEs that occurred during the study). 
This is not considered full withdrawal of consent, but the modified consent for limited follow-up 
should be noted in the medical record. 
 
Subjects who fully withdraw consent will not be contacted further. 
 
Subjects who withdraw from the study will not be replaced. 
 
4.7 
Discontinuation of Study Medication 
The investigator will instruct subjects to stop study medication for any of the following reasons: 
• The investigator becomes aware that the subject has renal insufficiency 
• Any other AE for which the investigator believes that continuation of the study medication 
would be detrimental to the subject 
• Subject is found to be pregnant 
• Subject is hospitalized within 5 days of enrollment 
 
The reason for discontinuation of the study agent is to be recorded in the source documentation 
and on the eCRF. All subjects who discontinue study drug will be encouraged to comply with the 


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study visit schedule including clinical and virologic assessment. In any event, AEs that lead to 
stopping study medication will be followed until resolution or stabilization if possible. 
 
4.8 
Discontinuation of Subject by Investigator 
The investigator has the right to withdraw subjects from the study. Subjects may be withdrawn 
from the study for any of the following reasons: 
◦ 
The subject is lost to follow-up 
◦ 
The subject experiences an AE, and the investigator believes that continuation in the 
study would be detrimental to the subject (in contrast to discontinuing the study 
medication and continuing follow-up as discussed in Section 4.7) 
◦ 
Subject is hospitalized within 5 days of enrollment 
 
The reason for withdrawal from the study is to be recorded on the eCRF. If a non-serious AE is 
unresolved at the time of discontinuation, efforts should be made to follow-up until the event 
resolves or stabilizes, the subject is lost to follow-up, or there is some other resolution of the 
event. The investigator is to make every attempt to follow all serious adverse events (SAEs) to 
resolution. 
 
Subjects who miss a study visit should be contacted to reschedule. If subjects cannot be 
contacted immediately, periodic attempts should continue until study completion (Study Day 28 
+3). Lost to follow-up is defined as unsuccessful contact after at least 3 documented telephone 
calls.  
 
Any subject withdrawn from the study will not be replaced.  
 
4.9 
Discontinuation of Study 
The National Institute of Allergy and Infectious Diseases (NIAID), as the study sponsor, has the 
right to terminate this study at one or all sites at any time. 
 
The reviewing IRB/IEC and any reviewing national regulatory agencies (if applicable) have the 
right to terminate the study at the sites it is responsible for at any time. Reasons for terminating 
the study may include, but are not limited to, the following: 
◦ 
The incidence or severity of an AE in this or other studies indicates a potential 
health hazard to subjects 
◦ 
Subject enrollment is unsatisfactory 
◦ 
Data recording is inaccurate or incomplete 
◦ 
Investigators do not adhere to the protocol or applicable regulatory guidelines in 
conducting the study 
 
4.10 
Participation in Other Protocols 
Subjects in this protocol may participate in other research protocols, as long as the other research 
protocol(s) does not require more than 100 mL of blood to be given in any 4-week period of time 
that overlaps with this study, and does not administer any unlicensed drug, unlicensed vaccine, 


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or any investigational treatment for influenza within the 30 days or 5 half-lives (whichever is 
longer) prior to enrollment or during the duration of this study.  
 
Note: The above may not represent the maximum amount of blood permitted to be collected by 
most IRBs/IECs. However, each site should ensure that these collection amounts are within the 
site’s institutional and local limits. 
 
4.11 
Emergency Unblinding 
Any pregnancy occurring on study will be immediately unblinded (regardless of known AE or 
known fetal toxicities).  
 
Any hospitalization occurring during treatment (Days 0-5 of this study) due to influenza 
symptoms will be unblinded, as knowing treatment may influence the subjects subsequent care 
(including choice of antivirals). 
 
If AEs occur and investigators are concerned about the treatment allocation, the treatment can be 
discontinued as discussed in Section 4.8. However, if all of the following three criteria are met, 
the subject’s randomization may be unblinded: 
 
1. The AE must be a SAE as also defined in Section 8.2 
2. The AE must be thought to be probably or definitely related to the study drug. 
3.  The treating clinician states that knowledge of the treatment arm may change the therapy 
provided to the patient. 
 
The procedure for unblinding will be detailed further in the Manual of Operations (MOP). 
 
5 
TREATMENT 
Subjects will be randomized to one of the following two arms (Table 3): 
 
  Table 3: Treatment Allocation 
Arm Drug 
Allocation Ratio 
Capsule 
1 
Oseltamivir  
1 
Oseltamivir 
2 
Oseltamivir placebo 
1 
Placebo 
   
5.1 
Method of Assignment to Treatment 
Subjects who meet all criteria for enrollment will be randomized using an interactive web-based 
system. A central randomization scheme will be prepared by the sponsor or designee.  
 
Additionally randomization will be stratified based on duration of symptoms prior to 
randomization: (0–24 hours and 25–48 hours). 
 


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5.2 
Study Regimens and Administration 
Each randomized subject will receive a study drug kit consisting of 5 days of study capsules. 
Subjects take one capsule twice daily, and each dose will consist of the following: 
• One of capsule A (Oseltamivir 75 mg) 
 
Total dose: 150 mg/day for 5 days 
OR 
• One of capsule B (matching placebo)  
 
Total dose: 2 placebo capsules/day for 5 days 
 
The Division of Clinical Research, NIAID, NIH (the sponsor), will supply the oseltamivir and 
matching placebo for the study regimen. 
 
The active capsule consists of commercial oseltamivir capsules over encapsulated with an 
opaque capsule.  The placebo capsule consists of the identical opaque capsule filled with 
microcrystalline cellulose. Assembled treatment kits will be supplied to the participating sites. 
 
Subjects should be instructed to take the study agent with food to avoid possible GI upset. 
 
5.3 
Justification of Dose 
Oseltamivir: 75 mg bid is the standard licensed dose for the treatment of influenza. 
 
5.4 
Surveillance 
During the conduct of this study the potential exists for the emergence of viruses resistant to 
oseltamivir. The protocol team will monitor the emergence of resistance to oseltamivir and 
current treatment recommendations. Should such a change occur where oseltamivir is no longer 
active for the majority of circulating strains (thus losing the ability to compare the two arms in 
the study), the study may be held or stopped. 
5.5 
Study Drug Acquisition 
Study drug will be stored in a central repository. Sites will be given an initial supply of study 
drug after the local IRB/IEC has approved the study, all applicable national regulatory agencies 
have granted the study safe to proceed, the sponsor has approved shipment of study agent, and 
after all import licenses have been obtained, as applicable. 
5.6 
Study Drug Accountability 
The investigator or his/her designee is required to maintain accurate drug accountability records. 
A binder containing instructions and the required accountability documentation will be provided 
to the investigator or his/her designee. When the study is completed, copies of the study drug 
accountability records will be maintained at the study site.  Copies of the drug accountability 
records must be maintained with the rest of the documentation for the study. All unused study 
drug must be disposed of upon authorization by NIAID or its designee. All records regarding the 
disposition of study drug must be available for inspection by the study monitors and regulatory 
authorities. 


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5.7 
Concomitant Medications 
Subjects will be monitored throughout the study for use of concomitant medications. Any 
prescription medications, over-the-counter (OTC) preparations, herbal remedies, and/or 
nutritional supplements taken during the study period must be recorded on the source document 
and in the eCRF.  
 
5.8 
Prohibited Medications 
 
Subjects may not receive investigational medications (other than the study drug provided) any 
time during the study. Their use would not be considered standard care, and therefore, 
withholding these compounds would still be consistent with best medical practice. This includes 
licensed drugs at non-approved doses, or drugs available under an Emergency Use Authorization 
(EUA). 
 
5.9 
Treatment Compliance 
 
Treatment compliance will be assessed by examination of subject’s remaining study product on 
each study visit.  Subjects should be asked to bring the study kit to each study visit and returned 
to the study team on Day 7. 
 
6 
STUDY PROCEDURES 
The following table (Table 4) outlines all of the assessments to be conducted during the study. A 
detailed presentation of assessments immediately follows the table. Total volumes of blood 
drawn are noted in the text for each study day. Details regarding the research samples (tubes, 
swabs, etc) will be detailed in the Manual of Procedures. The day when the subject is enrolled 
and randomized is denoted as Study Day 0, the first day after randomization is Study Day 1, etc. 
 


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 Table 4: Schedule of Assessments 
 
  
 
6.1 
Personnel and Location for Study Procedures 
All study assessments should be performed by members of the investigative team that are 
specifically designated to perform such activities (according to site practices, local law and as 
designated on the appropriate study documents). 
 
The initial screening evaluation and baseline visits should be performed within a health care 
facility (emergency rooms, medical clinics, inpatient units, or other health care settings).  
Subsequent visits may occur in a health care facility or at home according to site practices and 
local law. Any sites performing home visits should have: 
• IRB approval for home visits 
• Written study specific procedures including obtaining samples with the storage condition 
and timeframe of this protocol that are approved by the study team. 
• Documentation of institutional permission or policies permitting home visits including 
liability concerns 
• Adequate staff and resources to perform home visits (e.g., portable pulse oximeter for 
SaO2 measurements) 
 


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6.2 
Hospitalization 
Hospitalized subjects are excluded from this study. Subjects who initially are outpatients and are 
then hospitalized for influenza related symptoms should be unblinded to know the treatment 
obtained during this study and should receive antivirals as clinically indicated. 
 
6.3 
Detailed Description of Assessments 
6.3.1 
Study Day −1 to 0: Screening 
Screening is defined as the period of evaluation after signing the informed consent that is used to 
determine if a subject is eligible for randomization.  Up to 24 hours is permitted between 
enrollment (signing consent) and the first dose of study medication.  However, efforts should be 
made to minimize the time between enrollment and the first dose of study to the extent possible.  
6.3.1.1 Informed Consent 
The site investigator or designee is to review informed consent with the subject.  
 
6.3.1.2 Demographics 
The following information should be recorded: 
•  Age 
•  Sex 
•  Ethnicity  
•  Race 
 
6.3.1.3 Medical History 
The investigator (or designee) will take a medical history at the time of consent and conduct a 
complete physical examination. The following information should be recorded:  
•  Day and time of onset of influenza symptoms 
•  Influenza vaccination history  
•  History of chronic medical conditions 
•  Current use of prescription and OTC medications within the last 7 days  
•  History of allergies 
•  Participation in any recent research protocols (within the last 12 months) 
•  Smoking history 
 
Medical conditions noted at the time of consent (including influenza symptoms) should be 
recorded in the eCRF as part of the medical history (Pre-Existing Medical History eCRF). Any 
conditions that develop after consent should be recorded on the AE page of the eCRF if they are 
determined to be a recordable AE as outlined in section 8.3.1 . 
 
6.3.1.4 Physical Exam 
A brief physical exam including vital signs and SaO2, and major organ systems should be 
performed and will be used to ensure there are not medical conditions (either chronic or acute) 
that would increase a subject’s risk for participation in this study. 
 


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6.3.1.5 Laboratory Testing 
Subjects should have the following laboratory evaluations performed at screening:  
◦ 
Urine pregnancy test (serum pregnancy test may be substituted as needed) for females 
of childbearing potential. 
◦ 
Diagnostic test for influenza (PCR or rapid antigen).  If more than one influenza 
diagnostic test is performed, study teams can await subsequent diagnostic test prior to 
deciding about randomization.  Randomization may proceed in cases of discrepant 
results (one positive and one negative). 
 
No other laboratory testing is required for enrollment. This is consistent with the standard 
clinical use of oseltamivir where laboratory testing is often not performed. 
 
Results from laboratory tests obtained for clinical indications within 24 hours before 
screening/enrollment may be used if available, however, lab test results obtained nearest to 
randomization will be used for eligibility requirements. 
 
6.3.2 
Determination of Eligibility and Randomization  
6.3.2.1 Determination of Eligibility  
After the previously mentioned evaluations have been completed (i.e., medical history and 
laboratory tests), the investigator will review the inclusion/exclusion criteria and determine the 
subject’s eligibility for study participation. Any clinically obtained laboratory results should be 
reviewed for clinically significant findings; however no additional laboratory tests are required 
per protocol. 
 
6.3.2.2 Randomization 
Data from eligible subjects is then entered into the randomization system, subjects are then 
randomized, and a specific study drug kit number is provided by the system.  This study drug kit 
number must be provided to the pharmacist or designee. 
 
The following information will be collected on screening failures: demographics (age, screen 
number, sex, birth date, ethnicity, and race) and reason for ineligibility. Subjects who are found 
to be ineligible will be told the reason for ineligibility and may not be re-screened for the study.  
 
6.3.3 
Study Day 0: Baseline Evaluation 
Baseline evaluation must be completed prior to the first dose of study medication. 
6.3.3.1 Clinical Data on Day 0 
• Assessment for presence of complications of influenza (See Section 7.3.2) 
• Vital signs, including SaO2 and height (See section 7.3.3) 
o If this assessment is within 6 hours from the screening assessment, the 
screening vitals can be used, otherwise vital sign measurements should be 
repeated for this assessment 
• Assessment for AEs occurring after consent and prior to administration of study drug 
 


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6.3.3.2 Research Procedures on Day 0 
At baseline, the following research procedures will be performed: 
◦ 
Nasopharyngeal (NP) swab  
 
All subjects will also be instructed on self-collection of nasal swabs. The subject should perform 
the first self-collection at this time in the research facility/ clinic with the study staff present. The 
self-collection procedure can be found in the Manual of Operations (MOP) and will be described 
in written instructions that may be provided to the subject. 
 
