INA-RESPOND Observational Research on Infectious Disease Outbreaks and Difficult Cases of Unidentified Etiology in Indonesia
Conditions: Infectious Disease
Sponsor: Ina-Respond

 
 
 
 
 
   
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Protocol Number: INA107 
INA-RESPOND Observational 
Research on Infectious Disease 
Outbreaks and Difficult Cases of 
Unidentified Etiology in Indonesia 
      
Version: 1.3 
05 July 2021 
 
Sponsored by: 
Centre for Research and Development of Health Resources and 
Services, National Institute of Health Research and Development 
(NIHRD), Ministry of Health, Indonesia 
National Institute of Allergy and Infectious Diseases (NIAID), National 
Institutes of Health, United States  
Confidentiality Statement: 
This document is confidential and is to be distributed for review only to 
investigators, consultants, study staff, and applicable independent 
ethics committees or institutional review boards. The contents of this 
document shall not be disclosed to others without written authorization 
from NIAID or NIHRD. 

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Protocol Summary 
Long title 
INA-RESPOND Observational Research on Infectious Disease 
outbreaks and difficult cases of unidentified etiology in Indonesia 
Short title 
INA-ORCHID 
Study 
number 
INA107 
Clinical trial 
identifier 
NCT04339179 
Rationale 
Infectious diseases remain a significant source of morbidity and 
mortality in Indonesia, and sudden disease outbreaks can rapidly 
spread throughout the country and beyond. Containing outbreaks that 
might lead to pandemics is a crucial public health operation that is 
strengthened by clinical research studies on the etiologies, 
epidemiology, clinical manifestations, and case management 
processes of infectious diseases. The INA-RESPOND Network 
maintains an extensive and experienced research presence across 
Indonesia that is capable of conducting research on ongoing 
infectious disease outbreaks and difficult cases of unidentified 
etiology. This protocol will leverage the unique capacity of the INA-
RESPOND Network to rapidly study sudden disease outbreaks, 
difficult infectious disease cases of unidentified etiology, and samples 
collected during historical outbreaks and cases of unknown 
etiologies. The outcomes of this research will significantly improve our 
understanding of circulating diseases in Indonesia, particularly those 
that are most challenging to identify and of greatest outbreak concern. 
Objectives 
Aim 
To understand the scope of pathogens responsible for outbreaks and 
difficult clinical cases in Indonesia, and to characterize the clinical 
course of the diseases to better inform diagnostics, treatments, and 
prevention strategies. 
Objective 
Primary objective: 
To identify the causative agents and describe the clinical 
characteristics of presumptive infections reported during infectious 
diseases outbreaks or referred from difficult cases of unidentified 
etiology in Indonesia. 
Secondary objectives: 
• To describe the disease course and case management of the 
presumptive infections 
• To assess the accuracy of diagnostic tests of the presumptive 
infections 
• To assess treatments and short-term outcomes of the 
presumptive infections 
• To generate epidemiologic data to inform ongoing and future 
disease control and prevention efforts 

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Study 
design 
This is a study to identify the causative agents and describe the 
clinical characteristics of infectious disease outbreaks and difficult 
cases of unidentified etiology in Indonesia. It is a retrospective and 
prospective observational study with an exploratory design. There will 
be no intervention to the participants that is intended to affect their 
standard of care or clinical outcome. 
Retrospective study activities will be ongoing throughout the duration 
of the study. The INA-RESPOND Reference Lab will perform 
research tests on various specimens collected as part of historical 
outbreaks and previous difficult cases where an etiology was never 
identified. 
Prospective study activities will be initiated upon official request from 
health authorities and health facilities/institutions. Requests are 
expected to be filtered through and evaluated by the 20 active INA-
RESPOND Network sites before inclusion in the study. Samples 
collected during outbreaks and from difficult cases of unknown 
etiology will be analyzed at the INA-RESPOND Reference Lab at their 
own pace. Results from any research tests will be shared with the 
requesting authorities as research-use-only and are not intended to 
alter standard of care.  
Sample size This is a 5-year study that will enroll an estimated total of 2,000 
prospective cases, with a ceiling of 4,000 cases if necessary. The 
study will also include an estimated total of 500 retrospective cases, 
with a ceiling of 1,000 cases if necessary. 
Visit 
schedule for 
prospective 
study arm 
of ongoing 
patients 
providing 
informed 
consent 
Study Visit 1: Enrollment and Baseline Visit (Day 0) 
1. Demographics including, but not limited to: sex, age, residence, 
occupation. 
2. Medical history including, but not limited to: travel history, insect 
and animal exposure, vaccination history, medication use prior to 
enrollment. 
3. Clinical data including, but not limited to: current signs and 
symptoms, height and weight, vital signs, comorbidities, 
treatment, clinical outcome at this visit, available SoC laboratory 
or imaging results. 
4. Specimen collection (when possible): whole blood (5-15 mL) 
and clinically indicated non-invasive specimens such as sputum, 
urine, stool, nasopharyngeal swab, etc. Specimens collected 
under SoC can also be included in the study if leftover material is 
shared. 
5. Laboratory testing: routine hematology, blood chemistry, liver 
function tests, and renal function tests. 
Study Visit 2: Follow-Up Visit (between Day 7-14) 
1. Clinical data including, but not limited to: current signs and 
symptoms, height (if previously not done) and weight, vital signs, 
comorbidities, treatment, clinical outcome at this visit, available 
SoC laboratory or imaging results. 
2. Specimen collection (when possible): whole blood (5-15 mL) 
and clinically indicated non-invasive specimens such as sputum, 

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urine, stool, nasopharyngeal swab, etc. Specimens collected 
under SoC can also be included in the study if leftover material is 
shared. 
3. Clinical outcome data at hospital discharge or death (when 
applicable). 
Study Visits After Visit 2, if Needed 
1. Clinical data including, but not limited to: current signs and 
symptoms, height (if previously not done) and weight, vital signs, 
comorbidities, treatment, clinical outcome at this visit, available 
SoC laboratory or imaging results. 
2. Specimen collection (when possible): whole blood (5-15 mL) 
and clinically indicated non-invasive specimens such as sputum, 
urine, stool, nasopharyngeal swab, etc. Specimens collected 
under SoC can also be included in the study if leftover material is 
shared. 
3. Clinical outcome data at hospital discharge or death (when 
applicable). 
Interim Visits as part of Standard of Care 
At any time between study visits, clinical data and leftover specimen 
material collected as part of SoC visits could also be included in the 
study if shared by the attending clinician. These interim visits are 
independent of the study and may or may not occur depending on 
SoC procedures. 
 

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Table of Content 
Protocol Summary ................................................................................................................. i 
Table of Content ................................................................................................................... iv 
List of Figures and Table ....................................................................................................... vi 
List of Abbreviations and Acronyms ..................................................................................... vii 
Protocol Core Team ............................................................................................................ viii 
1. 
Introduction .................................................................................................................... 1 
2. 
Aim and Objectives ........................................................................................................ 2 
2.1. Aim…………. .......................................................................................................... 2 
2.2. Primary objective .................................................................................................... 2 
2.3. Secondary objectives .............................................................................................. 2 
3. 
Research Benefits ......................................................................................................... 2 
4. 
Methods ......................................................................................................................... 3 
4.1. Study Design .......................................................................................................... 3 
4.2. Sample Size and Study Duration ............................................................................ 6 
4.3. Overview of the Study Flow .................................................................................... 8 
4.3.1. Prospective Study .......................................................................................... 8 
4.3.1.1. Ongoing Patients with Difficult Infections of Unidentified Etiology ... 8 
4.3.1.2. Ongoing Patients in Outbreak Situations ........................................ 9 
4.3.2. Retrospective Study ..................................................................................... 10 
4.4. Study Instruments ................................................................................................. 11 
4.5. Prospective Study ................................................................................................. 11 
4.5.1. Eligibility Criteria .......................................................................................... 11 
4.5.1.1. Ongoing patients with difficult infections of unidentified etiology ... 11 
4.5.1.1.1. Inclusion ......................................................................... 11 
4.5.1.1.2. Exclusion........................................................................ 11 
4.5.1.2. Ongoing patients in outbreak situations ........................................ 11 
4.5.1.2.1. Inclusion ......................................................................... 11 
4.5.1.2.2. Exclusion........................................................................ 12 
4.5.2. Visit Schedule and Procedures .................................................................... 12 
4.5.2.1. Study Visit 1: Enrollment and Baseline Visit (Day 0) ..................... 13 
4.5.2.2. Study Visit 2: Follow-Up Visit (Day 7-14) ...................................... 13 
4.5.2.3. Study Visits After Visit 2 ................................................................ 14 
4.5.2.4. Interim Visits as part of Standard of Care ..................................... 14 
4.5.3. End of Study Criteria .................................................................................... 14 
4.6. Retrospective Study .............................................................................................. 15 
4.6.1. Eligibility Criteria .......................................................................................... 15 
4.6.1.1. Inclusion criteria ............................................................................ 15 
4.6.1.2. Exclusion criteria .......................................................................... 15 
4.6.2. End of study criteria ..................................................................................... 15 
4.7. Defining Difficult Cases of Unidentified Etiology .................................................... 15 
5. 
Specimen Collection and Testing ................................................................................. 16 
6. 
Data management and Analysis .................................................................................. 18 
6.1. Data Management ................................................................................................ 18 
6.2. Analysis ................................................................................................................ 19 
7. 
Tracking of Study Decisions......................................................................................... 19 
8. 
Assessment of Safety .................................................................................................. 20 
8.1. Specification of Safety Parameters ....................................................................... 20 

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8.2. Adverse Events .................................................................................................... 20 
8.3. Serious Adverse Events ....................................................................................... 20 
8.4. Unanticipated Problem ......................................................................................... 21 
8.5. Non-Compliance ................................................................................................... 21 
9. 
Safety Events Reporting .............................................................................................. 21 
9.1. Expedited Reporting to IRB .................................................................................. 21 
9.2. Annual Reporting to IRB ....................................................................................... 22 
10. Monitoring and Evaluation ........................................................................................... 22 
11. Human Participant Protection ...................................................................................... 22 
11.1. Ethical Review .................................................................................................... 22 
11.2. Potential Risk and Benefit to the Participants ...................................................... 23 
11.3. Participant Reimbursement ................................................................................. 23 
11.4. Special Population .............................................................................................. 23 
11.5. Informed Consent................................................................................................ 24 
11.6. Premature Withdrawal of a Participant from Study Participation .......................... 25 
11.7. Participant Confidentially ..................................................................................... 25 
12. Principal Investigator Curriculum Vitae ........................................................................ 26 
13. Appendix 1. General Guidance on Specimen Types .................................................... 33 
14. Appendix 2. General Guidance on Specimen Collection, Handling and Processing ..... 34 
15. Appendix 3. Implementing Arrangement on Infectious Diseases Research between US-
NIH and Indonesia-NIHRD ........................................................................................... 46 
16. Appendix 4. Extension of the Implementing Arrangement ............................................ 50 
17. Appendix 5 Molecular and serology tests at the INA-RESPOND Laboratory ................ 52 
 
 
 

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List of Figures and Table 
Table 1 Required sample size for estimating the prevalence of a generic binary outcome over 
a range of desired precision and true underlying prevalences ..................................................... 7 
Figure 2 Study flow for prospective study to ongoing patients with difficult infections of 
unidentified etiology ............................................................................................................................. 8 
Figure 3 Study flow for prospective study to ongoing patients in outbreak situations ............... 9 
Figure 4 Study flow for retrospective study to previously collected samples ............................ 10 
Figure 5 Study timeline for ongoing patients with difficult infections of unidentified etiology. 12 
Figure 6 Flow of specimen testing at the INA-RESPOND Reference Laboratory ................... 18 
 

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List of Abbreviations and Acronyms 
 
AE 
Adverse Events 
BAL 
Bronchoalveolar Lavage 
COVID-19 
Coronavirus Disease 
Co-PI 
Co-Principal Investigator 
CRF 
Case Report Form 
CSF 
Cerebrospinal Fluid 
DNA 
Deoxyribonucleic Acid 
EDMS 
Electronic Document Management System 
ICH-GCP 
International Conference on Harmonization Guidelines for Good 
Clinical Practice 
ICF 
Informed Consent Form 
ID 
Identification 
IEC 
Institutional Ethics Committee 
IgM 
Immunoglobulin M 
INA-RESPOND 
Indonesia Research Partnership on Infectious Diseases 
IRB 
Institutional Review Board 
LAR 
Legally Accepted Representative 
MERS 
Middle East Respiratory Syndrome 
MoH 
Ministry of Health of Indonesia 
MP 
Monitoring Plan 
MTA 
Material Transfer Agreement 
NIAID 
National Institute of Allergy and Infectious Diseases 
NIH 
National Institutes of Health 
NIH-HRPP 
National Institutes of Health Human Research Protection 
Program 
NIHRD 
National Institute of Health Research and Development 
NP 
Nasopharyngeal 
OHRP 
Office for Human Research Protections 
OP 
Oropharyngeal 
PBMC 
Peripheral Blood Mononuclear Cell 
PI 
Principal Investigator 
PII 
Personal Identifiable Information 
RE 
Reportable Event 
RT-PCR 
Reverse Transcription Polymerase Chain Reaction 
SAE 
Serious Adverse Event 
SARS 
Severe Acute Respiratory Syndrome 
UP 
Unanticipated Problem 
VTM 
Virus Transport Media 
 
 
 

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Protocol Core Team 
 
Coordinator  
 
 
: Dr. M. Karyana, MPH 
Principal Investigator 1  
: dr. Dona Arlinda, M.Sc 
Principal Investigator 2  
: dr. Retna Mustika Indah, MPH 
Co-Principal Investigator  
: Dr. Herman Kosasih, Ph.D. 
Co-Principal Investigator  
: Dr. Dewi Lokida, Sp.PK 
 
Investigators 
1. dr. Nurhayati 
2. dr. Tetra Fajarwati 
3. dr. Rossa Avrina 
 
Laboratory Specialists 
1. Ungke Anton Jaya 
2. Wahyu Nawang Wulan 
3. Deni Pepy Butar Butar 
4. Gustiani 
5. Rizki Amalia Sari 
 
Experts  
Experts will be determined on case by case 
basis.  
 
Data Management dan Statistics 
1. Kanti Laras 
2. Santi Maulintania 
3. Dwi Arie Pramanto 
4. Erry Algifarry 
5. Antonius Arditya Pradana  
6. dr. Nugroho Harry Susanto 
 
Secretariat  
1. Meity Siahaan 
2. Yayu Nuzulurrahmah 
3. dr. Venty Muliana Sari 
4. Maria Intan Josi  
5. Neneng Aini 
6. Maria Mila Erastuti 
7. Dedy Hidayat 
8. Yanti Triswan 

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1. Introduction 
Pandemics are large-scale outbreaks of infectious diseases that can significantly 
increase morbidity and mortality over a wide geographic area and cause 
significant economic, social, and political disruption. In the 21st century, the world 
has endured several prominent pandemics caused by severe acute respiratory 
syndrome (SARS) beta coronavirus, influenza A/H5N1, Middle East respiratory 
syndrome (MERS) beta coronavirus, influenza A/H1N1, Ebola virus, Zika virus, 
and currently the 2019 novel beta coronavirus (Covid-19). As pandemics 
generally begin from localized outbreaks, swiftly mitigating emerging outbreaks 
is crucial to global health. While a rapid public health investigation is essential to 
understand the epidemiology, clinical manifestations, and control of the 
suspected diseases, a scientific research response is necessary to 
systematically identify the best diagnostics, treatments, and prevention 
strategies.  
The Indonesia Research Partnership on Infectious Diseases (INA-RESPOND) is 
a nation-wide research network with 20 active hospital sites and a sophisticated 
central research laboratory capable of screening and identifying a variety of 
pathogens. In response to outbreaks, INA-RESPOND can leverage its extensive 
network and scientific experience to conduct the research needed to mitigate 
outbreaks, improve case management, select effective and efficient diagnostic 
tests, and develop treatment and prevention strategies. In addition to housing the 
capacity to conduct research during outbreaks, INA-RESPOND can also conduct 
research on suspected infectious disease cases of unidentified etiology reported 
by clinicians at healthcare facilities. Since outbreak pathogens are often 
unpredictable, and since each outbreak begins with a patient zero, it is important 
to monitor and strengthen the Indonesian healthcare system at all levels to help 
prevent outbreaks before they even begin. 
This observational study will investigate suspected infectious diseases of 
unknown etiology prospectively during outbreaks and at healthcare facilities, and 
retrospectively through historical samples where no etiology was ever 
determined. The study is designed to rapidly, flexibly, and consistently respond 
to any potential scenario in Indonesia, and the data collected will provide needed 

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insight into the landscape of infectious diseases in the country. By better 
understanding the infectious causes of outbreaks and difficult hospitalized cases, 
the Indonesian Ministry of Health will be able to more accurately and efficiently 
control infectious diseases and craft healthcare policies. Additionally, since 
pathogens do not respect regions or borders, the international community will 
benefit from an awareness of potential pandemic pathogens in Indonesia and the 
clinical knowledge generated by this study. 
2. Aim and Objectives 
2.1. Aim 
To understand the scope of pathogens responsible for outbreaks and difficult 
clinical cases in Indonesia, and to characterize the clinical course of the diseases 
to better inform diagnostics, treatments, and prevention strategies. 
2.2. Primary objective 
To identify the causative agents and describe the clinical characteristics of 
presumptive infections reported during infectious diseases outbreaks or referred 
from difficult cases of unidentified etiology in Indonesia. 
2.3. Secondary objectives 
• To describe the disease course and case management of the presumptive 
infections 
• To assess the accuracy of diagnostic tests of the presumptive infections 
• To assess treatments and short-term outcomes of the presumptive infections 
• To generate epidemiologic data to inform ongoing and future disease control 
and prevention efforts 
3. Research Benefits 
▪ 
This study offers no immediate or direct benefit to participants. Participants 
and their physicians may be provided the results of research tests, but any 
decisions related to disease diagnosis, case management, or treatment are 
made at the sole discretion of the attending clinician providing standard of 
care (SoC). 

