Coronavirus Pandemic

Challenges in the establishment of a biosafety testing laboratory for COVID-

19 in Bangladesh

SM Rashed Ul Islam1, Tahmina Akther1, Sharmin Sultana1, Paroma Deb1, Asish Kumar Ghosh1, Md.
Abdullah Omar Nasif1, Amirul Huda Bhuiyan1, Munira Jahan1, Afzalun Nessa1, Saif Ullah Munshi1,
Shahina Tabassum1
1
Department of Virology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Shahbag, Dhaka, Bangladesh

Abstract
At the beginning of the coronavirus disease 2019 (COVID-19) pandemic in Bangladesh, there was a scarcity of ideal biocontainment facilities
to detect the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a risk group of 3 organisms. Molecular detection of SARS-CoV-
2 must be performed in a BSL-2 laboratory with BSL-3-equivalent infection prevention and control practices. Establishing these facilities
within a short timeframe proved to be an enormous challenge, including locating a remote space distant from the university campus to establish
a laboratory, motivating the laboratory staff to work with a novel pathogen without any prior experience, allocation of funds for essential
equipment and accessories, and arrangement of a safe waste management system for environmental hazard reduction. This report also highlights
several limitations, such as the facility's architectural design that did not follow the biosafety guidelines, lack of continuous flow of funds, and
an inadequate number of laboratory personnel. This article describes various efforts taken to overcome the challenges during the establishment
of this facility that may be adopted to create similar facilities in other regions of the country. Establishing a BSL-2 laboratory with BSL-3-
equivalent infection prevention and control practices will aid in the early detection of a large number of cases, thereby isolating persons with
COVID-19, limiting the transmission of SARS-CoV-2, and promoting a robust public health response to contain the pandemic.

Key words: COVID-19; SARS-CoV-2; biosafety laboratory; challenges.

J Infect Dev Ctries 2021; 15(12):1833-1837. doi:10.3855/jidc.14415

(Received 28 November 2020 – Accepted 17 June 2021)

Copyright © 2021 Islam et al. This is an open-access article distributed under the Creative Commons Attribution License, which permits unrestricted use,
distribution, and reproduction in any medium, provided the original work is properly cited.

Introduction sole recognised COVID-19 testing facility in the

On March 11, 2020, the World Health Organization country [3].
(WHO) declared that the suppression of the coronavirus SARS-CoV-2, the causative organism of COVID-
disease-19 (COVID-19) pandemic must be through 19, belongs to the risk group three (RG3) infectious
isolation, treatment, and tracing [1]. Numerous severe agents; it should be handled in a Biosafety Level-3
acute respiratory syndrome-coronavirus-2 (SARS- (BSL-3) containment facility that permits the
CoV-2) RNA detection centers are required to meet this manipulation of pathogens transmitted via aerosols [4].
demand. At the onset of this pandemic, health systems There were limited biocontainment facilities in
in resource-limited settings, such as Bangladesh faced a Bangladesh before the onset of this pandemic that could
significant challenge in managing the situation. After be transformed to handle SARS-CoV-2. The purpose of
the first case was detected on March 8, 2020, the this study is to describe the efforts taken to overcome
Ministry of Health and Family Welfare (MOH&FW) of the challenges faced during the establishment and
the Government of Bangladesh decided to initiate operation of a molecular testing laboratory for COVID-
COVID-19 identification and expand SARS-CoV-2 19 in resource-constrained settings.
testing laboratories throughout the country to control
the spread of the virus [2]. In response, the Planning phase
Bangabandhu Sheikh Mujib Medical University Initially, relevant guidelines on COVID-19,
(BSMMU) took the initiative to provide COVID-19 biocontainment laboratory, biosafety levels, real-time
molecular testing support through the Department of reverse transcriptase-polymerase chain reaction (RT-
Virology. Until March 31, 2020, the Institute of PCR), and infection prevention and control (IPC)
Epidemiology, Disease Control and Research was the circulated by the Centers for Disease Control and
Islam et al. – Establishment of a COVID-19 biosafety laboratory J Infect Dev Ctries 2021; 15(12):1833-1837.

Prevention (CDC) [5] and the WHO [6] were Figure 1. The four-storied building in which the COVID-19
considered for the planning and establishment of a laboratory is located.
COVID-19 testing laboratory. Additionally, the risk
assessment steps were thoroughly followed to reduce
the operational risk hazards while maintaining a
functional biosafety laboratory at a minimal cost [7,8].
As SARS-CoV-2 is an RNA virus that belongs to a
group of RG3 organisms, it should be handled in a BSL-
3 facility. However, it can be considered that non-
propagative work with SARS-CoV-2 RNA would be
safe to be dealt with in a BSL-2 facility with additional
aerosol precautions [9]. Thus, to initiate COVID-19
testing within a short time, considering the gravity of
the situation, a BSL-2 facility was planned, and aerosol
precautions were taken based on BSL-3-equivalent
personal safety measures.