See Section 7.3.4 for an overview of the planned virology assessments. 
 
6.3.3.3 Reference Laboratory Tests on Day 0  
• Up to 20 mL of blood will be taken for the stored samples (see section 7.4) 
 
6.3.3.4 Study Day 0: Study Drug Distribution 
The study drug kit will be distributed to the subject, with instruction on how to take each dose 
every 12 hours. Treatment should begin as soon as possible. However up to 24 hours is permitted 
between enrollment (signing consent) and the first dose of study medication. To ensure timely 
administration of the first dose of the study mediation, it may be taken in the research facility/ 
clinic.  The time that the first dose is taken should be recorded.  
 
6.3.3.5 Distribution of Diary Cards 
A diary card booklet assessing fever, symptoms, and functional assessment, will be distributed to 
subjects.  Collection of baseline assessments and subject recalled pre-illness condition(s) (See 
Section 7.3.1) will be completed by the study team and instructions will be given to the subject 
on the completion of the diary card. 
 
6.3.4 
Day 1  
Subjects will collect nasal specimen per the self-collection procedure described in Section 
6.3.3.2, and will bring the specimen to the next study visit. 
 
6.3.5 
Day 2  
Subjects will collect the nasal specimen per the self-collection procedure described in Section 
6.3.3.2, and will bring the specimen to the next study visit. 
 
6.3.6 
Study Day 3 
6.3.6.1 Clinical Data on Day 3 
• Review and collection of diary card for fever, symptoms, and functional assessment (See 
Section 7.3.1) 
• Assessment for presence of complications of influenza (See Section 7.3.2) 
• Vital signs, including SaO2 (See section 7.3.3) 
• Review of study drug and assessment of compliance (see Section 7.5) 


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• Review of concomitant medications  
• Symptom targeted physical exam (for safety assessment, see Section 7.1.2) 
• Assessment for AEs 
 
6.3.6.2 Research Procedures on Day 3 
The following research procedures will be performed: 
◦ 
Nasopharyngeal swab  
◦ 
Subject sample self-collection as described in Section 6.3.3.2 
 
See Section 7.3.4 for an overview of the planned virology assessments 
 
6.3.7 
Reference Laboratory Tests on Day 3  
• Up to 20 mL of blood will be taken for the stored samples (see section 7.4) 
 
6.3.8 
Study Day 7 (+/- 1 Day) 
6.3.8.1 Clinical Data on Day 7 
• Review and collection of diary card for fever, symptoms, and functional assessment (See 
Section 7.3.1) 
• Assessment for presence of complications of influenza (See Section 7.3.2) 
• Vital signs, including SaO2 (See Section 7.3.3) 
• Review of study drug and assessment of compliance and collection of study agent kit (see 
Section 7.5) 
• Review of concomitant medications  
• Symptom targeted physical exam (for safety assessment, see Section 7.1.2) 
• Assessment for AEs 
 
6.3.8.2 Research Procedures on Day 7 
The following research procedures will be performed: 
◦ 
Nasopharyngeal swab  
 
See Section 7.3.4 for an overview of the planned virology assessments 
 
6.3.8.3 Reference Laboratory Tests on Day 7  
• Up to 20 mL of blood will be taken for the stored samples (see section 7.4) 
 
6.3.9 
Study Day 28 (+/- 3 Days) 
6.3.9.1 Clinical Data on Day 28 
• Review and collection of diary card for fever, symptoms, and functional assessment (See 
Section 7.3.1) 
• Assessment for presence of complications of influenza (See Section 7.3.2) 
• Vital signs, including SaO2 (See section 7.3.3) 


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• Review of concomitant medications  
• Symptom targeted physical exam (for safety assessment, see Section 7.1.2) 
• Assessment for AEs 
 
6.3.9.2 Reference Laboratory Tests on Day 28  
• Up to 20 mL of blood will be taken for the stored samples (see section 7.4) 
 
7 
MEASURES OF SAFETY, EFFICACY, AND COMPLIANCE  
7.1 
Safety Evaluations 
7.1.1 
Laboratory Evaluations 
All laboratory evaluations (except reference endpoint assays) will be performed at the local site.  
 
Urine (or serum) will be collected on females with childbearing potential at the time of screening 
for a pregnancy test. 
 
No other clinical laboratory testing will be performed as part of this study.  This would be 
consistent with the standard care treatment of influenza where oseltamivir is prescribed without 
any laboratory testing. 
 
7.1.2 
Other Safety Examinations 
A brief physical examination will be conducted at screening to ensure there are no medical 
conditions (either chronic or acute) that would increase a subject’s risk for participation in this 
study. Physical examinations may be completed by those authorized at a site according to local 
law and institutional policies.  Symptom-targeted physical examinations will be conducted at all 
other visits as needed to evaluate new complaints and possible AEs. Due to the variability and 
difficulty to standardize, the physical exam will not be used as efficacy data. 
 
7.2 
Influenza A Diagnostics 
7.2.1 
Determination of Influenza Infection 
This study will use a case definition published by the WHO for confirmed influenza virus 
infection. A subject will be classified as having laboratory-confirmed influenza by having one or 
more of the following: 
• Influenza virus isolation by RT-PCR at reference lab (not site diagnostics for influenza) 
• Influenza virus isolation by culture at reference lab (not site diagnostics for influenza) 
• Four-fold rise in virus-specific neutralizing or HAI antibodies 
 
7.2.2 
Site Influenza Testing 
Each site must have the ability to perform a diagnostic test for influenza, either rapid antigen or 
PCR. The methodology will be determined by the individual sites. 
 


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7.3 
Efficacy Evaluations 
7.3.1 
Diary Card for Fever, Symptoms, and Functional Assessment 
Subjects will maintain a diary card, and will be asked to make an entry twice daily 
(approximately 8AM and 8PM) through Day 7, and then every evening from Day 8 through 14. 
The subject completes the final diary card at the time of the final visit on Day 28. 
 
On Day 0, subjects will be instructed on the diary card, and the initial (baseline) assessment will 
be completed by the study team and collected.  Additionally, for the SF-36 physical domain, 
subjects will be asked to recall their status prior to enrollment. 
 
At each subsequent study visit, the diary card for the day(s) since the last visit will be reviewed 
and collected. This diary will contain the information listed below (Section 7.3.1.1 – 7.3.1.4). 
However, any influenza symptoms listed on the diary cards will not be captured as adverse 
events for this study in accordance with section 8.3.1 of this protocol. 
 
7.3.1.1 Fever 
Subjects will be asked to measure temperature orally at the time of completing the diary card and 
at anytime for symptoms of feverishness, and will be asked to record the maximal temperature 
since the time of entry for the previous diary card). 
 
7.3.1.2 Symptoms 
The symptoms assessed will be those assessed in previous licensure studies with oseltamivir 
(denoted by the ¶ symbol), [19, 20], as well as the addition of rhinorrhea and symptoms that are 
frequently a component of influenza (denoted by the § symbol). Using a 4-point scale (0 = 
absent, 1 = mild, 2 = moderate, 3 = severe), each symptom will be assessed for severity. Subjects 
will be asked to assess their symptoms twice daily for Study Days 0-7, and once daily for Study 
Days 8-14. 
 
The symptoms assessed are: 
• Cough ¶  
• Nasal obstruction ¶ 
• Sore throat ¶ 
• Fatigue ¶ 
• Headache ¶ 
• Myalgia ¶ 
• Feverishness ¶ 
• Rhinorrhea § 
• Nausea § 
• Vomiting § 
• Diarrhea § 
 
Symptoms present at the time of enrollment and not worsened during treatment will not be 
considered AEs.  Any new or worsened symptoms during treatment should be assessed for AEs 
in accordance with section 8.3.1. 


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7.3.1.3 Functional Status 
The 36-item Health Survey (SF-36 v1) is a frequently used health survey used for multiple 
disease states. [27] This study will assess the 10-item domain of physical function (specifically, 
questions 3-12 of the SF-36 v1) (see Table 5), and subjects will be asked to note the response 
once each study day (approximately 8PM – reflecting the function during that day). These 
include (as originally numbered in the SF-36 v1): 
 
  Table 5: SF-36 Physical Function Domain Questions 
Question 
Yes, 
Limited a 
Lot 
Yes, 
Limited a 
Little 
No, Not 
limited at 
All 
3. Vigorous activities, such as running, lifting 
heavy objects, participating in strenuous sports 
[1] 
[2] 
[3] 
4. Moderate activities, such as moving a table, 
pushing a vacuum cleaner, bowling, or playing golf 
[1] 
[2] 
[3] 
5. Lifting or carrying groceries 
[1] 
[2] 
[3] 
6. Climbing several flights of stairs 
[1] 
[2] 
[3] 
7. Climbing one flight of stairs 
[1] 
[2] 
[3] 
8. Bending, kneeling, or stooping 
[1] 
[2] 
[3] 
9. Walking more than a mile 
[1] 
[2] 
[3] 
10. Walking several blocks 
[1] 
[2] 
[3] 
11. Walking one block 
[1] 
[2] 
[3] 
12. Bathing or dressing yourself 
[1] 
[2] 
[3] 
 
7.3.1.4 Global Assessment 
Subjects will be asked the global assessment questions: 
 
“Are you feeling as good as you did before you had the flu?” With a yes/no response, referring to 
the status immediately prior to onset of influenza symptoms. 
 
“Are you functioning as well as you were before you had the flu?” With a yes/no response, 
referring to the status immediately prior to onset of influenza symptoms. 
 
7.3.2 
Assessment for Presence of Complications of Influenza  
Subjects will be assessed for the signs/symptoms suggestive of one of the following 
complications. 
◦ 
Sinusitis 
◦ 
Otitis Media 
◦ 
Bronchitis / Bronchiolitis 
◦ 
Pneumonia 
◦ 
Antibiotic use for reason other than above 


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In the event a complication occurs, additional information to support the diagnosis of the 
complication should be collected (e.g., microbiologic or radiographic data). The development of 
any of these complications may represent an adverse event and should be assessed as such. 
 
7.3.3 
Vital Signs, Including SaO2 
Vital signs assessments (BP, HR, temperature, respiration rate, and SaO2) will be taken at 
screening and on Study Days 0, 3, 7, and 28.  
 
7.3.4 
Virology Measures 
Standardization of virologic samples is critical for successful execution of the study and 
meaningful virologic data. The procedures for sample collection, labeling, local lab processing, 
storage and shipment are described in detail in the MOP.  The Virology Plan will detail the 
processing, testing, and reporting of the virologic studies. The virology analysis will be 
contained within the Statistical Analysis Plan. The differences in testing and analysis in the pilot 
study as compared to the main study will be discussed in these plans. 
 
The clinical virology plan to support this clinical study will be conducted in two tiers, each with 
a specific objective (see Table 6). The analyses in Tier 1 will determine the virus subtype (via 
HA subtyping), and viral shedding as a function of time. The objective of Tier 2 is to determine 
whether resistance is the cause of prolonged viral shedding.  
 
 
Table 6. Clinical Virology Plan 
Sampling Tier 
Objective 
Subject Population 
Analytical Method 
Tier 1 – pilot study 
- Determine HA subtype 
- Quantify viral shedding 
by TCID50 
- Quantify viral shedding 
by qPCR 
All subjects in pilot study 
(viral shedding at all time 
points, subtyping at 
baseline) 
- PCR of HA gene 
- TCID50 
 
- qPCR of M1 gene 
 
Tier 1 – main study 
- Determine HA subtype 
- Quantify viral shedding 
by either TCID50 or qPCR 
(as determined in pilot 
study) 
All subjects (viral 
shedding at all time points, 
subtyping at baseline) 
- PCR of HA gene 
- TCID50 or qPCR of M1 
gene 
 
Tier 2 
- Quantify if resistance 
emerged 
All subjects with virus 
isolated at Day 7, all time 
points 
- DNA Sequencing 
(Sanger or pyro) of M2, 
NA and HA 
 
 
 
7.3.4.1 Pilot Study - Tier 1 Analyses - HA Subtyping and Quantification of Virus  
Nasopharyngeal and throat swabs were obtained from the first 50 subjects at the specified time 
points according to the Schedule of Assessments (Table 4). Analyses involved HA subtyping of 
all patients at baseline and viral shedding quantitation of all time points by two methods, TCID50 
and qPCR.   
 


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HA subtyping has been performed on baseline samples by means of a multiplex real-time PCR, 
and the virus subtype will be reported as H1, H3, or H1 2009, or B. The viral shedding will be 
determined for all subjects at all study visits by quantitative viral culture and will be reported as 
log10 TCID50/mL, and by quantitative RT-PCR (qRT-PCR) and will be reported as log10 RNA 
copies/mL.  
 
Data from TCID50 and qPCR has been used in the pilot study analysis. This analysis assessed the 
variability of these sample-assay combinations in order to determine the analytical methodology 
for the remainder of the study. The variability at baseline between two swabs taken from the left 
and right sides (NPS x 2 versus OPS x 2) will be characterized using both PCR and TCID50, as 
described in the Virology Plan. 
 
7.3.4.2 Main Study - Tier 1 Analyses - HA Subtyping and Quantification of Virus 
Nasopharyngeal will be obtained from all subjects at the specified time points according to the 
Schedule of Assessments (Section 6, Table 4).  Analyses will involve HA subtyping of all 
patients at baseline (BL) and viral shedding quantitation of all time points by the method 
determined in the pilot study.   
 
