|POLICY AND PRACTICE
|Year : 2020 | Volume
| Issue : 2 | Page : 134-140
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
2 Faculty of Medicine, Padjadjaran University, Bandung, Indonesia
3 Directorate for Health and Community Nutrition, Ministry of National Development Planning/National Development Planning Agency, Jakarta, Indonesia
4 Indonesia One Health University Network, Universitas Indonesia, Depok, Indonesia
|Date of Web Publication||07-Sep-2020|
Dr Harimat Hendarwan
National Institute of Health Research and Development, Ministry of Health, Jakarta
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
|How to cite this article:|
Hendarwan H, Syachroni S, Aryastami NK, Su'udi A, Susilawati MD, Despitasari M, Mulyani UA, Sumiarsih M, Puspandari N, Indrati AR, Solikha DA, Riana DA, Wahyuni IR. Assessing the COVID-19 diagnostic laboratory capacity in Indonesia in the early phase of the pandemic. WHO South-East Asia J Public Health 2020;9:134-40
|How to cite this URL:|
Hendarwan H, Syachroni S, Aryastami NK, Su'udi A, Susilawati MD, Despitasari M, Mulyani UA, Sumiarsih M, Puspandari N, Indrati AR, Solikha DA, Riana DA, Wahyuni IR. Assessing the COVID-19 diagnostic laboratory capacity in Indonesia in the early phase of the pandemic. WHO South-East Asia J Public Health [serial online] 2020 [cited 2021 Jan 22];9:134-40. Available from: http://www.who-seajph.org/text.asp?2020/9/2/134/294307
| Background|| |
On 31 December 2019, the World Health Organization (WHO) Country Office for China was informed of cases of pneumonia of unknown aetiology detected in Wuhan, Hubei province. WHO declared a public health emergency of international concern on 31 January 2020, and on 11 March coronavirus disease 2019 (COVID-19) was characterized as a pandemic. The causal agent was named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Viruses on 11 February.
Indonesia reported its first two cases of COVID-19 on 2 March 2020, and by 31 March there had been 114 deaths from 1285 cases. Presidential Decree No. 11 of 31 March 2020 confirmed COVID-19 as a national public health emergency and announced various public health and social measures to prevent and mitigate the impact of COVID-19. This was prompted by the increasing number of cases and deaths, the spread across the country, and the impact on political, economic, defence and security aspects, as well as on the welfare of the people of Indonesia.
The Indonesian Ministry of Health was instrumental in issuing guidelines on prevention and control of COVID-19, issuing self-isolation protocols and establishing a referral hospital. The Ministry of Health also appointed the National Institute of Health Research and Development (NIHRD) as a diagnostic centre for COVID-19 samples. However, Indonesia is the largest archipelago in the world, with an estimated total of 17 504 islands, and has a population of more than 265 million. Concerns were therefore raised that having only one COVID-19 diagnostic laboratory for such a large geographical area and population would delay an effective response. Therefore, the Minister of Health issued three decrees: HK.01.07/Menkes/182/2020 on 16 March; HK.01.07/Menkes/214/2020 on 19 March; and HK.01.07/Menkes/216/2020 on 23 March. These decrees listed the facilities to be designated COVID-19 diagnostic laboratories by province and elevated the NIHRD laboratory to the status of national reference laboratory for COVID-19.
WHO interim guidance on laboratory testing for COVID-19 on 19 March 2020 was as follows: “Testing on clinical specimens from patients meeting the suspected case definition should be performed in appropriately equipped laboratories by staff trained in the relevant technical and safety procedures. National guidelines on laboratory biosafety should be followed in all circumstances. There is still limited information on the risk 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 facilities. Attempts to culture the virus require BSL-3 facilities at minimum.”
Rapid, accurate diagnosis of COVID-19 is essential for both patient management and contact-tracing purposes. An understanding of a country’s diagnostic laboratory capacity is therefore important to benchmark the ability of facilities to cope with increasing demand, and also to plan for equipment and laboratory requirements. We therefore undertook a rapid assessment of Indonesia’s COVID-19 laboratory testing capacity in the early phase of the pandemic response to identify key areas for strengthening and possible solutions. This assessment included a rapid survey of the laboratories newly designated as COVID-19 facilities.
| Approach|| |
This study involved rapid operational research to obtain key information on the current capacities of the 44 facilities that had been assigned by the Minister of Health’s Decree HK.01.07/Menkes/214/2020 to become COVID-19 diagnostic laboratories. Data were collected using a self-administered confidential questionnaire. The questionnaire was filled in by the manager of each laboratory. The completed questionnaire was then signed and approved by the head of the COVID-19 laboratory before being sent back to the researchers.
