Review Article

Laboratory diagnosis of COVID-19: current status and challenges


The magnitude and pace of global affliction caused by Coronavirus Disease-19 (COVID-19) is unprecedented in the recent past. From starting in a busy seafood market in the Chinese city of Wuhan, the virus has spread across the globe in less than a year, infecting over 76 million people and causing death of close to 1.7 million individuals worldwide. As no specific antiviral treatment is currently available, the major strategy in containing the pandemic is focused on early diagnosis and prompt isolation of the infected individuals. Several diagnostic modalities have emerged within a relatively short period, which can be broadly classified into molecular and immunological assays. While the former category is centered around real-time PCR, which is currently considered the gold standard of diagnosis, the latter aims to detect viral antigens or antibodies specific to the viral antigens and is yet to be recommended as a stand-alone diagnostic tool. This review aims to provide an update on the different diagnostic modalities that are currently being used in diagnostic laboratories across the world as well as the upcoming methods and challenges associated with each of them. In a rapidly evolving diagnostic landscape with several testing platforms going through various phases of development and/or regulatory clearance, it is prudent that the clinical community familiarizes itself with the nuances of different testing modalities currently being employed for this condition.

1. Contini C, Di Nuzzo M, Barp N, Bonazza A, De Giorgio R, Tognon M, et al. The novel zoonotic COVID-19 pandemic: An expected global health concern. J Infect Dev Ctries 2020; 14: 254-264.
2. Coronavirus disease (COVID-19) Weekly Epidemiological Update and Weekly Operational Update.
3. Ye F, Xu S, Rong Z, Xu R, Liu X, Deng P, et al. Delivery of infection from asymptomatic carriers of COVID-19 in a familial cluster. Int J Infect Dis 2020; 94: 133-138.
4. Arons MM, Hatfield KM, Reddy SC, Kimball A, James A, Jacobs JR, et al. Presymptomatic SARS-CoV-2 infections and transmission in a skilled nursing facility. N Engl J Med 2020; 382: 2081-2090.
5. Bai Y, Yao L, Wei T, Tian F, Jin DY, Chen L, et al. Presumed asymptomatic carrier transmission of COVID-19. JAMA 2020; 323: 1406-1407.
6. Hong H, Wang Y, Chung HT, Chen CJ. Clinical characteristics of novel coronavirus disease 2019 (COVID-19) in newborns, infants and children. Pediatr Neonatol 2020; 61: 131-132.
7. Yang X, Yu Y, Xu J, Shu H, Xia J, Liu H, et al. Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study. Lancet Respir Med 2020; 8: 475-481.
8. Lu R, Zhao X, Li J, Niu P, Yang B, Wu H, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet 2020; 395: 565-574.
9. Malik YS, Sircar S, Bhat S, Sharun K, Dhama K, Dadar M, et al. Emerging novel coronavirus (2019-nCoV)-current scenario, evolutionary perspective based on genome analysis and recent developments. Vet Q 2020; 40: 68-76.
10. Molecular assays to diagnose COVID-19: Summary table of available protocols.
11. Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DK, et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill 2020; 25:2000045.
12. Shirato K, Nao N, Katano H, Takayama I, Saito S, Kato F, et al. Development of genetic diagnostic methods for novel Coronavirus 2019 (nCoV-2019) in Japan. Jpn J Infect Dis 2020; 73: 304-307.
13. SARS-COV-2 Diagnostic Pipeline.
14. Xpert® Xpress SARS-CoV-2.
15. James AS, Alawneh JI. COVID-19 infection diagnosis: potential impact of isothermal amplification technology to reduce community transmission of SARS-CoV-2. Diagnostics (Basel) 2020; 10: 399.
16. Khan P, Aufdembrink LM, Engelhart AE. Isothermal SARS-CoV-2 diagnostics: tools for enabling distributed pandemic testing as a means of supporting safe reopenings. ACS Synth Biol 2020; 9: 2861-2880.
17. Yu L, Wu S, Hao X, Dong X, Mao L, Pelechano V, et al. Rapid detection of COVID-19 coronavirus using a reverse transcriptional loop-mediated isothermal amplification (RT-LAMP) diagnostic platform. Clin Chem 2020; 66: 975-977.
