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Policy and practice

Assessing the COVID-19 diagnostic laboratory capacity in


Indonesia in the early phase of the pandemic
Harimat Hendarwan1, Syachroni Syachroni1, Ni Ketut Aryastami1, Amir Su’udi1, Made Dewi Susilawati1, Mieska Despitasari1,
Ully Adhie Mulyani1, Mimi Sumiarsih1, Nelly Puspandari1, Agnes Rengga Indrati2, Dewi Amila Solikha3, Dyah Armi Riana1,
Indira Rezky Wahyuni4
1
National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia, 2Faculty of Medicine,
Padjadjaran University, Bandung, Indonesia, 3Directorate for Health and Community Nutrition, Ministry of National Development
Planning/National Development Planning Agency, Jakarta, Indonesia, 4Indonesia One Health University Network, Universitas
Indonesia, Depok, Indonesia
Correspondence to: Dr Harimat Hendarwan (harimat@litbang.kemkes.go.id)

Abstract
The coronavirus disease 2019 (COVID-19) pandemic has put a great burden on countries as a result
of the demand for laboratory diagnostic testing for severe acute respiratory syndrome coronavirus 2
(SARS-CoV-2). This paper reports our experiences in rapidly assessing Indonesia’s COVID-19
laboratory testing capacity in the early phase of the pandemic response. Through a questionnaire-
based survey carried out between 23 March and 2 April, we estimated the daily tests that could be
done by the 44 facilities, excluding the national referral laboratory, first assigned to be COVID-19
diagnostic laboratories. The capacity constraints were lack of reagents and equipment, and limited
human resources; because of these constraints, most of the laboratories were not yet operational. A
major hindrance was reliance on imported supplies and the associated procurement time. Expanding
real-time polymerase chain reaction testing capacity, through increased numbers of laboratories and
optimization of existing facilities, was clearly the main priority. We also assessed the potential yield
from using rapid molecular testing machines in the country’s referral hospitals. Even assuming this
potential could be tapped, several provinces would still be poorly served by diagnostic services in
the event of a surge in cases. Since this rapid assessment, the number of designated COVID-19
laboratories has increased and, by 1 July 2020, was 163. On 29 July 2020, for the first time, the
number of specimens examined in a day reached more than 30 000, achieving the WHO testing
capacity target of 1 in 1000 inhabitants per week.

Keywords: COVID-19, diagnosis, emergency response, Indonesia, laboratory testing

Background deaths, the spread across the country, and the impact on
political, economic, defence and security aspects, as well as
On 31 December 2019, the World Health Organization (WHO) on the welfare of the people of Indonesia.4
Country Office for China was informed of cases of pneumonia of The Indonesian Ministry of Health was instrumental in
unknown aetiology detected in Wuhan, Hubei province. WHO issuing guidelines on prevention and control of COVID-19,
declared a public health emergency of international concern issuing self-isolation protocols and establishing a referral
on 31 January 2020, and on 11 March coronavirus disease hospital. The Ministry of Health also appointed the National
2019 (COVID-19) was characterized as a pandemic.1 The Institute of Health Research and Development (NIHRD) as a
causal agent was named severe acute respiratory syndrome diagnostic centre for COVID-19 samples. However, Indonesia
coronavirus 2 (SARS-CoV-2) by the International Committee is the largest archipelago in the world, with an estimated total of
on Taxonomy of Viruses on 11 February.2 17 504 islands, and has a population of more than 265 million.5
Indonesia reported its first two cases of COVID-19 on Concerns were therefore raised that having only one COVID-19
2 March 2020, and by 31 March there had been 114 deaths diagnostic laboratory for such a large geographical area and
from 1285 cases.3 Presidential Decree No. 11 of 31 March population would delay an effective response.6 Therefore,
2020 confirmed COVID-19 as a national public health the Minister of Health issued three decrees: HK.01.07/
emergency and announced various public health and social Menkes/182/2020 on 16 March; HK.01.07/Menkes/214/2020
measures to prevent and mitigate the impact of COVID-19. on 19 March; and HK.01.07/Menkes/216/2020 on 23 March.7
This was prompted by the increasing number of cases and These decrees listed the facilities to be designated COVID-19