The main purpose of the survey was to ascertain the maximum capacity of each laboratory under the circumstances pertaining at that time. The questionnaire collected information on testing capacity; respondents were asked for the maximum capacity for specimen examinations in 1 day and the average daily number of specimens examined in the preceding week. They were also asked for the total number of laboratory personnel that were capable of COVID-19 testing and the number who had undergone specialist training. The questionnaire also had questions on the availability of testing equipment and reagents; total laboratory health-care and non-health-care personnel; laboratory apparatus, including if a biosafety cabinet was available; and the availability of personal protective equipment. The questions were developed by a team including a microbiologist and health service management experts, with input from the heads of two COVID-19 diagnostic laboratories.
The questionnaires were sent by email on 23 March and were to be returned by 2 April. Replies were cross-checked with respondents if additional clarification was needed. It was recognized at the outset that not all of the laboratories contacted would be able to answer all of the questions since most were not yet fully operational and the number of cases was still low; therefore, none of the questions was mandatory. The results of the survey were analysed descriptively to determine the capacity of each diagnostic laboratory. The survey was approved by the Health Research Ethics Committee, NIHRD (document number LB.02.01/2/KE.303/2020). We also collected Ministry of Health and National Agency for Disaster Management data on cumulative tests done and cases identified during the period from 2 March to 15 April, to identify changes coinciding with increasing laboratory capacity.
| Key findings|| |
Testing in the early phase of the pandemic response
This rapid survey was done at a highly dynamic time. The primary data collection for this study was conducted in 44 COVID-19 diagnostic laboratories. However, during the survey, on 26 March 2020, the government designated a further four laboratories, bringing the total number of COVID-19 diagnostic laboratories to 48. Initially, COVID-19 specimen examination was centralized and conducted only in the Ministry of Health’s NIHRD laboratory. As demand increased, it was impossible to continue with the NIHRD laboratory as the only COVID-19 diagnostic laboratory. Turnaround time for results increased 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, on 16 March the government expanded the testing programme by designating 12 new diagnostic laboratories ([Figure 1], point A), followed by more, bringing the total to 44 diagnostic laboratories on 19 March 2020 (Fig. 1, point B). Four more laboratories were designated on 26 March (Fig. 1, point C). Fig. 1 also shows that, in the initial weeks, there was not a significant increase in the number of specimens examined. Over time, a sharp increase in specimen examination by diagnostic laboratories and test results was seen, in line with the government’s policy of increasing the number of diagnostic laboratories in the network. In addition, there were increasing numbers of cases.
|Figure 1: Cumulative COVID-19 tests and cases in Indonesia, 2 March–15 April 2020|
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Distribution and capacities of COVID-19 diagnostic laboratories
At the outset of the survey, there were 44 COVID-19 diagnostic laboratories designated by ministerial decree. This meant that, of Indonesia’s 34 provinces, there were 12 without COVID-19 diagnostic laboratory facilities, namely Bengkulu, Lampung, East Nusa Tenggara, Central Kalimantan, East Kalimantan, North Kalimantan, Central Sulawesi, South-East Sulawesi, Gorontalo, West Sulawesi, North Maluku and West Papua. The government had appointed diagnostic laboratories located in other provinces to provide testing services for these provinces.
Of the 44 laboratories contacted, 36 (82%) responded to the survey; 11 were surveillance laboratories and 25 were non-surveillance laboratories. At the time of the survey, only 13 of these laboratories (in addition to the national referral laboratory) had tested specimens for SARS-CoV-2: seven of the 11 surveillance laboratories and six of the 25 non-surveillance laboratories. This finding was unsurprising because surveillance laboratories had been designated as COVID-19 diagnostic laboratories earlier than their non-surveillance counterparts. Lack of equipment and materials meant that most of the laboratories were not yet operational.
The capacity constraints reported in the survey were lack of reagents and equipment, and limited human resources. A major cause of lack of tools and reagents was procurement time, since all needed to be imported. With respect to equipment, in the 36 COVID-19 diagnostic laboratories, there were 38 real-time polymerase chain reaction (RT-PCR) machines. In addition, there were six conventional PCR machines plus 15 rapid molecular testing (RMT) machines. At the time of the survey, seven laboratories designated as COVID-19 diagnostic laboratories did not have an RT-PCR machine, and four laboratories had only an RMT machine.
A total of 23 laboratories provided estimates of the minimum and maximum capacities of the laboratory, based on the conditions at the time of the survey. As shown in [Table 1], between 22 March and 2 April 2020, the daily testing capacity of COVID-19 diagnostic laboratories (excluding the national referral laboratory) ranged from 12 to 200 specimens and the average maximum specimen examination capacity per day was higher for surveillance laboratories than for non-surveillance laboratories.
|Table 1: Estimated daily capacity of COVID-19 diagnostic laboratories, 22 March–2 April 2020|
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The capacity of a laboratory is the result of many factors, in particular the availability and adequacy of materials, workforce and equipment, and the speed and purity of RNA extraction. Funding, including overtime payments and other support for diagnostic staff, is also key. With respect to human resources, capacity is a product not only of the number of staff but also of their skills and training. Therefore, the capacities of different laboratories can vary even if they have the same number of staff and use the same RT-PCR equipment.