HA subtyping will be performed on baseline samples by means of a multiplex real-time PCR and 
the virus subtype will be reported as H1, H3, or B. The viral shedding will be determined for all 
subjects at all study visits by quantitative RT-PCR (qRT-PCR) and will be reported as log10 
RNA copies/mL. Data from qPCR will be used to assess primary and secondary endpoints (e.g., 
efficacy of treatment with combination antivirals as compared with oseltamivir alone in those 
subjects with confirmed influenza infection).  
 
7.3.4.3 Tier 2 Analyses: Resistance Typing of Known Regions via RNA Sequencing 
Virus from subjects who are actively shedding virus on Day 7 will be tested for resistance. The 
baseline samples and samples from Day 7 will be sequenced by the Sanger method at the M2, 
NA and HA genes. Resistance to amantadine will be reported as amino acid changes at codons 
known to confer resistance in M2. Resistance to oseltamivir will be reported as amino acid 
changes at codons known to confer resistance in NA. Other changes in amino acid sequence 
from baseline that are not known to confer resistance will be reported. 
 
7.3.4.4 Exploratory Virology 
If a mutation from Tier 2 is detected which has not previously been characterized, and if it is 
associated with a lack of response to therapy, phenotypic assays may be performed to confirm 
resistance to amantadine, and oseltamivir. The shift in EC50 compared with the baseline sample 
will be measured and reported. Further phenotypic analyses may be conducted using purified 
viruses, in which virus is amplified in the presence of drugs to maintain phenotype. Additional 
testing may examine other virus genotypic changes, replication kinetics, or other parameters to 
explore resistance in this population.   
 
Determination of subpopulations of viruses present during viral shedding may be performed by 
deep sequencing.  Other studies of the viruses may occur.   
 


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7.3.4.5 Self-Collected Samples 
This study will explore the utility of subject self-collected samples.  If self-collected samples 
provide the same quantitative information as study team-collected samples, self-collected 
samples could be utilized in future studies for more frequent assessment of viral shedding with 
fewer clinic visits.  For this study, a subject self-collected sample will be obtained once daily on 
Study Days 0, 1, and 2, and 3. 
 
7.4 
Serologic Analysis 
Serologic determination of influenza infection will be used those subjects that don’t have the 
influenza virus detected in the baseline (or any analyzed) virologic sample.  The serologic 
determination of influenza infection will be performed either by the hemagglutinin inhibition 
assay (HAI) and/or microneutralization (MN), and using samples on Day 0 and Day 28.  The 
serology assay will be performed for contemporary strains from the season the subject was 
enrolled. 
 
7.5 
Compliance Measures 
Treatment compliance will be assessed by examination of subject’s remaining study product at 
each study visit, and by asking subjects if they have missed doses.  No pharmacokinetics or other 
drug exposure testing is planned for this study. 
 
7.6 
Research Assays 
At visits noted in Section 6, blood will be obtained for other research laboratory tests that help 
characterize subject’s immune response to influenza. This could include antibody response to 
influenza and other biomarkers (including cytokines) of severity of disease.  No genetic testing is 
done on these samples.  Any use of these specimens beyond the above stated purposes will 
require review of the planned research by the IRB/IEC. 
 
8 
SAFETY MONITORING AND REPORTING  
8.1 
Documenting, Recording, and Reporting Adverse Events  
At each contact with the subject, information regarding adverse events will be elicited by 
appropriate questioning and examinations and documented, recorded and reported as specified in 
Section 8.3.1. 
 
8.2 
Definitions  
Adverse Event (AE) 
An adverse event is any untoward or unfavorable medical occurrence in a human subject, 
including any abnormal sign (e.g., abnormal physical exam or laboratory finding), symptom, or 
disease, temporally associated with the subject’s participation in the research, whether or not 
considered related to the research. 
 


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Adverse Reaction (AR) 
An adverse event that is caused by an investigational agent (drug or biologic). 
 
Suspected Adverse Reaction (SAR) 
An adverse event for which there is a reasonable possibility that the investigational agent caused 
the adverse event. ‘Reasonable possibility’ means that there is evidence to suggest a causal 
relationship between the drug and the adverse event. A suspected adverse reaction implies a 
lesser degree of certainty about causality than adverse reaction which implies a high degree of 
certainty. 
 
Serious Adverse Event (SAE) 
A Serious Adverse Event is an AE that results in one or more of the following outcomes: 
 
• death 
• a life threatening (i.e., an immediate threat to life) event 
• an inpatient hospitalization or prolongation of an existing hospitalization 
• a persistent or significant incapacity or substantial disruption of the ability to conduct 
normal life functions 
• a congenital anomaly/birth defect 
• a medically important event* 
 
* Medical and scientific judgment should be exercised in deciding whether expedited 
reporting is appropriate in other situations, such as important medical events that may not be 
immediately life threatening or result in death or hospitalization but they may jeopardize 
the subject or may require intervention to prevent one of the other outcomes listed above.  
 
Unexpected Adverse Event 
An AE is unexpected if it is not listed in the Investigator’s Brochure or Package Insert (for 
marketed products) or is not listed at the specificity or severity that has been observed.  It is the 
responsibility of the Sponsor to make this determination. 
 
Serious and Unexpected Suspected Adverse Reaction (SUSAR) 
A SUSAR is a Suspected Adverse Reaction that is both Serious and Unexpected.   
 
Unanticipated Problem (UP) 
An Unanticipated Problem is any event, incident, experience, or outcome that is 
 
1.  unexpected in terms of nature, severity, or frequency in relation to 
a. the research risks that are described in the IRB-approved research protocol and informed 
consent document; Investigator’s Brochure or other study documents; and 
b. the characteristics of the subject population being studied; and 
2. possibly, probably, or definitely related to participation in the research; and 
3. places subjects or others at a greater risk of harm (including physical, psychological, 
economic, or social harm) than was previously known or recognized. (Per the Sponsor, an 
AE with a serious outcome will be considered increased risk.) 
 


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Unanticipated Problem that is not an Adverse Event (UPnonAE) 
An incident, experience or outcome that is not associated with an adverse event which meets the 
3 criteria of a UP.  Examples include occurrences of breaches of confidentiality, accidental 
destruction of study records, and unaccounted-for study drug. 
 
Protocol Violation 
A Protocol Violation is any change, divergence, or departure from the study design or procedures 
in an IRB-approved research protocol that has a major impact on the subject’s rights, safety, or 
well-being and/or the completeness, accuracy or reliability of the study data. 
 
Protocol Deviation 
A Protocol Deviation is any change, divergence, or departure from the study design or 
procedures of an IRB-approved research protocol that does not have a major impact on the 
subject’s rights, safety or well-being, and/or the completeness, accuracy and reliability of the 
study data. 
 
8.3 
Investigator Assessment of Adverse Events  
8.3.1 
Determination of Adverse Event 
Oseltamivir was first licensed in 1999, and is currently licensed in most countries (including all 
countries participating in this study).  Cumulative safety and tolerability data for oseltamivir 
from over 4000 subjects in randomized controlled trials, as well as significant postmarketing 
surveillance for significant side effects has been published. [28] The most common side effects 
of oseltamivir include nausea with or without vomiting and headache. It is unlikely that this 
study will significantly contribute to what is known about oseltamivir safety and tolerability. 
 
Symptoms associated with influenza include: fever, headache, eye irritation, nasal congestion or 
discharge, sneezing, sore throat, cough, abdominal pain, diarrhea, dyspepsia, nausea, vomiting, 
chills, fatigue, arthralgia, myalgia, neck pain, malaise, ear congestion or discomfort.  Physical 
findings include the patient appearing flushed, oropharyngeal hyperemia, cervical 
lymphadenopathy, wheezing, and tachypnea. Recording influenza symptoms as adverse events is 
neither an appropriate way to capture this data nor is this study likely to significantly contribute 
to what is known about the signs and symptoms of influenza. 
 
Symptoms captured on the diary cards either in the structured assessment and/or as free text 
should be assessed to determine if it fits with known presentations of influenza or known side 
effects of oseltamivir.  
Therefore, this study will not capture in the source nor eCRF grade 1-3 adverse events that are 
known side effects of oseltamivir (as defined in the package insert) nor known signs and 
symptoms associated with influenza (as noted, or similar to what is noted above). 
 
However, the following still need to be recorded in the source records and the eCRF: 
• Adverse events that do not follow side effects of oseltamivir or known signs and 
symptoms associated with influenza (e.g. visual changes) 
• Complications of influenza (e.g. pneumonia, sinusitis, or myocarditis)  


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• Any adverse events that are judged by the site investigator to be clinically significant 
(e.g. new onset seizures, acute allergic reactions)  
• All Grade 4 (life-threatening) or Grade 5 (death) AEs regardless of association with 
influenza or oseltamivir 
• Serious Adverse Event (SAE) as defined in section 8.2 
• Unanticipated Problem that is not an Adverse Event as defined in section 8.2 
 
8.3.2 
Period of Assessment 
AEs that should be recorded (as defined above) occurring from the time the informed consent is 
signed through Day 28 will be documented, recorded, and reported. Additionally, after Day 28 
AE/SAE related to the pregnancy or the developing fetus will be reported.  After the end of the 
protocol-defined SAE reporting period, sites must report to the safety office serious, unexpected, 
clinically suspected adverse drug reactions if the study site staff becomes aware of the event on a 
passive basis. 
 
8.3.3 
Assessment of Adverse Event 
The Investigator will evaluate recorded AEs with respect to Seriousness (criteria listed above), 
Severity (grading), and Causality (relationship to study agent and relationship to research) 
according to the following guidelines. 
 
 
8.3.4 
Severity 
The Investigator will grade the severity of recorded AEs according to the “Division of AIDS 
Table for Grading the Severity of Adult and Pediatric Adverse Events” Version 1.0, December, 
2004: (Clarification August 2009) which can be found at:   
http://rsc.tech-
res.com/Document/safetyandpharmacovigilance/Table_for_Grading_Severity_of_Adult_Pediatri
c_Adverse_Events.pdf   
 
8.3.5 
Causality of Adverse Event to the Intervention 
The Investigator will assess recorded AEs for causality. A causal relationship means that the 
study intervention/procedure caused (or is reasonably likely to have caused) the AE. This usually 
implies a relationship in time between the intervention and the AE (e.g. the AE occurred shortly 
after the subject received the study intervention/procedure).  
 
The clinician who examines and evaluates the subject will determine the event’s causality. 
Acceptance that an AE is causally related to the intervention usually requires a plausible 
mechanism of action (i.e., a believable sequence of events by which the intervention brought 
about the AE).  
 
The best estimate of the Investigator at the time of reporting of the causal relationship between 
the experimental intervention and an adverse event and the degree of certainty about causality 
will be graded as follows:  


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Unrelated 
Adverse event is clearly due to extraneous causes (e.g., underlying disease, environment).  
For an “unrelated” designation of causality, there should be a clear and plausible cause that 
excludes the possibility that the adverse event could be caused by the study treatments. 
 
Unlikely (must have 2) 
Adverse event: 
1. does not have temporal relationship to intervention 
2. could readily have been produced by the subject’s clinical state 
3. could have been due to environmental or other interventions 
4. does not follow known pattern of response to intervention 
5. does not reappear or worsen with reintroduction of intervention 
 
Possible (must have 2) 
Adverse event: 
1. has a reasonable temporal relationship to intervention 
2. could not readily have been produced by the subject’s clinical state 
3. could not readily have been due to environmental or other interventions 
4. follows a known pattern of response to intervention 
 
Probable (must have 3) 
Adverse event: 
1. has a reasonable temporal relationship to intervention 
2. could not readily have been produced by the subject’s clinical state or have been due to 
 
environmental or other interventions 
3. follows a known pattern of response to intervention 
4. disappears or decreases with reduction in dose or cessation of intervention 
 
Definite (must have all 4) 
Adverse event: 
1. has a reasonable temporal relationship to intervention 
2. could not readily have been produced by the subject’s clinical state or have been due to 
 
environmental or other interventions 
3. follows a known pattern of response to intervention 
4. disappears or decreases with reduction in dose or cessation of intervention and recurs 
 
with re-exposure 
 
8.4 
Investigator Reporting Responsibilities to the Sponsor  
8.4.1 
Adverse Events 
AEs that are to be recorded for this study (as noted above) will be fully and completely 
documented on the AE eCRF and in the subject’s clinical chart.   
 


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In the event that the subject is withdrawn from the study due to an AE, it must be recorded on the 
eCRF as such. The subject should be followed and treated by the Investigator until the adverse 
event has resolved or stabilized, even if this extends past the 28 day follow up period.  It is up to 
the clinician to determine that the AE/SAE is resolved or has reached a stable state, after which 
no further follow-up is necessary. There should be documentation to support that determination.  
 
Once an AE or SAE is known, research team members at the study site should ensure that 
subjects receive appropriate care. All actions taken by the Investigator after observing an AE or 
SAE should be documented, including increased monitoring of the subject, suspension of the 
treatment, etc.  
 
Assessment of safety will include clinical observations and monitoring of hematological, blood 
chemistry, and immunologic parameters. The investigator must document all directly observed 
AEs and all spontaneously reported AEs. AEs will be documented on the AE eCRF in 
appropriate medical terminology. The severity and the relationship to the study intervention will 
be determined and reported on the eCRF. 
 
Any intermittent or as needed use of any medication (specifically, any newly prescribed 
medication) during the course of the study may indicate the occurrence of an AE that may need 
to be recorded on both the AE eCRF and the concomitant medication form. 
 
8.4.2 
Serious Adverse Events 
SAEs (whether or not they are also UPs) must be reported on the SAE/UP Report Form and sent to 
the Sponsor Clinical Safety Office (CSO) by fax or e-mail attachment. Deaths and immediately 
life threatening SAEs must be reported within 1 business day after the site becomes aware of the 
event. All other SAEs must be reported within 3 business days of site awareness.  
 