134 WHO South-East Asia Journal of Public Health | September 2020 | 9(2)
Hendarwan et al.: Indonesia’s COVID-19 diagnostic laboratory capacity

diagnostic laboratories by province and elevated the NIHRD most were not yet fully operational and the number of cases was
laboratory to the status of national reference laboratory for still low; therefore, none of the questions was mandatory. The
COVID-19. results of the survey were analysed descriptively to determine
WHO interim guidance on laboratory testing for COVID-19 the capacity of each diagnostic laboratory. The survey was
on 19 March 2020 was as follows: “Testing on clinical approved by the Health Research Ethics Committee, NIHRD
specimens from patients meeting the suspected case definition (document number LB.02.01/2/KE.303/2020). We also
should be performed in appropriately equipped laboratories by collected Ministry of Health and National Agency for Disaster
staff trained in the relevant technical and safety procedures. Management data on cumulative tests done and cases
National guidelines on laboratory biosafety should be followed identified during the period from 2 March to 15 April, to identify
in all circumstances. There is still limited information on the risk changes coinciding with increasing laboratory capacity.
posed by COVID-19, but all procedures should be undertaken
based on a risk assessment. Specimen handling for molecular
testing would require BSL-2 [biosafety level 2] or equivalent Key findings
facilities. Attempts to culture the virus require BSL-3 facilities
at minimum.”8 Testing in the early phase of the pandemic response
Rapid, accurate diagnosis of COVID-19 is essential for This rapid survey was done at a highly dynamic time. The
both patient management and contact-tracing purposes. An primary data collection for this study was conducted in 44
understanding of a country’s diagnostic laboratory capacity COVID-19 diagnostic laboratories. However, during the survey,
is therefore important to benchmark the ability of facilities to on 26 March 2020, the government designated a further four
cope with increasing demand, and also to plan for equipment laboratories, bringing the total number of COVID-19 diagnostic
and laboratory requirements. We therefore undertook a rapid laboratories to 48. Initially, COVID-19 specimen examination
assessment of Indonesia’s COVID-19 laboratory testing was centralized and conducted only in the Ministry of Health’s
capacity in the early phase of the pandemic response to NIHRD laboratory. As demand increased, it was impossible
identify key areas for strengthening and possible solutions. to continue with the NIHRD laboratory as the only COVID-19
This assessment included a rapid survey of the laboratories diagnostic laboratory. Turnaround time for results increased
newly designated as COVID-19 facilities. because of the geographical spread of the disease and the
increasing numbers of specimens requiring testing. At the same
time, demand for faster diagnosis was increasing. In response,
Approach on 16 March the government expanded the testing programme
by designating 12 new diagnostic laboratories (Fig. 1,
This study involved rapid operational research to obtain point A), followed by more, bringing the total to 44 diagnostic
key information on the current capacities of the 44 facilities laboratories on 19 March 2020 (Fig. 1, point B). Four more
that had been assigned by the Minister of Health’s Decree laboratories were designated on 26 March (Fig. 1, point C).
HK.01.07/Menkes/214/2020 to become COVID-19 diagnostic Fig. 1 also shows that, in the initial weeks, there was not a
laboratories.9 Data were collected using a self-administered significant increase in the number of specimens examined.
confidential questionnaire. The questionnaire was filled in by Over time, a sharp increase in specimen examination by
the manager of each laboratory. The completed questionnaire diagnostic laboratories and test results was seen, in line with
was then signed and approved by the head of the COVID-19 the government’s policy of increasing the number of diagnostic
laboratory before being sent back to the researchers. laboratories in the network. In addition, there were increasing
The main purpose of the survey was to ascertain the numbers of cases.
maximum capacity of each laboratory under the circumstances
pertaining at that time. The questionnaire collected information Distribution and capacities of COVID-19 diagnostic
on testing capacity; respondents were asked for the laboratories
maximum capacity for specimen examinations in 1 day and At the outset of the survey, there were 44 COVID-19 diagnostic
the average daily number of specimens examined in the laboratories designated by ministerial decree. This meant that,
preceding week. They were also asked for the total number of of Indonesia’s 34 provinces, there were 12 without COVID-19
laboratory personnel that were capable of COVID-19 testing diagnostic laboratory facilities, namely Bengkulu, Lampung,
and the number who had undergone specialist training. The East Nusa Tenggara, Central Kalimantan, East Kalimantan,
questionnaire also had questions on the availability of testing North Kalimantan, Central Sulawesi, South-East Sulawesi,
equipment and reagents; total laboratory health-care and non- Gorontalo, West Sulawesi, North Maluku and West Papua. The
health-care personnel; laboratory apparatus, including if a government had appointed diagnostic laboratories located in
biosafety cabinet was available; and the availability of personal other provinces to provide testing services for these provinces.
protective equipment. The questions were developed by a team Of the 44 laboratories contacted, 36 (82%) responded to
including a microbiologist and health service management the survey; 11 were surveillance laboratories and 25 were
experts, with input from the heads of two COVID-19 diagnostic non-surveillance laboratories. At the time of the survey, only
laboratories. 13 of these laboratories (in addition to the national referral
The questionnaires were sent by email on 23 March and laboratory) had tested specimens for SARS-CoV-2: seven
were to be returned by 2 April. Replies were cross-checked of the 11 surveillance laboratories and six of the 25 non-
with respondents if additional clarification was needed. It surveillance laboratories. This finding was unsurprising
was recognized at the outset that not all of the laboratories because surveillance laboratories had been designated as
contacted would be able to answer all of the questions since COVID-19 diagnostic laboratories earlier than their non-

