Cross-contamination in Molecular Diagnostic Laboratories in Low- and Middle-income Countries A Challenge to COVID-19 Testing

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Pia Marie Albano
Kin Israel Notarte
Imee Macaranas
Benedict Maralit


At the start of the pandemic, the Philippines had to send swab samples to the Victorian Infectious Diseases Reference Laboratory in Melbourne, Australia for COVID-19 confirmation. With the increasing number of  suspected cases needing confirmatory diagnostic testing, there was a demand to rapidly expand the capacity for widescale testing. Remarkably, within 200 days from announcement of the first confirmed COVID-19 case in the Philippines in January 30, 2020, the country has been able to expand its testing capacity from one national reference laboratory, the Research Institute for Tropical Medicine (RITM), to more than 100 licensed reverse transcription-polymerase chain reaction (RT-PCR) and cartridge-based PCR laboratories across the country. Due to the shortage of a trained clinical laboratory workforce, diagnostic centers are forced to hire additional personnel who have limited experience and technical knowledge and skills of molecular assays, especially in processing specimens, interpreting the results, identifying errors, and troubleshooting, in order to meet the demand of increased testing. Thus, the vulnerability to diagnostic errors, including cross-contamination, is increased and with the tendency for generating false positive results that can compromise the health of the patient and disrupt the efficacy of public health policies and public health response, surveillance programs, and restrictive measures for containing the outbreak. Hence, this review article aims to present the different sources of contamination in the laboratory setting where RT-PCR assays are conducted, as well as provide efficient, effective and feasible solutions to address these issues, most especially in low- and middle-income countries (LMICs) like the Philippines.


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How to Cite
Albano, P. M., Notarte, K. I., Macaranas, I., & Maralit, B. (2020). Cross-contamination in Molecular Diagnostic Laboratories in Low- and Middle-income Countries : A Challenge to COVID-19 Testing. Philippine Journal of Pathology, 5(2). Retrieved from
Author Biographies

Pia Marie Albano, University of Santo Tomas

Professor, College of Science and The Graduate School

Principal Investigator-Molecular Diagnostics Research Group (Cancer), Research Center for the Natural and Applied Sciences (RCNAS)

