Table 1. Summary of articles included in the review.
Author and Reference
Study Location
Sample Size
Specimen Sources/ Sample Type
Targeted pathogens
Virus Identified
Study Population
Type of study
Findings
Corwin et al. 1998 16
Irian Jaya
NA
NA
influenza virus
influenza A
Young adults between 15–44 years of age
Outbreak reporting, Case and control study
Young adults aged 15–44 years accounted for the largest percentage of influenza virus outbreak-related deaths
Djelantik et al. 2003 60 Lombok Island 2677 Nasopharyngeal washes RSV RSV Children between 0-2 years of age with severe lower respiratory illness Hospital based passive surveillance study For children 0-1 and 0-2 years of age, the estimated incidence of severe RSV LRI hospitalization was 25 per 1000 child-years and 14 per 1000 child-years respectively
Djelantik et al. 2003 59
Lombok Island
4351
NA
NA
RSV
Children 0-2 years of age admitted for pneumonia
Population based retrospective cohort study
Among children hospitalized for pneumonia, age < 4 months and hypoxia were identified as higher risk factors for death
Beckett et al. 2004 17
Jakarta, West Java, Yogyakarta, Makassar, Sulawesi, and Bali
1544
Nasal and pharyngeal swabs
influenza virus
influenza A (H1N1 and H3N2)
Adults (age, >14 years) and children (age, 4–14 years) with respiratory symptoms
Laboratory based passive surveillance study
Peak prevalence of influenza infection tended to coincide with the respective rainy seasons
Robertson et al. 2004 56 West Java 640 Nasopharyngeal specimens RSV RSV children between 0- 5 years of age Hospital based passive RSV surveillance The incidence of RSV-associated LRI per 1000 child-years was 34 in Indonesia. In Indonesia and Mozambique, RSV cases occurred primarily during the rainy season
Kandun et al. 2006 29
Jakarta
8
Serum, nasaland , throat swabs, tracheal aspirates
influenza A H5N1
influenza A H5N1
Patients between 1-38 years of age with avian influenza H5N1 infection
Outbreak investigation
Clusters of human infection with clade 2 H5N1 viruses included mild, severe, and fatal cases amongst family members
Sedyaningsih et al. 2007 34
West Java, North Sumatera
598
Throatand, nasal swab, serum, endotracheal aspirates and washes, lung-biopsy
influenza A H5N1
influenza A H5N1
Patients with suspected H5N1 virus infection with a median age of 18.5 years.
Outbreak investigation
Sporadic and family clusters of cases of avian influenza H5N1 infection, with a high case-fatality proportion, occurred throughout Indonesia during 2005–2006
Giriputro et al. 2008 30 Jakarta 296 NA influenza A H5N1 influenza A H5N1 Children and adults 1- 40 years of age Retrospective case series Most patients were younger and had indirect contact with infected poultry. The majority of cases were presented to the hospital after having systemic inflammatory response syndrome (SIRS)
Kandun et al. 2008 38
Indonesia (location not defined)
127
NA
influenza A H5N1
influenza A H5N1
Patients with a median age of 20 years with H5N1 infection
Case series
Early identification of suspected cases for treatment was difficult because of the very low incidence of the influenza and the common occurrence of ILI
Omer et al 2008 58 Lombok island 2878 Nasopharyngeal swabs RSV RSV Hospitalized children between 0-2 years of age Hospital based passive surveillance study for Haemophilus influenza type B (Hib) project Statistical association of monsoon-associated weather with localized RSV outbreaks suggested local factors influence RSV disease transmission
Santhia et al 2009 31
Bali
87
Serum, cloacal, tracheal swabs, throat and nasal swabs
influenza A H5N1
influenza A H5N1
Household participants from village with H5N1 outbreaks; Humans, Birds (poultry), pigs/swine survey at live bird markets
Behavioral, virological and seroepidemiological survey
Transmission of H5N1 to humans remained a rare event despite high levels of handling both healthy and sick birds
Adisasmito et al. 2010 39 Throughout Indonesia 93 NA influenza A H5N1 influenza A H5N1 Laboratory-confirmed H5N1 influenza cases with median age of 18 years Observational study Fatality, due to influenza A H5N1, may be related to delay in initiation of treatment after presentation