WHO South-East Asia Journal of Public Health | September 2020 | 9(2) 135
Hendarwan et al.: Indonesia’s COVID-19 diagnostic laboratory capacity

Fig. 1. Cumulative COVID-19 tests and cases in Indonesia, 2 March–15 April 2020

35 000
Cumulative cases Cumulative tests
30 000

25 000
Number of test/cases

A B C
20 000

15 000

10 000

5000

0
2-Mar-20 9-Mar-20 16-Mar-20 23-Mar-20 30-Mar-20 6-Apr-20 13-Apr-20
Date

Source: Task Force for the Acceleration of Handling COVID-19.10

surveillance counterparts. Lack of equipment and materials diagnostic staff, is also key. With respect to human resources,
meant that most of the laboratories were not yet operational. capacity is a product not only of the number of staff but also
The capacity constraints reported in the survey were lack of of their skills and training. Therefore, the capacities of different
reagents and equipment, and limited human resources. A major laboratories can vary even if they have the same number of
cause of lack of tools and reagents was procurement time, staff and use the same RT-PCR equipment.
since all needed to be imported. With respect to equipment,
in the 36 COVID-19 diagnostic laboratories, there were 38 Estimate of nationwide capacity
real-time polymerase chain reaction (RT-PCR) machines. As shown in Table 2, based on the responses from the 23
In addition, there were six conventional PCR machines plus laboratories and extrapolating to the rest, we estimated that the
15 rapid molecular testing (RMT) machines. At the time of testing capacity of the 44 COVID-19 diagnostic laboratories,
the survey, seven laboratories designated as COVID-19 excluding the national referral laboratory, was 2544 specimens
diagnostic laboratories did not have an RT-PCR machine, and per day. It was clear that there would be challenges not only
four laboratories had only an RMT machine. for the 12 provinces that did not have COVID-19 diagnostic
A total of 23 laboratories provided estimates of the minimum laboratories but also for Jakarta. Although Jakarta had seven
and maximum capacities of the laboratory, based on the COVID-19 diagnostic laboratories, including the national
conditions at the time of the survey. As shown in Table 1, referral laboratory, with the city being at the epicentre of the
between 22 March and 2 April 2020, the daily testing capacity COVID-19 outbreak, those laboratories would inevitably have
of COVID-19 diagnostic laboratories (excluding the national a heavy workload. In addition, several diagnostic laboratories
referral laboratory) ranged from 12 to 200 specimens and in Jakarta not only accommodated Jakarta’s needs but also
the average maximum specimen examination capacity per received specimens from other regions, as well as carrying out
day was higher for surveillance laboratories than for non- surveillance functions. The national referral laboratory was also
surveillance laboratories. carrying out various other functions: facilitating, monitoring and
The capacity of a laboratory is the result of many factors, in quality assurance for other COVID-19 diagnostic laboratories.
particular the availability and adequacy of materials, workforce The same problems were also faced by East Java province,
and equipment, and the speed and purity of RNA extraction. where most of the diagnostic laboratories had to support other
Funding, including overtime payments and other support for provinces.