Kin Israel Notarte, University of Santo Tomas

Former Faculty Member, College of Science and The Graduate School

Medical Student, Faculty of Medicine and Surgery

Imee Macaranas, University of Santo Tomas

Medical Student, Faculty of Medicine and Surgery

Benedict Maralit, University of the Philippines-Diliman, Quezon City

Director, DNA Sequencing Core Facility, Genome Center


[1] Jin Y, Yang H, Ji W, Wu W, Chen S, Zhang W, et al. Virology, epidemiology, pathogenesis, and control of COVID-19. Viruses 2020; 12(4):372.
[2] Wu F, Zhao S, Yu B, Chen YM, Wang W, Hu Y, et al. Complete genome characterisation of a novel coronavirus associated with severe human respiratory disease in Wuhan, China. bioRxiv 2020.
[3] Coronavirus Resource Center. COVID-19 Dashboard by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (JHU). [Online]. Available from: [Accessed on 06 August 2020].
[4] Chinese Center for Disease Control and Prevention. The epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (COVID-19) in China. Zhonghua Liu Xing Bing Xue Za Zhi 2020; 41(2):145-151.
[5] World Health Organization. Coronavirus Disease 2019 (COVID-19) Situation Report. [Online]. Available from: 2019/situation-reports/. [Accessed on 06 August 2020].
[6] Hopman J, Allegranzi B, Mehtar S. Managing COVID-19 in low-and middle-income countries. JAMA 2020; 323(16):1549-1550.
[7] Peto J. Covid-19 mass testing facilities could end the epidemic rapidly. BMJ 2020; 368:m1163.
[8] Kwon KT, Ko JH, Shin H, Sung M, Kim JY. Drive-through screening center for COVID-19: A safe and efficient screening system against massive community Outbreak. J Korean Med Sci 2020; 35(11):e123.
[9] Gonzales C. Philippines with Highest COVID-19 Cases in Southeast Asia? DOH Cites Different ‘Settings’ (Inquirer). [Online]. Available from: https://newsinfo.inquirer. net/1318069/ph-with-highest-covid-19-cases-in-se-asia-doh-cites-different-settings. [Accessed on 07 August 2020].
[10] Mietzner M. Populist anti-scientism, religious polarisation, and institutionalised corruption: How Indonesia’s democratic decline shaped its COVID-19 response. J Curr Southeast Asian Affairs 2020.
[11] Kobia F, Gitaka J. COVID-19: Are Africa’s diagnostic challenges blunting response effectiveness?. AAS Open Res 2020; 3:1-11.
[12] World Health Organization. Global Surveillance for Human Infection with Coronavirus Disease (COVID-19). [Online]. Available from: cations/i/item/global-surveillance-for-human-infection-with-novel-coronavirus-(2019-ncov). [Accessed on 06 August 2020].
[13] Sahajpal NS, Mondal AK, Njau A, Ananth S, Jones K, Ahluwalia PK, et al. Proposal of reverse transcription-PCR–based mass population screening for SARS-CoV-2 (COVID-19). J Mol Diagnostics 2020.
[14] Lippi G, Simundic AM, Plebani M. Potential preanalytical and analytical vulnerabilities in the laboratory diagnosis of coronavirus disease 2019 (COVID-19). Clin Chem Lab Med (CCLM) 2020; 58(7):1-7.
[15] Sheridan C. Coronavirus and the race to distribute reliable diagnostics. Nature Biotech 2020; 38(4):382.
[16] Aguilar K. ‘Manpower Shortage Hounding Bid to Boost COVID-19 Testing Capacity’ (Inquirer). [Online]. Available from: shortage-hounding-bid-to-boost-covid-19-testing-capacity. [Accessed on 06 August 2020].
[17] Giri AK, Rana DR. Charting the challenges behind the testing of COVID-19 in developing countries: Nepal as a case study. Biosafety Health 2020; 2:53-56.
[18] Piras A, Rizzo D, Longoni E, Turra N, Urru S, Saba PP, et al. Nasopharyngeal swab collection in the suspicion of Covid-19. Am J Otolaryngol 2020; 102551:1-2.
[19] Irving SA, Vandermause MF, Shay DK, Belongia EA. Comparison of nasal and nasopharyngeal swabs for influenza detection in adults. Clinical Med Res 2012; 10(4):215-8.
[20] Spencer S, Gaglani M, Naleway A, Reynolds S, Ball S, Bozeman S, et al. Consistency of influenza A virus detection test results across respiratory specimen collection methods using real-time reverse transcription-PCR. J Clin Microbiol 2013; 51(11):3880-3882.
[21] World Health Organization. Laboratory biosafety guidance related to coronavirus disease (COVID-19). [Online]. Available from: laboratory-biosafety-guidance-related-to-coronavirus-disease-(covid-19). [Accessed on 07 August 2020].
[22] Department of Health. Guidelines in securing a license to operate a COVID-19 testing laboratory. [Online]. Available from: [Accessed on 07 August 2020].
[23] Lv J, Yang J, Xue J, Zhu P, Liu L, Li S. Detection of SARS-CoV-2 RNA residue on object surfaces in nucleic acid testing laboratory using droplet digital PCR. Sci Total Environ 2020; 742:140370.
[24] Loh TP, Horvath AR, Wang CB, Koch D, Adeli K, Mancini N, et al. Operational considerations and challenges of biochemistry laboratories during the COVID-19 outbreak: an IFCC global survey. Clin Chem Lab Med 2020.
[25] Hong KH , Lee SW, Kim TS, Huh HJ, Lee J, Kim SY, et al. Guidelines for Laboratory Diagnosis of Coronavirus Disease 2019 (COVID-19) in Korea. Ann Lab Med 2020; 40:351-360.
[26] van Zyl G, Maritz J, Newman H, Preiser W. Lessons in diagnostic virology: expected and unexpected sources of error. Rev Med Virol 2019; 29(4):e2052.
[27] Mögling R, Meijer A, Berginc N, et al. Delayed Laboratory Response to COVID-19 Caused by Molecular Diagnostic Contamination. Emerg Infect Dis 2020; 26(8):1944-1946.
[28] Philippine News Agency. UP-NIH test kits recalled due to reagent contamination: FDA. [Online]. Available from: [Accessed on 08 August 2020].