Dilantika et al. 2010 18
Jakarta, Java, Yogyakarta, Bali, Sulawesi, North Sumatra
733
Stool samples, nasal and throat swabs
influenza virus
influenza A (H1N1 and H3N2) Influenza B
Pediatric patients (0-6 years of age) presenting with concurrent diarrhea and influenza-like illness
Hospital based passive surveillance study
In children, the influenza virus infection may be localized in the gastrointestinal tract and cause pediatric diarrhea
Ramadhany et al. 2010 19
8 provinces of Indonesia
549
Nasal and throat swabs
influenza virus
i influenza A (H1N1) and influenza B
SARI patients
Hospital based passive SARI surveillance
There were 21 (4%) cases caused by influenza A and 12 (2%) caused by influenza B
Vivi et al. 2010 36
Jakarta, Sukabumi
711
Sera
influenza A H5N1
influenza A H5N1
Poultry farmers and workers in poultry processing facilities
Observational study
Poultry workers were found to have asymptomatic H5N1 virus infection but no viral antibodies were detected among poultry farmers
Yupiana et al. 2010 37 Java 794 NA influenza A H5N1 influenza A H5N1 Humans and poultry Descriptive epidemiological study and outbreak investigation Human infection with avian influenza H5N1 was associated with poultry outbreaks
Aditama et al. 2011 67 Throughout Indonesia 139 NA influenza A H5N1 influenza A H5N1 Risk factors for avian influenza H5N1 infection were analyzed among a population all age groups. Outbreak investigation Avian influenza H5N1 infection is influenced by, and may even depend on, host genetic susceptibility
Simoes et al. 2011 57 Kota Bandung 2014 NA RSV RSV Children between 0-5 years of age Cohort study In children between 0-6 months old, the incidence of RSV associated lower respiratory infection was relatively low (less than 5%), most RSV-related disease occurred in older children
Yamaoka et al. 2011 68 East Java 635 Pharyngeal swabs influenza virus influenza A(H3N3, pandemic H1N1 2009), influenza B Patients ranging from all age groups. Hospital based passive ILI surveillance study Younger patients with milder symptoms were found to have pandemic (H1N1) 2009 viruses
Aditama et al. 2012 69
Throughout Indonesia
673
Serum, nasal and throat swabs
influenza A H5N1
influenza A H5N1
Children and adults from 0-30 years of age
Outbreak Investigation and disease transmission analysis
The overall household attack rate was 18.3% and secondary attack rate was 5.5%. The mean interval between onset of subsequent cases in outbreaks was 5.6 days.
Agustiningsih et al. 2012 70
Throughout Indonesia
230
Nasal and throat swabs, tracheal aspirate, bronchoalveolar lavage
influenza A/H5N1
influenza A, enteroviru, human rhinoviru, CoV 229E/NL 63, HADV, BoV, parainfluenza virus -1,2,3, 4
Hospitalized suspected influenza H5N1 patients with ARI Children: 0-17 years of age Adults:15- 60 years of age
NA
In children and adults, bacterial infections remain the most common etiologies of acute respiratory infections although there were infections caused by viruses. Bacterial and viral co-infections were identified among adults and children
Prawira et al. 2012 71 Jakarta 321 NA influenza A H5N1 influenza A H5N1 Hospitalized patients with influenza A H5N1 with median ages of 7 and 25 years of age for children and adults respectively, NA Patients usu­ally developed rapid clinical deterioration and fatal outcomes. Deaths were mostly due to Acute Respiratory Distress Syndrome and usually occurred on day 7. Adults had a higher mortality rate
Kosasih et al. 2013 13
Sumatra, Java, Kalimantan, Bali, Lombok, Sulawesi, Maluku, Timor, Papua
21030
Nasal and throat swabs
influenza Virus
influenza A(H3N2,H1N1), influenza A H5N1, Influenza B
ILI patients with a median age of 17 years (mean age, 21.1 years; range, 1 month- 90 years of age)
Primary health centers and hospitals based passive ILI surveillance
Among outpatients and hospitalized patients, influenza A and B showed year-round circulation and were important causes of ILI.