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▪ 
This study will provide a better understanding of the causative agents, 
clinical characteristics, and epidemiology of reported infectious disease 
outbreaks and difficult cases of unidentified etiology in Indonesia. 
▪ 
This study will generate data to support evidence-based recommendations 
to health authorities for disease diagnostics, treatment, and prevention. 
▪ 
This study will improve the INA-RESPOND Network’s capacity for 
conducting infectious disease research during dynamic outbreak scenarios, 
and it will strengthen the specialization of the Reference Laboratory to 
identify pathogens from very difficult cases of unidentified etiology. 
4. Methods 
4.1. Study Design 
This is a study to identify causative agents and describe clinical characteristics 
of infectious disease outbreaks and difficult cases of unidentified etiology in 
Indonesia. It is a retrospective and prospective observational study with an 
exploratory design. There will be no intervention to the participants that is 
intended to affect their SoC or clinical outcome. An outline of the study flow is 
described in Section 4.3. General guidance on specimen types, collection, 
handling, and processing is described in Appendices 1 and 2. The study is 
registered on ClinicalTrials.gov with identifier NCT04339179. 
Prospective study activities will be initiated upon official request from health 
authorities and health facilities/institutions. Requests are expected to be filtered 
through and evaluated by the 20 active INA-RESPOND Network sites before 
inclusion in the study. Cases will broadly fall into the two categories of difficult 
cases of unidentified etiology and outbreaks. For difficult cases, network sites, in 
consultation with the protocol core team, will first assess referred cases to 
determine whether they meet the criteria for inclusion in the study. If approved 
by the site’s principal investigator (PI) and the study PI and Co-PIs, the cases will 
be included. A documented informed consent or assent from participants with 
parental/legally accepted representative (LAR) consent will be sought prior to 
enrollment and study procedures. Demographics, medical history, clinical data, 
and biological specimens will be collected at study visit 1 (baseline visit at Day 

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0), and clinical data and biological specimens will be collected one time at study 
visit 2 (follow-up visit between Day 7-14), as well as at any necessary study visits 
after Visit 2. Blood samples (5-15 mL) and clinically indicated non-invasive 
samples such as sputum, urine, stool, nasopharyngeal swab, etc., will be 
collected from all participants at each study visit, when possible. If there is 
a risk to the participant’s safety, such as a bleeding disorder, or if the 
maximum allowable limits for sample collection have been reached by SoC 
procedures or other studies, then samples will not be collected. Specimens 
collected under SoC visit(s) could be included in the study if leftover specimen 
material is shared by the attending clinician. Clinical data collected as part of 
SoC visit(s) could also be included in the study if shared by the attending 
clinician. If SoC visits and procedures occur between study visits, the data 
and leftover specimens shared with the study from these visits and 
procedures will be considered as part of interim visits. These interim 
visit(s) are independent of the study and may or may not occur depending 
on SoC. Whenever possible, any specimen material remaining after study testing 
is complete will be cryopreserved and stored indefinitely for future research such 
as, but not limited to, developing and validating diagnostic tests, determining the 
evolution of pathogens, and determining host disease susceptibility. 
For outbreak cases, relevant site PIs and the study PI and Co-PIs will 
communicate closely with health authorities to determine how cases should be 
included in the study. Other subject matter experts and institutions may be 
consulted on a case-by-case basis. When cases are approved for study 
inclusion, data and specimen collection will be guided by the health authorities 
and may differ from data and specimens collected during difficult cases. A 
documented study informed consent will be sought from participants whenever 
possible, in addition to copies of any forms collected by the health authorities that 
have been signed by participants or their LAR. If the study team is unable to 
obtain a documented informed consent for reasons other than the patient 
declining participation in the study, the patient can still be enrolled in the study in 
a de-identified manner. The de-identification process will begin with the MoH, 
who is the sole owner and steward of clinical information collected during 
outbreak investigations. Given the obligation of the MoH to maintain patient 

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privacy, complete patient data will not be shared directly with INA-RESPOND or 
third parties for de-identification. Instead, MoH officials and the core study team 
will jointly review the general data collection form developed and implemented 
by the MoH for that individual outbreak. With consideration for the circumstances 
of the individual outbreak, appropriate data variables that cannot collectively be 
used for identification will be determined and agreed upon, with the final decision 
being left to the MoH. Any data collected by health authorities will then be 
scrubbed of personally identifiable information (PII) so that only the agreed upon 
variables are shared with the study team. Samples collected during outbreaks 
and from difficult cases of unknown etiology will be analyzed at the INA-
RESPOND Reference Laboratory at their own pace. Results from any research 
tests will be shared with the requesting authorities as research-use-only and are 
not intended to alter SoC. Upon approval from the relevant health authorities, 
any specimen material remaining after study testing is complete will be 
cryopreserved and stored indefinitely for future research such as, but not limited 
to, developing and validating diagnostic tests, determining the evolution of 
pathogens, and determining host disease susceptibility. 
Retrospective study activities will be ongoing throughout the duration of the 
study. The INA-RESPOND Reference Laboratory will perform research tests on 
various specimens collected as part of historical outbreaks and previous difficult 
cases where an etiology was never identified in order to identify the causative 
pathogen. Like the prospective arm of the study, retrospective cases will be 
evaluated by the study PI and Co-PIs to determine whether or not to include them 
in the study. If included, cases will be enrolled in a de-identified manner since 
obtaining informed consent is not possible. When the MoH is the owner of the 
samples and associated clinical data, the de-identification process described 
above will be followed. When the samples and associated clinical data are owned 
by another party, such as a university or private research entity, the core study 
team will jointly review the general data collection form used when the samples 
and data were originally collected. With consideration for the circumstances of 
the study or situation under which the data was collected, appropriate data 
variables that cannot collectively be used for identification will be determined and 

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agreed upon, with the final decision being left to the party of primary ownership. 
Samples and available, scrubbed metadata will then be obtained and analyzed. 
Depending on the complexities of the cases referred to this study, more detailed 
study plans, procedures, and CRFs may be developed, including specific or 
additional laboratory procedures not described in the Appendices 1 and 2. The 
plan will be written as an additional document (annex) to this general protocol, 
and the IRB will be notified. 
4.2. Sample Size and Study Duration 
The ORCHID study is an observational study with exploratory design to 
identify pathogenic etiology in outbreaks or difficult cases. There is no 
minimum number of cases that must be recruited in this study since the 
study is a 5-year open protocol to respond to research needs in outbreaks 
or difficult cases. The characteristics of the research is continuous and 
immediately adapts to current situation. The estimated sample size in the 
protocol is the upper limit of subjects that can be recruited for the study, 
based on the resources and capacity of the INA-RESPOND network to fulfil 
the primary and secondary objectives of the study properly. 
This is a 5-year study that will enroll an estimated total of 2,000 prospective 
cases, with a ceiling of 4,000 cases if necessary. The subjects as prospective 
cases will be recruited directly at the research site (in person visit), both in 
outbreak situations and difficult clinical cases. It is anticipated that all 19 INA-
RESPOND sites across Indonesia will participate in the study, which would result 
in approximately 21 patients enrolled per site per year. The study will also include 
an estimated total of 500 retrospective cases, with a ceiling of 1,000 cases if 
necessary. The retrospective cases come from the stored specimen at the 
site in which the etiology is to be determined. 
This study is designed to capture a broad range of diseases instead of a specific 
disease or subset of diseases. Dengue fever and typhoid fever are highly 
prevalent in Indonesia, but this study includes criteria to screen out dengue and 
typhoid in favor of less common and less understood diseases, such as 
rickettsiosis, leptospirosis, chikungunya, and hanta virus infection. Prevalence 

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estimates of these diseases in Indonesia are very poor and frequently unreliable. 
Consequently, the study sample size has been determined based on resource 
availability and INA-RESPOND Reference Laboratory capacity rather than 
expected disease prevalence or anticipated cases of a particular disease.     
This study is not meant to stand alone as a definitive survey of the distribution of 
causative agents of disease in Indonesia. The population from which samples 
are drawn from is likely to vary over both time and site, and testing methodology 
for each sample will be clinically informed and unlikely to follow a common 
algorithm. Thus, the data collected during this study is not intended to be 
analyzed completely together, as it will likely represent a dynamic mix of different 
populations.  
In the scenario that data from this study – or more likely, a subset of data from 
this study – is suitable for analysis, Table 1 summarizing the necessary sample 
size for estimating the prevalence of a generic binary outcome over a range of 
desired precision (+/-) and true underlying prevalence assumptions can be 
utilized. For example, with a true prevalence of 0.10 and a desired precision of 
0.02 (i.e. 95% confidence interval with a width of 0.04), one would require a 
sample size of 865. 
 
Table 1 Required sample size for estimating the prevalence of a generic binary 
outcome over a range of desired precision and true underlying prevalences 
 
 
True prevalence 
0.01 
0.02 
0.05 
0.10 
0.20 
0.50 
Desired 
precision 
(+/-) 
0.01 
381 
753 
1825 
3458 
6147 
9604 
0.02 
96 
189 
457 
865 
1537 
2401 
0.05 
16 
31 
73 
139 
246 
385 
0.10 
4 
8 
19 
35 
62 
97 
0.20 
1 
2 
5 
9 
16 
25 

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4.3. Overview of the Study Flow 
4.3.1. Prospective Study 
4.3.1.1. 
Ongoing Patients with Difficult Infections of Unidentified Etiology  
 
Figure 1 Study flow for prospective study to ongoing patients with difficult infections of unidentified etiology 

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4.3.1.2. 
Ongoing Patients in Outbreak Situations 
 
Figure 2 Study flow for prospective study to ongoing patients in outbreak situations 

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4.3.2. Retrospective Study 
 
 
Figure 3 Study flow for retrospective study to previously collected samples 

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4.4. Study Instruments  
The following instruments will be used in this study:  
a. Forms 
▪ Study informed consent (for prospective investigation) 
▪ Screening log 
▪ Enrollment log 
▪ Case Report Forms 
▪ Electronic data capture systems 
b. INA-RESPOND data and specimen database 
c. INA-RESPOND electronic document management system (EDMS) 
4.5. Prospective Study  
4.5.1. Eligibility Criteria 
4.5.1.1. 
Ongoing patients with difficult infections of unidentified etiology 
4.5.1.1.1. 
Inclusion  
1. Adult or child of any age hospitalized with a current episode of illness with 
a presumed infectious disease of unidentified etiology 
2. Negative for Dengue virus infection by an antigen-based and antibody-
based diagnostic test (i.e. NS1 antigen test and Dengue-specific IgM test) 
3. Negative for Salmonella Typhi infection by Standard of Care testing (i.e. 
blood culture, Widal test, or Tubex rapid test) 
4. Able to provide a documented informed consent 
5. Agrees to the collection and storage of specimens for laboratory testing 
and/or future research (participants may decline storage of specimens for 
future research) 
4.5.1.1.2. 
Exclusion  
1. Investigators’ discretion for patient safety and wellbeing 
4.5.1.2. 
Ongoing patients in outbreak situations 
4.5.1.2.1. 
Inclusion  
1. Adult or child of any age undergoing a current episode of illness with a 
presumed infectious disease of unidentified etiology 
2. Referral from the MoH as part of a suspected or identified outbreak of 
infectious disease 

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4.5.1.2.2. 
Exclusion  
1. None 
4.5.2. Visit Schedule and Procedures 
Clinical and laboratory evaluations will be performed for each participant after 
they have provided a documented informed consent or assent with parental/LAR 
consent. If the study team is unable to obtain a documented informed consent 
for reasons other than the patient declining participation in the study, the patient 
can still be enrolled in the study in a de-identified manner. Any data collected by 
health authorities as part of SoC will be scrubbed of personally identifiable 
information (PII), such as date of birth, residence, and other variables that may 
vary depending on the circumstances and/or scale of the individual outbreak. 
Prior to receiving any patient data, the core study team will consult with the 
relevant health authorities to determine what metadata will be included with the 
de-identified samples. 
See Appendices 1 and 2 for general specimen types and collection guidelines. A 
general study timeline for ongoing patients with difficult infections of unidentified 
etiology is shown in Figure 4. 
 
 
Figure 4 Study timeline for ongoing patients with difficult infections of unidentified 
etiology. 
 

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4.5.2.1. 
Study Visit 1: Enrollment and Baseline Visit (Day 0) 
Eligibility of ongoing patients with difficult infections of unidentified etiology must 
be verified before evaluations begin at the baseline visit (Day 0). If the participant 
is found to be eligible and consents, the participant is considered enrolled in the 
study. Foreign, non-Indonesian patients may also be enrolled in the study, but if 
they return to their home country before study completion, only the follow-up visit 
will not be conducted. This will not be considered a protocol deviation. 
The following procedures will be completed at the baseline visit (Day 0):  
1. Demographics including, but not limited to: sex, age, residence, occupation. 
2. Medical history including, but not limited to: travel history, human, insect and 
animal exposure, vaccination history, medication use prior to enrollment. 
3. Clinical data including, but not limited to: current signs and symptoms, height 
and weight, vital signs, comorbidities, treatment, clinical outcome at this visit, 
available SoC laboratory or imaging results. 
4. Specimen collection (when possible): whole blood (5-15 mL) and clinically 
indicated 
non-invasive 
specimens 
such 
as 
sputum, 
urine, 
stool, 
nasopharyngeal swab, etc. Specimens collected under SoC can also be 
included in the study if leftover material is shared.  
5. Laboratory testing: routine hematology, blood chemistry, liver function tests, 
and renal function tests. 
4.5.2.2. 
Study Visit 2: Follow-Up Visit (Day 7-14) 
The following procedures will be completed at the follow-up visit (one time 
between Day 7-14): 
1. Clinical data including, but not limited to: current signs and symptoms, height 
(if previously not done) and weight, vital signs, comorbidities, treatment, 
clinical outcome at this visit, available SoC laboratory or imaging results. 
2. Specimen collection (when possible): whole blood (5-15 mL) and clinically 
indicated 
non-invasive 
specimens 
such 
as 
sputum, 
urine, 
stool, 
nasopharyngeal swab, etc. Specimens collected under SoC can also be 
included in the study if leftover material is shared. 
3. Clinical outcome data at hospital discharge or death (when applicable). 

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4.5.2.3. 
Study Visits After Visit 2 
Study visits after Visit 2 may be necessary depending on the complexity of the 
ongoing case. Such cases could include those where convalescent specimens 
are needed to definitively identify an etiology, or those where long-term sequelae 
of interest are observed or anticipated. If study visits after Visit 2 are needed, 
then the following procedures will be completed: 
1. Clinical data including, but not limited to: current signs and symptoms, height 
(if previously not done) and weight, vital signs, comorbidities, treatment, 
clinical outcome at this visit, available SoC laboratory or imaging results. 
2. Specimen collection (when possible): whole blood (5-15 mL) and clinically 
indicated 
non-invasive 
specimens 
such 
as 
sputum, 
urine, 
stool, 
nasopharyngeal swab, etc. Specimens collected under SoC can also be 
included in the study if leftover material is shared. 
3. Clinical outcome data at hospital discharge or death (when applicable). 
4.5.2.4. 
Interim Visits as part of Standard of Care 
At any time between study visits, clinical data and leftover specimen 
material collected as part of SoC visits could also be included in the study 
if shared by the attending clinician. These interim visits are independent of 
the study and may or may not occur depending on SoC procedures. 
4.5.3. End of Study Criteria  
1. Completion of de-identified sample analysis 
2. Hospital discharge after Visit 2 
3. Completion of Visit 2 if discharged from hospital prior to Visit 2 
4. Participant or parent/LAR withdraws study participation 
5. Participant is lost to follow-up or moves away from the study area 
6. Participant dies 
7. Participant was inadvertently enrolled 
8. Investigator determines that further participation would be detrimental to 
the health or well-being of the participant 
9. The study is stopped for other administrative reasons 

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4.6. Retrospective Study  
4.6.1. Eligibility Criteria 
4.6.1.1. 
Inclusion criteria 
1. Samples from an adult or child of any age who experienced a presumed 
infectious disease of unidentified etiology 
2. Current episode of illness has ended 
4.6.1.2. 
Exclusion criteria 
1. Positive for Dengue virus infection, if results are available 
2. Positive for Salmonella Typhi infection, if results are available 
4.6.2. End of study criteria 
1. Completion of sample analysis 
2. Depletion of available samples 
4.7. Defining Difficult Cases of Unidentified Etiology 
While this study aims to assist clinicians at the hospitals when they have 
difficult infectious disease of unidentified etiology, it should be clear that 
this is a research study and not simply an advanced diagnostic laboratory. 
Sites may or may not receive etiology results before a patient is discharged 
Several etiologies can only be confirmed using fresh specimens and 
culture, for example, blood culture for sepsis, and urine culture for urinary 
tract infection. Therefore, it is expected that clinicians have conducted the 
search of the pathogens based on the available facilities at their hospitals 
and/or diagnostic laboratories in their region. INA-RESPOND laboratory 
does not have the capacity to test for pathogens that only can be identified 
by these cultures.  
Hospital should also take advantage of any other clinical testing they have 
on-site, such as microscopy or RDTs, so that the patient receives the fullest 
possible benefit. For screening dengue, sites should test for NS1 and 
IgM/IgG antibody using at least rapid diagnostic test and for screening 
typhoid fever using blood culture or tubex (>=6). Although clinicians may 
not think of these diseases as the causes of the diseases, ORCHID requires 
these tests to ensure that our study is not flooded with dengue and typhoid 

