Clinical laboratory role in viral pandemic response: Focus on COVID-19

Main Article Content

Ian C. Clift, PhD, MLS (ASCP)


Background: The global focus on COVID-19 provides a spotlight for the critical role of the clinical laboratory scientist in monitoring and managing pandemic disease. Laboratory management and the laboratory team must understand the signs, symptoms and routes of transmission of the pandemic infectious disease, ensure the safety of their employees, and determine the most effective testing methods for implementation in a rapid time frame.

Methods: An examination of the current literature regarding characteristics of airborne viral outbreaks, safety practices, and emergency use testing methods were compiled.

Results: The protection of laboratory employees is mediated by emergency preparedness plans prior to pandemic threats, insurance that personnel are vaccinated when possible and have appropriate PPE available; includes respirators or face masks. The primary method of early detection of novel pandemic viral threats, such as COVID-19, is molecular testing via nucleic acid extraction from patient specimens and rRT-PCR as indicated from the issuance of FDA Emergency Use Authorizations (EUAs) from February to April of 2020.

Conclusions: Prior pandemics and standard laboratory practice have prepared clinical laboratories for mitigating the spread of disease among employees. NAAT (nucleic acid amplification testing) has emerged as the earliest testing modality for monitoring pandemic viral disease presence and other methods include viral culture, serological assays, and biomarker testing will be used to monitor progression and treatment. The clinical laboratory investigations and response to viral pandemics has the benefit of increasing our technical knowledge in handling future pandemic threats.

Keywords: : COVID-19, NAAT, PCR, Pandemic, Viral, Infectious Disease, Laboratory Medicine

Article Details

How to Cite
CLIFT, Ian C.. Clinical laboratory role in viral pandemic response: Focus on COVID-19. Medical Research Archives, [S.l.], v. 8, n. 6, june 2020. ISSN 2375-1924. Available at: <>. Date accessed: 14 june 2024. doi:
Research Articles