Ikawati et al. 2014 26 Java 625 NA NA influenza A, influenza B, influenza A subtypes H1, H3, H5, pH1 Children between 0-5 years of age and adults >50 years of age Passive ILI surveillance using National institute of health research and development (NHRD) data ILI cases occurred most commonly in children aged 0-5 years old. Males tended to experience ILI more frequently than females. ILI cases occur mostly among children aged 0-5 and 6-12 years old. The incidence of ILI dropped in 13–17-year-olds but increased again in the 18-34 age groups.
WHO et al. 2014 72 Throughout Indonesia 3 NA influenza A H5N1 influenza A H5N1 NA NA NA
Pangesti et al. 2014 20 Throughout Indonesia 333 Serum, nasal and throat swabs influenza virus influenza A, H3, pH1, H5 Adults and children from all age groups Hospital based passive SARI surveillance Among the total SARI cases the proportion of influenza A was 5 % and influenza B was 1%.
Zaman et al. 2014 35
Azerbaijan, Indonesia, Pakistan and Turkey
259
NA
influenza A H5N1
influenza A H5N1
Patients with possible or confirmed H5N1 infection with a median age of 17 years
Used data from international patients registry for human cases of avain influenza
Confirmed cases were more likely to have had direct contact with another confirmed case. Unexplained respiratory illness, sore throat, excess sputum production, and rhinorrhea were more frequent in possible cases
Caini et al. 2015 73
Global
3653
NA
influenza virus
influenza A, influenza B
Outpatients and Inpatients
Passive surveillance, used data from national influenza centers of 43 countries.
Influenza B co-circulates with influenza A and accounts for roughly 20% of total cases in all regions of the world
Farida et al. 2015 74
Semarang
148
Sputum, throat swabs, blood, sera, urine
viruses and bacteria
influenza A, influenza B, rhino virus, parainfluenza virus, human coronavirus (HcoV OC43), adeno virus, human metapneumovirus, RSV
Adult patients admitted with community acquired pneumonia with a median age of 58 years
Prospective cohort study
Viruses and gram-negative bacilli are dominant causes of community acquired pneumonia in Semarang and Central Java
Prasetyo et al.2015 64 Central Java 106 Nasal and throat swabs respiratory viruses and torque teno viruses influenza A H3, influenza B virus, HMPV, HRV, adeno virus, human corona virus (HCoV-OC43), HPIV, TTV Adult patients with ARI, ILI, or SARI ranging from 0-20 and >81 years of age Hospital based passive ILI and SARI surveillance First report of the circulation of HMPV, human adenovirus B, HCoV-OC43, and HPIV-3 in Indonesia
Storms et al. 2015 21 East Jakarta 5065 NA influenza virus influenza A (pandemic (H1N1) 2009, H3), influenza A H5N1, influenza B Outpatients with ILI and hospitalized patients with SARI in all age groups. Hospital based passive ILI surveillance 34.5% of ILI cases and 15.4 % of SARI cases were tested positive for influenza A,
Wertheim et al. 2015 61
Thailand, Vietnam and Indonesia
225 (Indonesia )
Nasal, and throat swabs, nasopharyngeal, and tracheal aspirates, nasal wash, bronchoalveolar lavage
viruses and bacteria
entero virus, rhinovirus, boca virus, RSV, para influenza virus -1,2,3,4 adenovirus, influenza A, and B, HMPV, coronavirus (HCoV-OC43), coronavirus e229, enteroviruses, paraecho virus,
Patients hospitalized with suspected influenza 0-5 and > 65 years of age
Passive surveillance from archived samples
In patients hospitalized with ILI, respiratory viruses were the most commonly detected pathogen. Rhinovirus was the most frequently detected virus accounting for 32% of the patients in whom viral pathogens were detected.