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fever as it will reduce the essence of our aim. Furthermore, based on the 
AFIRE study, approximately 20% of unsuspected dengue at the hospitals 
were confirmed dengue at the reference laboratory.  
To accommodate difficult cases that have not been screened for dengue 
and typhoid fever, sites can include these cases in the retrospective 
component of the study. After discussion with the team on site and INA-
RESPOND secretariat, and approval from the chair of INA-RESPOND, 
specimens can be stored at INA-RESPOND sites and sent to INA-RESPOND 
laboratory on a regular basis. However, since retrospective samples will 
not come with the detailed CRF data that the difficult case samples come 
with, they are less ideal. There are also fewer retrospective case spots in 
the study, and the selection process for those samples will naturally be 
much more stringent. 
5. Specimen Collection and Testing 
Specimens included in this protocol will vary depending on the source of the 
participants. For ongoing patients with difficult infections of unidentified etiology, 
all specimens will be collected and handled at each study site by laboratory 
personnel or designees. Appropriate precautions will be determined and followed 
by all personnel in drawing, handling, transporting, and storing of all biological 
specimens. Specimens will be labelled accurately and legibly with a unique 
identifier/code that does not contain any information capable of directly linking 
the specimens to the study participants. Specimens will be logged and tracked 
using an electronic specimen tracking/database system, and only authorized 
personnel will have access to the participant code and the samples. 
For ongoing patients in outbreak situations, specimens will be received from 
designated Ministry of Health authorities unless MoH authorities refer 
participants to the study team to be seen. Specimen type determination and 
collection will occur independently of the study at the judgement of the health 
authorities unless MoH authorities refer participants to the study team to be 
seen. It is expected that participants will provide sample collection consent to 
health authorities but will not be asked to provide study consent unless the 
participants are seen by the study team. Therefore, these participants will be 

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enrolled in a de-identified manner, where coded samples without an identifying 
key are provided to the INA-RESPOND Reference Laboratory for analysis. 
Appropriate precautions will be followed in the handling, processing, and storage 
of all biological specimens, and the de-identified specimens will be logged and 
tracked using an electronic specimen tracking/database system. 
For previously collected specimens to be included in the retrospective arm of the 
study, specimen type determination and collection have occurred independently 
of the study. Unless documented informed consent permitting sample use in 
future research is obtained, these participants will be enrolled in a de-identified 
manner, where coded samples without an identifying key are provided to the INA-
RESPOND Reference Laboratory for analysis. Appropriate precautions will be 
followed in the handling, processing, and storage of all biological specimens, and 
the de-identified specimens will be logged and tracked using an electronic 
specimen tracking/database system. 
Etiology identification for all participants will occur at the INA-RESPOND 
Reference Laboratory. Other relevant clinical laboratory testing requiring freshly 
drawn samples can be completed at the INA-RESPOND study sites. The 
laboratory testing to be completed at the INA-RESPOND Reference Laboratory 
will focus on the identification and/or confirmation of suspected etiologic agents 
in order to meet the objective of the study. Additional, relevant exploratory 
activities may include, but are not limited to, research tests to: a) study immune 
markers that might enable better management or prediction of outcomes for 
patients, b) study pathogenicity, and c) identify genetic markers that may 
increases or decrease disease susceptibility. Routine laboratory tests may also 
be completed as needed. Whenever possible, any specimen material remaining 
after study testing is complete will be cryopreserved and stored indefinitely for 
future research such as, but not limited to, developing and validating diagnostic 
tests, determining the evolution of pathogens, and determining host disease 
susceptibility. 
The sharing of samples and/or data with entities outside of the study will follow 
regulations established in Material Transfer Agreements (MTAs). 

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If the initial testing fails to identify the suspected etiology, the study core team 
may develop and suggest a clinically-informed algorithm for further testing to be 
completed with the remaining specimens (Figure 5).  
 
Figure 5 Flow of specimen testing at the INA-RESPOND Reference Laboratory 
 
At the completion/termination of the study, specimens and data will either be 
destroyed or transferred to another existing protocol following approval from the 
INA-RESPOND Network Steering Committee and relevant IRBs. Any loss or 
unanticipated destruction of samples or data (i.e. due to freezer malfunction) that 
compromises the scientific integrity of the data collected for the study will be 
reported to the IRB.  
The capacity of the INA RESPOND Reference Laboratory for pathogen 
identification will be described in Appendix 5. 
6. Data management and Analysis 
6.1. Data Management 
For ongoing patients with difficult infections of unidentified etiology, participants 
will be coded with a unique identifier that does not contain any information 
capable of linking the data to the study participants. Only authorized personnel 
will have access to the participant code and the data. For ongoing patients in 
outbreak situations and retrospective patients, participants will also be coded 
with a unique identifier that does not contain any information capable of linking 
the data to the study participants. These participants will remain coded and de-

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identified throughout the study since it is anticipated that study informed consent 
will not be obtained. 
Data will be keyed and tracked using OpenClinica, RedCap, or other tools, as 
appropriate. Data will be periodically sent to the central data management center 
of INA-RESPOND and analyzed by the investigator team and approved partners. 
During the study and following study completion, data will be shared with the 
scientific community through peer-reviewed publications and presentations at 
local, national, and international meetings. IRB approval and approval from the 
INA-RESPOND Network Steering Committee must be sought prior to any sharing 
of data. Upon completion of the study, the final de-identified dataset will be made 
available to approved users under a specific data-sharing agreement as soon as 
possible, but no later than the acceptance for publication of the primary research 
manuscript. Any raw genome data and relevant associated metadata will be 
made available to the scientific community through submission to NCBI and 
appropriate databases such as GenBank. All study data will be shared in 
compliance with Indonesian legislation regarding the sharing of human 
participants data. 
6.2. Analysis 
Descriptive analyses will be performed, and data will be summarized using 
descriptive statistics along with appropriate distribution ranges. Continuous 
variables will be summarized using means and standard deviations for normally 
distributed variables, and medians and interquartile ranges for non-normally 
distributed variables. Categorical variables will be summarized with percentages 
in each category. Further specific and appropriate statistical analyses will be 
developed and applied as needed. 
7. Tracking of Study Decisions  
Each decision regarding the study plan, procedures, or analyses will be properly 
documented. This could include, for example, the determination of visit 
schedules, the decisions from laboratory evaluations and their underlying 
reasons, the rules for analyses, etc. 

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8. Assessment of Safety 
8.1. Specification of Safety Parameters 
Participant conditions may vary from healthy to complicated, with various 
underlying etiologies at baseline. Additionally, participant medical management 
will be SoC for those suspected illnesses and complications and will therefore 
not be part of the research process. Only Adverse Events (AEs) related to the 
research procedures, not the underlying disease states of the participants, will 
be followed in this protocol. Serious events not meeting the adverse event 
definition will be logged as Reportable Events (RE) and reported to the IRB within 
10 working days of the investigator’s awareness. 
8.2. Adverse Events 
An adverse event (AE) is any untoward or unfavorable medical occurrence in a 
human participant that occurs within 48 hours of study-related specimen 
collection (i.e. blood draw,) that is possibly, probably, or related to the specimen 
collection. Any event outside of this 48-hour window period will not be considered 
an AE for this study.  
8.3. Serious Adverse Events 
A serious adverse event (SAE) is defined as any AE that is possibly, probably, 
or definitely related to the research and meets one or more of the seriousness 
criteria below:  
• results in death;  
• is life-threatening (places the participant at immediate risk of death from the 
event as it occurred); 
• results in inpatient hospitalization or prolongation of existing hospitalization;  
• results in a persistent or significant disability/incapacity;  
• results in a congenital anomaly/birth defect;  
• results in important medical event based upon appropriate medical judgment 
that may jeopardize the participant’s health and may require medical or 
surgical intervention to prevent one of the other outcomes listed in this 
definition.  
Any event outside the AE definition that meet one/more of the seriousness 
criteria as mentioned above will be reported as Reportable Event (RE). 

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8.4. Unanticipated Problem 
An unanticipated problem (UP) is defined as any incident, experience, or 
outcome that is defined as:  
1. Unexpected in terms of nature, severity, or frequency in relation to:  
• the research risks that are described in the research protocol and informed 
consent document or other study documents; and  
• the characteristics of the participant population being studied; and  
2. Related or possibly related to the participation in the research; and  
3. Places participants or others at a greater risk of harm (including physical, 
psychological, economic, or social harm) than was previously known or 
recognized or is an SAE. 
8.5. Non-Compliance 
Non-compliance is defined as the failure to comply with applicable IRB 
requirements, or regulatory requirements for the protection of human 
participants. Non-compliance is further characterized as 
3. Serious: Non-compliance that: 
• Increases risks or causes harm, to participants. 
• Decreases potential benefits to participants. 
• Compromises the integrity of the National Institutes of Health Human 
Research Protection Program (NIH-HRPP). 
• Invalidates the study data.  
4. Continuing: Non-compliance that is recurring. 
5. Minor: Non-compliance that, is neither serious nor continuing. 
9. Safety Events Reporting 
9.1. Expedited Reporting to IRB 
Serious and non-serious UPs, serious or continuing non-compliance, and deaths 
will be reported within 10 working days of investigator awareness. SAEs that are 
possibly, probably, or definitely related to the research will be reported to the IRB 
within 10 working days of investigator’s awareness, regardless of expectedness. 
REs will be reported annually to IRB. 

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9.2. Annual Reporting to IRB 
The following items will be reported to the IRB in summary at the time of 
Continuing Review: 
• All deaths. 
• Summary of AEs, REs, SAEs, or Ups. 
• Non-compliance. 
• Any trends or events which in the opinion of the investigator should be 
reported. 
10. Monitoring and Evaluation 
The study will be conducted in compliance with this protocol, the International 
Conference on Harmonization (ICH) Guidelines for Good clinical Practice (GCP) 
and any applicable regulatory requirements. Independent monitors, under 
contract by the Sponsor, will visit the clinical research site to monitor the study 
implementation in accordance with the appropriate regulations. The details of 
monitoring visits will be described in Monitoring Plan (MP). The objectives of a 
monitoring visit, among others, will be:  
1. To verify the consistency of each participant’s records with the source 
documents. 
2. To ensure the compliance of study procedures to the protocol. 
3. To ensure the completeness and accuracy of records. 
4. To verify the prompt reporting of all data points, including reporting SAEs.  
The site investigator (or designee) will make the study documents (e.g., ICFs and 
CRFs) and pertinent hospital or clinical records readily available for inspection 
by the local institutional review board/ethics committee (IRB/IEC), the local and 
national regulatory authorities, and the site monitors for confirmation of the study 
data. 
11. Human Participant Protection 
11.1. Ethical Review 
Prior to implementation, the study protocol or a more specific study plan or 
procedures and any written information to be provided to participants for this 

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study will be submitted for approval to the appropriate IRB. Records of the IRB 
review and approval of all the documents pertaining to the study will be kept on 
file by the site investigator and will be made available for inspection at any time 
during the course of the study. Continuing reviews, including a study progress 
report will be submitted according to the requirement of the appropriate IRB, but 
not less than once a year at a minimum. 
11.2. Potential Risk and Benefit to the Participants 
Potential risks will include, but not limited to: 
• Risks inherent to specimen collection procedures, such as blood draw risk. 
The risks of blood drawing are minimal and consist of mild discomfort and or 
bleeding at the finger prick site, feelings of dizziness or faintness, bruising, 
swelling, and rarely fainting or local infection. Other risks will be detailed in 
the additional study plan/procedures that will be developed in response to the 
related outbreaks or referred infectious disease cases. 
Potential benefits will include, but not limited to: 
• Increasing health awareness. Participants may become more aware of their 
health, aided by contact by the study team to their doctor. 
• Increasing access to health care. Participants may become more aware of 
services that are available for infectious diseases. They may also have easier 
access to such services, by virtue of being integrated into the health care 
system. 
11.3. Participant Reimbursement 
Participant time and transportation cost to participate in the study will be 
reimbursed in accordance with the IRB approval. 
11.4. Special Population 
Pregnant and lactating women, adolescents, children of any age will be included 
in this study as needed. They will be managed according to the standard of care. 
There will be no investigational treatment or intervention assigned by this study. 
The study site team will ensure that their participation remains voluntarily without 
being coercive. The participants may withdraw participation from the study at any 
time for any reason. 

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11.5. Informed Consent  
Informed consent is a process in which information is presented to enable 
persons to voluntarily decide whether or not to participate as a research 
participant. It is an ongoing conversation between the human research 
participant and the researchers covering the essential information about the 
study which begins before consent is given and continues until the end of the 
participant’s involvement in the research.  
Informed consent forms (ICFs) describing in detail the purpose of the study, 
duration, procedures, alternatives, risks, and benefits are given to the participant 
and a documented informed consent is required prior to starting any study 
procedures. ICFs will be IRB-approved and the participant will be asked to read 
and review the document. Participants will have the opportunity to ask questions 
about the study and have their questions answered. The participants should have 
the opportunity to discuss the study with their surrogates or think about it prior to 
agreeing to participate. The participants may withdraw from study participation at 
any time throughout the course of the study. The rights and welfare of the 
participants 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 this study, participants may decline to have specimens stored for 
future research and/or genetic testing. 
Literate participants will document their provision of informed consent by signing 
their ICF. In case of illiterate participants, an oral consent will be obtained. The 
investigator or designee that perform the oral consent will sign and date the ICF. 
An impartial literate witness should be present during the entire informed consent 
discussion and should sign and date the ICF. The illiterate participants will be 
asked to document their informed consent by marking their ICF with a thumbprint 
in the presence of a literate witness. 
In case of minor participants, assent with parental or legally accepted 
representative (LAR) consent will be obtained and documented from those who 
are capable of providing assent. Informed consent for those under the age of 
consent will be provided by their parents/LAR. Once the child reaches the age of 
consent, they will be re-consented to this study. 

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In case of severely ill participants, informed consent will be obtained by LAR 
(Legally Authorized Representative) and at first opportunity of well episode, the 
participant will be reconsented. 
11.6. Premature Withdrawal of a Participant from Study Participation 
Participants may voluntarily withdraw from the protocol at any point in the study. 
Attempts will be made to determine the reason that the participant wishes to 
withdraw. 
11.7. Participant Confidentially 
All records will be kept confidential to the extent provided by the law. Records 
will be kept in a locked cabinet, and all computer entry and networking programs 
will be done with coded numbers only. Hospital information, attributable to the 
participant, will not be released without written permission of the participant, 
except as necessary for monitoring, the IRB/IEC, or Office for Human Research 
Protections (OHRP). The study monitors and other authorized representatives 
may inspect all documents and records required to be maintained by the site 
investigator, including, but not limited to, medical records. The results of the 
research study may be published according to the INA-RESPOND policy, but 
participant names or identities will not be revealed. 
 

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12. Principal Investigator Curriculum Vitae 
DONA ARLINDA 
 
 
Name 
: Dona Arlinda 
 
Sex 
: Female 
Date of birth 
: 05/December/1979 
Nationality 
: Indonesia 
Home 
address 
: Jalan Pipit 2 No. 183 RT. 06/10 
Perumnas Depok Jaya, Kota Depok, 
Jawa Barat, Indonesia – 16432  
Phone 
: Home +62-21-7521300 
Mobile +62-811813632 
Email 
: arlindona@ina-respond.net 
arlindona1@gmail.com  
arlindona@litbang.depkes.go.id  
Language 
: English (Professional level) 
Bahasa Indonesia (Native) 
 
Education 
 
2019  
Thammasat University  
Bangkok, Thailand 
 
M.Sc., Bioclinical Science (Pharmacology and Toxicology) 
2003 
Universitas Indonesia  
Indonesia 
 
MD. 
2001  
Universitas Indonesia  
Indonesia 
 
Bachelor of Medicine  
 
Work 
 
2011 – present  National Institute of Health Research and Development 
(NIHRD), Ministry of Health of Indonesia 
Jakarta, Indonesia 
 
Gedung 3 Lantai 1 Badan Litbangkes, Kementerian Kesehatan RI  
Jalan Percetakan Negara No. 29, Jakarta, Indonesia – 10560 
Phone: +62-21-4244375 
 
Researcher 
2003 – 2011  
Medical Emergency Rescue Committee (MER-C) 
Jakarta, Indonesia 
 
Jalan Kramat Lontar No. J-157 Paseban, Jakarta, Indonesia – 10440  
 
General Practitioner 
2003 – 2011  
Allia Health Clinic 
Depok, Indonesia 
 
Jalan Limo Raya, Kota Depok, Jawa Barat, Indonesia 
 
General Practitioner 
 
 

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Trainings/Conferences/Seminars 
 
2019 
Indonesia Research Partnership on Infectious Diseases 
(INA-RESPOND) 
Jakarta, Indonesia 
 
Protocol Writing Workshop  
2018 
Indonesia Research Partnership on Infectious Diseases 
(INA-RESPOND) 
Jakarta, Indonesia 
 
HIV Training 
2018 
Indonesia Research Partnership on Infectious Diseases 
(INA-RESPOND) 
Jakarta, Indonesia 
 
Research Ethics Workshops 
 
2018 
Indonesia National Agency of Drug and Food Control 
Jakarta, Indonesia 
 
Good Clinical Practice 
2017 
International AIDS Society (IAS) 
Paris, France 
 
9th IAS Conference on HIV Science 
2017 
International Antiviral Society – USA 
Seattle, USA 
 