Table 1.  Estimated daily capacity of COVID-19 diagnostic laboratories, 22 March–2 April 2020
Estimated capacity
Diagnostic laboratories n Mean Median Minimum Maximum
Surveillance function  7 99 96 32 200
Non-surveillance function 16 60 49 12 180
COVID-19 diagnostic laboratories (total) 23 72 50 12 200

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Hendarwan et al.: Indonesia’s COVID-19 diagnostic laboratory capacity

Table 2.  Estimated daily capacity for testing COVID-19 specimens in each province
Diagnostic laboratories assigned by Referral hospitals with RMT Referral hospitals
MoH decree machine and BSC with RMT machine only
Non-
Surveillance surveillance Estimated Estimated Estimated
Province (n) (n) capacity n capacity n capacity
Aceh 1 0 30 7 252 6 216
North Sumatera 0 2 140 1 36 4 144
West Sumatera a
0 1 60 2 72 0 0
Riaub 0 1 0 6 216 8 288
Jambib 0 1 0 1 36 5 180
South Sumatera a
1 1 126 7 252 16 576
Bengkuluc 0 0 0 0 0 7 252
Bangka Belitung 0 1 16 0 0 5 180
Lampung c
0 0 0 1 36 3 108
Riau Islanda 1 0 100 4 144 10 360
Jakartaa,b 3 3 548 7 252 1 36
West Java a,b
1 2 148 21 756 7 252
Central Javaa 0 3 200 30 1080 9 324
Yogyakarta 1 2 238 6 216 3 108
East Javaa,b 2 3 301 25 900 7 252
Banten 0 1 12 3 108 1 36
Bali b
0 2 0 6 216 2 72
West Nusa Tenggarab 0 1 0 5 180 5 180
East Nusa Tenggarac 0 0 0 2 72 9 324
West Kalimantan b
1 1 30 3 108 1 36
Central Kalimantanc 0 0 0 1 36 2 72
South Kalimantan 1 0 32 4 144 1 36
East Kalimantanc 0 0 0 7 252 2 72
North Kalimantanc 0 0 0 1 36 1 36
North Sulawesi a
1 1 160 2 72 1 36
Central Sulawesic 0 0 0 3 108 2 72
South Sulawesia 1 2 253 3 108 3 108
South-East Sulawesic 0 0 0 1 36 0 0
Gorontaloc 0 0 0 1 36 0 0
West Sulawesi c
0 0 0 0 0 2 72
Malukua 1 0 100 1 36 1 36
North Malukuc 0 0 0 2 72 5 180
Papua 1 0 50 2 72 2 72
West Papuac 0 0 0 1 36 1 36
Total 16 28 2544 166 5976 132 4752
BSC: biosafety cabinet; MoH: Ministry of Health; RMT: rapid molecular testing.
a
Laboratory capacity data missing for at least one COVID-19 diagnostic laboratory in the province.
b
At least one COVID-19 diagnostic laboratory in the province without a real-time polymerase chain reaction (RT-PCR) machine.
No COVID-19 diagnostic laboratory in the province.
c

Note: For surveillance laboratories that did not provide data, it was assumed that the maximum examination capacity was 100 specimens per day; meanwhile, non-
surveillance laboratories that did not provide data were assumed to have a maximum capacity of 60 specimens per day. Both assumptions were based on the calculation
of the average capacity for each type of laboratory shown in Table 1. For laboratories that did not have an RT-PCR machine, the maximum capacity was assumed to
be zero specimens.