Caini et al. 2016 28 Global 4231 NA influenza virus influenza A, influenza B NA Retrospective analysis of surveillance data (2000 -2014) Reliable surveillance data is not yet available for many countries in the intertropical belt
Wiyatno et al 2016 63 Bandung 209 Preserved sera coxsackievirus coxsackievirus Archived specimens available from non-dengue cases Retrospective study from archived samples The first case of coxsackievirus (CVB3) from an undifferentiated febrile illness specimen from Indonesia
Adam et al. 2017 75
Sumatra, Java, Kalimantan, Sulawesi, East Indonesia
334
Nasal and throat swabs
NA
influenza A, influenza B, RSV, rhinovirus adeno virus, enterovirus, parainfluenza virus, bocavirus ILI patients with a median age of 9 years
Hospital based passive ILI surveillance
The most frequent combination of viruses identified were adenovirus and human rhinovirus
Haji et al. 2017 32
Global
175 (Indonesia)
NA
influenza A H5N1
influenza A H5N1
Individuals 0-16 and >63 years of age
Retrospective analysis of data reported to WHO (1997-2017)
Mortality in Indonesia due to H5N1 remained high
Root et al. 2017 27 West Java 163014 Nasal and oropharyngeal swabs influenza virus influenza A (H3N2, H1N1 pdm09, H1N1), influenza B Patients between 0-5 years of age with ILI cases and symptoms Hospital based passive influenza surveillance In rural Indonesian households with young children and poultry, there was an increase in influenza A virus infections.
Amin et al. 2018 76
East Java
28,197
Oropharyngeal swabs
MERS-CoV
MERS-CoV
Returning Hajj Pilgrims with body temperature of > 38 °C accompanied by respiratory symptoms
Active surveillance
Absence of infection due to MERS-CoV
Pawestri et al. 2018 77
24 Provinces of Indonesia
4752
Nasopharyngeal and oropharyngeal swabs
influenza virus
influenza A( H1N1 pdm09)
Patients with ILI and SARI
Hospital based passive ILI and SARI surveillance
Indicated the first occurrence of oseltamivir resistant influenza A, (H1N1)pdm09 viruses in Indonesia
Susilarini et al. 2018 10 Yogyakarta, East Kalimantan, North Sumatera 1527 Respiratory specimens influenza virus Influenza A( H1N1 pdm09,H3N2), influenza B Inpatients screening for SARI, in patients 0-4 and > 70 years of age. Public health center and hospital based active SARI surveillance The overall estimated annual incidence of influenza-associated SARI ranged from 13-19 per 100 000 population Incidence was highest in children aged 0-4 years (82-114 per 100 000 population)
Wignjadiputro et al. 2018 78 North Sumatera, East Kalimantan, Yogyakarta, West Nusa Tenggara, North Sulawesi, Maluku 1806 Nasal and throat swabs influenza virus Influenza A(H3N2, H1N1)pdm09 and influenza B viruses. Patients with SARI cases from 0-1 and ≥65 years of age. Hospital based passive SARI surveillance study Indonesia’s SARI surveillance system is flexible to incorporate surveillance for other viruses
Wiyatno et al 2018 62
Jakarta
1
Serum, nasal swabs
rhinovirus C
rhinovirus C
4-year-old boy with increasing breathlessness for a week
Case report
In a child with acute onset of dilated cardiomyopathy, there was a possible association of rhinovirus C and myocarditis
Lafond et al. 2019 22
Jakarta
9819
Nasal and throat swabs
influenza virus
influenza A ( H1N1 pdm09, H3N2), influenza A H5N1, influenza B
ILI case patients, SARI case patients between 0-5 or ≥65 years of age.