Conference on Retroviruses and Opportunistic Infections (CROI) 
2016 
American Thorasic Society (ATS) – Indonesian Society of 
Respirology 
Jakarta, Indonesia 
 
Methods in Epidemiologic, Clinical and Operations Research (MECOR) 
2015 
Nagasaki University 
Nagasaki, Japan 
 
Product Research and Development Course 
2015 
Faculty of Medicine Universitas Gadjah Mada – WHO 
Tropical Disease Research (TDR)  
Yogyakarta, 
Indonesia 
 
Good Clinical Laboratory Practice 
2014 
Forum for Ethical Review Committees in the Asian & 
Western Pacific Region (FERCAP) – Thammasat University  
Bangkok, Thailand 
 
Research Ethics and Responsible Research Course 
2014 
Southeast Asian Ministers of Education Regional Centre 
for Food and Nutrition (SEAMEO-RECFON) 
Jakarta, Indonesia 
 
Research Methodology Course 
2014 
Indonesia Research Partnership on Infectious Diseases 
(INA-RESPOND) 
Jakarta, Indonesia 
 
Manuscript Writing Workshop 
2013 
Southeast Asian Ministers of Education Regional Centre 
for Food and Nutrition (SEAMEO-RECFON) 
Jakarta, Indonesia 
 
Biostatistics Course 
2011 
Indonesian Clinical Epidemiology and Evidence Based 
Medicine (ICE-EBM) Network 
Jakarta, Indonesia 
 
Basic Concept of Evidence-Based Medicine Workshop 
 
 
 
 
 
 

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Research Experience 
 
2018 – present  Indonesia Research Partnership on Infectious Diseases 
(INA-RESPOND) 
Jakarta, Indonesia 
 
D2EFT-Indonesia Research Project Coordinator 
Dolutegravir and Darunavir Evaluation in adults Failing Therapy 
2018 – present  Indonesia Research Partnership on Infectious Diseases 
(INA-RESPOND) 
Jakarta, Indonesia 
 
Schistosomiasis Research Project Coordinator 
Validation of the Schistosomiasis Point-of-Care Circulating Cathodic Antigen 
(POC-CCA) Rapid Urine Test for Qualitative Detection of Schistosoma japonicum 
2017 – present  Indonesia Research Partnership on Infectious Diseases 
(INA-RESPOND) 
Jakarta, Indonesia 
 
HIV Research Project Coordinator 
A Prospective Observational Cohort on HIV Infection and Risk-Related 
Coinfections/Comorbidities (INA-PROACTIVE) 
2015 – 2017  
National Institute of Health Research and Development 
(NIHRD) – Thammasat University 
Jakarta, Indonesia 
 
Principal Investigator 
Validation and Application of a Liquid Chromatography/ Tandem Mass 
Spectrometry (LC-MS/MS) Assay for Quantification of Dihydroartemisinin and 
Piperaquine in Plasma of Healthy Adults 
2014 – 2016  
National Institute of Health Research and Development 
(NIHRD) 
Jakarta, Indonesia 
 
Co-Investigator 
Hospital-based Tuberculosis-Diabetes Registry in Indonesia 
2013 – 2014  
National Institute of Health Research and Development 
(NIHRD) 
Jakarta, Indonesia 
 
Principal Investigator 
Systematic Review and Meta-Analysis of Inhaled Combination Therapy of 
Budesonide+Formoterol Versus Fluticasone+Salmeterol in Asthma  
2013 – 2014  
National Institute of Health Research and Development 
(NIHRD) 
Jakarta, Indonesia 
 
Principal Investigator 
Literature Review of Frambusia: A Neglected Tropical Disease 
2012 – 2013  
National Institute of Health Research and Development 
(NIHRD) 
Jakarta, Indonesia 
 
Principal Investigator 
Management of Type 2 Diabetes Mellitus in Primary Health Centers in Depok, 
West Java, Indonesia 
2012 – 2014  
National Institute of Health Research and Development 
(NIHRD) 
Jakarta, Indonesia 
 
Co-Investigator 
Hospital-based Stroke Registry in Indonesia 
2011 – 2012  
National Institute of Health Research and Development 
(NIHRD) 
Jakarta, Indonesia 
 
Technical Coordinator, Baubau District, South-East Sulawesi 
National Health Facilities Research 
 

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Publication 
 
2018 
Indonesian Society of Tropical and Infectious Diseases  
Bandung, Indonesia 
 
Oral presentation 
HIV Infection in Hospitalized Patients with Acute Fever in Indonesia 
2018 
Lembaga Penerbit Badan Penelitian dan Pengembangan 
Kesehatan  
Jakarta, Indonesia 
 
Book 
Panduan Penulisan Ilmiah (A Guide to Scientific Writing) 
2018 
International Conference on Interdisciplinary 
Academic Research and Innovation (IARI) 
Banjarmasin, 
Indonesia 
 
Proceeding 
Establishment of a Liquid Chromatography/Tandem Mass Spectrometry (LC-
MS/MS) Assay for Quantification of Dihydroartemisinin in Plasma for Monitoring 
of Antimalarial Resistance in Indonesia 
2017 
International Conference on Global Health (ICGH)  
Jakarta, Indonesia 
 
Poster presentation 
Assessment of Hospital Readiness for a Prospective Observational Cohort Study 
on HIV Infection and Related Coinfections/Comorbidities in Indonesia 
2017 
Media Litbangkes 
Indonesia 
 
Journal article 
Perbedaan Faktor Sosiodemografi Dan Status Gizi Pasien Tuberculosis Dengan 
Dan Tanpa Diabetes Berdasarkan Registry Tuberkulosis-Diabetes Melitus 2014  
(Differences in Sociodemographic Factors and Nutrition Status of Tuberculosis 
Patients With and Without Diabetes based on Tuberculosis-Diabetes Mellitus 
Registry 2014) 
2017 
Media Litbangkes 
Indonesia 
 
Journal article 
Pengaruh Diabetes Melitus terhadap Gambaran Klinis dan Keberhasilan 
Pengobatan Tuberkulosis di Tujuh RSU Kelas A dan B di Jawa dan Bali 
(The Effects of Diabetes Mellitus to Clinical Characteristics and Successful 
Treatment of Tuberculosis in Seven Public Hospitals Class A and B in Java and 
Bali) 
2017 
American Society of Tropical Medicine and Hygiene 
(ASTMH) 
Baltimore, USA 
 
Oral presentation 
Unfavorable Tuberculosis Outcome Associated with HIV, Drug Resistance, and 
Previous Treatment in Indonesia 
2016 
Asia Pacific Federation of Pharmacologists (APFP) 
Bangkok, Thailand 
 
Poster presentation 
High Performance Liquid Chromatographic Method for the Determination of 
Piperaquine in Plasma 
2016 
American Thoracic Society (ATS) 
San Francisco, USA 
 
Poster presentation 
Negative Interaction of Diabetes Mellitus with Clinical Characteristics and 
Treatment Success of Tuberculosis in Indonesia 
2015 
Lembaga Penerbit Badan Penelitian dan Pengembangan 
Kesehatan  
Jakarta, Indonesia 
 
Book 

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Kajian Penyakit Menular Neglected dan Non-Neglected  
(Literature Review of Neglected and Non-Neglected Infectious Diseases) 
2014 
Buletin Penelitian Kesehatan  
Jakarta, Indonesia 
 
Journal article 
Proporsi Seksio Sesarea dan Faktor yang Berhubungan dengan Seksio Sesarea di 
Jakarta  
(The Proportion of Caesarean Section and Associated Factors in Hospital of 
Jakarta) 
 
 
 
 
 

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RETNA MUSTIKA INDAH 
 
Basic Information 
 
 First name 
: Retna 
 Middle name 
: Mustika 
 Last name 
: Indah 
 Gender 
: Female 
 Place of Birth 
: Jakarta 
 Date of Birth 
: 8/21/1983 
 Office Address 
 
- Institution 
: Puslitbang Sumber Daya dan Pelayanan Kesehatan 
 
Badan Penelitian dan Pengembangan Kesehatan 
 
- Street 
: Jln. Percetakan Negara no. 29 
 
- City 
: Jakarta Pusat 
 
- Province 
: DKI Jakarta 
 
- Postal code 
: 10560 
 Office Telephone  & Fax Number 
: 62 21 4287 9189 ext 123 
 Office email address 
: retnaindah.sugiyono@ina-respond.net 
 Mobile Phone 
: 6281 1987 432 
 Home Address 
 
- Street 
: Jln. Janur Hijau 1 Blok HH, no. 10 
 
- City 
: Jakarta Utara 
 
- Province 
: DKI Jakarta 
 
- Postal code 
: 14230 
 Home telephone 
: - 
 Personal email address 
: retnaindah.sugiyono@gmail.com 
  
 
 
Education 
  
 
- Faculty of Medicine, Trisakti University (2000 – 2008) 
 
- Master of Health Economic, University of Indonesia Public Health Programme (2014 – 2017)  
 
Research Experiences 
  
 
- Hospital Coordinator for Solidarity Trial, Clinical Trial of COVID treatment (2020) 
 
- PROACTIVE (A Prospective Observational Cohort Study On Hiv Infection And Risk Related Coinfections/ 
Comorbidities In Indonesia) study protocol core team (2018 -2020) 
 
- TRIPOD (TB Study of INA RESPOND on Drug Resistance) study protocol core team (2015 -2020)  
 
- Hospital coordinator Indonesian Disease Registry (www.ina-registry.org) (2011 - 2016) 
 
- DSMB secretary for High dose rifampicin for treatment of adults with tuberculosis meningitis (TBM): a 
dose finding study (ReDEFINe), 2014-2015  
 
- 
 
- District coordinator of National Non-Communicable Research, Ministry of Health Republic of Indonesia, 
2015  
 
- District coordinator of National Basic Health Survey, Ministry of Health Republic of Indonesia, 2013  

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- District coordinator of National Health Facilities, Ministry of Health Republic of Indonesia, 2011 
 
- Attending physician in Wahana Clinic (Private Primary Health Care) in Jakarta (2009 - 2010) 
 
  
Professional Training 
  
 
- Good Clinic Practice Course & Workshop, IASMED (April 2020) 
 
- Understanding  The Process and Research Implementation of  The Health Policy, University of Gadjah 
Mada (November 2016) 
 
- Methods in Epidemiologic, Clinical and Operations Research (Level 2), American Thoracic Society (October 
2018) 
 
- Methods in Epidemiologic, Clinical and Operations Research (Level 1), American Thoracic Society (October 
2015) 
 
Publications 
  
 
- Article, Building capacity for advances in tuberculosis research; proceedings of the third RePORT 
international meeting (2018) 
 
- Book, Manuscript Writing Guidelines, Published by NIHRD (2017) 
 
- The Effects of Diabetes Mellitus to Clinical Characteristics and Successful Treatment of 
Tuberculosis in Seven Public Hospitals Class A and B in Java and Bali Published by NIHRD Media, 2017 
 
- Article, Differences of Sociodemography Factors and Nutrition Status of Tuberculosis Patients with and 
Without Diabetes Based on Tuberculosis-Diabetes Mellitus Registry 2014 Published by NIHRD Media, 2017 
 
- Abstract, Indonesia Tuberculosis-Diabetes Registry: Comparison of Sputum Smear and Culture Results for 
Tuberculosis Diagnosis in Patients with and without Diabetes comorbidity for the 47th Union World 
Conference on Lung Health, Liverpool, 2016  
Challenge on Tuberculosis Infection Control in Indonesia: High Close Contact History in 
 
- Abstract, Tuberculosis Patients with HIV and Diabetes Mellitus, ATS 2016 International Conference, San 
Fransisco, 2016  
 
- Article, A Glimmer of Hope for Tuberculosis Treatment, INA RESPOND News Letter (2015) 
 
- Article, Drug Resistance as Barrier in Treatment for Prevention, INA RESPOND News Letter (2015) 
 
- Article, Tobacco Smoking: New Leader to Tuberculosis Jeopardy, INA RESPOND News Letter (2015) 
  
 
 
 

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13. Appendix 1. General Guidance on Specimen Types 
 
Cases with Major 
Symptoms Criteria 
  
Sample Type 
Serum 
Acute 
(Day 0-
14) 
Serum 
Convalescent 
(after day 14) 
Whole blood 
EDTA 
Liquid 
Cerebrospinal 
(LCS) 
Oropharingeal/ 
Nasopharingeal 
swab) 
Sputum 
BAL 
Stool/  
Rectal 
swab in 
VTM 
Urine 
1.Respiratory infection  
√ 
√ 
  
  
√ 
√ 
√ 
  
  
2.Central Nervous 
System (CNS) infection 
√ 
√ 
√ 
√ 
  
√ 
√ 
√ 
  
3.Diarrhea 
√ 
√ 
  
  
√ 
  
  
√ 
  
4.Hepatobiliary or UTI 
(leptospirosis, Hantavirus 
and Hepatitis A/B/C/E)  
√ 
√ 
√ 
  
  
  
  
  
√ 
5. Unknown Fever or 
Fever with 
rash/hemorrhagic, or 
arthritis (up to 15 
bacterial and virus panel) 
suspected as dengue like 
ilness/Chikungunya 
infection. 
√ 
√ 
√ 
  
  
  
  
  
√ 
6. Unknown Fever or 
Fever with rash 
suspected for measles, 
HFMD/enterovirus 
infection. 
√ 
√ 
  
  
√ 
  
  
√ 
  
7. Unknown Fever 
√ 
√ 
√ 
√ 
√ 
√ 
√ 
√ 
  
 

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14. Appendix 2. General Guidance on Specimen Collection, Handling and 
Processing 
 
SPECIMEN COLLECTION GUIDELINES  
 
Purpose of this document  
The purpose of this document is to provide general specimen collection 
guidelines for healthcare providers and public health staff during an outbreak 
when the pathogen is unknown. The specimens listed in this document are those 
that may need to be collected to detect the etiologic agent during outbreak. When 
a specific pathogen is known or very strongly suspected, specimen collection 
should be tailored to the pathogen. 
Reference Testing  
Testing will be conducted by INA-RESPOND reference laboratories  
General principles  
1. Integrated approach.  
These guidelines are designed for use in an outbreak setting where the etiologic 
agent is unknown. Sensitive assays should allow for an efficient and coordinated 
approach to specimen collection and diagnostic testing to evaluate multiple 
potential viral, bacterial or fungal etiologies. Each pathogen requires a unique set 
of specimen types, collection methods and handling conditions to optimize 
diagnostic yield. Because these guidelines are designed for detection of multiple 
pathogens, the sensitivity of detection of any one agent may be compromised. If 
a particular agent is strongly suspected, please refer to 1 pathogen-specific 
materials. To rule out other pathogens, multiple specimens may be necessary.  
2. Recommended specimens 
A. Respiratory specimens 
a. Nasal (N), Nasopharynx (NP) and Oropharynx (OP)  
b. Nasopharyngeal wash aspirate 
c. Sputum or induced sputum 
d. Tracheal aspirate 
e. Bronchoalveolar lavage (BAL) fluid 
f. Pleural fluid 
B. Blood Specimens 
a. Serum or Plasma 
b. Whole Blood 
c. Buffy coat 

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d. PBMC 
e. Paxgene 
C. Urine 
D. Stool 
E. Other body fluid 
a. CSF 
b. Acites 
c. etc 
 
3. Timing of specimen collection.  
• Specimens should be collected as soon as possible in the course of the 
illness and before antimicrobic therapy begin, if possible. The likelihood of 
recovering most viruses and many bacteria diminishes markedly >72 hours 
after symptom onset and after the initiation of appropriate antimicrobial 
therapy.  
• If possible, Acute specimens should be collected within 72 hours of symptom 
onset and no later than 7 days after onset. While convalescence specimens 
should be collected after 14 days of symptoms 
 
4. Interpretation of results.  
The interpretation of laboratory test results should take into account whether 
proper specimen collection and handling occurred prior to receiving the 
specimen in the laboratory and pathogen specific test sensitivities and 
concurrent treatment. Also, some pathogens colonize the upper respiratory 
tract (e.g. S. pneumoniae and Hib), or can cause asymptomatic or 
symptomatic infection (e.g. rhinovirus or coronavirus). Therefore, each 
laboratory result needs to be interpreted individually for each pathogen. 
Combining results from selected cases may significantly improve the overall 
specificity for identifying the predominant cause or causes of an outbreak.  
 
Collection Specimens  
A. Collection of upper respiratory Specimens 
1. Nasal swabs, nasopharyngeal (NP) swabs and oropharyngeal (OP)  
a. Optimal timing.  
Acute specimens should be collected within 3 days of symptom onset and no 
later than 7 days from all patients meeting the case definition identified during 

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the outbreak, ideally prior to the initiation of antimicrobial chemoprophylaxis or 
therapy.  
b. Swab types.  
Use only sterile dacron or rayon swabs with plastic shafts or if available, 
flocked swabs. DO NOT use calcium alginate swabs or swabs with wooden 
sticks, as they may contain substances that inactivate some viruses and inhibit 
some molecular assays.  
d. Collecting Nasal swabs 
• Ask the patients to attempt to clear the discharge by “blowing” his/her nose 
into non-scented tissue paper. (Allow one attempt.)  
• Assist children whenever necessary.  
• Do not try to clear the discharge with swabs, as this might be excessively 
traumatic.  
• Insert swab into the nares 
• Insert the swab approximately 2 cm (approximately ¾ inches) into the naris.  
•  Rotate the swab against the anterior nasal mucosa for 3 seconds.  
• Using the same swab, repeat for other naris.  
• Place swab back into the transport tube. 
 
e. Collecting the NP swab.  
• Ask the patients  to attempt to clear the discharge by “blowing” his/her nose 
into nonscented tissue paper. (Allow one attempt.)  
• Assist children whenever necessary.  
• Do not try to clear the discharge with swabs, as this might be excessively 
traumatic.  
• Insert swab into the nares. 
• Insert flexible wire shaft swab through the nares parallel to the palate (not 
upwards) until resistance is encountered or the distance is equivalent to 
that from the ear to the nostril of the patient indicating contact with the 
nasopharynx.  
• Gently, rub and roll the swab. Leave the swab in place for several seconds 
to absorb secretions before removing.  
 