SPONSOR CLINICAL SAFETY OFFICE CONTACT INFORMATION:  
 
OCRPRO Clinical Safety Office 
5705 Industry Lane 
Frederick, MD 21704 
 
Phone 301-846-5301 
Fax 301-846-6224 
E-mail: rchspsafety@mail.nih.gov  
 
Non-US sites may have country specific SAE reporting requirements – refer to the MOPs for 
details. 
 
8.4.3 
Unanticipated Problems 
Non-Serious AEs that are UPs must also be reported on the SAE/UP Report Form and sent to the 
CSO by fax or e-mail attachment no later than 7 calendar days of site awareness of the event. 
The UPs that are not AEs are not reported to the Sponsor CSO.  
 


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8.4.4 
Pregnancy  
Pregnancy itself is not an AE. However, complications of pregnancies are AEs and may be 
SAEs.  Pertinent obstetrical information for all pregnancies will be reported to the CSO via fax 
or email within 3 business days from site awareness of the pregnancy.   
 
Pregnancy outcome data (e.g., delivery outcome, spontaneous or elective termination of the 
pregnancy) will be reported to the CSO within 3 business days of the site’s awareness on a 
protocol-specified form. 
 
In the event of a pregnancy, the subject’s treatment should be unblinded per the unblinding 
section of the protocol. 
 
Pregnancy Outcomes should be reported to the Clinical Safety Office.  However, if the 
Investigator learns at any time after a subject has completed the Day 28, End-of- Study visit, of 
an untoward medical occurrence that would have qualified as an SAE, and such event is 
reasonably related to previous study drug exposure, the Investigator should promptly notify the 
Sponsor and the IRB/IEC. 
 
8.5 
Investigator Reporting Responsibilities to the Site IRB/EC 
8.5.1 
Safety reports 
Investigators are responsible for submitting Safety Reports and UP summaries that are received 
from the Sponsor to their local IRB/Ethics Committee.  Investigators must also comply with all 
local IRB/Ethics Committee reporting requirements.   
 
8.5.2 
Expedited Reporting to the Site IRB/EC  
Unanticipated problems that are either AEs or non-AEs, (as defined above) and protocol 
violations which do not meet the definition of a UP will be reported within 7 calendar days of 
investigator awareness (or as required by the site IRB/EC).  
 
8.5.3 
Annual Reporting to the IRB/EC  
The following items will be reported to the IRB/EC in summary at the time of Continuing 
Review (or more frequently as required by the site IRB/ECs): 
• All unanticipated problems 
• All protocol deviations which in the opinion of the investigator should be reported 
• Summaries of AEs recorded for this study 
 
8.6 
Follow-up of Adverse Events and Serious Adverse Events  
AEs that occur following enrollment of the subject (by signing the informed consent) are 
followed until the final outcome is known or until the end of the study follow-up period (Study 
Day 28). 
 
SAEs that have not resolved by the end of the follow-up period are followed until final outcome 
is known. If it is not possible to obtain a final outcome for an SAE (e.g., the subject is lost to 


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follow-up), the reason a final outcome could not be obtained will be recorded by the investigator 
on the AE CRF (if the CRF is still open) and the SAE/UP Report Form.  
 
SAEs that occur after the study follow-up period that are reported to and are assessed by the 
Investigator to be possibly, probably, or definitely related must be reported to the CSO, as 
described above. 
8.7 
Safety Monitoring  
8.7.1 
Study Monitoring 
The trial will be conducted in compliance with this protocol, International Conference on 
Harmonization (ICH) Guidelines for Good Clinical Practice (GCP) and any applicable regulatory 
requirement(s). This study monitoring will be conducted according to the “NIAID Intramural 
Clinical Monitoring Guidelines.” Monitors under contract to the NIAID will visit the clinical 
research site to monitor all aspects of the study in accordance with the appropriate regulations. 
The objectives of a monitoring visit will be:  
1. To verify the prompt reporting of all data points, including reporting SAEs, and also 
check the availability of signed informed consent. 
2. To compare individual subjects records and the source documents (supporting data, 
laboratory specimen records and medical records to include physician progress notes, 
nurse’ notes, subjects’ hospital charts). 
3. To ensure compliance with the protocol, and accuracy and completeness of records.  
 
The monitors also will inspect the clinical site regulatory files to ensure that regulatory 
requirements (national requirements, US FDA) are being followed. During the monitoring visits, 
the Investigator (and/or designee) and other study personnel will be available to discuss the study 
progress and monitoring visit. 
 
The Investigator (and/or designee) will make study documents (e.g., consent forms and 
electronic case report forms (eCRFs)) and pertinent hospital or clinical records readily available 
for inspection by the local IRB/IEC, the local and national regulatory authorities, the US FDA, 
the site monitors, and the NIAID staff for confirmation of the study data.  
 
8.7.2 
Investigator Safety Monitoring 
Investigators participating in this clinical trial are responsible for: 
◦ 
Protecting the safety and welfare of subjects 
◦ 
Evaluating subject safety, including physician assessment of AEs for seriousness, 
severity, and causality 
◦ 
Notifying the sponsor of SAEs and immediately-reportable events (per 8.3) 
◦ 
Providing detailed written reports, including confirmatory tests promptly following 
immediate initial reports 
◦ 
Informing the IRB/IEC of SAEs as required by applicable regulatory requirements 
 
8.7.3 
Protocol Team Monitoring 
The protocol team will review the enrollment and study-related safety data (AEs and SAEs) from 
all sites periodically during the study. These reviews will occur at a minimum twice monthly 


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during active enrollment and follow-up.  During periods of low influenza activity when no 
enrollment is occurring, these reviews do not need to occur.  
 
8.7.4 
Medical Monitor 
A medical monitor representing the sponsor (OCRPRO) will be responsible for compliance with 
all safety requirements. In this capacity, the medical monitor will: 1) review all documented AEs 
on a regular basis (as determined by the medical monitor) throughout the study, 2) review all 
SAEs, 3) be available to advise the investigators on study-related medical questions or problems, 
and 4) evaluate cumulative subject safety data and make recommendations regarding the safe 
continuation of the study.  
 
8.7.5 
Data and Safety Monitoring Plan 
A DSMB will review the safety of this protocol including enrollment and outcomes. The DSMB 
will review the study to monitor the conduct of the protocol and to evaluate the scientific validity 
and integrity of the data.  All serious adverse events and all unanticipated problems will be 
reported to the DSMB at the same time as other oversight parties receive them. The PI will notify 
the DSMB of any cases of intentional or unintentional unblinding as soon as possible. The site PI 
will submit the written DSMB summary reports with recommendations to the IRB(s).  
 
The DSMB will review and approve a detailed monitoring plan before the study commences. 
 
The DSMB will review study-related data at the following intervals: 
• Before enrollment 
• Periodic safety review during the study (details below) 
• At least annually while the study is open for enrollment 
 
No interim efficacy analysis is planned. 
 
8.7.5.1 Before Enrollment 
Before any subjects are enrolled, the DSMB reviewed the protocol design, the informed consent 
form (ICF), the package insert, the safety monitoring plan, and the plans for data to be provided 
for the periodic safety reviews.  
 
8.7.5.2 Periodic Safety Review 
The DSMB members will receive safety data for periodic review at intervals requested by the 
DSMB. In addition, as long as subjects are enrolled into the study, the Board will review the 
study at least annually. 
9 
STATISTICAL CONSIDERATIONS  
This section briefly describes the statistical analyses to be used for the study. A Statistical 
Analysis Plan will provide further details. 


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9.1 
General Considerations 
All statistical inferences will be based on two-sided tests with an α-level of 0.05. Categorical 
data will be summarized by the number and percent of subjects falling within each category. 
Continuous variables will be summarized by descriptive statistics, including mean, standard 
deviation, minimum, maximum, median, and relevant percentiles. Time-to-event endpoints will 
be summarized by median durations, hazard ratios, and corresponding 95% confidence intervals. 
Study Day 0 will be defined as the day of randomization.  
 
The Statistical Analysis Plan will provide the procedure for accounting for missing, unused, and 
spurious data. 
 
9.2 
Sample Size and Power Calculations 
The original sample size was estimated using the AUC of the log10 TCID50 × h/mL reported in 
the Phase 3 oseltamivir study. [20] Because the values of the standard deviations of AUC were 
not given in the paper, we can only estimate the standard deviations based on the two reported p-
values. An additional constraint on the standard deviations of the three groups is required 
because there are three unknown parameters to be estimated in two equations. A common 
practice is to assume that the three groups have a common standard deviation of AUC. The last 
column of the following table (Table 7) gives the estimated value of the common standard 
deviation. This calculation is based on an assumed t-test between the treatments and control and 
assuming that the mean AUC is similar to the medians provided by Nicholson. Since Nicholson 
used the Wilcoxon rank sum test, our calculation is probably conservative. 
 
 
   Table 7: AUC Results from Previous Oseltamivir Studies 
 
 
 
 
 
 
Note: in this paper, a total of 350 subjects with viral shedding data were used in the analysis. We assume 
they are equally split among the three arms. Additionally, the 75 mg group had a greater treatment effect 
but a larger (less significant) p-value when compared with the 150 mg group. All calculations were based 
on the data as reported. If the p-values reported were reported incorrectly (inadvertently swapped), this 
would decrease the sample size by only 15-20%.  
 
Our design is for a two-arm study with an oseltamivir group (O) and a placebo group (P). The 
effect of P versus O in the previous study is approximately 131-(78+94)/2, or about 45. For 
sample size calculation, we assume that the standard deviation of the AUC is 140 log10 TCID50 
×h/mL. The estimated sample sizes are summarized in Table 8 for a two-sided alpha=.05 t-test 
assuming equal variances and treatment effects of 100%, 75%, and 50% of the estimated AUC 
difference in the previous study. 
 
Table 8: Sample Size Estimates Under Different Treatment Effects 
 
N 
Median AUC 
(log10 TCID50 ×h/mL) 
P-
value 
Common 
SD 
Placebo 
117 
130.8 
 
140 
Oseltamivir 75mg  
117 
78.2 
0.03 
Oseltamivir 150mg  
117 
94.4 
0.003 
AUC 
difference 
Fraction of 
O vs. P in 
Power 
 
Allocation 
ratio 
Total cases 
with viral 
Total 
cases¶ 
Total N§ 


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¶ Total flu cases is calculated by assuming that 90% of enrolled subjects have viral shedding data.  
§ Total enrollment is calculated by a 10% loss to follow-up rate among influenza patients. 
 
 
We see that if the O vs. P mean AUC difference is 45 log10 TCID50, or 100% of the effect seen in 
previous studies, a total sample size of 507 is required to achieve 90% power.  
 
The addition of 50 subjects randomized for the pilot study brought the initial sample size for this 
study to 560 subjects. 
 
9.2.1 
Sample Size Re-estimation 
After analysis of the pilot study data, the primary endpoint was chosen as the percentage of 
subjects shedding virus by PCR in NP swab at Day 3.  
 
Assumptions: 
• Pooled percentage of subjects with virus detectable by PCR at Day 3 combining both 
arms is 50% (based on pilot study data) 
• Require 90% power to detect difference between arms using two-sided Fisher’s Exact 
Test with Type I error rate of 0.05. 
• Proportion of participants with missing qPCR at Day 3 is 10% (due to losses to follow-
up, sample handling and laboratory assay problems). 
 
Magnitude of difference in 
proportions between arms 
(proportions in the two 
randomized arms) 
Sample size (combined across 
both arms) without adjustment 
for missing values 
Sample size (combined across 
both arms) with adjustment for 
10% with missing values & 
not accounting for the 50 
subjects in the pilot study) 
25% (37.5% vs 62.5%) 
174 
194 
20% (40% vs 60%) 
280 
312 
15% (42.5% vs 57.5%) 
490 
546 
 
Table 9:Re-estimated Sample Size Under Different Treatment Effects 
 
 
This sample size has been chosen to give approximately 90% power to detect an absolute 
difference of 15% in the proportion of subjects with undetectable virus shedding at Day 3 in NP 
swabs (e.g., a reduction of 15% from 57.5% in the oseltamivir arm to 42.5% in the placebo 
(O vs. P) 
the previous 
study 
(O:C) 
shedding data 
45 
1.0 
0.80 
1:1 
306 
340 
378 
 
 
0.90 
1:1 
410 
456 
507 
33.75 
0.75 
0.80 
1:1 
544 
604 
671 
 
 
0.90 
1:1 
726 
807 
897 
22.5 
0.5 
0.80 
1:1 
1218 
1353 
1503 
 
 
0.90 
1:1 
1630 
1811 
2012 


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arm).  Less than a 15% absolute difference in viral shedding is unlikely to be viewed as clinically 
meaningful. Therefore, the revised sample size calculations confirm keeping the sample size 560 
subjects, including 50 in the pilot study and 510 in the main study.  
 
This power calculation is based on the fact that approximately 50% of subjects in the pilot study 
had undetectable virus in NP swabs at Day 3 (pooled over randomized arms) and included 
allowance for 10% of subjects to have unavailable viral shedding results at Day 3.  The 
calculation assumed use of a t-test to compare proportions using a two-sided type I error rate of 
0.05. 
 
9.3 
Subject Populations 
Safety Population: The Safety Population will consist of all participants who are randomized and 
received at least one dose of the study drug. For interim reviews, this will be limited to data 
entered into the electronic database up to the cut-off date. 
 
Intention to Treat (ITT) Population: The ITT will be the same as the Safety Population. 
 