Public health centers based passive surveillance
31% of ILI case-patients and 15% of SARI case-patients tested positive for influenza virus Influenza A(H1N1)pdm09, influenza A(H3N2), and influenza B virus infections were detected for 3 years, and the epidemic season extended from November through May
Pawestri et al. 2019 33 15 provinces of Indonesia 180 Nasal, pharyngeal, pleural, tracheal, bronchial, rectal, fecal, blood specimens influenza A H5N1 influenza A H5N1 Patients with H5N1 infection, from 1- 67 years of age. Retrospective study from clinical specimens Of the 180 studied cases, 153 (85 %) were fatal. The case fatality rate increased from 73% in 2005 to 100% in 2012 and subsequent years
Setianingsih et al. 2019 23
Jakarta
13
Sputum, oropharyngeal swabs, nasal swabs, nasopharyngeal swabs, and serum
MERS-CoV, alphavirus,flavivirus, para myxovirus, herpes virus, henipa virus, hanta Virus, arenavirus and human metapneumovirus
influenza virus (H1N1,H3N2) enterovirus (EV D68, rhinovirus C, and A60) Coronavirus 229E, flavivirus, alphavirus, herpes simplex 1 virus, human metapneumovirus, dengue 3 virus
Hospitalized patients with suspected MERS-CoV infection.Majority of patients presented with pneumonia and symptoms of fever, dyspnea, and cough ranging from 32- 79 years of age
Observational study
The etiological agents detected in the samples were enterovirus D68, dengue virus type 3, rhinovirus C, HCoV-229E, HSV-1, influenza virus H1N1, influenza virus H3N2, HMPV, and rhinovirus A60
Anggraini et al. 2020 48 Surakarta 9 Blood, nasal and throat swabs NA SARS CoV-2 Pregnant women with SARS CoV-2 that were ≥20 years of age Observational study Pregnant women with neutrophil to lymphocyte ratio (NLR) of < 58 had a decreased risk of COVID-19
Asyary et al. 2020 40 Jakarta NA NA NA NA Patients with SARS CoV-2 Cross sectional study Higher duration of sunlight exposure was related to more cases of recovery from COVID-19 disease among patients
Burhan et al. 2020 79 Jakarta 3 NA SARS CoV-2 SARS CoV-2 Patients with SARS CoV-2 47-year-old man Case report CT-Scan might be a better diagnostic tool compared to RT-PCR in diagnosing COVID-19
Gasem et al. 2020 80 Jakarta, Bandung, Yogyakarta, Semarang, Suryabaya, Bali, Makassar 1,486 Blood, nasal swabs, sputum, feces, urine Pathogens causing febrile illness NA Children and adults ≥1 year of age, with body temperature of ≥38°C, and being hospitalized within the past 24 hours Longitudinal cohort study Indicated a lack of diagnosis of influenza in hospitals where most cases were diagnosed as non-specific upper respiratory tract infections or pneumonia
Gunadi et al. 2020 54 Yogyakarta 15 Nasopharyngeal swabs SARS-CoV-2 SARS-CoV-2 Hospitalized patients with COVID-19 between 30 – 53 years of age Observational study SARS-CoV-2 with the D614G mutation appears to become the major circulating virus in Indonesia
Hafiz et al. 2020 41 Yogyakarta and Central Java 30 Nasopharyngeal swabs SARS-CoV-2 SARS-CoV-2 Adult humans with SARS-CoV-2. 16 (53.3%) were male and 14 (46.6%) were female Observational case series Neutrophil-to-lymphocyte ratio (NLR) and CXR are cost effective findings and can be used as a disease severity marker in primary health care to determine further referral
Pitoyo et al. 2020 42 Jakarta 3 Serum, oropharyngealand nasopharyngeal swabs SARS-CoV-2, cytomegalovirus cytomegalovirus Adults above 60 years of age Case report Cytomegalovirus infection might be missed when depending only on CT scans and radiological reports
Putra et al. 2020 43 Jakarta 1 Oropharyngealand nasopharyngeal swabs SARS-CoV-2 SARS-CoV-2 29-year-old COVID with SARS-CoV-2 Case report A COVID-19 patient reported a pins and needles sensation, and exfoliation of the skin on their hands
Ravindran et al. 2020 81 Bali 41 NA SARS-CoV-2 SARS-CoV-2 The median age of cases was 31 years (range 3–64 years), which was similar to non-cases at 30 years (range 3–71 years) Retrospective cohort study Social gatherings play important roles in transmission of COVID-19