Estimate of nationwide capacity
As shown in [Table 2], based on the responses from the 23 laboratories and extrapolating to the rest, we estimated that the testing capacity of the 44 COVID-19 diagnostic laboratories, excluding the national referral laboratory, was 2544 specimens per day. It was clear that there would be challenges not only for the 12 provinces that did not have COVID-19 diagnostic laboratories but also for Jakarta. Although Jakarta had seven COVID-19 diagnostic laboratories, including the national referral laboratory, with the city being at the epicentre of the COVID-19 outbreak, those laboratories would inevitably have a heavy workload. In addition, several diagnostic laboratories in Jakarta not only accommodated Jakarta’s needs but also received specimens from other regions, as well as carrying out surveillance functions. The national referral laboratory was also carrying out various other functions: facilitating, monitoring and quality assurance for other COVID-19 diagnostic laboratories. The same problems were also faced by East Java province, where most of the diagnostic laboratories had to support other provinces.
|Table 2: Estimated daily capacity for testing COVID-19 specimens in each province|
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Expanding access to RT-PCR testing was the clear main priority, in addition to optimizing the laboratories owned by the NIHRD-Ministry of Health and the existing network of laboratories. Options also included allowing hospitals with biosafety cabinets and RT-PCR machines to carry out their own testing. As described below, we also assessed the potential for use of referral hospitals with RMT equipment.
Investigation of use of RMT laboratory facilities of referral hospitals
One of the fastest solutions to the deficit in testing capacity would be to optimize the 166 referral hospitals that had the capacity for RMT and also had a biosafety cabinet (Table 2). Assuming that each RMT machine had four modules (the most common type in Indonesia) and could do nine tests per day, 5976 specimens could be tested daily if all the requirements for COVID-19 examination were fulfilled (Table 2). The main challenges would be obtaining test cartridges for SARS-CoV-2 and the availability of trained personnel.
When we assessed the possibility of utilizing referral hospitals that own RMT machines and biosafety cabinets, it was clear that Bengkulu, Lampung, Central Kalimantan, North Kalimantan, South-East Sulawesi, Gorontalo, West Sulawesi and West Papua provinces would remain in a vulnerable position because of the absence of diagnostic laboratories and no or low availability of RMT plus a biosafety cabinet. We identified 132 referral hospital laboratories that had an RMT machine but did not yet have a biosafety cabinet. To enable these facilities to function as COVID-19 diagnostic laboratories, the government would have to provide biosafety equipment in addition to the cartridges for SARS-CoV-2. Using the same assumptions set out above, these additional facilities would provide an estimated testing capacity of 4752 specimens per day [Table 2]. This still left North Kalimantan, South-East Sulawesi, Gorontalo, West Sulawesi and West Papua provinces in an insecure position, so further identification of potential facilities was needed for these provinces.
| Lessons learnt and ways forward|| |
At the time of the assessment and survey discussed in this paper, the experience in China indicated to other countries that it would be essential to rapidly gain an understanding of the disease incidence and prevalence. Researchers used data from several sources to understand why COVID-19 had spread internationally from China at such great speed. They proposed that a reason was the large proportion of cases – estimated at 86% – that were contagious yet had mild, limited or no symptoms before the 23 January 2020 travel restrictions on Wuhan. The WHO–China joint mission on COVID-19 that was completed during 16–24 February 2020 reported that, in the context of meticulous case and contact tracing, between 1% and 5% of close contacts were subsequently laboratory-confirmed cases of COVID-19, depending on location.
In Indonesia, policy-making regarding the designation of diagnostic laboratories was dynamic. The government was aware of the need to be realistic about a possible surge in cases and the importance of speed of diagnosis for the management of patients. It was therefore clear that the 48 diagnostic laboratories and one national reference laboratory for COVID-19 would be insufficient. The Minister of Health therefore issued Circular Letter HK.02.01/Menkes/234/2020 on 7 April 2020, which provided guidelines for non-government laboratories on SARS-CoV-2 testing with RT-PCR equipment. This allowed other laboratories, such as those in universities and private facilities, to become diagnostic laboratories for COVID-19, providing they met the criteria set out in the guidelines. This policy was designed to deal with a challenging situation, and it was clear that a robust recording and reporting system would be needed to integrate data from the expanded and varied sources.