Development and establishment phase

Guidance documents and standard operating PCR cabinet (BIOBASE, China), dry shaking heating
procedures (SOPs) for laboratory detection of SARS- block, water bath, vortex mixer, refrigerated centrifuge,
CoV-2 RNA were prepared [10] and followed during 2-8 °C refrigerator, and -20 °C freezer. The pioneer
the functioning of the COVID-19 laboratory. The start- members of the COVID-19 laboratory comprised
up equipment consisted of real-time reverse faculties, residents, scientific officers, medical
transcription–polymerase chain reaction (RT-PCR) technologists, project-linked personnel, support staff,
(Applied Biosystems QuantStudio 5 and 7500 Real- and volunteers and were headed by the Chairman of the
Time PCR System, Thermo Fisher Scientific Inc. Department of Virology. All members underwent on-
USA), GeneXpert Systems (Cepheid, USA), biosafety campus training in basic techniques and skills required
cabinet (BSC)-Class II (Esco Lifesciences, Singapore), to operate the instruments and practiced IPC in a high-
containment laboratory before the commencement of
Figure 2. Naso-pharyngeal swab collection for COVID-19 operations in the COVID-19 laboratory. In particular,
testing. the participants were trained to maintain biosafety
precautions at all times, the use of personal safety
equipment according to the CDC guidelines, sample
collection techniques from the nasopharynx/throat,
molecular detection of SARS-CoV-2 RNA using
reagents and instruments, safe waste disposal, and
regular decontamination and maintenance of the
instruments.

Operational phase
A building completely separate from the main
university campus was selected to establish the
COVID-19 laboratory to avoid intermingling among
suspected and non-COVID-19 patients. The chosen
building is an old structure that belongs to the proposed
BSMMU administrative Block-1 (Figure 1). The
laboratory was established at the far end of the first
floor of the building to limit the number of people in the
area. A designated sample collection area for COVID-
19 testing was set up on the ground floor (Figure 2).
Several sample collection booths were constructed, and

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the long queue of patients was systematized by creating results were notified to each individual via text
prior online bookings for the daily testing slots. messages from a BSMMU-authorised mobile number
This laboratory received samples of suspected [12].
COVID-19 patients after evaluation at the fever clinic, The daily sample turnover at this facility usually
health care workers who developed COVID-19-like depends on the rate of infections in the country,
symptoms, and patients admitted under the hospital's publicised in the daily press released by the DGHS; a
COVID-19 and non-COVID-19 sections as directed by high rate of infection or high death rate due to COVID-
the University authority. Collection, transportation, and 19 makes more people screen for the disease when they
processing of samples followed by RT-PCR testing feel symptomatic. By May 31, 2021, about 144,067
were performed according to SOP guidelines. First, samples were tested for COVID-19 in this laboratory,
nasopharyngeal swabs were collected from patients, and on average 3,000 samples were received weekly for
and each swab was inserted into a sample storage tube testing.
containing 2 mL of normal saline with an RNase None of the laboratory personnel had laboratory-
inhibitor. In the laboratory, these samples were associated COVID-19 infections. However, many
processed using heat-inactivation and buffer-based admitted that they were infected through contact with
extraction methods. Real-time RT-PCR was performed family members or friends, probably resulting from
using a SARS-CoV-2 detection system (PCR- unenthusiastic health safety [13].
fluorescence probing) that utilised ORF1ab and N
genes as targets for the qualitative detection of SARS- Discussion
CoV-2 RNA. In addition, internal control targeting the The experience of establishing a COVID-19 testing
RNase P gene was used to monitor sample collection, center in Bangladesh indicates that collaborative efforts
sample handling, and molecular processes to avoid of all stakeholders, funding from the local budget, and
false-negative results. A cycle threshold (Ct) value of > the technical expertise of in-house researchers and
40 cycles indicated negative results, and the lowest scientists enabled the development of a biocontainment
limit of detection was 200 copies/mL. The organization laboratory within a short time and permitted operations
of the COVID-19 laboratory is shown in Figure 3. with acceptable quality in a resource-constrained
The results of the tested samples were sent to the situation. The establishment of a COVID-19 testing
Management Information System (MIS) under the center in the premises of the BSMMU was an enormous
Directorate General of Health Services (DGHS) that challenge, but it started functioning as a molecular
was added to the National Coronavirus COVID-19 COVID-19 laboratory within a short period.
Dashboard in 2020 [11]. Data shared with MIS and The initial challenge was to locate an ideal space for
DGHS were analyzed for COVID-19 detection a biocontainment facility that limited person-to-person
frequency in terms of locality, age-gender particulars, transmission due to the intermingling of COVID-19
recovery, and death numbers and compared with other patients with non-COVID-19 patients attending the
areas of the country that are included on the National hospital for other health-related services; this was
Coronavirus COVID-19 Dashboard, 2020, and managed by designating a separate building. The
circulated with a press release. Electronically generated second challenge was to motivate the laboratory
testing reports can be downloaded by the patients using personnel to deal with a new, unfamiliar pathogen
a web-based link from the DGHS website, and the without prior knowledge and to work while wearing