               
 
f. Collecting the OP swab.  
• Identify participant and explain the procedure. 

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• Put on personal protective equipment. 
• Check clearness, color, expiration date and absence of leakage of the 
collection tube. 
• Tilt participant’s head back and depress the tongue.  
• Note: For young children: have child sit on the parent’s lap facing forward 
with the child’s back against the parent’s chest. The parent should wrap 
one arm around the child in a manner that will restrain the child’s body and 
arms. Ask the parent to tilt the child’s head-backwards.  
• Firmly swab the tonsillar area on both sides and the pharyngeal arches 
and leave in place for 5-10 seconds to absorb secretions, then withdraw 
the swab. 
• Remove the cap from the VTM tube and insert the swab into the tube. 
• Break the swab shaft, replace the cap and close the collection tube tightly.  
Make sure the swab shaft is short enough to permit complete tightening 
of the cap. Insert swab into the posterior pharynx and tonsillar areas.  
• Rub swab over both tonsillar pillars and posterior oropharynx and avoid 
touching the tongue, teeth, and gums. 
• For suspected diphtheria, swab behind the pseudo membrane.  
                  
 
 
g. Specimen handling.  
• For virus : Place N, NP and OP swabs immediately into a sterile cryotube 
containing 1 ml of viral transport media without antibiotics. Both swabs can 
be 2 placed in the same cryotube, if desired. Aseptically, cut or break 
applicator sticks off near the tip to permit tightening of the cap.  
• For virus : If specimens will be examined within 48 hours after collection 
keep specimen at 4ºC and ship on wet ice or refrigerant gel-packs, 
otherwise store frozen at ≤-70ºC and ship on dry ice. Avoid freezing and 
thawing specimens. Viability of some pathogens from specimens that were 
frozen and then thawed is greatly diminished and may result in false-
negative test results 
• For bacteria : Place swab immediately in Bacterial transport media : Amies 
transport media  
• For bacteria : if specimens examined within 48 hours after collection, keep 
specimens in room temperature.  
• Label the vial with the patient’s name, ID number, specimen type, and date 
collected.  

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2. Nasopharyngeal wash/aspirate.  
This specimen is commonly collected in children  
a. Optimal timing.  
Specimens should be collected within 3 days of symptom onset and not later 
than 7 days from all patients meeting the case definition identified during the 
outbreak or case finding, ideally prior to the initiation of antimicrobial 
chemoprophylaxis or therapy.  
b. Specimen collection.  
• Have the patient sit with head tilted slightly backward. Instill 1 ml-1.5 ml of 
non-bacteriostatic saline (pH 7.0) into one nostril. Flush a plastic catheter 
or tubing with 2 ml-3 ml of saline.  
• Insert the tubing into the nostril parallel to the palate (not upwards). Aspirate 
nasopharyngeal secretions.  
• If permitted, repeat this procedure for the other nostril.  
 
c. Specimen handling.  
• Collect the specimens in sterile vials.  
• Label each specimen container with the patients name, ID number, 
specimen type, and the date collected.  
• If specimens will be examined within 48 hours after collection, keep 
specimen at 4ºC and ship on wet ice or refrigerant gel-packs, otherwise 
store frozen at ≤-70ºC and ship on dry ice.  
• Avoid freezing and thawing specimens. Viability of some pathogens (e.g. 
respiratory syncytial virus) from specimens that are frozen and then thawed 
is greatly diminished and may result in false-negative test results.  
 

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B. Collection of Lower Respiratory Tract Specimens  
1. Sputum, induced sputum, tracheal aspirate, bronchoalveolar lavage (BAL) 
fluid, pleural fluid 
Due to the increased technical skill and equipment needs, collection of 
specimens other than sputum from the lower respiratory tract may be limited 
to patients presenting with more severe disease, including persons admitted 
to the hospital and/or fatal cases.  
a. Optimal timing.  
These specimens may be obtained at any time during the clinical course, but 
ideally prior to initiation of antimicrobial therapy.  
b. Specimen types.  
• Acceptable lower respiratory tract specimens include sputum, tracheal 
aspirate, BAL fluid, pleural fluid, or lung biopsy.  
• Specimens with less chance for upper airway contamination (i.e., BAL fluid, 
pleural fluid, lung biopsy) are preferred.  
c. Specimen collection.  
i. BAL fluid, tracheal aspirate, pleural fluid Collect specimens in sterile 
containers.  
• These specimens will be collected by a physician or other suitably 
qualified person by local practice.  
• The lavage fluids will be collected into a sterile container. 
• Label the specimen container with the participants ID number, date and 
time of the sample was collected. 
• Transfer the sample to the study site laboratory. 
• Aliquot 1.0 mL of sample into cryovials.  If the laboratory cannot aliquot 
soon after receipt, store the sample in the refrigerator until ready to aliquot. 
• Label each specimen container with the participants ID number, date, time 
and specimen type  
• Store at -20oC or below until shipment  
 
ii. Sputum and induced sputum 
• Note, a specimen may be obtained by sterile suction technique only by 
physician order. 
• If possible, have the participant rinse mouth and gargle with water prior 
to sputum collection. Instruct the participant not to spit saliva or 
postnasal discharge into the container. 
• A Gram stain smear result on sputum specimens will show epithelial 
cells. A sputum specimen containing >25 epithelial cells per low power 

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field has been contaminated with oropharyngeal secretions during 
collection, indicating a poor quality specimen for culture. 
• Educate the patient about the difference between sputum and oral 
secretions.  
• Have the patient rinse the mouth with water and then expectorate deep 
cough sputum directly into a sterile screw-cap collection cup or sterile 
dry container.  
d. Specimen handling.  
• Label the vial or container with the patient’s name, ID number, specimen 
type, and date collected. Store fixed cells at room temperature.  
• If unfixed specimens will be examined within 48 hours after collection, keep 
specimen at 4ºC and ship on wet ice or refrigerant gel-packs, otherwise store 
frozen at ≤-70ºC and ship on dry ice. Avoid freezing and thawing specimens. 
Viability of some pathogens from specimens that were frozen and then 
thawed is greatly diminished and may result in false-negative test results.  
 
C. Collection of Blood Components 
1. Acute and convalescent serum/plasma specimens.  
If possible, acute and convalescent sera should be obtained from all patients 
identified during the outbreak. For most respiratory pathogens, both acute and 
convalescent sera must be collected to permit a definitive diagnosis. Antibody 
titers against suspected bacteria or viruses may be measured in sera and 
provide an important adjunct to or confirmation of PCR and culture results. 
However, these results are not timely enough to guide clinical care.  
a. Optimal timing.  
i. Acute. Acute serum/plasma specimens should be collected within one 
week of symptom onset as soon as possible. 
ii. Convalescent. Convalescent specimens should be collected and 
submitted at day after day 14th after the acute specimen was collected.  
b. Collecting the sera.  
• For each serum specimen, collect 5 ml of whole blood into a serum 
separator tube (Red top or SST top).  
• Centrifuge 3000 rpm for 15 minutes. Pipette serum using transfer pipette 
or clinipipette into cryo (NUNC) tube 
• A minimum of 1 ml of whole blood is needed for testing of pediatric 
patients.  
• Labeled cryo (NUNC) tube. Store at temperature - 70ºC or -80ºC.  
• Ship with dry ice 
 
c. Collecting the plasma & Buffy coat.  

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• For each plasma specimen, collect 2 x 3 ml EDTA tubes. 
• Centrifuge 3000 rpm for 15 minutes.  
• Pipette plasma using transfer pipette or clinipette. 
• If aliquoting is performed, divide the sera into 0.5 ml aliquots in cryotube. 
• After plasma separated from above process, transfer buffy coat using 
clinipipette yellow tip or transfer pipette ± 200 ul from each EDTA tube 3 
ml into cryo (NUNC) tube.  
• Label each vial with the patient’s name, ID number, specimen type, and 
date collected.  
• Store refrigerated at 4ºC or frozen (-70ºC), and ship on refrigerant gel 
packs or dry ice. 
  
d. Collecting the PBMC 
• For each PBMC specimen, collect 2 x 3 ml Heparin tubes or 1 CPT 
tubes  
• Processing blood as soon as possible 
• Label the tube with the patient’s name, ID number, specimen type, and 
date collected.  
• Store PBMC in liquid nitrogen 
e. Collecting the paxgene 
• Label the tube with the patient’s name, ID number, specimen type, and 
date collected.  
• Draw blood using a winged blood collection set  
• The PAXgene tube must remain upright during collection. 
• Full 2.5 ml of blood must be collected 
• Invert tube 8-10 times after blood is collected 
• Place tube in a wire rack. 
• Store tube at -20ºC for 24 hours until frozen. 
• After frozen, store the tube in the rack to freezer -80ºC  
 
2. Whole blood for Culture.  
This specimen may be limited to patients with more severe disease including 
persons admitted to the hospital.  
a. Optimal timing.  
Whole blood should be collected as soon as possible after illness onset 
and ideally before initiation of antimicrobial chemoprophylaxis or therapy.  
For fatal cases, postmortem whole blood should always be obtained at 
autopsy.  
b. Collection.  
Collect whole blood in bottles (culture media) ex: Bactec or BaTallert 
according to clinical laboratory guidelines.  

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c. Specimen handling.  
Label the bottle with the patient’s name, ID number, specimen type, and 
date collected.  
Store and ship specimens in room temperature. 
 
D. Urine  
a. Optimal timing.  
Urine may be collected within 7 days of symptom onset  
 
b. Specimen collection.  
• Random midstream urine will be collected if urine analysis is requested 
by the attending physician.   
• Urine samples will be collected according to standard procedures. If 
standard procedures are not available then provide the participant with 
a sterile, plastic, preservative-free screw-top urine collection cup and 
instruct them to clean the labia or retract the foreskin prior to specimen 
collection.  
•  The participant should be asked to direct the first part of the urine void 
into the toilet, collect the middle part into the sterile cup and void the 
remaining urine into the toilet. Then the participant should screw the 
lid tightly onto the cup after collection.  
• Collect 10-20 ml of mid stream urine in a container.  
• Divide urine into 5 barcodes labeled cryo (NUNC) tube, each: 1000 uL. 
Store at temperature 70ºC or -80ºC. 
 
c. Specimen handling.  
• Label the container(s) with the patient’s name, ID number, specimen 
type(s), and date collected.  
• Store refrigerated at 4ºC and ship on dry ice or refrigerant gel packs.  
 
E. Stool/Rectal Swab  
a. Optimal timing.  
Stool/Rectal Swab may be collected within 14 days of symptom onset from 
patients hospitalized as part of an disease outbreak (e.g. from SARS CoV 
suspect cases for RT-PCR).  
b. Stool Specimen collection.  
• Collect 3 ml watery stool  or 3 grams stool in a clean, dry, leak-proof 
container.  
• Stool specimens should be collected into a clean, dry, leak-proof 
container. 

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• Label each specimen container with the participants ID number, date and 
time of the sample was collected. 
• Transfer the sample to the study site laboratory.  
• Take 3 grams of stool to 15 ml centrifuge tube. Dilute stool with PBS with 
ratio 1:1 (gr/volume solid or volume/volume watery stool) and centrifuge 
at 2000 rpm for 5 mins. Then aliquot 0.2 mL of the supernatant into  6 
cryovials. 
• Label each specimen vial with the participants ID number, date, time and 
specimen type which is classified by the color. 
• Store at - 20 or below until shipment (See section 
c. Rectal swab specimen collection.  
• Identify participant and explain the procedure. 
• Put on personal protective equipment. 
• Check clearness, colour, expiration date and absence of leakage of the 
collection tube.  
• Have participant lie on his/her back or side with upper legs and knees 
flexed towards the abdomen (crouching position). 
• Moisten swab in normal saline or water. 
• Carefully insert the swab through the anus in the participant’s rectum 
(See Figure) and gently rotate a few times, leave in place for 5-10 
seconds to absorb secretions, then withdraw swab carefully. 
• Put the swab into the transport media tube 8. Label specimen transport 
tube with participants ID, date and time of sample collection. 9. Transfer 
the sample to the study site laboratory.   10. Affix the sample tube with 
the color sticker (see section 7.3). 11. Store at -20oC or below until 
shipment 
• For bacterial examination, put the swab into the bacterial transport media 
(example: amies).  
• For viral examination, put the swab into the VTM (Virus Transport Media) 
example: Hank's Solution  
 
 
 

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d. Specimen handling.  
• Label the container(s) with the patient’s name, ID number, specimen 
type(s), and date collected.  
• If specimens will be examined within 48 hours after collection, they can 
be refrigerated at 4ºC; otherwise store frozen at -70ºC and ship on dry 
ice. 
 
F. OTHER BODY FLUID (Cerebrospinal Fluid / CSF, Acites, Pus etc) 
a. Optimal timing.  
Specimens may be collected within 7 days of symptom onset  
 
d. Specimen collection.  
• CSF specimens will be collected according to the attending 
physician’s decision. 2.  
• The CSF fluid will be collected into a sterile container. 
•  Label the specimen container with the participants ID number, date 
and time of the sample was collected.  
• Transfer the sample to the study site laboratory.  * (CSF specimens 
should be transported to a microbiology laboratory as soon as 
possible. Specimens for culture should not be refrigerated or 
exposed to extreme cold, excessive heat, or sunlight. They should 
be transported at temperatures between 20°C and 35°C). 
• Aliquot 1.0 mL of sample into cryovials. 
 
e. Specimen handling.  
• Label the container(s) with the patient’s name, ID number, specimen 
type(s), and date collected.  
• Store refrigerated at 4ºC or 20oCand ship on dry ice or refrigerant gel 
packs.  
 
G. OTHER SPECIMENS (SWAB VESICLE OR SKIN LESSION) 
 
 
 

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A. For virus : swabs immediately into a sterile cryotube containing 1 ml of 
viral transport media without antibiotics. Aseptically, cut or break 
applicator sticks off near the tip to permit tightening of the cap.  
B. For virus : If specimens will be examined within 48 hours after collection 
keep specimen at 4ºC and ship on wet ice or refrigerant gel-packs, 
otherwise store frozen at ≤-70ºC and ship on dry ice. Avoid freezing and 
thawing specimens. Viability of some pathogens from specimens that 
were frozen and then thawed is greatly diminished and may result in false-
negative test results 
C. For bacteria : Place swab immediately in Bacterial transport media : Amies 
transport media  
D. For bacteria : if specimens examined within 48 hours after collection, keep 
specimens in room temperature.  
E. Label the vial with the patient’s name, ID number, specimen type, and date 
collected.  
 