1. Hansen V, Oren E, Dennis LK, Brown HE. Infectious Disease Mortality Trends in the United States, 1980-2014. Jama. 2016;316(20):2149-2151.
2. Armstrong GL, Conn LA, Pinner RW. Trends in infectious disease mortality in the United States during the 20th century. Jama. 1999;281(1):61-66.
3. Hinman AR. Global progress in infectious disease control. Vaccine. 1998;16(11-12):1116-1121.
4. Iwen PC, Stiles KL, Pentella MA. Safety Considerations in the Laboratory Testing of Specimens Suspected or Known to Contain the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). American journal of clinical pathology. 2020;153(5):567-570.
5. Sivanandy P, Zi Xien F, Woon Kit L, Tze Wei Y, Hui En K, Chia Lynn L. A review on current trends in the treatment of human infection with H7N9-avian influenza A. J Infect Public Health. 2019;12(2):153-158.
6. Lim W, Ng KC, Tsang DN. Laboratory containment of SARS virus. Ann Acad Med Singapore. 2006;35(5):354-360.
7. Yang Y, Peng F, Wang R, et al. The deadly coronaviruses: The 2003 SARS pandemic and the 2020 novel coronavirus epidemic in China. J Autoimmun. 2020:102434.
8. Pavan K. Bhatraju MD, Bijan J. Ghassemieh MD, Michelle Nichols MD, et al. Covid-19 in Critically Ill Patients in the Seattle Region — Case Series. The New England journal of medicine. 2020:1-11.
9. Reusken CB, Ieven M, Sigfrid L, Eckerle I, Koopmans M. Laboratory preparedness and response with a focus on arboviruses in Europe. Clin Microbiol Infect. 2018;24(3):221-228.
10. Ogunremi T, Defalco K, Johnston BL, et al. Preventing transmission of bloodborne viruses from infected healthcare workers to patients: Summary of a new Canadian Guideline. Can Commun Dis Rep. 2019;45(12):317-322.
11. Syed S, Saleem A. Severe Acute Respiratory Syndrome Epidemiology and Control. Laboratory Medicine. 2004;35(2):112-116.
12. Salgado CD, Giannetta ET, Hayden FG, Farr BM. Preventing nosocomial influenza by improving the vaccine acceptance rate of clinicians. Infect Control Hosp Epidemiol. 2004;25(11):923-928.
13. Park SH, Kim YS, Jung Y, et al. Outbreaks of Middle East Respiratory Syndrome in Two Hospitals Initiated by a Single Patient in Daejeon, South Korea. Infect Chemother. 2016;48(2):99-107.
14. Coronavirus disease (COVID-19) outbreak situation. 2020; Accessed 4/18/2020, 2020.
15. Bundy KL, Foss ML, Stubbs JR. Transfusion service disaster planning. Immunohematology. 2008;24(3):93-101.
16. Delany JR, Pentella MA, Rodriguez JA, Shah KV, Baxley KP, Holmes DE. Guidelines for Biosafety Laboratory Competency CDC and the Association of Public Health Laboratories. MMWR Suppl. 2011;60:1-6.
17. Lippi G, Plebani M. The critical role of laboratory medicine during coronavirus disease 2019 (COVID-19) and other viral outbreaks. Clin Chem Lab Med. 2020.
18. Sharma PP, Friesen T, Waites KB. Influenza testing in the diagnostic laboratory. Labmedicine. 2006;37(6):366-370.
19. Miller JM, Astles R, Baszler T, et al. Guidelines for safe work practices in human and animal medical diagnostic laboratories. Recommendations of a CDC-convened, Biosafety Blue Ribbon Panel. MMWR Suppl. 2012;61(1):1-102.
20. Interim Infection Prevention and Control Recommendations for Patients with Suspected or Confirmed Coronavirus Disease 2019 (COVID-19) in Healthcare Settings. 2020; Accessed 4/1/2020, 2020.
21. Wang X, Zhang X, He J. Challenges to the system of reserve medical supplies for public health emergencies: reflections on the outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in China. Biosci Trends. 2020;14(1):3-8.
22. Broussard IM, Kahwaji CI. Universal Precautions. StatPearls. Treasure Island (FL)2020.
23. Radonovich LJ, Jr., Simberkoff MS, Bessesen MT, et al. N95 Respirators vs Medical Masks for Preventing Influenza Among Health Care Personnel: A Randomized Clinical Trial. Jama. 2019;322(9):824-833.
24. MacIntyre CR, Chughtai AA, Rahman B, et al. The efficacy of medical masks and respirators against respiratory infection in healthcare workers. Influenza Other Respir Viruses. 2017;11(6):511-517.
25. Ma QX, Shan H, Zhang HL, Li GM, Yang RM, Chen JM. Potential utilities of mask wearing and instant hand hygiene for fighting SARS-CoV-2. J Med Virol. 2020.
26. Eisfeld AJ, Neumann G, Kawaoka Y. At the centre: influenza A virus ribonucleoproteins. Nat Rev Microbiol. 2015;13(1):28-41.
