Molecular tests for the detection of SARS-CoV-2
Keywords:
COVID-19, molecular tests, RT-PCR, sequencing.Abstract
Introduction: Coronaviruses cause respiratory, hepatic or neurological diseases, with variable severity in their host. Real-time reverse transcriptase polymerase chain reaction is the reference methodology to confirm the detection of the SARS-CoV-2 virus. A bibliographic review was carried out in the period from July to November 2021, in the resources available in MEDLINE, SciELO, Pubmed and Elsevier. Of the total queries, 34 references were cited.Objective: Describe molecular tests for the detection of SARS-CoV-2.
Development: Three types of rRT-PCR assays have been designed for the detection of SARS-CoV-2. The tests described are specific for RNA polymerase dependent RNA (RdRp) genes, E (upE) genes, and Nnes (N) genes. The United States Centers for Disease Control and Prevention (CDC) have developed rRT-PCR directed at the N protein of the nucleocapsid of the SARS-CoV-2 genetic material, the gene E assays (upE) and protein gene 1b (ORF 1b) can be complemented for detection and confirmation.
Conclusions: The targets used for the specific detection of the SARS-CoV-2 genome by real-time RT-PCR are found in the ORF1a and 1b, RdRp, N, S and E regions of the viral RNA.
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References
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20. Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu D, 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
21. Corman VM, Müller MA, Costabel U, Timm J, Binger T, Meyer B, et al. Assays for laboratory confirmation of Novel human Coronavirus (hCoV-EMC) Infections. Euro Surveill. 2012; 17(49): 20334. DOI: 10.2807/ese.17.49.20334-en
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23. 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 (COVID19) in China: a report of 1014 cases. Radiology. 2020; 96(2): 32-40. DOI: 10.1148/radiol.2020200642
24. Long C, Xu H, Shen Q, Zhang X, Fan B, Wang C, et al. Diagnosis of the coronavirus disease (COVID-19): rRT-PCR or CT? Eur J Radiol. 2020; 126: 108961. DOI: 10.1016/j.ejrad.2020.108961
25. Shen Z, Xiao Y, Kang L, Ma W, Shi L, Zhang L, et al. Genomic diversity of SARS-CoV-2 in coronavirus disease 2019 patients. Clin Infect Dis. 2020; 71(15):713-720. DOI:10.1093/cid/ciaa203
26. Folegatti PM, Bittaye M, Flaxman A, Lopez FR, Bellamy D, Kupke A, et al. Safety and immunogenicity of a candidate Middle East respiratory syndrome coronavirus viral-vectored vaccine: a dose-escalation, open-label, non-randomised, uncontrolled, phase 1 trial. Lancet Infect Dis. 2020; 20(7):816-26. DOI: 10.1016/S1473-3099(20)30160-2
27. Pan American Health Organization / World Health Organization. Epidemiological Update: Novel Coronavirus (2019 nCoV) 20 January 2020. Washington, D.C.: PAHO/WHO; 2020.[acceso: 03/03/2020]. Disponible en: https://iris.paho.org/handle/10665.2/51851
28. Richardson P, Griffin I, Tucker C, Smith D, Oechsle O, Phelan A, et al. Baricitinib as potential treatment for 2019-nCoV acute respiratory disease. Lancet. 2020; 395(10223): e30-e31. DOI: 10.1016/S0140-6736(20)30304-4
29. Li Y, Xie Z, Lin W, Cai W, Wen C, Guan Y, et al. Efficacy and Safety of Lopinavir/Ritonavir or Arbidol in Adult Patients with Mild/Moderate COVID-19: An Exploratory Randomized Controlled Trial. Med (NY). 2020;1(1):105-113.e4. DOI: 10.1016/j.medj.2020.04.001
30. Pitts J, Li J, Perry J, Du Pont V, Riola N, Rodriguez L, et al. Remdesivir and GS-441524 retain antiviral activity against Delta, Omicron, and other emergent SARS-CoV-2 variants. BioRxiv. 2022;1(1):1-46.DOI: 10.1101/2022.02.09.479840
31. Ionescu MI. An Overview of the Crystallized Structures of the SARS-CoV-2. Protein J. 2020; 39(6): 600-18.DOI: 10.1007/s10930-020-09933-w
32. Lisa M. IL-6 blockers tested against COVID-19. C&EN. 2020; 98(11):13-20. DOI: 10.1021/cen-09811-buscon3
