Volume 32, Issue 3 (June 2021)                   Studies in Medical Sciences 2021, 32(3): 156-174 | Back to browse issues page

XML Persian Abstract Print


Download citation:
BibTeX | RIS | EndNote | Medlars | ProCite | Reference Manager | RefWorks
Send citation to:

Bakhshi Mofrad Kashani A, Asalani Mehr M, Abedi Elkhichi P. CHALLENGES OF LABORATORY SAMPLING AND DIAGNOSIS OF SARS-COV-2 VIRUS OF DISEASE (COVID-19). Studies in Medical Sciences 2021; 32 (3) :156-174
URL: http://umj.umsu.ac.ir/article-1-5310-en.html
Medical Microbiology Associate Professor Qazvin University of Medical Sciences Research Center, Qazvin, Iran (Corresponding Author) , dr.aslanimehr@gmail.com
Abstract:   (4013 Views)
Background & Aims: Given the prevalence of SARS-CoV-2 worldwide, it is essential to identify people infected with the virus and determine its different types to control the global outbreak of COVID-19. The results of the studies are controversial, so this study examines these diagnostic challenges, including the types of diagnostic methods, the type and time of sampling, and even the clinical condition of the disease.
Materials & Methods: In this systematic review, studies conducted from 2003 to May 2020 in English on the challenges of laboratory sampling and diagnostics of coronaviruses and SARS-CoV-2 virus were reviewed. These articles were obtained by searching for keywords in databases, PubMed, Scopus and Embace as well as Google scholar search engine and duplicate articles were removed from the study.
Results: In the initial search, 98 articles were extracted that after eliminating duplicates and evaluating the title and abstract, finally 64 articles had the necessary conditions for review and were included in the study. The results of the studies showed that, although RT-PCR is the gold standard for the diagnosis of Covid-19 disease, but it requires a sufficient concentration of viral RNA in the patient sample for proper evaluation of the sample. Since the concentration of viral RNA in the patient sample is not constant, this can affect the results obtained. Although the best sample to detect the virus in the first days is the nasopharyngeal swab and in the following days, samples taken from the lower respiratory tract, but also numerous samples such as throat swabs and feces can also be used for identification. However, the percentage of viral RNA isolation in these samples is significantly reduced.
Conclusion: Due to the global prevalence of Covid-19 disease, early diagnosis of patients, quarantine and timely treatment are of great importance in controlling the epidemic. The use of correct diagnostic tests allows physicians to perform immediate interventions for patients. Although molecular diagnosis is the best method, studies show that it is better not to be satisfied with the results of an experiment and to use a combination of different methods and tests to solve diagnostic challenges.
Full-Text [PDF 707 kb]   (7065 Downloads)    
Type of Study: Review article | Subject: ویروس شناسی