27. Zhu N, Zhang D, Wang W, et al. A Novel Coronavirus from Patients with Pneumonia in China, 2019. The New England journal of medicine. 2020;382(8):727-733.
28. Noda T. Native morphology of influenza virions. Front Microbiol. 2011;2:269.
29. Review of preparations used for hand hygiene. WHO Guidelines on Hand Hygiene in Health Care: First Global Patient Safety Challenge Clean Care Is Safer Care. Geneva2009.
30. Gebel J, Exner M, French G, et al. The role of surface disinfection in infection prevention. GMS Hyg Infect Control. 2013;8(1):Doc10.
31. Devnani M. Factors associated with the willingness of health care personnel to work during an influenza public health emergency: an integrative review. Prehosp Disaster Med. 2012;27(6):551-566.
32. Garcia E, Kundu I, Kelly M, Soles R. The American Society for Clinical Pathology's 2018 Vacancy Survey of Medical Laboratories in the United States. American journal of clinical pathology. 2019;152(2):155-168.
33. Garcia E, Kundu I, Fong K. The American Society for Clinical Pathology’s 2017 Wage Survey of Medical Laboratories in the United States. American journal of clinical pathology. 2018;151(1):29-52.
34. Costello MJ, Morrow SL, Laney S, Yungbluth M. Guidelines for Specimen Collection, Transportation, and Test Selection. Laboratory Medicine. 1993;24(1):19-24.
35. NxTAG® CoV Extended PanelAssay Package Insert [package insert]. Luminex Corporation. 2020.
36. QIAstat-Dx®Respiratory SARS-CoV-2 Panel Instructions for Use (Handbook) [package insert]. QIAGEN. 2020.
37. Cellex qSARS-CoV-2 IgG/IgM Rapid Test [package insert]. Cellex Inc. 2020.
38. Chan JF, Sridhar S, Yip CC, Lau SK, Woo PC. The role of laboratory diagnostics in emerging viral infections: the example of the Middle East respiratory syndrome epidemic. J Microbiol. 2017;55(3):172-182.
39. CDC Grows SARS-CoV-2, the virus that causes COVID-19, in Cell Culture. 2020; Accessed 4/2/2020, 2020.
40. Azar MM, Landry ML. Detection of Influenza A and B Viruses and Respiratory Syncytial Virus by Use of Clinical Laboratory Improvement Amendments of 1988 (CLIA)-Waived Point-of-Care Assays: a Paradigm Shift to Molecular Tests. J Clin Microbiol. 2018;56(7).
41. Hahn A, Podbielski A, Meyer T, et al. On detection thresholds-a review on diagnostic approaches in the infectious disease laboratory and the interpretation of their results. Acta Trop. 2020;205:105377.
42. Pang J, Wang MX, Ang IYH, et al. Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review. J Clin Med. 2020;9(3).
43. Mahony JB, Petrich A, Smieja M. Molecular diagnosis of respiratory virus infections. Critical reviews in clinical laboratory sciences. 2011;48(5-6):217-249.
44. Obande GA, Banga Singh KK. Current and Future Perspectives on Isothermal Nucleic Acid Amplification Technologies for Diagnosing Infections. Infect Drug Resist. 2020;13:455-483.
45. ID NOW COVID-19 [package insert]. In: Abbott, ed. Rev. 1 ed: Abbott; 2020.
46. Emergency Use Authorizations. Accessed 4/2/2020, 2020.
47. Merckx J, Wali R, Schiller I, et al. Diagnostic Accuracy of Novel and Traditional Rapid Tests for Influenza Infection Compared With Reverse Transcriptase Polymerase Chain Reaction: A Systematic Review and Meta-analysis. Ann Intern Med. 2017;167(6):394-409.
48. Xpert® Xpress SARS-CoV-2 Instructions for Use: For Use with GeneXpert Xpress System (point of care system) [package Insert]. Cepheid Innovation. 2020;302-3750.
49. Reusken C, Broberg EK, Haagmans B, et al. Laboratory readiness and response for novel coronavirus (2019-nCoV) in expert laboratories in 30 EU/EEA countries, January 2020. Euro Surveill. 2020;25(6).
50. Ginocchio CC, McAdam AJ. Current Best Practices for Respiratory Virus Testing. Journal of Clinical Microbiology. 2011;49(9 Suppl):S44-S48.
51. Hospital Respiratory Protection Program Toolkit. Vol 2015-117. DHHS (NIOSH); 2015.
52. Modes of transmission of virus causing COVID-19: implications for IPC precaution recommendations. 2020; Accessed 4/6/2020, 2020.
53. Thatcher SA. DNA/RNA preparation for molecular detection. Clin Chem. 2015;61(1):89-99.
54. Spackman E, Senne DA, Myers TJ, et al. Development of a real-time reverse transcriptase PCR assay for type A influenza virus and the avian H5 and H7 hemagglutinin subtypes. J Clin Microbiol. 2002;40(9):3256-3260.
55. Tewari D, Zellers C, Acland H, Pedersen JC. Automated extraction of avian influenza virus for rapid detection using real-time RT-PCR. J Clin Virol. 2007;40(2):142-145.
