Real-time RT-PCR internal quality control optimization for qualitative detection of SARS-CoV-2

Authors

  • Giancarlo Torres-Gamarra Escuela Académico Profesional de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad Nacional Hermilio Valdizán (UNHEVAL). Huánuco-Perú

DOI:

https://doi.org/10.35434/rcmhnaaa.2023.161.1657

Keywords:

Optimization, Internal quality control, Real-time RT-PCR, SARS-CoV-2

Abstract

Objective: To optimize the internal quality control of real-time RT-PCR for the qualitative detection of SARS-CoV-2, using the Cq values ​​of negative and positive controls. Material and method: Prospective-longitudinal study. The sample consisted of 143 Cq values ​​for the negative aliquot and extraction controls, as well as for the positive control. The normal distribution of Cq values ​​was analyzed using the Anderson-Darling (AD) test and randomness tests were applied. Control limits were calculated from 51 Cq values, and then, using control charts, to monitor 92 Cq values ​​obtained from November 2020 to March 2021. Lot acceptance and Cpk indices were evaluated as optimization indicators. The calculations were made with the Minitab program. Results: The batches of Cq values ​​were accepted and Cpk indices higher than 1.33 were obtained for the three types of control. Discussion: There are no published studies that apply statistical quality control to the qualitative detection of SARS-CoV-2. Conclusions: It is possible to use the Cq values ​​of the controls to optimize the internal quality control of real-time RT-PCR for qualitative detection of SARS-CoV-2, as if it were a quantitative technique.

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Author Biography

Giancarlo Torres-Gamarra, Escuela Académico Profesional de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad Nacional Hermilio Valdizán (UNHEVAL). Huánuco-Perú

1. Tecnólogo médico

References

Pe BO, Rinc B, Jairo J, Le C. SARS-CoV-2 : Generalidades bioquímicas y métodos de diagnóstico. :11–33.

Lizaraso Caparó F, del Carmen Sara JC. Coronavirus y las amenazas a la salud mundial. Horiz Médico. 2020;20(1):4–5.

ThermoFisher. Realtime PCR handbook. Realt PCR Handb [Internet]. 2015;1–68. Available from: https://www.thermofisher.com/content/dam/LifeTech/Documents/PDFs/PG1503-PJ9169-CO019861-Update-qPCR-Handbook-branding-Americas-FLR.pdf%0Ahttp://www.nature.com/doifinder/10.1038/tp.2014.12%5Cnhttp://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=405504

Westgard S, Lucic D. Sigma Metrics for Assessing Accuracy of Molecular Testing. Clin Microbiol Newsl. 2015 Jul 1;37(13):103–10.

Wikramaratna PS, Paton RS, Ghafari M, Lourenço J. Estimating the false-negative test probability of SARS- CoV-2 by RT-PCR. Eurosurveillance [Internet]. 2020;25(50):1–10. Available from: http://dx.doi.org/10.2807/1560-7917.ES.2020.25.50.2000568

Rao S, Manissero D, Steele V, Pareja J. Clinical utility of cycle threshold values in the context of COVID-19. 2020;1–23.

García AF, Melón S, Navarro D. Organización del diagnóstico de SARS-CoV-2 y estrategias de optimización [Internet]. España; 2020. Available from: https://seimc.org/contenidos/documentoscientificos/recomendaciones/seimc-rc-2020-COVID19-OrganizacionDiagnostico.pdf

Westgard JO. Prácticas Básicas de Control de Calidad [Internet]. 4ta ed. USA, Madison: QC Westgard, Inc.; 2013. 326 p. Available from: https://www.ifcc.org/media/333582/2015_Prácticas_Básicas_de_Control_de_Calidad.pdf

Shahsiah R, Nili F, Ardalan FA, Pourgholi F, Borumand MA. Application of quality control planning methods for the improvement of a quantitative molecular assay. J Virol Methods. 2013 Nov 1;193(2):683–6.

Serrano-Cumplido A, Ruiz A, Segura-Fragoso A. Aplicación del valor umbral del número de ciclos (Ct) de PCR en la COVID-19. Med Fam. 2020;47(January):337–41.

Public Health England. Understanding cycle threshold (Ct) in SARS-CoV-2 RT-PCR A guide for health protection teams. 2020;1–12. Available from: https://www.gov.uk/government/publications/cycle-threshold-ct-in-sars-cov-2-rt-pcr

Zhang ZL, Hou YL, Li DT, Li FZ. Laboratory findings of COVID-19: a systematic review and meta-analysis. Scand J Clin Lab Invest [Internet]. 2020;0(0):1–7. Available from: https://doi.org/10.1080/00365513.2020.1768587

Westgard SA, Westgard QC. Six Sigma Metric Analysis for Analytical Testing Processes [Internet]. USA; 2009. Available from: https://www.corelaboratory.abbott/sal/whitePaper/SixSigma_WP_MAATP_ADD-00058830.pdf

Gutiérrez, H.; De la Vara R. Control estadístico de calidad y seis sigma. 2da ed. México D.F: McGraw-Hill; 2009. 502 p.

Palacios López M, Gisbert Soler V. Control estadístico de la calidad: una aplicación práctica.. Editorial Científica 3Ciencias; 2018.

Siemens. FTD SARS CoV 2. Vol. 2. USA; 2014.

Parra-Ortega I, Carbajal-Franco E, Vilchis-Ordoñez A, Ángeles-Floriano T, Nieto-Rivera B, López-Martínez I, et al. Distribución de los valores del Ct en la RT-PCR para SARS-CoV-2 al momento del diagnóstico en pacientes pediátricos mexicanos. Rev Mex Patol Clínica y Med Lab. 2020;67(4):176–82.

Ben-Ami R, Klochendler A, Seidel M, Sido T, Gurel-Gurevich O, Yassour M, et al. Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection. Clin Microbiol Infect. 2020;26(9):1248–53.

Khodare A, Padhi A, Gupta E, Agarwal R, Dubey S, Sarin S. Optimal size of sample pooling for RNA pool testing: An avant-garde for scaling up severe acute respiratory syndrome coronavirus-2 testing. Indian J Med Microbiol [Internet]. 2020;38(1):18–23. Available from: https://doi.org/10.4103/ijmm.IJMM_20_260

Borillo GA, Kagan RM, Baumann RE, Fainstein BM, Umaru L, Li HR, et al. Pooling of Upper Respiratory Specimens Using a SARS-CoV-2 Real-time RT-PCR Assay Authorized for Emergency Use in Low-Prevalence Populations for High-Throughput Testing. Open Forum Infect Dis. 2020;7(11):1–7.

Published

2023-06-18

How to Cite

1.
Torres-Gamarra G. Real-time RT-PCR internal quality control optimization for qualitative detection of SARS-CoV-2. Rev. Cuerpo Med. HNAAA [Internet]. 2023 Jun. 18 [cited 2024 May 14];16(1):71-7. Available from: http://cmhnaaa.org.pe/ojs/index.php/rcmhnaaa/article/view/1657