33. Cision PR Newswire. Inovio Accelerates Timeline for COVID-19 DNA Vaccine INO-4800. Pensilvania: Inovio Pharmaceuticals; 2020.[acceso: 03/03/2020]. Disponible en: https://www.prnewswire.com/news-releases/inovio-accelerates-timeline-for-covid-19-dna-vaccine-ino-4800-301015031.html
34. HusseyC. Moderna ships mRNA vaccine against novel coronavirus (mRNA-1273) for phase 1 study. Cambridge, Mass: Business Wire; 2020.[acceso: 24/02/2020]. Disponible en: https://www.bloomberg.com/press-releases/2020-02-24/moderna-ships-mrna-vaccine-against-novel-coronavirus-mrna-1273-for-phase-1-study
2. Gloza-Rausch F, Ipsen A, Seebens A, Göttsche M, Panning M, Drexler JF, et al. Detection and prevalence patterns of group I coronaviruses in bats, northern Germany. Emerg Infect Dis. 2008;14(4):626-31. DOI: 10.3201/eid1404.071439
3. Hamre D, Procknow JJ. A new virus isolated from the human respiratory tract. Proc Soc Exp Biol Med. 1966;121(1):190-3. DOI: 10.3181/00379727-121-30734
4. Drosten C, Günther S, Preiser W, van der Werf S, Brodt HR, Becker S. Identification of a novel coronavirus in patients with severe acute respiratory syndrome. N Engl J Med. 2003; 348(20):1967-76. DOI: 10.1056/NEJMoa030747
5. Fouchier RA, Hartwig NG, Bestebroer TM, Niemeyer B, de Jong JC, Simon JH, et al. A previously undescribed coronavirus associated with respiratory disease in humans. Proc Natl Acad Sci USA. 2004;101(16):6212-6. DOI: 10.1073/pnas.0400762101
6. Woo PC, Lau SK, Chu CM, Chan KH, Tsoi HW, Huang Y. Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. J Virol. 2005; 79(2):884-95. DOI: 10.1128/JVI.79.2.884-895.2005
7. Zlateva KT, Coenjaerts FE, Crusio KM, Lammens C, Leus F, Viveen M. No novel coronaviruses identified in a large collection of human nasopharyngeal specimens using family-wide CODEHOP-based primers. Archives of Virology. 2013;158(1):251-5. DOI: 10.1007/s00705-012-1487-4
8. Lan L, Dan X, Guangming Y. Positive RT-PCR Test Results in Patients Recovered From COVID-19. JAMA. 2020;323(15):1502-03. DOI:10.1001/jama.2020.2783
9. Peng W, Xinxin H, Eric H Y, Jessica Y, Kathy S, Joseph T, et al. Real-time tentative assessment of the epidemiological characteristics of novel coronavirus infections in Wuhan, China. Euro Surveill Bull. 2020;25(3):pii=2000044. DOI: 10.2807/1560-7917.ES.2020.25.3.2000044
10. Paules CI, Marston HD, Fauci AS. Coronavirus Infections-More Than Just the Common Cold. JAMA. 2020;323(8):707-8. DOI:10.1001/jama.2020.0757
11. Cuadra TE, Guadrón Meléndez AA, Cruz Aguilar R de J, Vásquez Rodriguez EA. Factores relevantes sobre el ensayo RT-PCR para la detección de SARS-CoV-2, virus causante del COVID-19. Alerta.2021;4(1): 31-9. DOI:10.5377/alerta.v4i1.10060
12. Palm D, Pereyaslov D, Vaz J, Broberg E, Zeller H, Gross D, et al.Laboratory capability for molecular detection and confirmation of novel coronavirus in Europe, November 2012. Euro Surveill. 2012;17(49):20335. DOI: 10.2807/ese.17.49.20335-een
13. Van Boheemen S, de Graaf M, Lauber C, Bestebroer TM, Raj VS, Zaki AM, et al. Genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans. mBio. 2012;3(6): e00473-12. DOI: 10.1128/mBio.00473-12
14. Timothy M, Bernstein H, Bradley J, Englund J, File T, Gravenstein S, et al. Clinical Practice Guidelines by the Infectious Diseases Society of America: 2018 Update on Diagnosis, Treatment, Chemoprophylaxis, and Institutional Outbreak Management of Seasonal Influenza. Clinical Infectious Diseases. 2019; 68 (6): 1-47. DOI: 10.1093/cid/ciy866
15. Corman VM, Eckerle I, Bleicker T, Zaki A, Landt O, Eschbach-Bludau M. Detection of a novel human coronavirus by real-time reverse-transcription polymerase chain reaction. Euro Surveill. 2012;17(39): 20285. DOI: https://DOI.org/10.2807/ese.17.39.20285-en
16. Herzog P, Drosten C, Müller M. Plaque assay for human coronavirus NL63 using human colon carcinoma cells. Virol J. 2008;5(1):138-142. DOI: https://DOI.org/10.1186/1743-422X-5-138