18. Huang WE, Lim B, Hsu CC, Xiong D, Wu W, Yu Y, et al. RT-LAMP for rapid diagnosis of coronavirus SARS-CoV-2. Microb Biotechnol 2020; 13: 950-961.
19. Zhang Y, Odiwuor N, Xiong J, Sun L, Nyaruaba RO, Wei H, et al. Rapid molecular detection of SARS-CoV-2 (COVID-19) virus RNA using Colorimetric LAMP. medRxiv 2020;
20. Kellner MJ, Koob JG, Gootenberg JS, Abudayyeh OO, Zhang F. SHERLOCK: nucleic acid detection with CRISPR nucleases. Nat Protoc 2019; 14: 2986-3012.
21. Ding X, Yin K, Li Z, Lalla RV, Ballesteros E, Sfeir MM, et al. Ultrasensitive and visual detection of SARS-CoV-2 using all-in-one dual CRISPR-Cas12a assay. Nat Commun 2020; 11: 4711.
22. Wang R, Qian C, Pang Y, Li M, Yang Y, Ma H, et al. opvCRISPR: One-pot visual RT-LAMP-CRISPR platform for SARS-cov-2 detection. Biosens Bioelectron 2021; 172:112766.
23. Ding X, Yin K, Li Z, Lalla RV, Ballesteros E, Sfeir MM, et al. Ultrasensitive and visual detection of SARS-CoV-2 using all-in-one dual CRISPR-Cas12a assay. Nat Commun 2020; 11: 4711.
24. Rauch JN, Valois E, Solley SC, Braig F, Lach RS, Baxter NJ, et al. A Scalable, easy-to-deploy, protocol for Cas13-based detection of SARS-CoV-2 genetic material. bioRxiv 2020.
25. Javalkote VS, Kancharla N, Bhadra B, Shukla M, Soni B, Sapre A, et al. CRISPR-based assays for rapid detection of SARS-CoV-2. Methods 2020; S1046-2023(20)30217-6.
26. Islam KU, Iqbal J. An update on molecular diagnostics for COVID-19. Front Cell Infect Microbiol 2020; 10: 560616.
27. Andre NM, Cossic B, Davies E, Miller AD, Whittaker GR. Distinct mutation in the feline coronavirus spike protein cleavage activation site in a cat with feline infectious peritonitis-associated meningoencephalomyelitis. JFMS Open Rep 2019; 5: 2055116919856103.
28. Phan T. Genetic diversity and evolution of SARS-CoV-2. Infect Genet Evol 2020; 81:104260.
29. Serology Testing for COVID-19 at CDC.
30. CHEMBIO Diagnostic Systems Inc. DPP® COVID-19 IgM/IgG System. 2020.
31. Wu JL, Tseng WP, Lin CH, Lee TF, Chung MY, Huang CH, et al. Four point-of-care lateral flow immunoassays for diagnosis of COVID-19 and for assessing dynamics of antibody responses to SARS-CoV-2. J Infect 2020; 81: 435-442.
32. EUA Authorized Serology Test Performance.
33. Loeffelholz MJ, Tang YW. Laboratory diagnosis of emerging human coronavirus infections - the state of the art. Emerg Microbes Infect 2020; 9: 747-756.
34. Hogan CA, Sahoo MK, Pinsky BA. Sample pooling as a strategy to detect community transmission of SARS-CoV-2. JAMA 2020, 323: 1967-1969.
35. Singh AK, Nema RK, Joshi A, Shankar P, Nema S, Raghuwanshi A, et al. Evaluation of pooled sample analysis strategy in expediting case detection in areas with emerging outbreaks of COVID-19: A pilot study. PLoS One 2020; 15(9): e0239492.
36. Praharaj I, Jain A, Singh M, Balakrishnan A, Dhodapkar R, Borkakoty B, et al. Pooled testing for COVID-19 diagnosis by real-time RT-PCR: A multi-site comparative evaluation of 5- & 10-sample pooling. Indian J Med Res 2020; 152: 88-94.
37. Wolfel R, Corman VM, Guggemos W, Seilmaier M, Zange S, Muller MA, et al. Virological assessment of hospitalized patients with COVID-2019. Nature 2020; 581: 465-469.
38. Medeiros da Silva RC, Nogueira Marinho LC, de Araújo Silva DN, Costa de Lima K, Pirih FQ, Luz de Aquino Martins AR. Saliva as a possible tool for the SARS-CoV-2 detection: A review. Travel Med Infect Dis 2020; 38: 101920.
39. Yan Y, Chang L, Wang L. Laboratory testing of SARS-CoV, MERS-CoV, and SARS-CoV-2 (2019-nCoV): Current status, challenges, and countermeasures. Rev Med Virol 2020; 30(3):e2106.
IssueVol 13 No 1 (2021) QRcode
SectionReview Article(s)
COVID-19; SARS-CoV-2; Coronavirus; Diagnosis; COVID-19 nucleic acid testing; Enzyme-linked immunosorbent assay

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Creative Commons License This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
How to Cite
Mathew B, Vyas A, Khare P, Gupta S, Nema R, Nema S, Gupta S, Chaurasiya S, Biswas D, Singh A. Laboratory diagnosis of COVID-19: current status and challenges. Iran J Microbiol. 13(1):1-7.