Primary Efficacy Population: The Primary Efficacy Population will consist of all randomized (as 
defined in Section 3.2) subjects with confirmed influenza (as defined in Section 7.3.4, not site 
diagnostics for influenza). Primary efficacy analyses will be based on this subject population.  
 
9.4 
Statistical Analysis  
Details of the planned analysis are presented in the Statistical Analysis Plan. 
 
9.5 
Pilot Study (completed) 
Due to the lack of reliable data concerning the AUC virologic endpoint, an “external” pilot study 
was conducted on the first 50 patients randomized to identify a primary endpoint and method of 
analysis, and to possibly modify the sample size.  To ensure no effect on the type I error rate, 
data from these 50 patients will be excluded from the primary and secondary efficacy analyses 
but will be used in other analyses of secondary objectives and regression analyses between 
clinical and virologic endpoints.  The study continues to enroll into the main study while the 
results of the pilot study are being analyzed. The pilot study will not change what data and 
samples are collected, but rather how the collected data and samples are analyzed. 
 
Data in the pilot study included duplicate samples for both throat and nose locations and for both 
methods of measuring virus. Duplicate sampling was only done at baseline. Bland-Altman plots, 
regression, and correlation were used to assess the reproducibility and variability of both 
methods of counting virions. Additionally, post randomization viral and clinical endpoints were 
assessed by study arm to examine the distribution and possibly treatment effect of different 
clinical and virologic endpoints. This analysis was conducted by a statistician who conveyed the 
results blinded to treatment allocation to the Pilot Study Analysis Group who recommended a 
method to the protocol team for a final decision. The analyzing statistician was not part of the 
group making decisions on which endpoint to use in the main study. Further details for analysis 
of the Pilot Study will be presented in the Statistical Analysis Plan. 
 


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10 
DATA MANAGEMENT AND MONITORING 
10.1 
Source Documents 
The primary source document for this study will be the subject’s medical record. If the 
investigators maintain separate research records, both the medical record and the research 
records will be considered the source documents for the purposes of auditing the study. The 
investigator will retain a copy of source documents. The investigator will permit monitoring and 
auditing of the data, and will allow NIAID, Social & Scientific Systems, Inc. (SSS) and other 
NIAID contractors, IRB/IEC, and regulatory authorities access to the original source documents, 
regardless of media. 
 
The investigator is responsible for ensuring that the data collected is complete, accurate, and 
recorded in a timely manner. Source documentation (the point of initial recording of information) 
should support the data collected on the eCRF. All eCRFs should be reviewed by the investigator 
and signed as required with written or electronic signature, as appropriate. Data for eCRFs will 
be collected directly from subjects, clinical assessments, and tests during study visits or will be 
abstracted from subjects’ medical records. The subjects’ medical records must record their 
participation in the clinical trial, including obtaining informed consent, concomitant medications 
(with doses and frequency), medical interventions or treatments that were administered, and 
adverse reactions experienced during the trial. 
 
10.2 
Data Management Plan 
Study data will be collected at the study sites and maintained on eCRFs. These forms are to be 
completed on an ongoing basis during the study. Corrections on any study related source record 
must be made by striking through the incorrect entry with a single line (taking care not to 
obliterate or render the original entry illegible) and entering the correct information adjacent to 
the incorrect entry. Corrections to paper source documents must be initialed and dated by the 
person making the correction. 
 
10.3 
Data Capture Methods 
Clinical data will be entered into an Internet Data Entry System (IDES) (US 21 CFR 11-
compliant). The data system includes password protection and internal quality checks, to identify 
data that appear inconsistent, incomplete, or inaccurate. 
 
10.4 
Study Record Retention 
The investigator is responsible for retaining all essential documents listed in the ICH Good 
Clinical Practice Guideline. Since this is a non-IND study, NIH policy requires that study records 
be retained for at least 3 years after completion of the research.  These records are also to be 
maintained in compliance with IRB/IEC, state, and federal medical records retention 
requirements, whichever is longest.  
 
All stored records are to be kept confidential to the extent provided by national and local law. It 
is the investigator’s responsibility to retain copies of source documents until receipt of written 


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notification to the contrary from OCRPRO/DCR/NIAID. No study document should be 
destroyed without prior written agreement from OCRPRO/DCR/NIAID. Should the investigator 
wish to assign the study records to another party and/or move them to another location, the 
investigator must provide written notification of such intent to OCRPRO/DCR/NIAID with the 
name of the person who will accept responsibility for the transferred records and/or their new 
location.  
 
OCRPRO/DCR/NIAID must be notified in writing and written OCRPRO/DCR/NIAID 
permission must be received by the site prior to destruction or relocation of research records. 
 
11 
HUMAN SUBJECTS 
11.1 
IRB/IEC Approval  
This protocol, informed consent document, diary cards, relevant supporting information, and all 
types of patient recruitment or advertisement information must be submitted to the IRB/IEC for 
review and must be approved before the study is initiated. 
 
Any amendments must also be approved by the IRB/IEC prior to implementing changes in the 
study.  
 
The investigator is responsible for keeping the IRB/IEC apprised of the progress of the study as 
deemed appropriate, but in any case at least once a year. The investigator must also keep the 
IRB/IEC informed of any significant AEs. 
 
11.2 
Compliance with Good Clinical Practices (GCP) 
This study will be conducted in compliance with the conditions stipulated by NIAID and local 
IRB/IEC, informed consent regulations, local regulatory agencies, and supported by ICH/GCP 
guidelines. In addition, all local regulatory requirements will be adhered to, in particular those 
which afford greater protection to the safety of the trial subjects. 
 
11.3 
Informed Consent Process 
Informed consent is a process wherein information is presented to enable persons to voluntarily 
decide whether or not to participate as a research subject. It is an on-going conversation between 
the human research subject and the researchers about the essential information about the study, 
which begins before consent is given and continues until the end of the subject's involvement in 
the research. Discussions of essential information about the research will include the study's 
purpose, duration, experimental procedures, alternatives, risks, and benefits, and subjects will 
have the opportunity to ask questions and have them answered.  
 
The subjects will sign the informed consent document prior to any procedures being done 
specifically for the study. The subjects may withdraw consent at any time throughout the course 
of the trial. A copy of the informed consent document will be given to the subjects for their 
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record. The rights and welfare of the subjects will be protected by emphasizing to them that the 
quality of their medical care will not be adversely affected if they decline to participate in this 
study.  
 
In the case of illiterate subjects, the consent can be read to the subjects. IRB/IEC approval for 
use of the oral consent process will be obtained if required by the policy at the individual site. As 
warranted, translated copies of the informed consent documents (into Spanish or other languages 
as dictated by a given sites usual demographics) may be provided. The translated ICF will be 
approved by the site’s IRB/IEC prior to use. 
 
11.4 
Anonymity and Confidentiality  
As each subject is consented and then enrolled, he or she will be allocated a unique study ID 
number. To ensure participant confidentiality, these numeric codes will substitute for personal 
identifiers on all paper documents, computer records, and blood sample vials. The information 
obtained during the conduct of this clinical study is confidential, and disclosure to third parties 
other than those noted is prohibited. The results of the research study may be published, but 
subjects’ names or identities will not be revealed. Records will remain confidential. To maintain 
confidentiality, the principal investigator will keep records in locked cabinets, and the results of 
tests will be coded to prevent association with subjects’ names. It is expected that these data will 
be reported in scientific journals and scientific meetings. Confidentiality of subjects will be 
maintained in all forms of reporting. Subjects will be informed in general terms of the results as 
soon as possible.  
 
11.5 
Conflict of Interest 
  
There is no real or apparent conflict of interest. 
 
11.6 
Compensation 
 
Each site is responsible for generating a compensation scheme as applicable (accounting for 
travel cost and time lost from work for outpatient visits), and that fits the local legal and 
regulatory requirements as well as the cultural norm. Any compensation must be reviewed by the 
local IRB/IEC.  The site may use a site specific “Appendix A”, or other method to convey this 
information to the IRB/IEC without changing the protocol. 
 
12 
RESEARCH USE OF STORED HUMAN SAMPLES, SPECIMENS, AND DATA 
12.1 
Intended Use of the Samples/Specimens/Data 
Samples and data collected under this protocol may be used to study the clinical features, 
immunology, and virology of human influenza. 
 


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12.2 
Storage of Samples/Specimens/Data  
As part of this protocol, samples will be stored for further research. Any future research (aside 
from the scope of research listed within this protocol and performed at a future date) will require 
approval from the IRB/IEC. Samples and data will be stored using codes assigned by the sponsor 
or its designee. Data will be kept in password-protected computers, which are located in locked 
rooms. Samples will be stored in locked facilities.  
 
Stored samples are coded and linked to a specific patient ID (PID).  However, neither the stored 
samples nor data in the database can be linked to a particular subject. Only the site will have the 
ability to link the subject ID to the actual person. 
 
12.3 
Storage of Genetic Sample 
No samples are being stored for genetic testing on the subjects (genetic testing of influenza 
viruses may occur). 
 
12.4 
Tracking Samples/Specimens/Data 
Samples will be tracked by a commercial software program. 
 
12.5 
Use of Samples/Specimens/Data at the Completion of the Protocol 
Samples will be maintained for further laboratory testing for up to 5 years after completion (or 
termination) of the protocol. This length of time for storing samples may be extended only after 
permission of the IRB/IEC. 
 
In the future, other investigators besides those listed in this protocol may wish to study these 
samples and/or data. In that case, IRB/IEC approval will be sought prior to any sharing of 
samples. Any clinical information shared about the sample with or without subject identifiers 
would similarly require prior IRB/IEC approval.  
12.6 
Reporting Loss or Destruction of Samples/Specimens/Data  
Any loss or unanticipated destruction of locally maintained samples (for example, due to freezer 
malfunction) or data (for example, misplacing a printout of data with identifiers) will be reported 
to the corresponding IRB/IECs. 
 
Any loss or unanticipated destruction of centrally maintained samples or data will be reported to 
all IRB/IECs.  
 
 


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13 
REFERENCES 
1. Thompson WW, Shay DK, Weintraub E, et al. Mortality associated with influenza and 
respiratory syncytial virus in the United States. JAMA 2003;289:179-86 
2. Monto AS. Vaccines and antiviral drugs in pandemic preparedness. Emerging Infect Dis 
2006;12:55-60 
3. Moscona A. Oseltamivir resistance--disabling our influenza defenses. N Engl J Med 
2005;353:2633-6 
4. High levels of adamantane resistance among influenza A (H3N2) viruses and interim 
guidelines for use of antiviral agents--United States, 2005-06 influenza season. MMWR Morb 
Mortal Wkly Rep 2006;55:44-6 
5. Update: influenza activity--United States, September 28-November 29, 2008. MMWR Morb 
Mortal Wkly Rep 2008;57:1329-32 
6. Update: drug susceptibility of swine-origin influenza A (H1N1) viruses, April 2009. MMWR 
Morb Mortal Wkly Rep 2009;58:433-5 
7. Memoli MJ, Hrabal RJ, Hassantoufighi A, Eichelberger MC, Taubenberger JK. Rapid 
Selection of Oseltamivir- and Peramivir-Resistant Pandemic H1N1 Virus during Therapy in 2 
Immunocompromised Hosts. Clin Infect Dis 2010 
8. Englund JA, Champlin RE, Wyde PR, et al. Common emergence of amantadine- and 
rimantadine-resistant influenza A viruses in symptomatic immunocompromised adults. Clin 
Infect Dis 1998;26:1418-24 
9. Bright RA, Shay DK, Shu B, Cox NJ, Klimov AI. Adamantane resistance among influenza A 
viruses isolated early during the 2005-2006 influenza season in the United States. JAMA 
2006;295:891-4 
10. Fiore AE, Shay DK, Broder K, et al. Prevention and control of influenza: recommendations 
of the Advisory Committee on Immunization Practices (ACIP), 2008. MMWR Recomm Rep 
2008;57:1-60 
11. http://www.cdc.gov/H1N1flu/recommendations.htm#e.  
12. Bautista E, Chotpitayasunondh T, Gao Z, et al. Clinical aspects of pandemic 2009 influenza 
A (H1N1) virus infection. N Engl J Med 2010;362:1708-19 
13. von Itzstein M, Wu WY, Kok GB, et al. Rational design of potent sialidase-based inhibitors 
of influenza virus replication. Nature 1993;363:418-23 
14. Colman PM. Influenza virus neuraminidase: structure, antibodies, and inhibitors. Protein Sci 
1994;3:1687-96 
15. Wood N, Aitken M, Sharp S,  Evison H. Tolerability and pharmacokinetics of the influenza 
neuraminidase inhibitor Ro-64-0802 (GS4071) following oral administration of the prodrug Ro-
64-0796 (GS4104) to healthy male volunteers, . In: 37th Interscience Conference on 
Antimicrobial Agents and Chemotherapy. Toronto, Ontario, 1997 
16. Eisenberg E, Bidgood A, Cundy K. Penetration of GS4071, a novel influenza neuraminidase 
inhibitor, into rat bronchoalveolar lining fluid following oral administration of the prodrug 
GS4104. . In: Antimicrobial Agents & Chemotherapy 1997 
17. He G, Massarella J, Ward P. Clinical pharmacokinetics of the prodrug oseltamivir and its 
active metabolite Ro 64-0802. Clin Pharmacokinet 1999;37:471-84 
18. Roche. Tamiflu Package Insert.  
19. Treanor JJ, Hayden FG, Vrooman PS, et al. Efficacy and safety of the oral neuraminidase 
inhibitor oseltamivir in treating acute influenza: a randomized controlled trial. US Oral 
Neuraminidase Study Group. JAMA 2000;283:1016-24 