Figure 3. Organization of the COVID-19 laboratory: Specimen processing room (A), RNA isolation and reagent mixture preparation (B),
Amplification room (C).

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Islam et al. – Establishment of a COVID-19 biosafety laboratory J Infect Dev Ctries 2021; 15(12):1833-1837.

various safety gears. This department has a long the services and maintenance of instruments. A
experience in molecular detection of blood-borne decrease in the efficacy of instruments is already being
pathogens [14], and after intensive training, the staff noticed owing to overuse under the current
acquired a basic understanding of testing and IPC circumstances. Third, there has been a shortage of labor
procedures. The third challenge was to reduce aerosol that persisted despite few appointments, and many staff
formation during sample collection and molecular members were already exhausted as there were no
testing to avoid laboratory-associated infections. backup laboratory members. Moreover, the lack of
Preventing contact with the aerosol formed during short-term assignments or stipends for volunteers and
sample collection was minimised by collecting the risk allowances for the working personnel at the
samples inside the designated booths or kiosks. In the laboratory failed to motivate them to continue work, as
laboratory, the sample tubes were placed in a dry observed in the initial phase [17]. Finally, accreditation
heating block inside a biosafety cabinet II that degraded of the COVID-19 testing laboratory, necessary for
the virus envelope, making it non-infectious [15]. quality assurance and follow-up calibration
Fourthly, there was a shortage of Personal protective certification for continued testing and equipment,
equipment (PPE) with accessories during the initial respectively, could not be obtained due to the ongoing
stages because of increased global demand; necessities pandemic in the country.
were met through imports from foreign countries.
Subsequently, rapid initiatives taken by the local Conclusions
readymade garments (RMG) industry to manufacture This experience has taught us that, despite several
all the components of PPE made safety gear readily limitations and financial barriers, the concerted efforts
available [16]. Fifthly, there was a gradual increase in of all stakeholders can enable the establishment and
sample turnover, causing difficulty in delivering results functioning of a biocontainment facility that is
in due time; this issue was resolved by the emergency beneficial to the community in the current pandemic.
employment of a few laboratory technologists from Nonetheless, it is essential to set long-term goals, and
DGHS. Lastly, the waste management system was financing should be made available to sustain
another challenge that was resolved by merging it with continuous functioning and improve the quality of
the University waste disposal protocol. Hence, all the COVID-19 laboratories.
challenges were overcome, and a COVID-19 testing
laboratory has been established that has already earned
the confidence of the local community. Acknowledgements
We are grateful for the support of the Administration,
Limitations Bangabandhu Sheikh Mujib Medical University (BSMMU),
Directorate General of Health Services, Ministry of Health
Despite all efforts, there are certain drawbacks to
and Family Welfare, and Government of Bangladesh. We
the COVID-19 laboratory setup. First, the construction sincerely appreciate the tireless contributions of numerous
of the laboratory was on a temporary basis, and we had university staff during the establishment and continuance of
to compromise with the old architectural design of the the services.
building. For this reason, the laboratory design did not
include the ideal biosafety precautions and sequences. Author contribution
Moreover, the sample collection and processing rooms Conceptualization: SRUI, ST, SUM; fund acquisition: SUM;
could not be designed as negative pressure rooms with designing the facility: SRUI, SUM, MJ, AN, AKG;
a controlled HEPA-filtered airflow. Furthermore, the developing the facility: SRUI, AKG, PD, MAON, SUM;
establishment lacked a self-closing double-door air- performing the experiments and reporting the results: SRUI,
PD, AKG, MAON, TA, AHB; literature search and drafting
showered facility and a pass-through box between the
the manuscript: SRUI, PD, AKG, TA, AHB; data analysis:
biocontainment rooms. Additionally, on-site SS, MAON, AHB; reviewing, editing, and revising the
autoclaving and effluent decontamination systems manuscript: SRUI, ST, SS, TA; approving the final version
could not be arranged. Second, the duration of the of the manuscript: SRUI, ST.
pandemic cannot be predicted; therefore, there have
been challenges in bearing the operational expenses of
the support and supplies in a resource-constrained References
situation. Although the essential instruments were 1. World Health Organization (2020) WHO Director-General's
obtained and the establishment cost was covered, the opening remarks at the media briefing on COVID-19 - 11
March 2020. Available: https://www.who.int/director-
uncertainty of continued financial support may hamper general/speeches/detail/who-director-general-s-opening-