References
1. Escalera-Antezana JP, Lizon-Ferrufino NF, Maldonado-Alanoca A, Alarcón-De-la-Vega G, Alvarado-Arnez LE, Balderrama-Saavedra MA, et al. Clinical features of cases and a cluster of Coronavirus Disease 2019 (COVID-19) in Bolivia imported from Italy and Spain. TRAVEL MED INFECT DI. 2020:101653. [DOI:10.1016/j.tmaid.2020.101653] [PMID] [PMCID]
2. Ge H, Wang X, Yuan X, Xiao G, Wang C, Deng T, et al. The epidemiology and clinical information about COVID-19. Eur J Clin Microbiol Infect Dis. 2020:1. [DOI:10.1007/s10096-020-03874-z] [PMID] [PMCID]
3. Dong X, Cao Yy, Lu Xx, Zhang Jj, Du H, Yan Yq, et al. HFNC 2019. Allergy. 2020.
4. Padhi A, Kumar S, Gupta E, Saxena SK. Laboratory Diagnosis of Novel Coronavirus Disease 2019 (COVID-19) Infection. Coronavirus Disease 2019 (COVID-19, J Res Health Sci , Springer; 2020. p. 95-107. [DOI:10.1007/978-981-15-4814-7_9] [PMCID]
5. Moccia F, Gerbino A, Lionetti V, Miragoli M, Munaron L, Pagliaro P, et al. COVID-19-associated cardiovascular morbidity in older adults: a position paper from the Italian Society of Cardiovascular Researches. JCR. 2020:1-29. [DOI:10.1007/s11357-020-00198-w] [PMID] [PMCID]
6. Cheng MP, Papenburg J, Desjardins M, Kanjilal S, Quach C, Libman M, et al. Diagnostic testing for severe acute respiratory syndrome-related coronavirus-2: A narrative review. Ann Intern Med . 2020. [DOI:10.7326/M20-1301] [PMID] [PMCID]
7. Zhou P, Yang X-L, Wang X-G, Hu B, Zhang L, Zhang W, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. nature. 2020;579(7798):270-3. [DOI:10.1038/s41586-020-2012-7] [PMID] [PMCID]
8. Luan J, Jin X, Lu Y, Zhang L. SARS‐CoV‐2 spike protein favors ACE2 from Bovidae and Cricetidae. J Med Virol. 2020. [URL]
9. Valencia DN. Brief review on COVID-19: the 2020 pandemic caused by SARS-CoV-2. Cureus. 2020;12(3). [DOI:10.7759/cureus.7386]
10. Yan C, Cui J, Huang L, Du B, Chen L, Xue G, et al. Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription loop-mediated isothermal amplification assay. Clin Microbiol Infect. 2020. [DOI:10.1016/j.cmi.2020.04.001] [PMID] [PMCID]
11. 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(10224):565-74. [DOI:10.1016/S0140-6736(20)30251-8]
12. Wu A, Peng Y, Huang B, Ding X, Wang X, Niu P, et al. Genome composition and divergence of the novel coronavirus (2019-nCoV) originating in China. CELL HOST MICROBE. 2020. [DOI:10.1016/j.chom.2020.02.001] [PMID] [PMCID]
13. Walls AC, Park Y-J, Tortorici MA, Wall A, McGuire AT, Veesler D. Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell. 2020. [DOI:10.1101/2020.02.19.956581]
14. Wrapp D, Wang N, Corbett KS, Goldsmith JA, Hsieh C-L, Abiona O, et al. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science. 2020;367(6483):1260-3. [DOI:10.1126/science.abb2507] [PMID] [PMCID]
15. Yuan M, Wu NC, Zhu X, Lee C-CD, So RT, Lv H, et al. A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV. Science. 2020;368(6491):630-3. [DOI:10.1126/science.abb7269] [PMID] [PMCID]
16. Tavakoli A, Vahdat K, Keshavarz M. Novel coronavirus disease 2019 (COVID-19): an emerging infectious disease in the 21st century. ISMJ. 2020;22(6):432-50. [DOI:10.29252/ismj.22.6.432]
17. Heymann DL, Shindo N. COVID-19: what is next for public health? Lancet. 2020;395(10224):542-5. [DOI:10.1016/S0140-6736(20)30374-3]
18. Pang J, Wang MX, Ang IYH, Tan SHX, Lewis RF, Chen JI-P, et al. Potential rapid diagnostics, vaccine and therapeutics for 2019 novel coronavirus (2019-nCoV): a systematic review. Clin Med. 2020;9(3):623. [DOI:10.3390/jcm9030623] [PMID] [PMCID]