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Hendarwan et al.: Indonesia’s COVID-19 diagnostic laboratory capacity

Expanding access to RT-PCR testing was the clear main diagnostic laboratories and one national reference laboratory
priority, in addition to optimizing the laboratories owned by for COVID-19 would be insufficient. The Minister of Health
the NIHRD-Ministry of Health and the existing network of therefore issued Circular Letter HK.02.01/Menkes/234/2020
laboratories. Options also included allowing hospitals with on 7 April 2020, which provided guidelines for non-government
biosafety cabinets and RT-PCR machines to carry out their own laboratories on SARS-CoV-2 testing with RT-PCR equipment.14
testing. As described below, we also assessed the potential for This allowed other laboratories, such as those in universities
use of referral hospitals with RMT equipment. and private facilities, to become diagnostic laboratories
for COVID-19, providing they met the criteria set out in the
Investigation of use of RMT laboratory facilities of guidelines. This policy was designed to deal with a challenging
referral hospitals situation, and it was clear that a robust recording and reporting
One of the fastest solutions to the deficit in testing capacity system would be needed to integrate data from the expanded
would be to optimize the 166 referral hospitals that had the and varied sources.
capacity for RMT and also had a biosafety cabinet (Table 2). The capacity constraints clearly highlighted by the rapid
Assuming that each RMT machine had four modules (the most survey of 44 government laboratories were lack of reagents
common type in Indonesia) and could do nine tests per day, and equipment, and limited human resources. At the time of
5976 specimens could be tested daily if all the requirements the survey, some laboratories had no RT-PCR equipment
for COVID-19 examination were fulfilled (Table 2).11 The main or were not BSL-2. Some laboratories were obliged to rely
challenges would be obtaining test cartridges for SARS-CoV-2 on manual extraction processes that require more time to
and the availability of trained personnel. complete a series of examinations, thus limiting the testing
When we assessed the possibility of utilizing referral frequency per day. Delays between processes were also
hospitals that own RMT machines and biosafety cabinets, it introduced by the time taken to prepare tools and materials.
was clear that Bengkulu, Lampung, Central Kalimantan, North For these reasons, some laboratories were unable to carry out
Kalimantan, South-East Sulawesi, Gorontalo, West Sulawesi testing at their maximum capacity. The scarcity of imported
and West Papua provinces would remain in a vulnerable supplies, including RNA extraction kits, reagent kits, primers,
position because of the absence of diagnostic laboratories probes, positive and negative controls, and master mix, was a
and no or low availability of RMT plus a biosafety cabinet. We serious challenge, and developing a strategy for a sustainable
identified 132 referral hospital laboratories that had an RMT supply needs to be seriously considered.
machine but did not yet have a biosafety cabinet. To enable The geography of Indonesia makes any reporting system
these facilities to function as COVID-19 diagnostic laboratories, highly dependent on rapid transport of specimens. Adequacy
the government would have to provide biosafety equipment in of tools and materials that support temperature stability during
addition to the cartridges for SARS-CoV-2. Using the same transport is therefore another vital requirement. The sample
assumptions set out above, these additional facilities would transport guidance in Indonesia stipulates that the temperature
provide an estimated testing capacity of 4752 specimens at the time of delivery should be 2–8 °C, to be achieved by
per day (Table 2). This still left North Kalimantan, South- placing the specimen in a cool box or using dry ice for the
East Sulawesi, Gorontalo, West Sulawesi and West Papua duration of transport for up to 3 days.15 A retrospective review
provinces in an insecure position, so further identification of of the performance of the Victorian Infectious Diseases
potential facilities was needed for these provinces. Reference Laboratory, Australia, during the initial stage of
the influenza A/H1N1pdm pandemic noted that transport of
specimens had been a challenge. The review also noted that
Lessons learnt and ways forward pandemic planning had focused primarily on internal laboratory
resources and processes. However, for optimal functioning
At the time of the assessment and survey discussed in this of the whole testing cycle, the transport of specimens and
paper, the experience in China indicated to other countries accompanying data from patient to testing site and the
that it would be essential to rapidly gain an understanding provision of results to the patients’ caregivers also needed to
of the disease incidence and prevalence. Researchers used be optimal.16 In an outbreak situation where there are transport
data from several sources to understand why COVID-19 and flight restrictions, the government must facilitate the
had spread internationally from China at such great speed. delivery of specimens, tools and materials so that laboratories
They proposed that a reason was the large proportion of can carry out their functions properly.
cases – estimated at 86% – that were contagious yet had The increase in COVID-19 cases in Indonesia created
mild, limited or no symptoms before the 23 January 2020 a need to enlarge the number of laboratories to leverage
travel restrictions on Wuhan.12 The WHO–China joint mission capacity for COVID-19 specimen examination. Expanding RT-
on COVID-19 that was completed during 16–24 February PCR testing capacity was clearly the main priority, in addition
2020 reported that, in the context of meticulous case and to optimizing laboratories owned by the NIHRD-Ministry of
contact tracing, between 1% and 5% of close contacts were Health and the existing network of laboratories. Options also
subsequently laboratory-confirmed cases of COVID-19, included allowing hospitals with biosafety cabinets and RT-
depending on location.13 PCR machines to carry out their own testing.
In Indonesia, policy-making regarding the designation of There was also the option of using SARS-CoV-2-specific kits
diagnostic laboratories was dynamic. The government was that have been developed for use with RMT platforms that are
aware of the need to be realistic about a possible surge in currently deployed for tuberculosis diagnosis or HIV viral load
cases and the importance of speed of diagnosis for the testing.11 This option was supported on 27 April 2020 by the
management of patients. It was therefore clear that the 48 Director General of Prevention and Control of Disease through