Rozaliyani et al. 2020 44 Jakarta 4052 Nasal and pharyngeal swabs SARS-CoV-2 SARS-CoV-2 Participants’ age range was 0-9 and 70 years of age. The mean age of the patients were 45.8 years Retrospective cohort study Older age, dyspnea, pneumonia, and pre-existing hypertension were associated with SARS-CoV-2 related deaths
Soedarsono et al. 2020 49 Surabaya, East Java 4 NA SARS-CoV-2 SARS-CoV-2 Adults 34- 58 years old with SARS-CoV-2 Case studies Infection caused by SARS-CoV-2 can present with different clinical manifestations. Some patients that had no symptoms initially, developed symptoms later on
Somasetia et al. 2020 50 Bandung 1 NA SARS-CoV-2 SARS-CoV-2 6-year-old male with SARS-CoV-2 infection Case report The patient was presented without classic upper respiratory symptoms of SARS-CoV-2, conjunctivitis, or rash and was instead presented with fever, acute abdominal pain, and shock
Tenda et al. 2020 45 Jakarta 3 Oropharyngeal andnasopharyngeal swabs SARS-CoV-2 SARS-CoV-2 Older adults between 37- 57 years of age with SARS-CoV-2 Case studies Fever was the most common symptom of SARS-CoV-2. Gastrointestinal symptoms in the form of diarrhea appeared in only one patient. Only one patient had dry cough
Widhidewi et al. 2020 24
Bali
200
Throat swabs
Family of paramyxoviridae, herpesviridae, coronaviridae, hantaviridae, adenoviridae, arenaviridae Genus of enterovirus, henipavirus, influenza A virus, bocavirus, Pneumovirinae viruses, Sub- family of RSV, human metapneumovirus influenza A virus(H1N1, H1N2, ), enterovirus 84, coxsackievirus A6, and A24, rhinovirus A, and C, coxsackievirus B3, human adenovirus B2, B3, and C measles D8, and parainfluenza virus 3, bocavirus, RSV A, B, human metapneumovirus, human coronavirus OC43, cytomegalovirus
Children and adults 0-6 and 80 years of age with acute respiratory tract infections
Cohort studies of children and adults with Acute respiratory infections
Positive detection rate of respiratory viruses was 490 % The most common viruses detected were herpesviridae, enterovirus, influenza A and RSV
Widysanto et al. 2020 52 Tangerang City 1 NA SARS-CoV-2 SARS-CoV-2 48 year old male patient Case report Survival with hypoxia in a critical COVID-19-positive ICU hospitalized patient from Indonesia
Wirawan et al. 2020 82 Bali NA NA SARS-CoV-2 SARS-CoV-2 NA Modeling Study NA
Yasmin et al. 2020 51 Bangdung 1 Nasopharyngeal, and pharyngeal specimens SARS-CoV-2 SARS-CoV-2 64-year-old female Case report Proposed a synergistic concept of lethal arrhythmia due to direct SARS-CoV-2-associated cardiac injury, hyperinflammatory response, and drug-induced arrhythmia
Aman et al. 2021 25 Bandung, Denpasar, Jakarta, Makassar, Semarang, Surabaya, and Yogyakarta 420 Blood, nasopharyngeal swabs, sputum, urine, feces influenza virus, RSV, chikungunya virus, measles virus, human coronavirus OC-43, enterovirus, herpes virus, human metapneumovirus influenza, RSV, chikungunya virus, measles, human coronavirus OC-43 enterovirus, herpesvirideae virus, human metapneumovirus Adults and children either 0-1 or ≥60 years of age with SARI Hospital based passive SARI surveillance Implementation of the SARI criteria in tertiary referral hospitals would help identify potential influenza infections
Baskara et al. 2021 46 Yogyakarta 1 Nasopharyngeal and oropharyngeal swabs SARS-CoV-2 SARS-CoV-2 42 year old diabetic male with SARS-CoV-2 Case report First case of COVID-19 disease with active primary tuberculosis in Indonesia. Limited or no protection against COVID-19 is one of the problems that leads to co-infection
Kadriyan et al. 2021 53 Nusa Tenggara Barat 2 Nasopharyngeal, and oropharyngeal swabs SARS-CoV-2 SARS-CoV-2 26-year-old woman and 19-year-old man Case report The SARS- CoV2 gene remains detected in the tonsil and detritus even after the negative PCR report
Riawati et al. 2021 47 Yogyakarta 7 Nasopharyngeal, and oropharyngeal swabs SARS-CoV-2 SARS-CoV-2 Young and older adults (36- 71 years of age) Case reports Chest X-ray (CXR) is considered more effective and useful for initial screening and follow-up of the progress of patients with COVID-19