17. Rabenau HF, Cinatl J, Morgenstern B, Bauer G, Preiser W, Doerr HW. Stability and inactivation of SARS coronavirus. Med Microbiol Immunol. 2005;194(1-2):1-6. DOI: 10.1007/s00430-004-0219-0
18. Yong CY, Ong HK, Yeap SK, Ho KL, Tan WS. Recent Advances in the Vaccine Development Against Middle East Respiratory Syndrome-Coronavirus. Front. Microbiol. 2019; 10:1781. DOI: 10.3389/fmicb.2019.01781
19. 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: 172-5. DOI: 10.1016/j.cca.2020.03.009
20. Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu D, 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
21. Corman VM, Müller MA, Costabel U, Timm J, Binger T, Meyer B, et al. Assays for laboratory confirmation of Novel human Coronavirus (hCoV-EMC) Infections. Euro Surveill. 2012; 17(49): 20334. DOI: 10.2807/ese.17.49.20334-en
22. 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. 2020; 58(7):1070-1076. DOI: 10.1515/cclm-2020-0285
23. 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 (COVID19) in China: a report of 1014 cases. Radiology. 2020; 96(2): 32-40. DOI: 10.1148/radiol.2020200642
24. Long C, Xu H, Shen Q, Zhang X, Fan B, Wang C, et al. Diagnosis of the coronavirus disease (COVID-19): rRT-PCR or CT? Eur J Radiol. 2020; 126: 108961. DOI: 10.1016/j.ejrad.2020.108961
25. Shen Z, Xiao Y, Kang L, Ma W, Shi L, Zhang L, et al. Genomic diversity of SARS-CoV-2 in coronavirus disease 2019 patients. Clin Infect Dis. 2020; 71(15):713-720. DOI:10.1093/cid/ciaa203
26. Folegatti PM, Bittaye M, Flaxman A, Lopez FR, Bellamy D, Kupke A, et al. Safety and immunogenicity of a candidate Middle East respiratory syndrome coronavirus viral-vectored vaccine: a dose-escalation, open-label, non-randomised, uncontrolled, phase 1 trial. Lancet Infect Dis. 2020; 20(7):816-26. DOI: 10.1016/S1473-3099(20)30160-2
27. Pan American Health Organization / World Health Organization. Epidemiological Update: Novel Coronavirus (2019 nCoV) 20 January 2020. Washington, D.C.: PAHO/WHO; 2020.[acceso: 03/03/2020]. Disponible en: https://iris.paho.org/handle/10665.2/51851
28. Richardson P, Griffin I, Tucker C, Smith D, Oechsle O, Phelan A, et al. Baricitinib as potential treatment for 2019-nCoV acute respiratory disease. Lancet. 2020; 395(10223): e30-e31. DOI: 10.1016/S0140-6736(20)30304-4
29. Li Y, Xie Z, Lin W, Cai W, Wen C, Guan Y, et al. Efficacy and Safety of Lopinavir/Ritonavir or Arbidol in Adult Patients with Mild/Moderate COVID-19: An Exploratory Randomized Controlled Trial. Med (NY). 2020;1(1):105-113.e4. DOI: 10.1016/j.medj.2020.04.001
30. Pitts J, Li J, Perry J, Du Pont V, Riola N, Rodriguez L, et al. Remdesivir and GS-441524 retain antiviral activity against Delta, Omicron, and other emergent SARS-CoV-2 variants. BioRxiv. 2022;1(1):1-46.DOI: 10.1101/2022.02.09.479840
31. Ionescu MI. An Overview of the Crystallized Structures of the SARS-CoV-2. Protein J. 2020; 39(6): 600-18.DOI: 10.1007/s10930-020-09933-w
32. Lisa M. IL-6 blockers tested against COVID-19. C&EN. 2020; 98(11):13-20. DOI: 10.1021/cen-09811-buscon3
33. Cision PR Newswire. Inovio Accelerates Timeline for COVID-19 DNA Vaccine INO-4800. Pensilvania: Inovio Pharmaceuticals; 2020.[acceso: 03/03/2020]. Disponible en: https://www.prnewswire.com/news-releases/inovio-accelerates-timeline-for-covid-19-dna-vaccine-ino-4800-301015031.html
34. HusseyC. Moderna ships mRNA vaccine against novel coronavirus (mRNA-1273) for phase 1 study. Cambridge, Mass: Business Wire; 2020.[acceso: 24/02/2020]. Disponible en: https://www.bloomberg.com/press-releases/2020-02-24/moderna-ships-mrna-vaccine-against-novel-coronavirus-mrna-1273-for-phase-1-study
Published
2022-07-05
How to Cite
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Oliva Menacho JE. Molecular tests for the detection of SARS-CoV-2. Rev Cubana Med Milit [Internet]. 2022 Jul. 5 [cited 2025 Mar. 14];51(3):e02201756. Available from: https://revmedmilitar.sld.cu/index.php/mil/article/view/1756
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