19. Moghissi K, Dixon K, Gibbins S. Does PDT have potential in the treatment of COVID 19 patients? Photodiagnosis Photodyn Ther. 2020:101889. [DOI:10.1016/j.pdpdt.2020.101889] [PMID] [PMCID]
20. Kim ES, Chin BS, Kang CK, Kim NJ, Kang YM, Choi J-P, et al. Clinical course and outcomes of patients with severe acute respiratory syndrome coronavirus 2 infection: a preliminary report of the first 28 patients from the Korean cohort study on COVID-19. J Korean Med Sci. 2020;35(13). [DOI:10.3346/jkms.2020.35.e142] [PMID] [PMCID]
21. Burhan E, Prasenohadi P, Rogayah R, Isbaniyah F, Reisa T, Dharmawan I. Clinical Progression of COVID-19 Patient with Extended Incubation Period, Delayed RT-PCR Time-to-positivity, and Potential Role of Chest CT-scan. Acta Med Indones. 2020;52(1):80. [PMID]
22. Eze EC, Chenia HY, El Zowalaty ME. Acinetobacter baumannii biofilms: effects of physicochemical factors, virulence, antibiotic resistance determinants, gene regulation, and future antimicrobial treatments. Infect. Drug Resist. 2018;11:2277. [DOI:10.2147/IDR.S169894] [PMID] [PMCID]
23. Wu F, Zhao S, Yu B, Chen Y-M, Wang W, Song Z-G, et al. A new coronavirus associated with human respiratory disease in China. Nature. 2020;579(7798):265-9. [DOI:10.1038/s41586-020-2008-3] [PMID] [PMCID]
24. Carter LJ, Garner LV, Smoot JW, Li Y, Zhou Q, Saveson CJ, et al. Assay techniques and test development for COVID-19 diagnosis. J Am Chem Soc; 2020. [DOI:10.1021/acscentsci.0c00501] [PMID] [PMCID]
25. Waller JV, Allen IE, Lin KK, Diaz MJ, Henry TS, Hope MD. The Limited Sensitivity of Chest Computed Tomography Relative to Reverse Transcription Polymerase Chain Reaction for Severe Acute Respiratory Syndrome Coronavirus-2 Infection: A Systematic Review on COVID-19 Diagnostics. Invest Radiol. 2020. [DOI:10.1097/RLI.0000000000000700] [PMID] [PMCID]
26. Tutar U, Çelik C, Karaman İ, Ataş M, Hepokur C. Anti-biofilm and antimicrobial activity of Mentha pulegium L essential oil against multidrug-resistant Acinetobacter baumannii. Trop J Pharm Res. 2016;15(5):1039-46. [DOI:10.4314/tjpr.v15i5.20]
27. Chan JF-W, Yip CC-Y, To KK-W, Tang TH-C, Wong SC-Y, Leung K-H, et al. Improved molecular diagnosis of COVID-19 by the novel, highly sensitive and specific COVID-19-RdRp/Hel real-time reverse transcription-PCR assay validated in vitro and with clinical specimens. J. Clin. Microbiol. 2020;58(5). [DOI:10.1128/JCM.00310-20] [PMID] [PMCID]
28. Ye Q, Wang B, Mao J, Fu J, Shang S, Shu Q, et al. Epidemiological analysis of COVID‐19 and practical experience from China. J Med Virol. 2020. [DOI:10.1002/jmv.25813] [PMID] [PMCID]
29. 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. [DOI:10.1056/NEJMoa2001191] [PMID] [PMCID]
30. Long Q-X, Liu B-Z, Deng H-J, Wu G-C, Deng K, Chen Y-K, et al. Antibody responses to SARS-CoV-2 in patients with COVID-19. Nat Med. 2020:1-4. [Google Scholar]
31. Richards JJ, Reed CS, Melander C. Effects of N-pyrrole substitution on the anti-biofilm activities of oroidin derivatives against Acinetobacter baumannii. Bioorg Med Chem Lett. 2008;18(15):4325-7. [DOI:10.1016/j.bmcl.2008.06.089] [PMID]
32. Singh R, Nadhe S, Wadhwani S, Shedbalkar U, Chopade BA. Nanoparticles for control of biofilms of Acinetobacter species. Materials. 2016;9(5):383. [DOI:10.3390/ma9050383] [PMID] [PMCID]
33. Ohadi M, Forootanfar H, Dehghannoudeh G, Eslaminejad T, Ameri A, Shakibaie M, et al. Antimicrobial, anti-biofilm, and anti-proliferative activities of lipopeptide biosurfactant produced by Acinetobacter junii B6. Microb Pathog. 2020;138:103806. [DOI:10.1016/j.micpath.2019.103806] [PMID]