1836
Islam et al. – Establishment of a COVID-19 biosafety laboratory J Infect Dev Ctries 2021; 15(12):1833-1837.

remarks-at-the-media-briefing-on-covid-19---11-march-2020. http://103.247.238.92/webportal/pages/covid19.php.
Accessed: 10 November 2020. Accessed: 6 December 2021.
2. Ministry of Health and Family Welfare (2020) Bangladesh 12. Directorate General of Health Services (2020) Corona.
preparedness and response plan for COVID-19. Available: Available:
http://www.mohfw.gov.bd/index.php?option=com_docman&t https://dghs.gov.bd/index.php/en/component/content/article?i
ask=doc_download&gid=23359&lang=en. Accessed: 20 d=5393. Accessed: 6 December 2021.
October 2020. 13. Cheng HY, Jian SW, Liu DP, Ng TC, Huang WT, Lin HH,
3. bdnews24.com, Bangladesh (2020) BSMMU begins COVID- Taiwan COVID-19 Outbreak Investigation Team (2020)
19 testing, DMCH is ready. Available: Contact tracing assessment of COVID-19 transmission
https://bdnews24.com/health/2020/04/02/bsmmu-begins- dynamics in Taiwan and risk at different exposure periods
covid-19-testing-dmch-is-ready. Accessed: 25 October 2020. before and after symptom onset. JAMA Intern Med 180: 1156-
4. Buchan BW, Mahlen SD, Relich RF (2019) Interim clinical 1163.
laboratory guideline for biological safety. The American 14. Rashed-Ul Islam SM, Jahan M, Tabassum S (2015) Evaluation
Society for Microbiology. Available: of a rapid one-step real-time PCR method as a high-throughput
https://asm.org/ASM/media/Policy-and-Advocacy/Biosafety- screening for quantification of hepatitis B virus DNA in a
white-paper-2019.pdf. Accessed: 10 October 2020. resource-limited setting. Euroasian J Hepatogastroenterol 5:
5. Centers for Disease Control and Prevention (2020) Overview 11-15.
of testing for SARS-CoV-2 (COVID-19). Available: 15. Wang Y, Song W, Zhao Z, Chen P, Liu J, Li C (2020) The
https://www.cdc.gov/coronavirus/2019-ncov/hcp/testing- impacts of viral inactivating methods on quantitative RT-PCR
overview.html. Accessed: 2 November 2020. for COVID-19. Virus Res 285: 197988.
6. World Health Organization (2020) Diagnostic testing for 16. The daily star (2020) Factories rise to the occasion, join hands
SARS-CoV-2. Available: https://www.who.int/publications- to make PPE. Available:
detail-redirect/diagnostic-testing-for-sars-cov-2. Accessed: 10 https://www.thedailystar.net/business/news/factories-rise-the-
October 2020. occasion-join-hands-make-ppe-1886101. Accessed: 28 May
7. Bangladesh Biosafety and Biosecurity Society (2019) 2021.
Bangladesh biosafety and biosecurity society guidelines for 17. Giri AK, Rana DRSJB (2020) Charting the challenges behind
handling and disposal of biohazardous materials, first edition. the testing of COVID-19 in developing countries: Nepal as a
Available: case study. Biosafety and Health 2: 53-56.
https://bdbiosafetysecurity.org/uploads/documents/Banglades
h_Biosafety_and_Biosecurity_Guidelines.pdf Accessed: 10 Corresponding author
October 2020. SM Rashed Ul Islam, M. Phil, MPH
8. Li N, Hu L, Jin A, Li J (2019) Biosafety laboratory risk Associate Professor
assessment. J Biosaf Biosecur 1: 90-92. Department of Virology
9. World Health Organization (2020) Laboratory biosafety Bangabandhu Sheikh Mujib Medical University (BSMMU)
guidance related to the novel coronavirus (2019-nCoV). Shahbag, Dhaka-1000, Bangladesh.
Available:https://www.who.int/docs/default- Phone.: +8801713236399
source/coronaviruse/laboratory-biosafety-novel-coronavirus- Fax: +02-55165609
version-1-1.pdf?sfvrsn=912a9847_2. Accessed: 25 May 2021. Email: [email protected]
10. Islam SMRUI (2020) Guidance and standard operating
procedure for SARS-CoV-2 detection. doi: Conflict of interests: No conflict of interests is declared.
10.5281/zenodo.3903995.
11. COVID-19 dynamic dashboard for Bangladesh (2020)
Available:

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