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20. Nicholson KG, Aoki FY, Osterhaus AD, et al. Efficacy and safety of oseltamivir in treatment 
of acute influenza: a randomised controlled trial. Neuraminidase Inhibitor Flu Treatment 
Investigator Group. Lancet 2000;355:1845-50 
21. Whitley RJ, Hayden FG, Reisinger KS, et al. Oral oseltamivir treatment of influenza in 
children. Pediatr Infect Dis J 2001;20:127-33 
22. Hayden FG, Jennings L, Robson R, et al. Oral oseltamivir in human experimental influenza 
B infection. Antivir Ther 2000;5:205-13 
23. Hayden FG, Treanor JJ, Fritz RS, et al. Use of the oral neuraminidase inhibitor oseltamivir in 
experimental human influenza: randomized controlled trials for prevention and treatment. JAMA 
1999;282:1240-6 
24. Kaiser L, Wat C, Mills T, Mahoney P, Ward P and Hayden F. Impact of oseltamivir 
treatment on influenza-related lower respiratory tract complications and hospitalizations. Arch 
Intern Med 2003;163:1667-72 
25. Bowles SK, Lee W, Simor AE, et al. Use of oseltamivir during influenza outbreaks in 
Ontario nursing homes, 1999-2000. J Am Geriatr Soc 2002;50:608-16 
26. Dutkowski R, Thakrar B, Froehlich E, Suter P, Oo C,  Ward P. Safety and pharmacology of 
oseltamivir in clinical use. Drug Safety : an international journal of medical toxicology and drug 
experience 2003;26:787-801 
27. Contopoulos-Ioannidis DG, Karvouni A, Kouri I, Ioannidis JP. Reporting and interpretation 
of SF-36 outcomes in randomised trials: systematic review. BMJ 2009;338:a3006 
28.  Smith JR, Rayner CR, Donner B, Wollenhaupt M, Klumpp K, Dutkowski R. Oseltamivir in 
seasonal, pandemic, and avian influenza: a comprehensive review of 10-years clinical 
experience. Adv Ther. 2011 Nov;28(11):927-59 
 
 
 
 

SAP_000.pdf: 
Statistical Analysis Plan IRC004 
Page 1 of 17  
 
 
 
 
 
 
 
 
Number: IRC-004 
 
ClinicalTrials.gov ID: NCT01314911 
 
 
A Randomized Double-Blind Study Comparing Oseltamivir versus Placebo 
for the Treatment of Influenza in Low Risk Adults 
 
VERSION 2.0  
 
August 3, 2016 
 
This is IRC004 SAP Version 2.0 with names of authors, names of publication writing team members and 
analysis timeline redacted. 
 


Statistical Analysis Plan IRC004 
Page 2 of 17  
Table of Contents 
INTRODUCTION........................................................ ERROR! BOOKMARK NOT DEFINED. 
KEY UPDATES TO IRC004 STATISTICAL ANALYSIS PLAN, VERSION 1.0 .... ERROR! 
BOOKMARK NOT DEFINED. 
TABLE OF CONTENTS ............................................................................................................. 2 
PROTOCOL SUMMARY ........................................................................................................... 3 
1 
GENERAL ANALYSIS CONSIDERATIONS .................................................................. 5 
2 
APPLICATION VALIDATION.......................................................................................... 5 
3 
VISIT AND EVALUATION SCHEDULE ......................................................................... 5 
4 
ANALYSIS PLAN ................................................................................................................ 6 
4.1 
ANALYSIS POPULATIONS ................................................................................................. 6 
4.2 
ACCRUAL, ELIGIBILITY VIOLATIONS AND EXCLUSIONS FROM ANALYSES (ENROLLED 
POPULATION) ............................................................................................................................... 6 
4.3 
SELECTED CHARACTERISTICS OF PARTICIPANTS AT DAY 0 (DAY OF RANDOMIZATION) 
PRIOR TO STARTING STUDY TREATMENT ...................................................................................... 7 
4.3.1 
Demographics and other characteristics: (Enrolled population and ITT) ............. 7 
4.3.2 
Influenza infection (ITT) ......................................................................................... 7 
4.3.3 
Disease and vaccination status (ITT) ..................................................................... 7 
4.3.4 
Virology Measures (ITT and PEP) [team collected swabs] ................................... 8 
4.3.5 
Virology Measures (ITT and PEP) [self-collected swabs] ..................................... 9 
4.4 
STUDY STATUS OF PARTICIPANTS AND LOSS TO FOLLOW-UP (ITT) ................................... 9 
4.5 
STUDY TREATMENT [SDCOMP1] (ITT) .......................................................................... 9 
4.6 
MORTALITY, HOSPITALIZATION[EVENT3 AND AE2] (ITT) ........................................... 9 
4.7 
SAFETY ANALYSIS ......................................................................................................... 10 
4.7.1 
Serious Adverse Events (Enrolled population and ITT) ....................................... 10 
4.7.2 
Adverse Events (Enrolled population, and ITT) ................................................... 11 
4.8 
EFFICACY ANALYSIS ...................................................................................................... 11 
4.8.1 
Primary Endpoint [IRCRSLT] (population for the primary analysis and PEP) .. 11 
4.8.2 
Secondary Endpoints: Virologic Endpoints [IRCRSLTS]  (PEP and ITT) ........... 12 
4.9 
SECONDARY ENDPOINTS: CLINICAL ENDPOINTS [DIARY1] (PEP AND ITT) ................. 12 
4.9.1 
Association of viral shedding to clinical symptoms and fever (PEP and ITT) ..... 15 
4.10 
EVALUATION OF SELF-COLLECTED SAMPLES (PEP AND ITT) ......................................... 15 
4.11 
EMERGENCE OF ANTIVIRAL RESISTANCE. (ITT) ............................................................. 17 
 
 
 


Statistical Analysis Plan IRC004 
Page 3 of 17  
 PROTOCOL SUMMARY 
 
Full Title:  A Randomized Double-Blind Study Comparing Oseltamivir versus Placebo for the 
Treatment of Influenza in Low Risk Adults 
 
Short Title: IRC-004 
 
Sponsor: Office of Clinical Research Policy and Regulatory Operations (OCRPRO), Division of 
Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID) 
 
Conducted by: NIAID Influenza Research Collaboration (NIRC) 
 
Sample Size: N= 560 subjects 
 
Accrual Ceiling: Up to 800 subjects will be screened to randomize 560 subjects 
 
Study Population: Outpatient subjects at low risk for complications and morbidity from 
influenza (using US CDC criteria), and that have a diagnosis of influenza by rapid antigen or 
PCR. 
 
Study Design: This randomized double-blind study will evaluate whether oseltamivir modifies 
viral shedding in an ambulatory population with uncomplicated influenza. This study is also 
designed to explore the relationship between virologic effects and clinical effects, and to start 
understanding if improvements to virologic shedding correlate with improvements in clinical 
outcomes.  This is a multicenter international study.  Up to approximately 50 sites may 
participate in this protocol. 
 
Subjects with an influenza-like illness will be screened for the study, and those found positive for 
influenza will be randomized in a 1:1 manner to receive a blinded study treatment consisting of 
either oseltamivir or placebo for 5 days. Subjects will be assessed on Study Day 0 (pre-dose), 
and on Study Days 3, 7, and 28. All subjects will undergo a series of efficacy and safety 
assessments during the study. Subjects will have a NP swab to test for influenza virus on Days 0, 
3, 7, and blood samples will be collected on Days 0, 3, 7, and 28. Subjects will also perform self-
collection of nasal swabs for the detection of influenza virus on Days 0, 1, 2, and 3. 
 
Study Agent: Oseltamivir versus placebo. 
 
Primary Objective:  
The overall objective of the study is to evaluate the antiviral efficacy of oseltamivir compared to 
placebo in the treatment of subjects with confirmed influenza infection (Primary Efficacy 
Population) as measured by percentage of subjects with virus detectable by PCR in NP swab at 
Day 3. 
 
Secondary Objectives:  


Statistical Analysis Plan IRC004 
Page 4 of 17  
1. Evaluate the antiviral efficacy of treatment with oseltamivir compared with placebo in those 
subjects with confirmed influenza infection (primary efficacy population) and intention to treat 
(ITT) population as assessed by the following parameters: 
 
Virologic: (by PCR in NP swab) 
◦ AUC of viral shedding 
◦ Duration of viral shedding  
◦ Percent cessation of viral shedding on Days 3 and 7 
◦ Frequency of emergence of antiviral resistance 
 
Clinical: 
◦ Time to alleviation of influenza clinical symptoms 
◦ Time to absence of fever  
◦ Time to resolution of all symptoms AND fever 
◦ Time to resumption of normal activity 
                  Note: in this analysis, this objective will be assessed by: 
o Time to feeling as good as before the onset of the influenza illness (as measured 
by a global assessment question) 
o Time to return to pre-influenza illness level of function (as measured by a global 
assessment question) 
o Time to return to pre-influenza illness level of physical function (as measured by 
SF-36 physical score) 
◦ Proportion of subjects who require hospitalization 
◦ Proportion of subjects who develop bronchitis, pneumonia, or other complications of 
influenza 
 
2. Evaluate the association of viral shedding (both qualitative and quantitative) to clinical 
symptoms and fever. 
 
3. Evaluate if changes in viral shedding by antiviral treatment predict changes in clinical 
symptoms and fever.  
 
4.  Evaluate subject self-collected nasal samples compared with study team collected samples for 
the determination of viral shedding. 
 
5. Evaluate the variability in the sample collection. (pilot study only) [NOTE: This is not 
addressed in this SAP]  
 
 
Endpoints: 
 
Primary Endpoint 
Percentage of subjects shedding virus by PCR in NP swab at day 3.  
 
Secondary Endpoints 
Clinical Endpoints: 


Statistical Analysis Plan IRC004 
Page 5 of 17  
 Time to alleviation of influenza clinical symptoms  
 Time to absence of fever  
 Time to resumption of normal activity 
Note: in this analysis, the following endpoints will be used to represent “resumption of 
normal activity”: 
o Time to feeling as good as before the onset of the influenza illness (as measured 
by a global assessment question) 
o Time to return to pre-influenza illness level of function (as measured by a global 
assessment question) 
o Time to return to pre-influenza illness level of physical function (as measured by 
SF-36 physical score) 
 Number of premature study treatment discontinuations 
 Proportion of subjects who develop bronchitis, pneumonia, or other complications of 
influenza 
 Proportion of subjects who require hospitalization 
 28-day mortality  
 
Virologic Endpoints: (assessed by PCR in NP swab) 
 Duration of viral shedding 
 Change in viral shedding as a function of time 
 AUC of viral shedding 
 Frequency of emergence of antiviral resistance  
 
1 
General analysis considerations  
Unless otherwise specified, data summaries and analyses will be presented overall and by 
randomized arm.  
 
To help protect participant confidentiality, listings of individual patient level data will be 
minimized as much as possible.  Dates will also not be presented in listings; instead, for 
example, listings will present details as days since randomization. 
2 
Application validation 
All study-specific programs for creation of derived datasets for derivation of the endpoint 
defined in this document will require application validation and verification per written Standard 
Operating Procedures as appropriate. 
3 
Visit and Evaluation Schedule 
The expected schedule for clinic visits (per protocol) is shown in Table 1 below. To allow for 
possible deviations from these, the visit windows have been expanded for analysis purposes as 
indicated.  If there are multiple measurements within a window, then the one closest to the 
scheduled time will be used in analysis. 
 
   


Statistical Analysis Plan IRC004 
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Table 1. IRC003 Study days and analysis windows 
Days since randomization 
Visit 
Day 0 
(Baseline*) 
Day 1 
(Home) 
Day 2 
(Home) 
Day 3 
Day 7 
Day 28 
Per protocol (Days) 
0 
1 
2 
3 
7±1 
28±3 
Analysis (Days) 
0 (-1 if 0 not 
available) 
1 
2 
3±1 
7±2 
28±7 
 *  Baseline evaluation must be completed prior to the first dose of study medication. 
 
For the diary cards, the auto-populated study day (‘stday’) on the CRF will be used to select the 
measurements at each time point. If there are multiple measurements within a window, the 
calculated study day (i.e. date of evaluation - randomization date), will be used to choose the one 
closest to the scheduled time. 
4 
Analysis Plan 
Unless otherwise stated, all tables and figures will show results by randomized arms.   
 
Throughout this analysis plan, annotations in square brackets ([XXX]) provide the source 
table/view names and, in some cases, target fields in the IRC004 database. 
 
Per protocol, at study entry, results from laboratory tests obtained for clinical indications within 
24 hours before randomization may be used if available.  
 