138 WHO South-East Asia Journal of Public Health | September 2020 | 9(2)
Hendarwan et al.: Indonesia’s COVID-19 diagnostic laboratory capacity

Circular Letter No. HK. 02.02/V/6664/2020.17 GeneXpert® Authorship: HH developed the concept; HH and UAM designed the
(Cepheid, Sunnyvale, United States of America), which is an study; HH, NKA, AS and MDS defined the intellectual content; HH,
RMT machine that can be operated by laboratory personnel SS, NKA, MDS, UAM, MS, NP, ARI, DAS, DAR and IRW carried out
with minimal training.18 The Food and Drug Administration the literature search; HH collected the data; HH and SS analysed the
of the United States of America has granted emergency data; HH, SS, MD and UAM prepared the manuscript; HH, SS, MS
authorization for the Xpert® Xpress SARS-CoV-2 cartridge; and MD edited the manuscript; all authors reviewed and approved the
the assay is fully automated and provides results within about manuscript.
45 minutes. Difficulties encountered relate to the availability of
the Xpert® Xpress SARS-CoV-2 cartridges. How to cite this paper: Hendarwan H, Syachroni S, Aryastami NK,
At present, there are hundreds of RMT machines spread Su’udi A, Susilawati MD, Despitasari M, Mulyani UA, Sumiarsih M,
across all health service facilities in Indonesia. Since 2015, Puspandari N, Indrati AR, Solikha DA, Riana DA, Wahyuni IR.
they have been used to diagnose drug-sensitive and drug- Assessing the COVID-19 diagnostic laboratory capacity in Indonesia
resistant tuberculosis. The aim should be to transfer some in the early phase of the pandemic. WHO South-East Asia J Public
RMT machines from testing for tuberculosis to testing for Health. 2020;9(2):134–140. doi:10.4103/2224-3151.294307.
COVID-19 without halting or affecting the sustainability of the
tuberculosis programme.
The results of the survey show that there are 166 COVID-19 References
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