34. Loeffelholz MJ, Tang Y-W. Laboratory diagnosis of emerging human coronavirus infections-the state of the art. Emerg Microbes Infect. 2020;9(1):747-56. [DOI:10.1080/22221751.2020.1745095] [PMID] [PMCID]
35. Vashist SK. In vitro diagnostic assays for COVID-19: recent advances and emerging trends. MDPI; 2020. [DOI:10.3390/diagnostics10040202] [PMID] [PMCID]
36. Krüttgen A, Cornelissen CG, Dreher M, Hornef M, Imöhl M, Kleines M. Comparison of four new commercial serologic assays for determination of SARS-CoV-2 IgG. J Clin Virol. 2020:104394. [DOI:10.1016/j.jcv.2020.104394] [PMID] [PMCID]
37. Muzammil S, Khurshid M, Nawaz I, Siddique MH, Zubair M, Nisar MA, et al. Aluminium oxide nanoparticles inhibit EPS production, adhesion and biofilm formation by multidrug resistant Acinetobacter baumannii. Biofouling. 2020;36(4):492-504. [DOI:10.1080/08927014.2020.1776856] [PMID]
38. Bruning A, Aatola H, Toivola H, Ikonen N, Savolainen-Kopra C, Blomqvist S, et al. Rapid detection and monitoring of human coronavirus infections. New Microbes New Infect. 2018;24:52-5. [DOI:10.1016/j.nmni.2018.04.007] [PMID] [PMCID]
39. Long Q-X, Tang X-J, Shi Q-L, Li Q, Deng H-J, Yuan J, et al. Clinical and immunological assessment of asymptomatic SARS-CoV-2 infections. Nat. Med. 2020:1-5. [DOI:10.1038/s41591-020-0965-6] [PMID]
40. Bastos ML, Tavaziva G, Abidi SK, Campbell JR, Haraoui L-P, Johnston JC, et al. Diagnostic accuracy of serological tests for covid-19: systematic review and meta-analysis. BMJ. 2020;370. [PMID] [PMCID]
41. Yan Y, Chang L, Wang L. Laboratory testing of SARS‐CoV, MERS‐CoV, and SARS‐CoV‐2 (2019‐nCoV): Current status, challenges, and countermeasures. J Med Virol . 2020;30(3):e2106. [DOI:10.1002/rmv.2106] [PMID] [PMCID]
42. Babapour E, Haddadi A, Mirnejad R, Angaji S-A, Amirmozafari N. Biofilm formation in clinical isolates of nosocomial Acinetobacter baumannii and its relationship with multidrug resistance. Asian Pac J Trop Biomed. 2016;6(6):528-33. [DOI:10.1016/j.apjtb.2016.04.006]
43. Deeks JJ, Dinnes J, Takwoingi Y, Davenport C, Leeflang MM, Spijker R, et al. Diagnosis of SARS‐CoV‐2 infection and COVID‐19: accuracy of signs and symptoms; molecular, antigen, and antibody tests; and routine laboratory markers. Cochrane Database Syst Rev. 2020(4). [DOI:10.1002/14651858.CD013596] [PMCID]
44. Lin D, Liu L, Zhang M, Hu Y, Yang Q, Guo J, et al. Evaluations of the serological test in the diagnosis of 2019 novel coronavirus (SARS-CoV-2) infections during the COVID-19 outbreak. Eur J Clin Microbiol Infect Dis. 2020:1-7. [DOI:10.1101/2020.03.27.20045153]
45. Ching L, Chang SP, Nerurkar VR. COVID-19 Special Column: Principles Behind the Technology for Detecting SARS-CoV-2, the Cause of COVID-19. Hawaii J Health Soc. 2020;79(5):136. [] [PMID] [PMCID]
46. Nguyen T, Duong Bang D, Wolff A. 2019 novel coronavirus disease (COVID-19): paving the road for rapid detection and point-of-care diagnostics. Micromachines. 2020;11(3):306. [DOI:10.3390/mi11030306] [PMID] [PMCID]
47. Zhou P, Yang X-L, Wang X-G, 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. BioRxiv. 2020. [DOI:10.1101/2020.01.22.914952]
48. Xiao AT, Gao C, Zhang S. Profile of specific antibodies to SARS-CoV-2: the first report. J. Infect. 2020. [DOI:10.1016/j.jinf.2020.03.012] [PMCID]
49. Ramachandran R, Sangeetha D. Antibiofilm efficacy of silver nanoparticles against biofilm forming multidrug resistant clinical isolates. J Pharm Innov. 2017;6(11, Part A):36. [Google Scholar]