Unless otherwise stated, data will be presented in tables.  For tables with categorical variables, 
the number (%) will be presented.  For tables with continuous variables, the mean, standard 
deviation, median, 25th and 75th percentiles, min and max will be presented. The number with 
missing values will also be shown.  In calculation of percentages, subjects with missing data will 
not be included in the denominator. Data presented as listings or figures noted. 
4.1 
Analysis Populations 
All tables and figures will note the analysis population used: 
 Enrolled Population includes all subjects who had a signed informed consent form for 
screening. 
 Intention To Treat (ITT) Population includes all subjects who were randomized and who 
received at least one dose of study drug (as defined in Section 7.2.1 of the protocol).  
 Primary Efficacy Population (PEP) includes subjects in the ITT population with influenza 
infection confirmed in central laboratory testing.  Given the virology needed to analyze 
the primary endpoint, this is defined as having an influenza virus isolated and typed in the 
qualitative PCR evaluation at Day 0 from central laboratory testing (or Day -1 if Day 0 
not available).  
 The population for the primary analysis is defined as the subgroup of the PE Population 
that excludes the subjects who participated in the pilot study (because efficacy results for 
those subjects were used in selecting the primary endpoint for the study). 
4.2 
Accrual, eligibility violations and exclusions from analyses (Enrolled Population) 
 


Statistical Analysis Plan IRC004 
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a. Number (%) enrolled (i.e. having a signed informed consent form for screening): 
overall and by month/year.  Dates of first and last subject’s enrollments. [STEP] 
b. Screen failures: Number (%) by reason. [SCRVIS3] 
c. Number (%) randomized: overall and by month/year.  Dates of first and last 
randomizations. [STEP] 
d. Table: Number (%) randomized by site. 
e. List: Description of violations/deviations of eligibility criteria among subjects 
randomized: Randomized arm, subject ID, site, age, sex, study treatment 
dispensed (yes or no), whether in PE Population, subject’s study status 
(completed 28 days, died, or discontinued early from study including reason for 
discontinuation), category of issue (violation or deviation) and description of 
issue (site narrative). [DEVTRK] 
f. List: Description of exclusions from analyses among subjects randomized but who 
did not have study treatment dispensed: Randomized arm, site, subject ID, reason 
study treatment not dispensed. [Note: The only randomized subjects who will be 
excluded from all analyses are those subjects who did not have study treatment 
dispensed]. 
 
 
All following analyses will be restricted to the ITT Population (or further to the Primary 
Efficacy Population where noted).  
 
4.3 
Selected characteristics of participants at Day 0 (day of randomization) prior to 
starting study treatment 
 
4.3.1 
Demographics and other characteristics: (Enrolled population and ITT) 
a. Age [CASE] 
b. Sex [PATIENT] 
c. Ethnicity [PATIENT] 
d. Race [PATIENT] 
e. Country [CURRENT] 
 
4.3.2 
Influenza infection (ITT) 
a. Site test for influenza used to determine eligibility [SCRVIS3] 
b. Results of influenza diagnostic test at sites (positive or negative) [SCRVIS3] 
c. Influenza type/subtype by local testing at sites [SCRVIS3] 
d. Confirmed influenza infection status (yes or no) [as defined in the protocol] by 
nasopharyngeal(NP) swab tested by PCR at central virology laboratory [IRCRSLTS] 
e. Confirmed influenza type/subtype by NP swab tested by PCR at central virology 
laboratory [IRCRSLTS] 
 
4.3.3 
Disease and vaccination status (ITT) 
a. Hours since onset of influenza-like illness to screening (as defined in protocol section 
4.3, item 4) [SCRVIS3] 


Statistical Analysis Plan IRC004 
Page 8 of 17  
b. Hours from screening to randomization  
c. Hours from randomization to treatment initiation [SDCOMP1] 
d. Influenza vaccination the season of (and anytime prior to) enrollment 
e. Vital signs: Blood pressure (diastolic and systolic), heart rate, mean arterial pressure, 
temperature [VITALS2] 
f. Smoking status (current, previous, never) 
g. Anthropometric measurements: weight, height, body mass index [VITALS2] 
h. SaO2 and SaO2 category (<93% vs. ≥93%) [VITALS2] 
i. Presence of fever (≥38°C) [DIARY1] 
j. Symptom score for each of the following symptoms (scored on a 4-point scale: 
0=absent, 1=mild, 2=moderate, 3=severe) [DIARY1] 
 Cough 
 Nasal obstruction 
 Sore throat 
 Fatigue 
 Headache 
 Myalgia 
 Feverishness 
 Rhinorrhea 
 Nausea 
 Vomiting 
 Diarrhea 
 Other (as specified by study participant) 
k. Overall symptom score (defined as the sum of scores for the preceding list of 
symptoms) 
l. Functional status pre-illness (assessed using subjects pre-illness recall of the 10-item 
domain of Physical Function from the SF-36) [DIARY1] 
m. Functional status on Day 0 (assessed using the 10-item domain of Physical Function 
from the SF-36) [DIARY1] 
n. Presence of each of the following complications of influenza [EVENTS3]: 
 Sinusitis 
 Otitis media 
 Bronchitis / bronchiolitis 
 Pneumonia 
 Antibiotic use for reason other than above   
 
4.3.4 
Virology Measures (ITT and PEP) [team collected swabs] 
a. Viral shedding in nasopharyngeal (NP) swab by qPCR:  number (%) <LOD, LOD-
<LLOQ, ≥LLOQ, and summary of quantitative values on log10 scale [IRCRSLTS] 
b. Housekeeping (HK) gene levels by qPCR: number (%) <LOD, LOD-<LLOQ, 
≥LLOQ-≤ULOQ, >ULOQ, and summary of quantitative values on log10 scale 
[IRCRSLTS] 
c. Viral shedding in nasopharyngeal (NP) swab by qPCR by housekeeping gene 
detection [IRCRSLTS]:   


Statistical Analysis Plan IRC004 
Page 9 of 17  
 NP virus <LOD: % HK <LOD, % HK LOD-<LLOQ, % HK ≥LLOQ-≤ULOQ, % 
HK >ULOQ 
 NP virus LOD-<LLOQ: % HK <LOD, % HK LOD-<LLOQ, % HK ≥LLOQ-
≤ULOQ, % HK >ULOQ 
 NP virus ≥LLOQ: % HK <LOD, % HK LOD-<LLOQ, % HK ≥LLOQ-≤ULOQ, 
% HK >ULOQ  
4.3.5 
Virology Measures (ITT and PEP) [self-collected swabs] 
a. Viral shedding in self- collected swabs by qPCR:  number (%) <LOD, LOD-<LLOQ, 
≥LLOQ, and summary of quantitative values on log10 scale [IRCRSLTS] 
b. Cross-tabulation of the viral test results for self- and team-collected swabs on Day 0 
swab by whether or not virus was detected at Day 0. Comparison will use first 
available team-collected swab and the daytime self-collected swab on Day 0. 
 
4.4 
Study status of participants and loss to follow-up (ITT) 
a. 
Died prior to Day 28 evaluation [DEATH2] 
b. 
Lost to follow-up before completing Day 28 evaluation (with subcategories showing 
reason for loss) [OFFSDY2] 
c. 
Completed Day 28 evaluation [OFFSDY2] 
d. 
List: Randomized arm, days from randomization to last study visit, site, subject ID, 
protocol version, age, sex, confirmed influenza infection status, days from 
randomization to last contact, text reason for off study (sort by randomized arm, day 
of last study visit, subject ID). [OFFSDY2] 
e. 
Figure: Kaplan-Meier plot (with log rank test comparing randomized arms) of time 
from randomization to last study visit prior to loss to follow-up (censoring at 28 days 
if completed Day 28 visit or died before 28 days). [OFFSDY2] 
 
4.5 
Study treatment [SDCOMP1] (ITT) 
a. 
Number of days with all study drug reported as taken : number (%) in following 
categories 
 5 days (i.e. completed 5 days) 
 Partial course (i.e. did not complete 5 days) : 0 day to 5 days 
b. 
List:  Reasons for receiving the partial course of treatment or not receiving full 
planned first course of treatment: randomized arm, number of days with all study 
drug reported as taken, site, subject ID, influenza type/subtype by central lab testing, 
reason for not receiving full planned  course of treatment.  
List of subjects who were randomized properly but received wrong 
study treatment: randomized arm, subject ID, site, age, sex, reasons 
for not receiving the correct treatment as assigned.  
 
4.6 
Mortality, Hospitalization[EVENT3 and AE2] (ITT) 
 
a. Number (%) dying showing whether or not the death occurred on or before 28 days 
versus greater than 28 days from randomization.  


Statistical Analysis Plan IRC004 
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b. List of deaths: Randomized arm, days from randomization to death, subject ID, age, 
sex, site, confirmed influenza infection status, days from the last dose of study 
treatment taken to death, primary cause of death, relatedness to study intervention.  
List to include all deaths reported, irrespective of time from randomization to the date 
of death (i.e. including any deaths reported after 28 days).  Sort by randomized arm, 
days from randomization to death and subject ID.   
c. Figure and Analysis: Kaplan-Meier plot of time from randomization to death 
(censoring at Day 28 visit date if completed, or at date of last contact if lost to follow-
up prior to Day 28 visit), with associated table showing: number censored and number 
(%) dying; p-value from log-rank test. 
d. The percentage of subjects dying by 28 days will estimated from the Kaplan-Meier 
curves and Greenwood’s formula for the standard error of this estimate will be used to 
construct 95% confidence intervals for the mortality rates and the difference between 
treatments in the mortality rates. 
e. If the number of hospitalizations is small in one randomized arm, an alternative 
confidence interval will be constructed by inverting an exact binomial test of the actual 
percentages (but ignoring loss to follow-up). 
f. Analyses of time to hospitalization and the derivation of 28-days percentage of 
subjects being hospitalized will be analyzed in a similar manner to that for time to 
death.  
 
4.7 
Safety Analysis 
4.7.1 
Serious Adverse Events (Enrolled population and ITT) 
a. Enrolled Population: Number (%) of subjects with an SAE by MedDRA System 
Organ Class (SOC) and Preferred Term (PT); number (%) of subjects with any SAE.  
This table will include all SAEs, irrespective of time from randomization to the date of 
onset of the SAE (i.e. including any SAEs reported before randomization or after 28 
days).   
 Table repeated to show total number of SAEs (i.e. allowing a subject to be 
represented more than once per row, SOC header, and in total numbers). 
 ITT Population: Number (%) of subjects with an SAE by MedDRA System Organ 
Class (SOC) and Preferred Term (PT); number (%) of subjects with any SAE 
through to the date of the Day 28 visit (or death on/before 28 days). 
 Table repeated to show total number of SAEs (i.e. allowing a subject to be 
represented more than once per row, SOC header, and in total numbers). 
b. Enrolled Population: List of SAEs: Randomized arm, days from randomization to first 
SAE experienced by a subject, subject ID, site, confirmed influenza infection status, 
days from randomization to the date of the SAE, days from first and from last dose of 
study treatment to the date of SAE, SAE (MedDRA SOC and PT, and verbatim 
description), severity grade, relatedness to study intervention, outcome (e.g. 
died/resolved/ongoing) (sort by randomized arm, days from randomization to first 
SAE, subject ID, and, if a subject has multiple SAEs, days from randomization to 
SAE). 
 


Statistical Analysis Plan IRC004 
Page 11 of 17  
4.7.2 
Adverse Events (Enrolled population, and ITT) 
a. Enrolled Population: Number (%) of subjects with an AE (as defined above) by 
MedDRA System Organ Class (SOC) and Preferred Term (PT); number (%) of 
subjects with all AEs irrespective of time since randomization (i.e. including any 
reported before randomization or after Day 28).   
 Table repeated to show total number of AEs (i.e. allowing a subject to be 
represented more than once per row, SOC header, and in total numbers). 
b. ITT Population: Number (%) of subjects with an AE (as defined above) by MedDRA 
System Organ Class (SOC) and Preferred Term (PT); number (%) of subjects with all 
AEs from Day 0 to Day 28. 
 Table repeated to show total number of AEs (i.e. allowing a subject to be 
represented more than once per row, SOC header, and in total numbers). 
c. ITT Population: Number (%) of subjects with an AE (as defined above) by MedDRA 
System Organ Class (SOC) and Preferred Term (PT); number (%) of subjects with all 
related AEs (definitely related, probably related, possibly related) from Day 0 to Day 
28. 
 Table repeated to show total number of AEs (i.e. allowing a subject to be 
represented more than once per row, SOC header, and in total numbers). 
d. Enrolled Population: List of AEs: Randomized arm, days from randomization to first 
AE experienced by a subject, subject ID, site, confirmed influenza infection status, 
days from randomization to AE, days from last dose of study treatment, AE 
(MedDRA SOC and PT, and verbatim description), severity grade, relatedness to 
study intervention, outcome, e.g., died/resolved/ongoing, sorted by randomized arm, 
days from randomization to first AE, subject ID, and, if a subject has multiple AEs, 
days from randomization to AE. 
 
4.8 
Efficacy Analysis 
The following efficacy analyses will be presented for the Primary Efficacy Population (study 
participants with confirmed influenza) and also for the Intent to Treat Population. The primary 
analysis of the primary endpoint will exclude the 50 subjects enrolled in the pilot study.  A 
secondary analysis will, however, be undertaken which includes these 50 subjects. All analyses 
of secondary efficacy endpoints will be undertaken including the 50 subjects enrolled in the pilot 
study.   
 
4.8.1 
Primary Endpoint [IRCRSLT] (population for the primary analysis and PEP) 
The primary endpoint is defined as the percentage of subjects shedding virus by PCR in 
nasopharyngeal swabs obtained at Day 3.     
a. Completeness of viral shedding results showing number (%) at Day 0, 3 and 7 who: 
 had qPCR result  
 were lost to follow-up prior to the visit 
 were in follow-up but had missing value 
b. Primary Analysis: Among subjects with Day 3 qPCR results, number (%) with 
detectable viral shedding at Day 3. Comparison of randomized arms with associated 
95% confidence interval and p-value based on the normal approximation to the 
binomial distribution. 