 
 
 
 

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15. Appendix 3. Implementing Arrangement on Infectious Diseases 
Research between US-NIH and Indonesia-NIHRD 
 
 
 
 
 

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16. Appendix 4. Extension of the Implementing Arrangement  
 
 

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17. Appendix 5 Molecular and serology tests at the INA-RESPOND 
Laboratory 
 
Pathogen 
Methods 
Confirmation 
Dengue virus 
Molecular: real-time PCR(1) and 
nested PCR(2) 
DENV RNA was detected 
Antigen detection (Focus Technology, 
US) 
NS1 antigen was detected 
Serology assay: ELISA IgM and IgG 
(Focus Technology, US) 
Sero-conversion in IgM and or IgG between acute and 
convalescent specimens; four-fold increase of IgG in 
the absence of IgM; detectable IgM, supported by IgG 
and clinical manifestations. 
Salmonella typhi/ 
Salmonella paratyphi 
Blood culture (Bactec or ViTek) 
Identified by API 
Molecular: S. typhi(3), S. paratyphi(4) 
S. typhi/S. paratyphi DNA was detected 
S. typhi antibodies by ELISA 
(MyBioSource, US) IgM and IgG 
 
Sero-conversion or increasing of IgM and/or IgG 
antibodies titer. Detection of IgM in acute samples, 
supported by clinical manifestations. 
Rickettsia typhi 
Molecular: Rickettsia spp.(5), R. 
typhi(6) 
R. typhi DNA was detected, if only Rickettsia spp. is 
detectable, it is supported by R. typhi IgM and IgG 
antibodies 
R. typhi ELISA IgM/IgG antibodies 
using ELISA (Fuller, US) 
 
Murine typhus IFA (Focus, US) 
Sero-conversion or increasing titers of R. typhi IgM 
and IgG antibodies in convalescent specimens. 
Increase in Fluorescein level in convalescent 
specimens, in line with ELISA results  
Orientia tsutsugamuchi 
Molecular: Orientia tsutsugamuchi(5) 
O. tsutsugamuchi DNA was detected 
Scrub typhus ELISA IgM and IgG 
antibodies (InBios, US) 
 
Sero-conversion or increasing titers of IgM and/or IgG 
O. tsutsugamuchi antibodies in convalescent 
specimens 
 
Leptospira 
Micro agglutination test (MAT) in a 
few specimens 
Four-fold increase of Leptospira antibodies to certain 
species, or a high titer (1/320) of antibodies in a single 
acute specimen 
Molecular: real time PCR(7) 
Leptospira DNA was detected 
ELISA IgM leptospira (PanBio, Aus), 
IgG Leptospira (Serion, Germany) 
Sero-conversion or increasing IgM and IgG titers in 
convalescent specimens 
Chikungunya virus 
Molecular: real time PCR(8) 
Chikungunya RNA was detected 
ELISA IgM and IgG chikungunya 
antibodies (Euroimmune, Germany) 
Sero-conversion or increasing titers of IgM and IgG in 
convalescent specimens 
Malaria 
Thick blood smear (microscopic) or 
Rapid Antibody test (SD Bioline, US) 
Plasmodium was detected 
Antibody was detected 
Mycobacterium 
tuberculosis 
Acid fast bacilli smear (microscopic) 
Acid fast bacilli was detected 
Mycobacterium leprae 
Acid fast bacilli smear (microscopic)  
Acid fast bacilli was detected 
Amoeba coli/ 
Amoeba histolytica 
Microscopic examination 
Amoeba was detected 
Helminthiasis 
Microscopic examination 
Helmith eggs or spores were detected 
Other parasites 
Microscopic examination 
A parasite was detected 
Seoul virus 
Molecular: conventional PCR(9) 
Seoul virus RNA was detected 
ELISA IgM and IgG Hantavirus 
Antibodies (Focus diagnostics) 
Sero-conversion or increasing titers of IgM and IgG 
Hantavirus anti bodies in convalescent specimens 
Rubella virus 
ELISA Rubella virus IgM and IgG 
antibodies (Serion, Germany) 
Sero-conversion or increasing titers of IgM and IgG 
antibodies in convalescent specimens 
Influenza virus 
Molecular: multiplex real-time 
PCR(10) 
Influenza RNA virus was detected 
ELISA Influenza A and B virus IgM 
and IgG antibodies (Serion, Germany) 
Two fold increase of IgM and/or IgG influenza A or 
Influenza B antibodies in convalescent specimens 
Respiratory syncitial virus  
Molecular: multiplex real-time 
PCR(10) 
RSV RNA was detected 
ELISA RSV IgM and IgG antibodies 
(Serion, Germany) 
Sero-conversion or increasing of IgM or IgG RSV 
antibodies in convalescent specimens 
Para- influenza viruses 
Melecular: multiplex real-time 
PCR(10) 
Para influenza virus RNA was detected 
Adenovirus 
Melecular: multiplex real-time 
PCR(10) 
Adenovirus RNA was detected 
Cor OC43 
Melecular: multiplex real-time 
PCR(10) 
CorOC43 virus RNA was detected 
Parechovirus 
Melecular: multiplex real-time 
PCR(10) 
Parechovirus RNA was detected 
Bocavirus 
Melecular: multiplex real-time 
PCR(10) 
Bocavirus RNA was detected 

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Rhinovirus 
Melecular: multiplex real-time 
PCR(10) 
Rhinovirus RNA was detected 
Metapneumovirus 
Melecular: multiplex real-time 
PCR(10) 
Metapneumovirus RNA was detected 
Measles virus 
 
 
Molecular: conventional(11) 
Measles virus RNA was detected 
ELISA measles virus IgM and IgG 
antibodies (Serion, Germany) 
Sero-conversion or increase titers of IgM and/or IgG 
antibodies in convalescent specimens 
HHV-6 
Conventional PCR(12) 
HHV-6 virus DNA was detected 
Real-time PCR(13) 
>1,000 copies/ul 
Enterovirus 
Real-time PCR(14) 
Enterovirus RNA was detected 
Flavivirus 
Conventional PCR(15) 
Flavivirus RNA was detected 
Zikavirus 
Real-time PCR(16) 
Zikavirus RNA was detected 
Rotavirus 
Real-time PCR(17) 
Rotavirus RNA was detected 
Norovirus 
Real-time PCR(18) 
Norovirus RNA was detected 
Adenovirus (ent) 
Real-time PCR(17) 
Adenovirus RNA was detected 
Astrovirus 
Real-time PCR(18) 
Astrovirus RNA was detected 
Chlamydia pneumonia 
Real-time PCR(19) 
C. pneumonia DNA was detected 
Chlamydia psitacci 
Real-time PCR(20) 
C. pistacci DNA was detected 
Streptococcus pneumonia 
Real-time PCR(21) 
S. pneumoniae DNA was detected 
Haemophilus influenza 
Real-time PCR(21) 
H. influenza DNA was detected 
Bordetella pertussis 
Real-time PCR(22) 
B. pertussis DNA was detected 
Legionella pneumoniae 
Real-time PCR(23) 
L. pneumoniae DNA was detected 
Mycoplasma pneumoniae 
Real-time PCR(24) 
M. pneumoniae DNA was detected 
Staphylococcus aureus 
Real-time PCR25 
S. aureus DNA was detected 
Klebsiella pneumoniae 
Real-time PCR25 
K. pneumoniae DNA was detected 
16S r RNA 
Real-time PCR(7) 
Bacterial DNA was detected 
HIV 
Real-time PCR26 
Rapid Test SD®, Oncoprobe® 
ELISA 4th generation (Biorad®) 
HIV RNA was detected, HIV antibody was negative, 
4th generation ELISA was positive 
References: 
1. Hue KD, Tuan TV, Thi HT, et al. Validation of an internally controlled one-step real-time multiplex 
RT-PCR assay for the detection and quantitation of dengue virus RNA in plasma. J Virol Methods 
2011; 177(2):168–73. 
2. Lanciotti RS, Calisher CH, Gubler DJ, Chang GJ, Vorndam AV. Rapid detection and typing of dengue 
viruses from clinical samples by using reverse transcriptase-polymerase chain reaction. J Clin 
Microbiol 1992; 30(3):545–51. 
3. Hatta M, Smits HL. Detection of Salmonella typhi by nested polymerase chain reaction in blood, urine, 
and stool samples. Am J Med Trop Med Hyg 2007; 76(1):139–43. 
4. Pratap CB, Kumar G, Patel SK, et al. Mix-infection of S. typhi and paratyphi A in typhoid fever and 
chronic typhoid carriers: a nested PCR based study in North India. J Clin Diagn Res 2014; 8(11):DC09–
DC14. 
5. Jiang J, Chan TC, Temenak JJ, Dasch GA, Ching WM, Richards AL. Development of a quantitative 
real-time polymerase chain reaction assay specific for Orientia tsutsugamushi. Am J Med Trop Med 
Hyg 2004; 70(4):351–6. 
6. Henry KM, Jiang J, Rozmajzl PJ, Azad AF, Macaluso KR, Richards AL. Development of quantitative 
real-time PCR assays to detect Rickettsia typhi and Rickettsia felis, the causative agents of murine 
typhus and flea-borne spotted fever. Mol Cell Probes 2007; 21(1):17–23. 
7. Thaipadungpanit J, Chierakul W, Wuthiekanun V, et al. Diagnostic accuracy of real-time PCR assays 
targeting 16S rRNA and lipL32 genes for human leptospirosis in Thailand: a case-control study. PLoS 
One 2011; 6(1). 
8. Lanciotti RS, Kosoy OL, Laven JJ, et al. Chikungunya virus in US travelers returning from India, 2006. 
Emerg Infect Dis 2007; 13(5):764–7. 
9. Dekonenko A, Ibrahim MS, Schmaljohn CS. A colorimetric PCR-enzyme immunoassay to identify 
hantaviruses. Clin Diagn Virol 1997; 8(2):113–21. 
10. Jansen RR, Schinkel J, Koekkoek S, et al. Development and evaluation of a four-tube real time 
multiplex PCR assay covering fourteen respiratory viruses, and comparison to its corresponding single 
target counterparts. Clin Diagn Virol 2011; 51(3):179–85. 
11. Chibo D, Birch CJ, Rota PA, Catton MG. Molecular characterization of measles viruses isolated in 
Victoria, Australia, between 1973 and 1998. J Gen Virol 2000; 81(Pt 10):2511–8. 
12. Huang LM, Kuo PF, Lee CY, Chen JY, Liu MY, Yang CS. Detection of human herpesvirus-6 DNA by 
polymerase chain reaction in serum or plasma. J Med Virol 1992; 38(1):7–10. 
13. Sedlak RH, Cook L, Huang ML, et al. Identification of chromosomally integrated human herpesvirus 
6 by droplet digital PCR. Clin Chem 2014; 60(5):765–72. 

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14. Beld M, Minnaar R, Weel J, et al. Highly sensitive assay for detection of enterovirus in clinical 
specimens by reverse transcription-PCR with an armored RNA internal control. J Clin Microbiol 2004; 
42(7):3059–64.  
15. Kuno G, Chang G-JJ, Tsuchiya KR, Karabatsos N, Cropp CB. Phylogeny of the genus Flavivirus. J 
Virol 1998; 72(1 ):73–83. 
16. Lanciotti RS, Kosoy OL, Laven JJ, et al. Genetic and serologic properties of zika virus associated with 
an epidemic, Yap State, Micronesia, 2007. Emerg Infect Dis 2008; 14(8). 
17. Logan C, O'Leary JJ, O'Sullivan N. Real-time reverse transcription-PCR for detection of rotavirus and 
adenovirus as causative agents of acute viral gastroenteritis in children. J Clin Microbiol 2006; 
44(9):3189–95  
18. Logan C, O’Leary JJ, O'Sullivan N. Real-time reverse transcription PCR detection of norovirus, 
sapovirus and astrovirus as causative agents of acute viral gastroenteritis. J Virol Methods 2007; 146(1-
2):36–44. 
19. Heddema ER PY, Langerak AA, Beld M, Duim B. Development of an internally controlled Taqman 
based PCR assay for the detection of Chlamydia pneumoniae in the Lightcycler 2.0 system. Ned Tijschr 
Med Microbiol 2004; 12(s1:s61). 
20. Heddema ER, Beld MGHM, Wever Bd, Langerak AAJ, Pannekoek Y, Duim B. Development of an 
internally controlled real-time PCR assay for detection of Chlamydophila psittaci in the LightCycler 
2.0 system. Clin Microbiol Infect 2006; 12(6):571–5. 
21. Corless CE, Guiver M, Borrow R, Edwards-Jones V, Fox AJ, Kaczmarski EB. Simultaneous Detection 
of Neisseria meningitidis, Haemophilus influenzae, and Streptococcus pneumoniae in suspected cases 
of meningitis and septicemia using real-time PCR. J Clin Microbiol 2001; 39(4):1553–8  
22. Reischl U, Lehn N, Sanden GN, Loeffelholz MJ. Real-time PCR assay targeting IS481 of Bordetella 
pertussis and molecular basis for detecting Bordetella holmesii. J Clin Microbiol 2001; 39(5):1963–6. 
23. Wilson DA, Yen-Lieberman B, Reischl U, Gordon SM, Procop GW. Detection of Legionella 
pneumophila by real-time PCR for the mip gene. J Clin Microbiol 2003; 41(7):3327–30. 
24. Pitcher D, Chalker VJ, Sheppard C, George RC, Harrison TG. Real-time detection of Mycoplasma 
pneumoniae in respiratory samples with an internal processing control. J Med Microbiol 2006; 55:149–
55. 
25. Gadsby NJ, McHugh MP, Russell CD, Mark H, Conway Morris A, Laurenson IF, Hill AT,  Templeton 
KE.  2015. Development of two real-time multiplex PCR assays for the detection and quantification of 
eight key bacterial pathogens in lower respiratory tract infections. Clin Microbiol Infect 2015; 21: 
788.e1–788.e13 
26. Palmer S, Wiegand AP, Maldarelli F, et al. New real-time reverse transcriptase-initiated PCR assay 
with single-copy sensitivity for Human Immunodeficiency Virus type 1 RNA in plasma. J Clin 
Microbiol 2003; 41(10):4531–6 
 
 
 
 
 
 

INA107 Annex INA-ORCHID  
 
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Annex ORCHID-COVID-19 Ver 1.2.1 Dated 21 JUL 2020 
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Annex 1. In Response to SARS-CoV-2 Pandemic (ORCHID-COVID-19 Study) 
 
This document outlines the procedures to identify and characterize Corona Virus Disease 
2019 (COVID-19) in the INA-ORCHID study. 
 
Background 
Fifteen years after the Avian Influenza epidemic, Indonesia was recently hit by another 
respiratory outbreak, COVID-19, caused by the novel SARS-CoV-2. This virus belongs 
to Coronaviridae family, genus betacoronavirus, together with SARS-CoV and MERS-
CoV. SARS-CoV-2 was first reported on 31 December 2020 in Wuhan, China, and then 
it rapidly spread globally to infect more than 10 million people in more than 200 countries 
by 15 July 2020. SARS-CoV-2 has infected more than 80,000 people in all provinces in 
Indonesia,and has caused approximately 5% death. In response to this pandemic, a 
scientific research is necessary to systematically collect epidemiological and clinical data, 
along with biological specimens. Data and specimens obtained from this study are very 
important for identifying the best diagnostics, treatments, and prevention strategies in 
order to control the disease.  
 
Objectives  
Consistent with the objectives in the main protocol, focus on COVID-19. 
Primary Objective: 
To identify COVID-19 and other respiratory infectious disease cases from hospitalized 
suspected COVID-19 patients. 
Secondary Objectives:  
• To describe the disease course and case management of COVID-19 
• To assess the accuracy of diagnostic tests of COVID-19 
• To better understand the pathogenesis of COVID-19 
• To assess treatments and short-term outcomes of COVID-19 
• To generate epidemiologic data to inform ongoing and future disease control and 
prevention efforts of COVID-19 
 
Study Benefit  
Consistent with the objectives in the main protocol, focus on COVID-19. 
• Provide a better understanding of COVID-19, its epidemiology and clinical 
characteristics in Indonesia. 
• Generate data to support evidence-based recommendations to health authorities 
for COVID-19 disease diagnostics, treatment, and prevention. 

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• Improve the INA-RESPOND Network’s capacity for conducting infectious disease 
research during dynamic outbreak scenarios, and it will strengthen the 
specialization of the Reference Laboratory to identify SARS-CoV-2 and other 
respiratory pathogens. 
 
Sample Size and Study Duration 
As a part of the INA-ORCHID study that will enrol 4000 subjects over 5 years, this 
ORCHID-COVID-19 study will enrol 500 suspected COVID-19 subjects from 5 hospitals 
over 1 year.  
 
Study Method 
This study will enrol suspected COVID-19 subjects to the prospective arm in outbreak 
situation of the INA-ORCHID study. It is an observational study with exploratory design. 
There will be no intervention that will affect standard of care or clinical outcome. 
Study visit and Procedure: 
Consistent with the main protocol, subjects will be seen during enrolment (visit 1), 7-14 
days later (visit 2), and if necessary, one additional visit after visit 2 without specific time 
frame. Data and specimens collected also refer to the main protocol.  
Inclusion criteria (consistent with the main protocol, focus on COVID-19): 
 
• Adult or child of any age undergoing a current episode of illness that is presumed 
COVID-19 
Exclusion criteria: none (consistent with the main protocol). 
 
Study Flow: 
Of the 500 suspected COVID-19 patients who sign the consent form and are enrolled in 
the study, demographic and clinical data, clinical specimens are collected following INA-
ORCHID protocol. COVID-19 RT-PCR is the hospital standard of care. As PCR results 
are usually available 24-72 hours later, other tests (dengue using NS1/IgM&IgG RDT, 
influenza virus using RDT, S typhi and paratyphi and other bacteria using blood culture) 
should be performed. Although confirmed dengue diagnosis even by positive NS1 will not 
exclude COVID-19, early dengue diagnosis will be very useful for patients, clinicians and 
hospital management. Blood culture during enrolment is recommended as it is the gold 
standard for S typhi and S paratyphi infections and should use blood before antibiotics 
are given to the patients. This blood culture may also identify other bacteria circulating in 
the blood. By conducting these tests, we are able to confirm COVID-19, dengue, 
influenza, S typhi, S parathyphi, other bacteria, and co-infections among them.  

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We expect 100 COVID-19 cases will be identified; however, the majority of cases may 
remain undiagnosed. For these cases, testing will be conducted at the reference lab 
based on clinical syndromes 1) COVID-19 that may be missed (viral shedding has 
passed, diagnosis will be based on serology). 2) dengue that may be missed (NS1 is 
often negative in secondary infection, diagnostic tests will use ELISA in paired sera and/or 
RT-PCR, 3) Salmonellas may be missed from blood culture and the only feasible 
diagnosis is using tubex test in paired sera. Sputum from pneumonia patients will be 
tested for virus and bacteria pneumonia panel.  For testing other pathogens, the algorithm 
will be based on clinical syndromes and will be discussed with INA-RESPOND core and 
lab team and the sites.  
All these 500 patients will follow INA-ORCHID study procedures during visit 1,2, and if 
necessary, visit 3. 
Specimens from confirmed COVID-19 cases will be tested to understand the kinetics of 
the virus, IgM and IgG antibodies over-time, and to explore if there is certain people are 
more susceptible to contract severe disease. Data from COVID-19 cases can be used to 
better understand the epidemiology, disease progress and treatment outcomes.  All the 
tests will be conducted at the reference lab.  
The diagram of this study procedure is below. 
 