50. Yueying W, Song W, Zhao Z, Chen P, Liu J, Li C. The Impacts of Viral Inactivating Methods On Quantitative RT-PCR for COVID-19. Virus Res. 2020:197988. [DOI:10.1016/j.virusres.2020.197988] [PMID] [PMCID]
51. Yip CC, Ho CC, Chan JF, To KK, Chan HS, Wong SC, et al. Development of a Novel, Genome Subtraction-Derived, SARS-CoV-2-Specific COVID-19-nsp2 Real-Time RT-PCR Assay and Its Evaluation Using Clinical Specimens. Int J Mol Sci. 2020;21(7). [DOI:10.3390/ijms21072574] [PMID] [PMCID]
52. Yip CC-Y, Ho C-C, Chan JF-W, To KK-W, Chan HS-Y, Wong SC-Y, et al. Development of a novel, genome subtraction-derived, SARS-CoV-2-specific COVID-19-nsp2 real-time RT-PCR assay and its evaluation using clinical specimens. Int J Mol Sci. 2020;21(7):2574. [DOI:10.3390/ijms21072574] [PMID] [PMCID]
53. Awadasseid A, Wu Y, Tanaka Y, Zhang W. Initial success in the identification and management of the coronavirus disease 2019 (COVID-19) indicates human-to-human transmission in Wuhan, China. Int J Biol Sci. 2020;16(11):1846. [DOI:10.7150/ijbs.45018] [PMID] [PMCID]
54. 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. [DOI:10.1056/NEJMoa2001017] [PMID] [PMCID]
55. Becherer L, Borst N, Bakheit M, Frischmann S, Zengerle R, von Stetten F. Loop-mediated isothermal amplification (LAMP)-review and classification of methods for sequence-specific detection. Anal. Methods. 2020;12(6):717-46. [DOI:10.1039/C9AY02246E]
56. Tripathy S, Kabir R, Arafat SY, Saxena SK. Futuristic Technologies for Advanced Detection, Prevention, and Control of COVID-19. Diagnostic Strategies for COVID-19 and other Coronaviruses: Springer; 2020. p. 161-73. [DOI:10.1007/978-981-15-6006-4_8]
57. Yin C. Genotyping coronavirus SARS-CoV-2: methods and implications. Genomics. 2020;112(5):3588-96. [DOI:10.1016/j.ygeno.2020.04.016] [PMID] [PMCID]
58. Bryant JE, Azman AS, Ferrari MJ, Arnold BF, Boni MF, Boum Y, et al. Serology for SARS-CoV-2: apprehensions, opportunities, and the path forward. Sci Immunol. 2020;5(47). [DOI:10.1126/sciimmunol.abc6347] [PMID]
59. Deeks JJ, Dinnes J, Takwoingi Y, Davenport C, Spijker R, Taylor-Phillips S, et al. Antibody tests for identification of current and past infection with SARS‐CoV‐2. Cochrane Database Syst Rev. 2020(6). [DOI:10.1002/14651858.CD013652] [PMID] [PMCID]
60. Wang Y, Wang Y, Chen Y, Qin Q. Unique epidemiological and clinical features of the emerging 2019 novel coronavirus pneumonia (COVID‐19) implicate special control measures. J Med Virol. 2020;92(6):568-76. [DOI:10.1002/jmv.25748] [PMID] [PMCID]
61. Salehi S, Abedi A, Balakrishnan S, Gholamrezanezhad A. Coronavirus disease 2019 (COVID-19): a systematic review of imaging findings in 919 patients. AJR Am J Roentgenol. 2020;215(1):87-93. [DOI:10.2214/AJR.20.23034] [PMID]
62. Garg M, Gupta P, Maralakunte M, Kumar-M P, Sinha A, Kang M, et al. Diagnostic accuracy of CT and radiographic findings for novel coronavirus 2019 pneumonia: Systematic review and meta-analysis. Clin Imaging. 2020. [DOI:10.1016/j.clinimag.2020.11.021] [PMID] [PMCID]
63. Lan L, Xu D, Ye G, Xia C, Wang S, Li Y, et al. Positive RT-PCR test results in patients recovered from COVID-19. JAMA. 2020;323(15):1502-3. [DOI:10.1001/jama.2020.2783] [PMID] [PMCID]
64. 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(3):2000045. [DOI:10.2807/1560-7917.ES.2020.25.3.2000045] [PMID] [PMCID]

Add your comments about this article : Your username or Email:
CAPTCHA

Send email to the article author


Rights and permissions
Creative Commons License This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

© 2024 CC BY-NC 4.0 | Studies in Medical Sciences

Designed & Developed by : Yektaweb