Statistical Analysis Plan IRC004 
Page 12 of 17  
c. Sensitivity Analyses (PEP only): to assess potential impact of missing measurements. 
Repeat the primary analysis (above) considering missing measurements in turn as (a) 
above the limit of detection, or (b) below the limit of detection, or (c) above the limit 
of detection in one randomized arm and below in the other arm (so as to maximize the 
difference between arms), or (d) the opposite of (c) (so as to minimize the difference 
between arms). 
d. Sensitivity Analyses (PEP only): Repeat the primary analysis above but restricted (a) 
to samples in which one or more housekeeping genes had detectable levels (hence 
indicating adequate sample); and (b) to samples in which all housekeeping genes had 
detectable levels. 
e. Subgroup Analyses (PEP only): Comparison of randomized treatments will be 
undertaken by sex (male vs female), influenza type (A vs B), and country/race 
(US/white vs US/non-white vs Thailand vs other countries).  To assess whether the 
difference between randomized treatments varies by subgroup, a treatment by 
subgroup interaction test will be undertaken using logistic regression.   
 
4.8.2 
Secondary Endpoints: Virologic Endpoints [IRCRSLTS]  (PEP and ITT) 
Viral shedding will be assessed by quantitative RT-PCR (reported as log10 RNA copies/mL) with 
measurements obtained on Days 0, 3, and 7.  These measurements will be used to define the 
following variables: 
a. Figure and associated table showing number (%) of subjects who had values <LOD, 
LOD-<LLOQ, ≥LLOQ at each visit. 
b. Figure and associated table showing number of subjects and minimum, maximum, 
median, 25% and 75% percentile of the value of viral shedding at each visit (subjects 
with values <LOD will be ranked as lower than detectable values in this analysis; 
minimum and maximum in table only). Comparison of randomized arms at each of 
Day 3 and Day 7 will be based on the extension of Wilcoxon’s test to handle censoring 
of measurements which are <LLOQ.  
c. Number (%) of subjects with undetectable viral load at both Day 3 and Day 7;  
detectable at Day 3 and undetectable at Day 7; detectable at Day 7 (irrespective of 
whether or not detectable at Day 3).  Analysis will be restricted to subjects with 
measurements at both Day 3 and Day 7.  Comparison of percentages of subjects in this 
table using the Wilcoxon Test.  
d. Above tables/figures/analyses will be repeated for the subset of subjects who had 
detectable viral load at Day 0. 
 
 
4.9 
Secondary Endpoints: Clinical Endpoints [DIARY1] (PEP and ITT) 
Many of the clinical endpoints rely on data collected on diary cards completed by the 
study participants.  The subjects are asked to complete these twice a day (at 8AM and 
8PM) on Days 0 through 14 and then again on Day 28.  Fever is recorded for the 
preceding 12 hour period at both times each day, and symptoms are recorded at both 
times for Days 0 to 7 and then once daily on Days 8 to 14. Functional status (based on the 
Physical Function domain questions from the SF-36) and two questions giving a global 
assessment of status are completed daily at 8AM. 


Statistical Analysis Plan IRC004 
Page 13 of 17  
 
a. Duration of clinical symptoms. Duration of clinical symptoms is defined as the 
time from Day 0 to the first of two successive measurements at which all clinical 
symptoms are grade 0 (absent) or 1 (mild).  A measurement is considered to be 
the 8AM or 8PM assessment during Days 0 to 7 (so two measurements are 
obtained per day) and then the daily assessment thereafter.  Time will then be 
calculated in half-days through to Day 7.  For the purposes of defining the 
endpoint, if the subjects’ first two assessments on (baseline assessment and first 
subsequent diary card assessment) satisfy this criterion, then the duration will be 
set to zero.  Missing values will be ignored [this is equivalent to assuming that a 
missing value would have (a) indicated at least one grade 2+ symptom if the 
preceding record includes a grade 2+ symptom or if the first Day 0 value is 
missing; (b) indicated no grade 2+ symptoms if the preceding and succeeding 
assessments show no grade 2+ symptoms; and (c) indicated a grade 2+ symptom 
if the preceding assessment shows no grade 2+ symptom and the succeeding value 
shows a grade 2+ symptom].  Times will be considered as discrete (i.e. based on 
the schedule of completion of diary cards) and subjects not having two succeeding 
assessments with only grade 0 or 1 symptoms at any time during follow-up will 
be censored immediately after Day 14 (the last scheduled measurement time on 
which an endpoint can occur). 
 
 Kaplan-Meier plot (and associated table) of the percent of subjects without 
clinical symptoms per the above definition over time, with the median 
duration of time to alleviation of such symptoms and its 95% confidence 
interval. 
 P-value comparing randomized arms from the log rank test. 
 Sensitivity analyses assuming (a) that missing values would include grade 2+ 
symptoms, (b) that missing values would not include grade 2+ symptoms, (c) 
that missing values would include grade 2+ symptoms in one randomized arm 
and would not include grade 2+ symptoms in the other arm (so as to maximize 
the difference between arms), and (d) the opposite of (c) (so as to minimize 
the difference between arms). 
 
Note: Secondary analyses restricting to those with at least one grade2 (moderate) 
or grade 3 (severe) clinical symptom based on the Diary Card at randomization, 
will be conducted for section a described above. 
 
b. Absence of fever Time to the absence of fever is defined as the time from Day 0 
to the first of two successive assessments (through to Day 7) or the first 
assessment (Day 8 to Day 28) at which no fever ≥38.0°C is reported during the 
prior 12 hours and no antipyretics have been taken during the 24 hours. Time will 
then be calculated in half-days through to Day 7.  For the purposes of defining the 
endpoint, if the first two assessments on Day 0 or 1 satisfy this criterion, then the 
duration will be set to zero.  Missing values will be ignored [this is equivalent to 
assuming that a missing value would have (a) indicated fever if the preceding 
record includes fever or if the first Day 0 value is missing; (b) indicated no fever 


Statistical Analysis Plan IRC004 
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if the preceding and succeeding assessments show no fever; and (c) indicated 
fever if the preceding assessment shows no fever and the succeeding value shows 
fever].  Times will be considered as discrete (i.e. based on the schedule of 
completion of diary cards) and subjects not having a 24-hour period without fever 
at any time during follow-up will be censored immediately after Day 14 (the last 
scheduled measurement time on which an endpoint can occur). 
 
 Analysis for duration of fever will follow the same approach as for duration of 
clinical symptoms. 
 
c. Resolution of Symptoms and Fever. Time to resolution of all symptoms AND 
Fever is defined as the time from Day 0 to the first of two successive 
measurements at which all clinical symptoms are grade 0 (absent) or 1 (mild) and 
no fever ≥38.0°C is reported during the prior 12 hours and no antipyretics have 
been taken during the 24 hours. 
 
 Analysis for duration of clinical symptoms and fever will follow the same 
approach as for duration of clinical symptoms. 
 
 
d. Global assessment:  Times to “feeling as good as you did before you had the flu” 
and “functioning as well as you did before you had the flu” will be defined as the 
times of two successive measurements with “yes” responses to the respective 
global assessment questions. 
 
 The details of the definition, handling of missing values and analysis will 
follow that for duration of clinical symptoms. 
 
e. Functional status: This is assessed using the 10-item domain of Physical Function 
from the SF-36, and calculated as the average of the scores of all 10 items.  
Functional status is evaluated daily through to Day 14 and then at Day 28. 
 
 Scoring, including handling of missing values, will be undertaken per the 
standard instructions for the RAND 36-Item Health Survey 1.0 instrument 
(located at: 
http://www.rand.org/health/surveys_tools/mos/mos_core_36item_scoring.htm
l ).  If all 10 components are not scored, the pre-illness functional status will 
be scored as missing. 
 
 Figure and associated Table: Median, 25th and 75th percentiles, (and min and 
max value in table), with sample size, at each required measurement time. 
 
 Figure and associated Table: Median, 25th and 75th percentiles, (and min and 
max value in table), with sample size, change from Day 0 at each required 
measurement time. 
 


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 Statistical comparison between randomized arms of changes in score will be 
undertaken at Days 3, 7, 14 and 28 using Wilcoxon’s test.  
 
 Time to return of physical function to pre-illness level is defined as the time 
from Day 0 to the first of two successive measurements at which the physical 
function score equals or is better than the pre-illness score (obtained by recall 
at enrollment).  Time will be calculated in daily increments through to Day 
14.  For the purposes of defining the endpoint, if a subject’s Day 0 and Day 1 
assessments satisfy this criterion, then the duration will be set to zero.  
Missing values will be ignored.  Times will be considered as discrete (i.e. 
based on the schedule of completion of diary cards) and subjects not having 
two successive assessments with scores equal to or better than the pre-illness 
score will be censored immediately after Day 14 (the last scheduled 
measurement time on which an endpoint can occur). 
 
 Kaplan-Meier plot (and associated table) of the percent of subjects returning 
to pre-illness level per the above definition over time, with the median 
duration of time to return and its 95% confidence interval. 
 
 P-value comparing randomized arms from the log rank test. 
 
f. The following outcomes are targeted in the protocol: 
 
 Bronchitis / bronchiolitis 
 Pneumonia 
 Other complications 
 
For each of these, the percentage of subjects experiencing the event during 
follow-up will be obtained with the associated 95% confidence interval and 
comparison of arms will be based on the normal approximation to the binomial 
distribution, or exact methods based on the binomial distribution if numbers are 
small. 
 
4.9.1 
Association of viral shedding to clinical symptoms and fever (PEP and ITT) 
Association between viral shedding and clinical symptoms and fever is listed as a 
secondary objective.  The analysis depends on what is seen in virology results, and 
therefore the analysis is not presented in this analysis plan.  The planned analysis will be 
detailed in a later analysis plan.  
 
4.10 
Evaluation of self-collected samples (PEP and ITT) 
Self-collected NP are collected on Day 0 (prior to treatment initiation), Day 0 evening, 
Day 1, Day 1 evening, Day 2, Day 2 evening and Day 3. Viral shedding will be assessed 
using these self-collected swabs by the same assay used for the team collected swabs, i.e., 
quantitative RT-PCR (reported as log10 RNA copies/mL).  


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a. Completeness of viral shedding results showing number (%) at Day 0, Day 0 evening, 
Day 1, Day 1 evening, Day 2, Day 2 evening and Day 3 who: 
 had swab taken (i.e. submitted) 
 had qPCR result  
 died prior to visit 
 were lost to follow-up prior to the visit 
 were in follow-up but had missing value 
 
b. Among subjects with Day 3 qPCR results, number (%) with detectable viral shedding 
at Day 3. Comparison of randomized arms with associated 95% confidence interval 
and p-value based on the normal approximation to the binomial distribution. 
This table can be compared to table 4.8.1a, the primary endpoint, to determine if the 
self-swabs would have similar treatment effects 
 Repeat analysis in the population for the primary analysis (PEP  excluding 
pilot study) to allow direct comparison with primary endpoint.  
 
c. Bland-Altman plot showing the agreement between the result from the self-collected 
swabs and team-collected swabs across all available swabs 
 
d. Bland-Altman plot showing the agreement between the result from the self-collected 
swabs and team-collected swabs on Day 0 and Day 3.  
 
e. Table: Mean, standard deviation, median, min, max, 25% and 75% percentiles of the 
viral load difference between self-collected swabs and team-collected swabs on Day 
0, Day1, Day 2 and Day 3. P-values comparing the difference based on normal 
approximation or Wilcoxon signed rank test, as appropriate for the data.  
 
f. Plots of associations between viral load based on self-collected swabs and viral load 
based on team-collected swabs on Day 0, Day 1, Day 2 and Day 3. Spearman 
correlation coefficients, along with their 95% confidence intervals, will be provided. 
Plots of associations and estimated correlation coefficients will be provided both over 
all subjects and by strata defined by quartile of the viral load based on team-collected 
swabs at each time point.  
  
g. AUCs will be calculated for the self-collected swabs.  This is defined as the area 
below the line formed by joining the measured values at each successive scheduled 
measurement time and above the limit of detection.  This will be calculated using the 
trapezoidal rule.  Missing values will be ignored (this is equivalent to imputing a 
missing value using linear interpolation between the previous and succeeding 
available values).  If the Day 0 value is missing, then the subject will be excluded 
from the analysis.  
 Figure and associated table showing number of subjects and minimum, 
maximum, median, 25% and 75% percentile of the value of viral shedding at 
each scheduled measurement time.  This will be presented (a) imputing values 


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as defined above for the calculation of AUC, and (b) using observed values 
only. 
 Table showing number of subjects and minimum, maximum, median, 25% 
and 75% percentile of the AUC, both over all subjects and by strata defined 
by quartile of Day 0 measurement. 
 P-value comparing randomized arms from Wilcoxon rank sum test stratified 
by quartile of Day 0 measurement. 
 
 
4.11 
Emergence of antiviral resistance. (ITT) 
Due to technical demands and cost of sequencing, resistance will be evaluated only in subjects 
that have virus present at Day 7, i.e., subjects that stop viral shedding by Day 7 will be 
considered as not having clinically significant resistance. All subjects with virus isolated at Day 
7 will have Day 0 and 7 samples evaluated by DNA Sequencing (Sanger method) of M2, NA and 
HA genes.  As this is primarily descriptive data of genetic sequences, and not statistical analysis, 
this data will be presented in a separate report.   
a. Number (% of subjects with Day 7 measurement) of subjects with detectable viral 
shedding at Day 7. 
b. The number (% of number) of subjects with samples sequenced. 
c. The number (% of number) of subjects with detectable viral load, but were not 
sequenced as the viral load was near the limits of quantification (suggesting resistance 
is unlikely). 
d. Listing, separated by strain (H1N1, H3N2, and B) of subject ID, study day, viral load, 
amino acid substitutions tested (those known to convey amantadine or oseltamivir 
resistance), amino acids detected in the sample at the given position. 
e. Interpretation if any amino acid substitutions detected are likely to confer resistance 
(based on literature review).