Detection of SARS-CoV-2 using real-time polymerase chain reaction in different clinical specimens: A critical review

Main Article Content

Anees Muhammad
Hajira Ameer
Syed Adnan Haider
Ihsan Ali


COVID-19, Nasopharyngeal Specimens, SARS-CoV-2, RT-PCR


Coronavirus disease 2019 (COVID-19) is a disease caused by a new strain of coronavirus named as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Globally, since the outbreak, more than seven million confirmed cases of COVID-19 have been reported. The rapid spread and increase in the number of new cases is due to person-to-person transmission. To further control its transmission, early laboratory diagnosis of both asymptomatic and symptomatic patients is crucial. Presently, the COVID-19 diagnosis of infected individuals is dependent on computed tomography scanning and real-time polymerase chain reaction (PCR). The latter is considered more sensitive and efficient for early diagnosis. In this review, general comparisons are made (cases, fatality rate, incubation period, clinical features, and reservoirs) and diag-nostic laboratory procedures (specimens, extraction methods, and positive rates by real-time PCR) are compared between SARS, Middle East Respiratory Syndrome, and SARS-2. In total, 8982 SARS-2 suspected patients specimen data were retrieved, in which 40.9% (n = 3678) were detected as positive by real-time PCR. The specimen-wise high detection rate was observed from bronchoalveolar lavage, followed by saliva, nasal swabs, and sputum. As the COVID-19 cases are persistently increasing, the selection of appropriate specimens and laboratory assay would help in rapid and timely diagnosis.

Abstract 38 | PDF Downloads 24 XML Downloads 0 HTML Downloads 0


1. Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, et al. A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med. 2020;382:727–33.

2. Chen Y, Liu Q, Guo D. Emerging coronaviruses: genome structure, replication, and pathogenesis. J Med Virol. 2020;92:418–23.

3. Wang D, Hu B, Hu C, Zhu F, Liu X, Zhang J, et al. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China. JAMA. 2020;323:1061–69.

4. Su S, Wong G, Shi W, Liu J, Lai AC, Zhou J, et al. Epidemiology, genetic recombination, and pathogenesis of coronaviruses. Trends Microbiol. 2016;24:490–502.

5. Zaki AM, Van Boheemen S, Bestebroer TM, Osterhaus AD, Fouchier RA. Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. N Engl J Med. 2012;367:1814–20.

6. Chan-Yeung M, Xu RH. SARS: Epidemiology. Respirology. 8(Suppl) S9–14.

7. Watts J. China culls wild animals to prevent new SARS threat. Lancet. 2004;363:134.

8. Lee JY, Kim YJ, Chung EH, Kim DW, Jeong I, Kim Y, et al. The clinical and virological features of the first imported case causing MERS-CoV outbreak in South Korea, 2015. BMC Infect Dis. 2017;17:498.

9. Lee J, Chowell G, Jung E. A dynamic compartmental model for the Middle East respiratory syndrome outbreak in the Republic of Korea: A retrospective analysis on control interventions and superspreading events. J Theor Biol. 2016;408:118–26.

10. Coleman CM, Frieman MB. Growth and quantification of MERS–CoV infection. Curr Protoc Microbiol. 2015;37:15E–2.

11. Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, et al. Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin. Bio Rxiv. 2020;10:22-914952.

12. World Health Organization. WHO statement on the first meeting of the International Health Regulations (2005) Emergency Committee on Zika virus and observed increase in neurological disorders and neonatal malformations 2016 [Internet]. [Cited 25 Sept 2016]. Updated 1 February 2016;.

13. World Health Organization. Coronavirus disease 2019 (COVID-19): Situation report, 140. Geneva, Switzerland: WHO.

14. Perlman S. Another decade, another coronavirus. N Engl J Med. 2020;382:760–2.

15. Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020;579:270–3.

16. Holshue ML, DeBolt C, Lindquist S, Lofy KH, Wiesman J, Bruce H, et al. First case of 2019 novel coronavirus in the United States. N Engl J Med. 2020;382:929–36.

17. Rothe C, Schunk M, Sothmann P, Bretzel G, Froeschl G, Wallrauch C, et al. Transmission of 2019-nCoV infection from an asymptomatic contact in Germany. N Engl J Med. 2020;382:970–1.

18. Cong Y, Ren X. Coronavirus entry and release in polarized epithelial cells: A review. Rev Med Virol. 2014;24:308–15.

19. Shereen MA, Khan S, Kazmi A, Bashir N, Siddique R. COVID-19 infection: origin, transmission, and characteristics of human coronaviruses. J Adv Res. 2020;24:91–8.

20. Hussain S, Chen Y, Yang Y, Xu J, Peng Y, Wu Y, et al. Identification of novel subgenomic RNAs and noncanonical transcription initiation signals of severe acute respiratory syndrome coronavirus. J Virol. 2005;79:5288–95.

21. Cui J, Li F, Shi ZL. Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol. 2019;17:181–92.

22. Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y, et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet. 2020;395:497–506.