56. Marzoratti L, Iannella HA, Gomez VF, Figueroa SB. Recent advances in the diagnosis and treatment of influenza pneumonia. Curr Infect Dis Rep. 2012;14(3):275-283.
57. Mackay IM. Real-time PCR in the microbiology laboratory. Clin Microbiol Infect. 2004;10(3):190-212.
58. Drolet BS, Weingartl HM, Jiang J, et al. Development and evaluation of one-step rRT-PCR and immunohistochemical methods for detection of Rift Valley fever virus in biosafety level 2 diagnostic laboratories. J Virol Methods. 2012;179(2):373-382.
59. Applied Biosystems 7500 Real-Time PCR System and Applied Biosystems 7500 Fast Real-Time PCR System: A Real Fast and Real Versatile Approach to Real-Time PCR. Applied Biosystems; 2004.
60. EUROIMMUN is one of the first European manufacturers of diagnostic tests to provide CE-marked antibody detection systems to support COVID-19 diagnostics. 2020; Accessed 3/29/2020, 2020.
61. Liu DX, Fung TS, Chong KK, Shukla A, Hilgenfeld R. Accessory proteins of SARS-CoV and other coronaviruses. Antiviral Res. 2014;109:97-109.
62. Ou X, Liu Y, Lei X, et al. Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV. Nature communications. 2020;11(1):1620.
63. Zhao J, Yuan Q, Wang H, et al. Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019. Clin Infect Dis. 2020.
64. Okba NMA, Müller MA, Li W, et al. 'SARS-CoV-2 specific antibody responses in COVID-19 patients'. medRxiv [preprint]. 2020.
65. Green DA, StGeorge K. Rapid Antigen Tests for Influenza: Rationale and Significance of the FDA Reclassification. J Clin Microbiol. 2018;56(10).
66. Parry JV, Easterbrook P, Sands AR. One or two serological assay testing strategy for diagnosis of HBV and HCV infection? The use of predictive modelling. BMC Infect Dis. 2017;17(Suppl 1):705.
67. Meyer B, Drosten C, Muller MA. Serological assays for emerging coronaviruses: challenges and pitfalls. Virus Res. 2014;194:175-183.
68. Haveri A, Smura T, Kuivanen S, et al. Serological and molecular findings during SARS-CoV-2 infection: the first case study in Finland, January to February 2020. Euro Surveill. 2020;25(11).
69. Leland D, Clift IC. Viral Serology. In: Clift IC, ed. Clinical immunodiagnostics : laboratory principles and practices. First edition. ed. Burlington, MA: Jones & Bartlett Learning; 2021:175-198.
70. NCI brings serological test validation to COVID-19 fight. 2020; Accessed 5/7/2020, 2020.
71. Laurie KL, Huston P, Riley S, et al. Influenza serological studies to inform public health action: best practices to optimise timing, quality and reporting. Influenza Other Respir Viruses. 2013;7(2):211-224.
72. Liu Y, Yang Y, Zhang C, et al. Clinical and biochemical indexes from 2019-nCoV infected patients linked to viral loads and lung injury. Sci China Life Sci. 2020;63(3):364-374.
73. Chen WH, Strych U, Hotez PJ, Bottazzi ME. The SARS-CoV-2 Vaccine Pipeline: an Overview. Curr Trop Med Rep. 2020:1-4.
74. Lydon EC, Ko ER, Tsalik EL. The host response as a tool for infectious disease diagnosis and management. Expert Rev Mol Diagn. 2018;18(8):723-738.
75. Shanmugaraj B, Siriwattananon K, Wangkanont K, Phoolcharoen W. Perspectives on monoclonal antibody therapy as potential therapeutic intervention for Coronavirus disease-19 (COVID-19). Asian Pac J Allergy Immunol. 2020;38(1):10-18.
76. Hussain M, Jabeen N, Raza F, et al. Structural Variations in Human ACE2 may Influence its Binding with SARS-CoV-2 Spike Protein. J Med Virol. 2020.
77. Yang P, Gu H, Zhao Z, et al. Angiotensin-converting enzyme 2 (ACE2) mediates influenza H7N9 virus-induced acute lung injury. Sci Rep. 2014;4:7027.
78. Yu F, Yan L, Wang N, et al. Quantitative Detection and Viral Load Analysis of SARS-CoV-2 in Infected Patients. Clin Infect Dis. 2020.
79. To KK, Tsang OT, Leung WS, et al. Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study. Lancet Infect Dis. 2020.
80. Mantel C, Cherian T. New immunization strategies: adapting to global challenges. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz. 2020;63(1):25-31.
81. Bernasconi V, Kristiansen PA, Whelan M, et al. Developing vaccines against epidemic-prone emerging infectious diseases. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz. 2020;63(1):65-73.
82. Clift IC. Diagnostic Flow Cytometry and the AIDS Pandemic. Lab Med. 2015;46(3):e59-64.