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Study Diagram for ORCHID-COVID-19 Study 
 Suspected COVID 
Baseline Procedures 
- PCR/Xpert SARS-CoV-2 (SoC) 
- Dengue NS1 & IgM 
- Blood Culture (one side) 
- Influenza Testing 
ICF enrolled 
Test @ sites 
500 subjects 
Pathogen confirmed 
Not confirmed 
Covid+other(s) 
COVID 
Dengue  
Typhoid 
Other bacteria 
Follow-up  
Algorithm based on 
Clinical Syndromes for 
pathogen identification 
Follow-up 
Follow-up 
100 subjects 
ORCHID COVID-19 
Follow-up  
400 subjects  
ORCHID non-COVID-19 
Influenza 

 
 
Informed Consent Form for Pediatrics and Assent Version 1.1 Dated 05MAY2020 
Based on INA107 Protocol Version 1.1 Dated 05MAY2020 
 
 
Page 1 of 9  
 
Informed Consent Form for Pediatrics and Assent 
Part I: Information Sheet 
 
Title of study:  
 
INA-RESPOND Observational Research on Infectious 
Disease Outbreaks and Difficult Cases of Unidentified 
Etiology in Indonesia 
Protocol number:  
INA107 
Protocol PI: 
Dr. Muhammad Karyana, MPH 
Gedung 3 Lantai 1 Badan Litbangkes 
Jl. Percetakan Negara No. 29 Jakarta, Indonesia - 10560 
mkaryana@gmail.com  
Site Number: 
 
Site PI: 
 
Participant’s Name: 
 
Participant’s ID: 
 
 
I am [insert name of Site Investigator], working for [indicate Site name] of the Indonesia 
Reseach Partnership on Infectious Diseases (INA-RESPOND). The INA-RESPOND is 
a research collaboration on infectious diseases between the National Institute of Health 
Research and Development, Ministry of Health of Indonesia and the National Institute of 
Allergy and Infectious Diseases, National Institutes of Health of the United States of America. 
We are doing research on [indicate name of disease], which is affecting a lot people 
in Indonesia. I am going to give you information and invite your child to be part of the 
study we are conducting. Before you decide whether your child will participate or not, 
you can talk to a friend, a family member or anyone else you feel comfortable with. 
We will do our best to facilitate the communication.  
If I use some words that you do not understand, please ask me to stop and I will take 
time to explain.  If you have questions later, you can ask them of me or [indicate all 
research staff with whom participant will be in contact, e.g. study nurse, study 
physicians, etc]. 
This Informed Consent Form has two parts:  
 
• Information Sheet (to share information about the study with you)  
 
• Consent Form (for signatures if you agree to take part) 
 
Why is this research being done? 
Your child are being asked to take part in this research because your child have been 
clinically diagnosed with [indicate name of disease] OR because we suspect your child 
have [indicate name of disease] OR because your child have been in contact with 
someone who has [indicate name of disease]. This research aims to understand the 
scope of pathogens (agent or organism that causes disease) responsible for outbreaks 
and difficult clinical cases in Indonesia, and to characterize the clinical course of the 
diseases to better inform diagnostics, treatments and prevention strategies. 
 
What is the study about? 
This study is about identifying the causative agents and describe the clinical conditions 
or characteristics of presumptive infections. It will involve data collection on 
demographics, medical history and clinical examination, and blood samples collection.  

 
 
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Page 2 of 9  
 
 
Is study participation mandatory? 
Participation in research is entirely voluntary. It is your choice whether to participate 
or not. Whatever your decision, you will still access all health care services at your 
local clinic or hospital. If you decide to participate, you will be asked to sign the consent 
form at the end of this document to show that you agree. You can decide to participate 
now and change your mind later during the study. This will have no negative 
consequence for you or your child health. 
 
How many people will be in this study?  
The study is being conducted in Indonesia, particularly in 19 hospitals member of the 
INA-RESPOND Network (RSUPN Dr. Cipto Mangunkusumo, RS Persahabatan, and 
RSPI Prof. Dr. Sulianti Saroso, RS St. Carolus, Jakarta; RSUD Kab. Tangerang, 
Banten; RSUP Dr. Hasan Sadikin, Bandung; RSUP Dr. Sardjito, Yogyakarta; RSUP 
Dr. Kariadi, Semarang; RSUD Dr. Soetomo, Surabaya; RSUP Dr. Wahidin 
Sudirohusodo, Makassar; RSUP Sanglah, Denpasar; RSUP Adam Malik, Medan; RS 
Budi Kemuliaan, Batam; RSUD Zainoel Abidin, Banda Aceh;  RSUD Ansari Saleh, 
Banjarmasin; RSUD Abdul Wahab Sjahranie, Samarinda; RSUD Soedarso, 
Pontianak; RSUD TC Hilers, Sikka; RSUD Abepura, Jayapura) for five years from 
2020 to 2025. We plan to include up to 5,000 participants. We are inviting all adults 
OR all children with [indicate name of disease] to participate in the study.  
 
What will happen if you decide your child to participate in this study? 
If you agree that your child to be part of the study, your child will be asked to complete 
the study visits twice, at enrolment and baseline visit (day 0) and follow up visit (day 
7-14) to conduct data and blood sample collection. 
 
Screening 
We will evaluate your child eligibility to take part in this study. The screening 
procedures will take up to 30 minutes. 
Your child may be enrolled in this study if your child meets all the following criteria: 
1. Child of any age hospitalized with a current episode of illness with a presumed 
infectious disease of unidentified etiology 
2. Your child tested negative for Dengue virus infection by an antigen-based and 
antibody-based diagnostic test (i.e. NS1 antigen test and Dengue-specific IgM test) 
3. Your child tested negative for Salmonella Typhi infection by Standard of Care 
testing (i.e. blood culture, Widal test, or Tubex rapid test) 
4. You are able to provide a documented informed consent 
5. You agree to the collection and storage of specimens of your child for laboratory 
testing and/or future research (you may decline storage of specimens for future 
research) 
However, if your Site PI advised your child not to take part in this study to protect your 
child safety and wellbeing, your child may not be enrolled in this study. 
 
 
Enrolment and Baseline Visit (Day 0) 

 
 
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Page 3 of 9  
 
After your child are enrolled in this study, we will collect your child baseline information. 
This procedure may take up to 30 minutes to 2 hours, your child will have the following 
done: 
• We will ask you some questions about your general information, such as age, 
gender, residence and occupation. We will also ask you some questions about 
your child medical history, such as your child travel history, contact history to 
suspected human cases, insect or animal exposure, vaccination history, and 
medication use prior to enrolment. 
• We will check your child height and weight, blood pressure, heart and 
respiratory rate, body temperature, and current signs and symptoms. We will 
also collect information on other diseases or conditions, results on laboratory 
and imaging tests done by your physicians, treatment and clinical outcome at 
this visit. 
• About 0.5-1 tablespoon (5-15 mL) of your child blood will be drawn through the 
vein in your child forearm. We will also collect other non-invasive (not breaking, 
cutting, or entering the skin) samples such as sputum, urine, stool, 
nasopharyngeal swab, etc. if clinically indicated. Samples collected by your 
child physicians can be included if leftover specimen is shared.  
• 
Based on your child’s weight, the amount of blood drawn in one take will be adjusted 
according to the table below: 
Your child’s body weight 
(Kilograms) 
Maximum blood volume 
per one take 
4.5 – 6.8 
5 ml 
7.3 – 18.2 
10 ml 
>18.2 
15 ml 
• Routine hematology, blood chemistry, liver and renal function tests will be done 
to the collected blood samples. The remaining blood samples and other 
available samples will be processed for pathogen identification tests at INA-
RESPOND Reference Laboratory. 
• The remaining blood samples and other available samples will be processed 
and stored for future research (you may decline storage of specimens of your 
child for future research). 
 
Follow Up Visit (Day 7-14) 
Approximately 1-2 weeks after baseline evaluation, the study staff will contact you and 
continue with the study follow up. During which, your child will have the following done 
for up to 30 minutes to 2 hours:  
• We will check your child height (if previously not done) and weight, blood 
pressure, heart and respiratory rate, body temperature, and current signs and 
symptoms. We will also collect information on other diseases or conditions, 
results on laboratory and imaging tests done by your physicians, treatment and 
clinical outcome at this visit. 
• About 0.5-1 tablespoon (5-15 mL) of your blood will be drawn trough the vein 
in your child forearm. We will also collect other non-invasive (not breaking, 
cutting, or entering the skin) samples such as sputum, urine, stool, 

 
 
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nasopharyngeal swab, etc. if clinically indicated. Samples collected by your 
child physicians can be included if leftover specimen is shared.  
• 
Based on your child’s weight, the amount of blood drawn in one take will be 
adjusted according to the table below: 
Your child’s body weight 
(Kilograms) 
Maximum blood volume 
per one take 
4.5 – 6.8 
5 ml 
7.3 – 18.2 
10 ml 
>18.2 
15 ml 
• The blood samples and other available samples will be processed for pathogen 
identification tests at INA-RESPOND Reference Laboratory. 
• The remaining blood samples and other available samples will be processed 
and stored for future research (you may decline storage of specimens of your 
child for future research). 
  
Additional Study Visit (Beyond Day 14 up to one month) 
If your child current episode of illness is deemed complex, where convalescent 
specimens (specimen that taken in recovering phase) are needed to identify etiology 
or where long-term sequelae are observed or anticipated, it is possible that additional 
follow up visit is conducted. Your child will have the following done for up to 30 minutes 
to 2 hours:  
• We will check your child height (if previously not done) and weight, blood 
pressure, heart and respiratory rate, body temperature, and current signs and 
symptoms. We will also collect information on other diseases or conditions, 
results on laboratory and imaging tests done by your child physicians, treatment 
and clinical outcome at this visit. 
• About 0.5-1 tablespoon (5-15 mL) of your child blood will be drawn through the 
vein in your child forearm. We will also collect other non-invasive (not breaking, 
cutting, or entering the skin) samples such as sputum, urine, stool, 
nasopharyngeal swab, etc. if clinically indicated. Samples collected by your 
child physicians can be included if leftover specimen is shared.  
• Based on your child’s weight, the amount of blood drawn in one take will be 
adjusted according to the table below: 
Your child’s body weight 
(Kilograms) 
Maximum blood volume 
per one take 
4.5 – 6.8 
5 ml 
7.3 – 18.2 
10 ml 
>18.2 
15 ml 
• The blood samples and other available samples will be processed for pathogen 
identification tests at INA-RESPOND Reference Laboratory.    
• The remaining blood samples and other available samples will be processed 
and stored for future research (you may decline storage of specimens of your 
child for future research). 

 
 
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Your child involvement in the study will last for up to 2 weeks to 1 month, unless there 
are situations or circumstances that may cause your child participation in this study to 
be dropped early. 
 
What are the risks and possible discomforts of being in this study? 
There is an anticipated risks and discomforts associated with blood draw. These 
include slight pain and redness or bruising at the site where the blood is drawn and in 
rare cases, fainting. Bruising may be alleviated by a warm compress. There is a very 
small chance the site where the blood is drawn may become infected. This is unlikely 
since the person drawing the blood will clean the site with alcohol before blood is taken 
and use a sterile needle and blood drawing material. 
 
What Happens If your Child Injured? 
We will provide immediate medical care for study-related injuries e.g. an infection 
where blood has been taken. The study cannot pay for long-term disability that may 
have resulted from the participant’s illness. 
 
 
What are the possible benefits of being in this study? 
Your child will not directly benefit from being in this study, except that if your child is in 
the study, your child will have closer medical follow-up than if you are not. Others in 
the future may benefit from knowledge gained during this research, as the study 
results may guide the future treatment OR diagnosis OR prevention of [indicate name 
of disease]. 
 
What are your responsibilities if your child participates? 
If you agree that your child to participate in the study, we expect you and your child to 
comply with the study visit schedule and procedure as previously described. You may 
decide at any time that you or your child do not want to take part in the study anymore. 
If you do so, we may ask your child to come for a final medical visit to check that 
everything is alright.  
 
Will you be paid to take part in this study? 
You and your child will not be paid to take part in this study, but we will reimburse you 
for your time and travel to and from the clinic for your child study visits for up to Rp 
150,000.00 per visit. Participating in the study will not incur any additional cost for you 
and your child. However, you will still have to pay for all the treatment you 
received as part of the hospital's medical treatment 
 
What will happen to the samples collected during the study? 
Samples collected during the study will be sent to INA-RESPOND Reference 
Laboratory for storage and analysis. If you agree, the stored samples may be used for 
future research on [indicate name of disease]. If we incidentally discover that your child 
has a severe, un-diagnosed disease we will inform you through your child physicians 
and make sure you have access to appropriate health care. 
 
How will we protect confidentiality? 
We will not share you and your child identity or that of any other study participant 
outside of the clinic. The only people who will know that your child is in the study are 

 
 
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members of the study team.  No information about you and your child or provided by 
you and your child during the study, will be disclosed to others, except under the 
circumstances described below. 
Your child name will not be mentioned on any sample, nor on the data collected during 
the study. Your child will be given a unique number, which will be used to identify the 
samples and data collected. If the results of this study get published in a scientific 
journal, your child name will not appear on the publication. All members of the study 
team commit to protect the confidentiality of the information you and your child provide. 
The members of the Ethics Committee, auditors, members of the drug regulatory 
authorities and the sponsor’s representatives may conduct assessments of the study 
and verify it is conducted according to best research practices. In doing so they may 
have to access your child personal information, however, all these people have to 
respect the confidentiality, and your personal information will not be revealed publicly. 
In addition, the Ministry of Health or designee may request access to your child 
personal information to prevent the further spread of [indicate name of disease] in your 
community.  
 
A description of this study will be available on www.ina-registry.org and 
www.ClinicalTrials.gov .These Web sites will not include information that can identify 
your child. At most, the Web sites will include a summary of the results. You can search 
this Web sites at any time. 
 
Will you and your child be informed of study findings? 
The knowledge that we gain from doing this research will be shared with you and your 
child through community meetings or through your child physicians. Likewise, during 
the course of the study, you and your child will be informed of any significant new 
findings, such as changes in the risks or benefits resulting from participation in the 
study or new alternatives to participation, that might cause you or your child to change 
your mind about continuing in the study.   
 
What should you do if you or your child want to stop taking part in the study? 
You and your child can stop being in the study at any time, and without providing any 
justification for this decision. If you or your child decide to withdraw from the study, it 
will not affect the quality of your child care, and your child will still receive treatment 
for [indicate name of disease], according to the standard of care in use in [indicate 
name of study site]. Any information collected up to the point of your child withdrawal 
cannot be removed from the study. This includes any sample collected up until the 
date of withdrawal, which will be kept and analyzed.  If you or your child decide to stop 
participating, please inform your study physicians or nurse.  
 
What situations or circumstances that may cause your child participation in this study 
to be dropped early? 
Your child involvement in the study will last for up to 2 weeks to 1 month, unless there 
are situations or circumstances that may cause your child participation in this study to 
be dropped early due to meet with below criteria: 
• 
Your child specimen has been identified for the pathogens based on the specimen 
analysis  
• 
Your child has discharged from hospital after Visit 2 

 
 
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• 
Your child has discharged from hospital and then completed Visit 2 and not require 
for additional visit 
• 
Your child decides to withdraw from study participation 
• 
You cannot be contacted and lost to follow-up or moves away from the study area 
• 
Participant dies 
• 
Your child was inadvertently enrolled such as not meeting the eligibility criteria 
• 
Investigator determines that further participation would be detrimental to your child 
health or well-being  
• 
The study is stopped for other administrative reasons 
 
If you or your child have questions or concerns about this study, whom can you call?  
If you have questions, concerns, or believe your child may have developed an injury 
related to this study, contact [indicate Principal Investigator name] at [give PI direct 
phone number]. 
This study protocol has been reviewed and approved by [indicate name of IRB], which 
is a committee whose task it is to make sure that study participants are protected from 
harm. If you wish to find out more about the Institutional Review Board (IRB), contact 
[name and phone number].   
 
 
 

 
 
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Informed Consent Form for Pediatrics 
Part II: Parental Consent Form 
INA-RESPOND Observational Research on Infectious Disease Outbreaks and 
Difficult Cases of Unidentified Etiology in Indonesia 
 
 I have read the study information sheet, or the information sheet has been read to 
me. I have had the opportunity to ask questions about it and any questions I have 
asked has been answered to my satisfaction. I have been explained that I may 
withdraw from this study at any time. 
 I freely and voluntarily choose my child to participate in this study. I will be given a 
copy of this information sheet and signed consent form to keep for my reference. 
 
I agree to the storing of my child blood for future research. 
☐  YES 
☐  NO 
 
 
Participant/Child Name: 
___________________ 
Date of birth: 
___/___/____ (dd/mm/yy) 
Parental relationship or legal 
custodianship with the child: 
___________________ 
Date of Consent: 
___/___/____ (dd/mm/yy) 
 
 
Time of Consent: 
___________________ 
Name of Parent/Legal 
Guardian: 
___________________ 
Signature*: 
___________________ 
 
 
 
 
 
 
 
 
 
Name of the Investigator: 
_____________________ 
Signature: 
___________________ 
Date of Consent: 
___/___/___   (dd/mm/yy) 
Time of Consent: 
___________________ 
 
 
 
 
 
 
 
 
 
 
 
 
Name of Witness: 
_____________________ 
Signature: 
___________________ 
Date of Consent: 
___/___/___   (dd/mm/yy) 
Time of Consent: 
___________________ 
 
 
 
 
*a thumb print can be used if the person cannot write 
 
 
 

 
 
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Informed Consent Form for Pediatrics 
Part II: Assent Consent Form 
INA-RESPOND Observational Research on Infectious Disease Outbreaks and 
Difficult Cases of Unidentified Etiology in Indonesia 
 
 
I have read the study information sheet, or this information sheet has been read to me. I 
have had the opportunity to ask questions about it and any questions I have asked to have 
been answered to my satisfaction. I have been explained that I may withdraw from this 
study at any time. 
 
I freely and voluntarily choose to participate in this study. I will be given a copy of this 
information sheet and signed consent form to keep for my reference. 
 