23. Lin C, Xiang J, Yan M, Li H, Huang S, Shen C. Comparison of throat swabs and sputum specimens for viral nucleic acid detection in 52 cases of novel coronavirus (SARS-Cov-2) infected pneumonia (COVID-19). Clin Chem Lab Med. 2020 Jun 25;58(7):1089-94.

24. Xie X, Zhong Z, Zhao W, Zheng C, Wang F, Liu J. Chest CT for typical 2019-nCoV pneumonia: Relationship to negative RT-PCR testing. Radiology. 2020;296(2):200343.

25. Tortorici MA, Veesler D. Structural insights into coronavirus entry. Adv Virus Res. 2019;105:93–116.

26. Wu Z, McGoogan JM. Characteristics of and important lessons from the coronavirus disease 2019 (COVID-19) outbreak in China: Summary of a report of 72,314 cases from the Chinese Center for Disease Control and Prevention. JAMA. 2020;323:1239–42.

27. Ai T, Yang Z, Hou H, Zhan C, Chen C, Lv W, et al. Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: A report of 1014 cases. Radiology. 2020;296(2):200642.

28. Winichakoon P, Chaiwarith R, Liwsrisakun C, Salee P, Goonna A, Limsukon A, et al. Negative nasopharyngeal and oropharyngeal swab does not rule out COVID-19. J Clin Microbiol. 2020;58(5):00297–20.

29. Wu J, Liu J, Zhao X, Liu C, Wang W, Wang D, et al. Clinical characteristics of imported cases of COVID-19 in Jiangsu Province: A multicenter descriptive study. Clin Infect Dis. 2020;71(15):706-712.

30. Yu F, Yan L, Wang N, Yang S, Wang L, Tang Y, et al. Quantitative detection and viral load analysis of SARS-CoV-2 in infected patients. Clin Infect Dis. 2020;71(15):793-798.

31. Lu R, Wang J, Li M, Wang Y, Dong J, Cai W. SARS-CoV-2 detection using digital PCR for COVID-19 diagnosis, treatment monitoring and criteria for discharge. medRxiv 2020.

32. Wang W, Xu Y, Gao R, Lu R, Han K, Wu G, et al. Detection of SARS-CoV-2 in different types of clinical specimens. JAMA. 2020;323:1843–4.

33. World Health Organization. Laboratory testing for coronavirus disease 2019 (COVID-19) in suspected human cases: Interim guidance, 2 March 2020. Geneva, Switzerland: World Health Organization; 2020.

34. Lu X, Whitaker B, Sakthivel SK, Kamili S, Rose LE, Lowe L, et al. Real-time reverse transcription-PCR assay panel for Middle East respiratory syndrome coronavirus. J Clin Microbiol. 2014;52:67–75.

35. Zhao Z, Cui H, Song W, Ru X, Zhou W, Yu X. A simple magnetic nanoparticles-based viral RNA extraction method for efficient detection of SARS-CoV-2. bioRxiv 2020.

36. China CDC. Specific primers and probes for detection 2019 novel coronavirus [Internet]. [2020]. Available from:

37. Chu DK, Pan Y, Cheng SM, Hui KP, Krishnan P, Liu Y, et al. Molecular diagnosis of a novel coronavirus (2019-nCoV) causing an outbreak of pneumonia. Clinic Chem. 2020;66:549–55.

38. Nao N, Shirato K, Katano H, Matsuyama S, Takeda M. Detection of second case of 2019-nCoV infection in Japan (corrected version). National Institute of Infectious Diseases; 2020.

39. Health, T.M.o.P. Diagnostic detection of novel coronavirus 2019 by real time RT-PCR [Internet]. 2020. Available from: detection-of-ncov-rirl-nat-inst-health-t.pdf?sfvrsn=4227

40. US CDC. 2019-Novel coronavirus (2019-nCoV) Real-time rRT-PCR panel: Primers and probes [Internet]. [cited 2020]. Available from:

41. 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. Eurosurveillance. 2020;25:2000045.

42. Zheng S, Fan J, Yu F, Feng B, Lou B, Zou Q, et al. Viral load dynamics and clinical disease severity in patients with SARS-CoV-2 infection. SSRN. 2020.

43. Zhang J, Wang S, Xue Y. Fecal specimen diagnosis 2019 novel coronavirus-infected pneumonia. J Med Virol. 2020;92:680–682.

44. To KK, Tsang OT, Yip CC, Chan KH, Wu TC, Chan JM, et al. Consistent detection of 2019 novel coronavirus in saliva. Clin Infect Dis. 2020;71(15):841-843.

45. Yang Y, Yang M, Shen C, Wang F, Yuan J, Li J, et al. Laboratory diagnosis and monitoring the viral shedding of 2019-nCoV infections. medRxiv 2020.

46. Liu R, Han H, Liu F, Lv Z, Wu K, Liu Y, et al. Positive rate of RT-PCR detection of SARS-CoV-2 infection in 4880 cases from one hospital in Wuhan, China, from Jan to Feb 2020. Clin Chim Acta. 2020;505:172–175.

47. Ren X, Liu Y, Chen H, Liu W, Guo Z, Chen C, et al. Application and optimization of RT-PCR in diagnosis of SARS-CoV-2 infection. SSRN 2020.