The capacity constraints clearly highlighted by the rapid survey of 44 government laboratories were lack of reagents and equipment, and limited human resources. At the time of the survey, some laboratories had no RT-PCR equipment or were not BSL-2. Some laboratories were obliged to rely on manual extraction processes that require more time to complete a series of examinations, thus limiting the testing frequency per day. Delays between processes were also introduced by the time taken to prepare tools and materials. For these reasons, some laboratories were unable to carry out testing at their maximum capacity. The scarcity of imported supplies, including RNA extraction kits, reagent kits, primers, probes, positive and negative controls, and master mix, was a serious challenge, and developing a strategy for a sustainable supply needs to be seriously considered.
The geography of Indonesia makes any reporting system highly dependent on rapid transport of specimens. Adequacy of tools and materials that support temperature stability during transport is therefore another vital requirement. The sample transport guidance in Indonesia stipulates that the temperature at the time of delivery should be 2–8 °C, to be achieved by placing the specimen in a cool box or using dry ice for the duration of transport for up to 3 days. A retrospective review of the performance of the Victorian Infectious Diseases 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 pandemic planning had focused primarily on internal laboratory resources and processes. However, for optimal functioning of the whole testing cycle, the transport of specimens and accompanying data from patient to testing site and the provision of results to the patients’ caregivers also needed to be optimal. In an outbreak situation where there are transport and flight restrictions, the government must facilitate the delivery of specimens, tools and materials so that laboratories can carry out their functions properly.
The increase in COVID-19 cases in Indonesia created a need to enlarge the number of laboratories to leverage capacity for COVID-19 specimen examination. Expanding RT-PCR testing capacity was clearly the main priority, in addition to optimizing laboratories owned by the NIHRD-Ministry of Health and the existing network of laboratories. Options also included allowing hospitals with biosafety cabinets and RT-PCR machines to carry out their own testing.
There was also the option of using SARS-CoV-2-specific kits that have been developed for use with RMT platforms that are currently deployed for tuberculosis diagnosis or HIV viral load testing. This option was supported on 27 April 2020 by the Director General of Prevention and Control of Disease through Circular Letter No. HK. 02.02/V/6664/2020. GeneXpert® (Cepheid, Sunnyvale, United States of America), which is an RMT machine that can be operated by laboratory personnel with minimal training. The Food and Drug Administration of the United States of America has granted emergency authorization for the Xpert® Xpress SARS-CoV-2 cartridge; the assay is fully automated and provides results within about 45 minutes. Difficulties encountered relate to the availability of the Xpert® Xpress SARS-CoV-2 cartridges.
At present, there are hundreds of RMT machines spread across all health service facilities in Indonesia. Since 2015, they have been used to diagnose drug-sensitive and drug-resistant tuberculosis. The aim should be to transfer some RMT machines from testing for tuberculosis to testing for COVID-19 without halting or affecting the sustainability of the tuberculosis programme.
The results of the survey show that there are 166 COVID-19 referral hospitals that have both an RMT machine and support facilities. In addition, there are 132 COVID-19 referral hospitals that are equipped with only an RMT machine. However, using these alternatives would still not increase capacity enough, because several provinces would still be in a vulnerable position if case numbers surged. Each of these provinces should be provided with one RT-PCT unit. There are several laboratories that are BSL-3 or BSL-2 and have PCR facilities that are located in non-health institutions, such as faculties of agriculture or veterinary medicine. In addition, laboratories in the Ministry of Agriculture and the Ministry of State-owned Enterprises can also play a role in increasing COVID-19 testing capacity.
WHO has noted that, when testing facilities are limited, available facilities tend to be located in or near a capital city, making timely access to testing difficult for people living in other parts of the country. In these circumstances, mobile laboratories or automatic integrated nucleic acid amplification test systems that can be operated in remote areas and by staff with minimal training can be alternatives. In line with this, mobile BSL-2 laboratories are being developed by the Agency for the Assessment and Application of Technology and the Indonesian Institute of Sciences.
On 1 July 2020, the Minister of Health’s Decree No. HK.01.07/Menkes/405/2020 increased the number of COVID-19 diagnostic laboratories to 163. It also created a mandate for the establishment of further COVID-19 diagnostic laboratories. This extension of the number COVID-19 diagnostic laboratories has increased the coverage of the COVID-19 testing programme. 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. Further increases in testing capacity for COVID-19 in Indonesia will require developing and establishing a laboratory network system and laboratory referral mechanisms, in addition to increasing the capacity of the laboratory workforce in terms of size and skills.
Source of support: The survey was funded by the National institute of Health Research and Development, Ministry of Health, Indonesia.
Conflict of interest: None declared.
Authorship: HH developed the concept; HH and UAM designed the study; HH, NKA, AS and MDS defined the intellectual content; HH, SS, NKA, MDS, UAM, MS, NP, ARI, DAS, DAR and IRW carried out the literature search; HH collected the data; HH and SS analysed the data; HH, SS, MD and UAM prepared the manuscript; HH, SS, MS and MD edited the manuscript; all authors reviewed and approved the manuscript.
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[Table 1], [Table 2]