I agree to the storing of my blood for future research. 
  YES  
  NO 
 
 
Participant Name: 
___________________ 
Date of birth: 
___/___/____ (dd/mm/yy) 
 
 
 
 
Signature*: 
___________________ 
Age: 
___________________ 
 
 
 
 
Date of Consent: 
___/___/____ (dd/mm/yy) 
Time of Consent: 
___________________ 
 
 
 
 
Parental relationship or 
legal custodianship with 
the child: 
___________________ 
Date of Consent: 
___/___/____ (dd/mm/yy) 
 
 
Time of Consent: 
___________________ 
Name of Parent/Legal 
Guardian: 
___________________ 
Signature*: 
___________________ 
 
 
 
 
 
 
 
 
 
Name of the Investigator: 
_____________________ 
Signature: 
___________________ 
Date of Consent: 
___/___/___   (dd/mm/yy) 
Time of Consent: 
___________________ 
 
 
 
 
 
 
 
 
 
 
 
 
Name of Witness: 
_____________________ 
Signature: 
___________________ 
Date of Consent: 
___/___/___   (dd/mm/yy) 
Time of Consent: 
___________________ 
 
 
 
 
*a thumb print or mark “X” can be used if the person cannot write or illeterate 
 

 
 
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Page 1 of 8  
Informed Consent Form for Adults 
Part I: Information Sheet 
Title of study:  
 
INA-RESPOND Observational Research on Infectious Disease 
Outbreaks and Difficult Cases of Unidentified Etiology in 
Indonesia 
Protocol number:  INA107 
Sponsors: 
National Institute of Health Research and Development, Ministry 
of Health of Indonesia and the National Institute of Allergy and 
Infectious Diseases, National Institutes of Health of the United 
States of America 
Site Number: 
 
Site PI Name: 
 
Site Address: 
 
Site PI Contact: 
 
Participant’s 
Name: 
 
Participant’s ID: 
 
 
I am [insert name of Site Investigator or designee], working for [indicate Site name] of 
the Indonesia Reseach Partnership on Infectious Diseases (INA-RESPOND). The 
INA-RESPOND is a research collaboration on infectious diseases between the 
National Institute of Health Research and Development, Ministry of Health of 
Indonesia and the National Institute of Allergy and Infectious Diseases, National 
Institutes of Health of the United States of America.  
We are doing research on [indicate name of disease], which is affecting a lot people 
in Indonesia. I am going to give you information and invite you to be part of the study 
we are conducting. Before you decide whether you will participate or not, you can talk 
to a friend, a family member or anyone else you feel comfortable with. We will do our 
best to facilitate the communication.  
If I use some words that you do not understand, please ask me to stop and I will take 
time to explain.  If you have questions later, you can ask them of me or [indicate all 
research staff with whom participant will be in contact, e.g. study nurse, study 
physicians, research assistants, etc]. 
This Informed Consent Form has two parts:  
 
• Information Sheet (to share information about the study with you)  
 
• Consent Form (for signatures if you agree to take part) 
 
Why is this research being done? 
You are being asked to take part in this research because you have been clinically 
diagnosed with [indicate name of disease] OR because we suspect you have [indicate 
name of disease] OR because you have been in contact with someone who has 
[indicate name of disease]. This research aims to understand the scope of pathogens 
(agent or organism that causes disease) responsible for outbreaks and difficult clinical 

 
 
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Page 2 of 8  
cases in Indonesia, and to characterize the clinical course of the diseases to better 
inform diagnostics, treatments and prevention strategies. 
 
What is the study about? 
This study is about identifying the causative agents and describe the clinical conditions 
or characteristics of presumptive infections. It will involve data collection on 
demographics, medical history and clinical examination, and blood samples collection.  
 
Is study participation mandatory? 
Your participation in this study is entirely voluntary. It is your choice whether to 
participate or not. Whatever your decision, you will still access all health care services 
at your local clinic or hospital. If you decide to participate, you will be asked to sign the 
consent form at the end of this document to show that you agree. You can decide to 
participate now and change your mind later during the study. This will have no negative 
consequence for you or your health. 
 
How many people will be in this study?  
The study is being conducted in Indonesia, particularly in 19 hospitals member of the 
INA-RESPOND Network (RSUPN Dr. Cipto Mangunkusumo, RS Persahabatan, and 
RSPI Prof. Dr. Sulianti Saroso, RS St. Carolus, Jakarta; RSUD Kab. Tangerang, 
Banten; RSUP Dr. Hasan Sadikin, Bandung; RSUP Dr. Sardjito, Yogyakarta; RSUP 
Dr. Kariadi, Semarang; RSUD Dr. Soetomo, Surabaya; RSUP Dr. Wahidin 
Sudirohusodo, Makassar; RSUP Sanglah, Denpasar; RSUP Adam Malik, Medan; RS 
Budi Kemuliaan, Batam; RSUD Zainoel Abidin, Banda Aceh;  RSUD Ansari Saleh, 
Banjarmasin; RSUD Abdul Wahab Sjahranie, Samarinda; RSUD Soedarso, Pontianak; 
RSUD TC Hilers, Sikka; RSUD Abepura, Jayapura) for five years from 2020 to 2025. 
We plan to include up to 5,000 participants. We are inviting all adults OR all children 
with [indicate name of disease] to participate in the study.  
 
What will happen if you decide to participate in this study? 
If you agree to be part of the study, you will be asked to complete the study visits twice, 
at enrolment and baseline visit (day 0) and follow up visit (day 7-14) to conduct data 
and blood sample collection. 
 
Screening 
We will evaluate your eligibility to take part in this study. The screening procedures will 
take up to 30 minutes. 
You may be enrolled in this study if you meet all the following criteria: 
1. You are adult of any age hospitalized with a current episode of illness with a 
presumed infectious disease of unidentified etiology 
2. You tested negative for Dengue virus infection by an antigen-based and antibody-
based diagnostic test (i.e. NS1 antigen test and Dengue-specific IgM test) 
3. You tested negative for Salmonella Typhi infection by Standard of Care testing (i.e. 
blood culture, Widal test, or Tubex rapid test) 
4. You are able to provide a documented informed consent 
5. You agree to the collection and storage of specimens for laboratory testing and/or 
future research (you may decline storage of specimens for future research) 

 
 
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However, if your Site PI advised you not to take part in this study to protect your safety 
and wellbeing, you may not be enrolled in this study. 
 
Enrolment and Baseline Visit (Day 0) 
After you are enrolled in this study, we will collect your baseline information. This 
procedure may take up to 30 minutes to 2 hours, you will have the following done: 
• We will ask you some questions about your general information, such as age, 
gender, residence and occupation. We will also ask you some questions about 
your medical history, such as your travel history, contact history to suspected 
human cases, insect or animal exposure, vaccination history, and medication 
use prior to enrolment. 
• We will check your height and weight, blood pressure, heart and respiratory 
rate, body temperature, and current signs and symptoms. We will also collect 
information on other diseases or conditions, results on laboratory and imaging 
tests done by your physicians, treatment and clinical outcome at this visit. 
• About 0.5-1 tablespoon (5-15 mL) of your blood will be drawn through the vein 
in your forearm. We will also collect other non-invasive (not breaking, cutting, 
or entering the skin) samples such as sputum, urine, stool, nasopharyngeal 
swab, etc. if clinically indicated. Samples collected by your physicians can be 
included if leftover specimen is shared.  
• Routine hematology, blood chemistry, liver and renal function tests will be done 
to the collected blood samples. The remaining blood samples and other 
available samples will be processed for pathogen identification tests at INA-
RESPOND Reference Laboratory. 
• The remaining blood samples and other available samples will be processed 
and stored for future research (participants may decline storage of specimens 
for future research). 
 
Follow Up Visit (Day 7-14) 
Approximately 1-2 weeks after baseline evaluation, the study staff will contact you and 
continue with the study follow up. During which, you will have the following done for 
up to 30 minutes to 2 hours:  
• We will check your height (if previously not done) and weight, blood pressure, 
heart and respiratory rate, body temperature, and current signs and symptoms. 
We will also collect information on other diseases or conditions, results on 
laboratory and imaging tests done by your physicians, treatment and clinical 
outcome at this visit. 
• About 0.5-1 tablespoon (5-15 mL) of your blood will be drawn trough the vein 
in your forearm. We will also collect other non-invasive (not breaking, cutting, 
or entering the skin) samples such as sputum, urine, stool, nasopharyngeal 
swab, etc. if clinically indicated. Samples collected by your physicians can be 
included if leftover specimen is shared.  
• The blood samples and other available samples will be processed for pathogen 
identification tests at INA-RESPOND Reference Laboratory. 

 
 
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• The remaining blood samples and other available samples will be processed 
and stored for future research (participants may decline storage of specimens 
for future research). 
  
Additional Study Visit (Beyond Day 14 up to one month) 
If your current episode of illness is deemed complex, where convalescent specimens 
(specimen that taken in recovering phase) are needed to identify etiology or where 
long-term sequelae are observed or anticipated, it is possible that additional follow up 
visit is conducted. you will have the following done for up to 30 minutes to 2 hours:  
• We will check your height (if previously not done) and weight, blood pressure, 
heart and respiratory rate, body temperature, and current signs and symptoms. 
We will also collect information on other diseases or conditions, results on 
laboratory and imaging tests done by your physicians, treatment and clinical 
outcome at this visit. 
• About 0.5-1 tablespoon (5-15 mL) of your blood will be drawn through the vein 
in your forearm. We will also collect other non-invasive (not breaking, cutting, 
or entering the skin) samples such as sputum, urine, stool, nasopharyngeal 
swab, etc. if clinically indicated. Samples collected by your physicians can be 
included if leftover specimen is shared.  
• The blood samples and other available samples will be processed for pathogen 
identification tests at INA-RESPOND Reference Laboratory.    
• The remaining blood samples and other available samples will be processed 
and stored for future research (participants may decline storage of specimens 
for future research). 
 
Your involvement in the study will last for up to 2 weeks to 1 month, unless there are 
situations or circumstances that may cause your participation in this study to be 
dropped early. 
 
What are the risks and possible discomforts of being in this study? 
There is an anticipated risks and discomforts associated with blood draw. These 
include slight pain and redness or bruising at the site where the blood is drawn and in 
rare cases, fainting. Bruising may be alleviated by a warm compress. There is a very 
small chance the site where the blood is drawn may become infected. This is unlikely 
since the person drawing the blood will clean the site with alcohol before blood is taken 
and use a sterile needle and blood drawing material. 
 
What Happens If I Am Injured? 
We will provide immediate medical care for study-related injuries e.g. an infection 
where blood has been taken. The study cannot pay for long-term disability that may 
have resulted from the participant’s illness. 
 
What are the possible benefits of being in this study? 
You will not directly benefit from being in this study, except that if you are in the study, 
you will have closer medical follow-up than if you are not. Others in the future may 
benefit from knowledge gained during this research, as the study results may guide 
the future treatment OR diagnosis OR prevention of [indicate name of disease]. 
 

 
 
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What are your responsibilities if you participate? 
If you agree to participate in the study, we expect you to comply with the study visit 
schedule and procedure as previously described. You may decide at any time that you 
do not want to take part in the study anymore. If you do so, we may ask you to come 
for a final medical visit to check that everything is alright.  
 
Will you be paid to take part in this study? 
You will not be paid to take part in this study, but we will reimburse you for your time 
and travel to and from the clinic for your study visits for up to Rp 150,000.00 per visit. 
Participating in the study will not incur any additional cost for you. However, you will 
still have to pay for all the treatment you received as part of the hospital's 
medical treatment. 
 
What will happen to the samples collected during the study? 
Samples collected during the study will be sent to INA-RESPOND Reference 
Laboratory for storage and analysis. If you agree, the stored samples may be used for 
future research on [indicate name of disease]. If we incidentally discover that you have 
a severe, un-diagnosed disease we will inform you through your physicians and make 
sure you have access to appropriate health care. 
 
How will we protect confidentiality? 
We will not share your identity or that of any other study participant outside of the clinic. 
The only people who will know that you are in the study are members of the study 
team.  No information about you, or provided by you during the study, will be disclosed 
to others, except under the circumstances described below. 
Your name will not be mentioned on any sample, nor on the data collected during the 
study. You will be given a unique number, which will be used to identify the samples 
and data collected. If the results of this study get published in a scientific journal, your 
name will not appear on the publication. All members of the study team commit to 
protect the confidentiality of the information you provide. The members of the Ethics 
Committee, auditors, members of the drug regulatory authorities and the sponsor’s 
representatives may conduct assessments of the study and verify it is conducted 
according to best research practices. In doing so they may have to access your 
personal information, however, all these people have to respect the confidentiality, 
and your personal information will not be revealed publicly. 
In addition, the Ministry of Health or designee may request access to your personal 
information to prevent the further spread of [indicate name of disease] in your 
community.  
 
A description of this study will be available on www.ina-registry.org and 
www.ClinicalTrials.gov. These Web sites will not include information that can identify 
you. At most, the Web sites will include a summary of the results. You can search this 
Web sites at any time. 
 
Will you be informed of study findings? 
The knowledge that we gain from doing this research will be shared with you through 
community meetings or through your physicians. Likewise, during the course of the 
study, you will be informed of any significant new findings, such as changes in the 

 
 
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risks or benefits resulting from participation in the study or new alternatives to 
participation, that might cause you to change your mind about continuing in the study.   
 
What should you do if you want to stop taking part in the study? 
You can stop being in the study at any time, and without providing any justification for 
this decision. If you decide to withdraw from the study, it will not affect the quality of 
your care, and you will still receive treatment for [indicate name of disease], according 
to the standard of care in use in [indicate name of study site]. Any information collected 
up to the point of your withdrawal cannot be removed from the study. This includes 
any sample collected up until the date of withdrawal, which will be kept and analyzed.  
If you decide to stop participating, please inform your study physicians or nurse.  
 
What situations or circumstances that may cause your participation in this study to be 
dropped early? 
Your involvement in the study will last for up to 2 weeks to 1 month, unless there are 
situations or circumstances that may cause your participation in this study to be 
dropped early due to meet with below criteria: 
• 
Your specimen has been identified for the pathogens based on the specimen analysis  
• 
You have discharged from hospital after Visit 2 
• 
You have discharged from hospital and then completed Visit 2 and not require for 
additional visit 
• 
You decide to withdraw from study participation 
• 
You cannot be contacted and lost to follow-up or moves away from the study area 
• 
Participant dies 
• 
You were inadvertently enrolled such as not meeting the eligibility criteria 
• 
Investigator determines that further participation would be detrimental to your health 
or well-being  
• 
The study is stopped for other administrative reasons 
 
If you have questions or concerns about this study, whom can you call?  
If you have questions, concerns, or believe you may have developed an injury related 
to this study, contact [indicate Principal Investigator name] at [give PI direct phone 
number]. 
This study protocol has been reviewed and approved by [indicate name of IRB], which 
is a committee whose task it is to make sure that study participants are protected from 
harm. If you wish to find out more about the Institutional Review Board (IRB), contact 
[name and phone number].  
 

 
 
Informed Consent Form for Adults Version 1.1 Dated 05MAY2020 
Based on INA107 Protocol Version 1.1 Dated 05MAY2020 
 
 
Page 7 of 8  
Informed Consent Form for Adults 
Part II: Consent Form 
INA-RESPOND Observational Research on Infectious Disease Outbreaks and 
Difficult Cases of Unidentified Etiology in Indonesia 
 
 I have read the study information sheet, or the information sheet has been read to 
me. I have had the opportunity to ask questions about it and any questions I have 
asked has been answered to my satisfaction. I have been explained that I may 
withdraw from this study at any time. 
 I freely and voluntarily choose to participate in this study. I will be given a copy of 
this information sheet and signed consent form to keep for my reference. 
 
I agree to the storing of my blood for future research. 
☐  YES 
☐  NO 
 
Printed Name of 
Participant: 
_____________________ 
Date of birth: 
___/___/____ (dd/mm/yy) 
Signature: 
 
Date: 
___/___/____ (dd/mm/yy) 
 
 
_____________________ 
Time of 
Consent: 
_____________________ 
 
 
 
 
 
 
 
 
Printed Name of 
the Investigator: 
_____________________ 
Signature: 
_____________________ 
Date: 
___/___/____ (dd/mm/yy) 
Time of 
Consent: 
_____________________ 
 
 
 
 
 
 
 
 
Printed Name of 
Witness: 
_____________________ 
Signature: 
_____________________ 
Date: 
___/___/____ (dd/mm/yy) 
Time of 
Consent: 
_____________________ 
 
 
 
 
 
 
 

 
 
Informed Consent Form for Adults Version 1.1 Dated 05MAY2020 
Based on INA107 Protocol Version 1.1 Dated 05MAY2020 
 
 
Page 8 of 8  
**COMPLETE THIS SECTION ONLY IF THE PARTICIPANT IS UNCONSCIOUS OR TOO ILL TO 
CONSENT 
Participant Name: 
_____________________ 
Date of birth: 
___/___/____ (dd/mm/yy) 
Relationship with the 
Participant: 
_____________________ 
Date of Consent: 
___/___/____ (dd/mm/yy) 
 
 
Time of Consent: 
___________________ 
Name of Parent/ Spouse/ 
Legal Guardian: 
_____________________ 
Signature*: 
___________________ 
Name of the Investigator: 
_____________________ 
Signature: 
___________________ 
Date of Consent: 
___/___/___   (dd/mm/yy) 
Time of Consent: 
___________________ 
Name of Witness: 
_____________________ 
Signature: 
___________________ 
Date of Consent: 
___/___/___   (dd/mm/yy) 
Time of Consent: 
___________________ 
 
 
 
 
*A thumbprint or mark “X” can be used if the person cannot write or illiterate 
** In case of severely ill participants, informed consent will be obtained by LAR (Legally Authorized 
Representative) and at first opportunity of well episode, the participant will be reconsented.