Research Article
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Year 2023, Volume: 9 Issue: 5 - September 2023, 1142 - 1148, 04.09.2023
https://doi.org/10.18621/eurj.1341822

Abstract

References

  • 1. Dioni L, Orlandi A, Renteria SU, Favero C, Solazzo G, Oggioni M. Digital RT-PCR Chip method for detection of SARS-CoV-2 virus. J Immunol Methods 2022;509: 113339.
  • 2. Ciottia M, Ciccozzi M, Pieric M, Bernardini S. The COVID-19 pandemic: viral variants and vaccine efficacy. Crit Rev Clin Lab Sci 2022;59:66-75.
  • 3. Ontiveros N, Adol Bosque Aguirre DA, Gonzalez Urquijo M, Gonzalez DEH, Martinez Resendez FM, Schang L. Nasopharyngeal viral load at admission is not an independent predictor of thromboembolic complications in unvaccinated COVID 19 hospitalized patients. J Thromb Thrombolysis 2023;55:282-8.
  • 4. Burjanivova T, Lukacova E, Lucansky V, Samec M, Podlesniy P, Kolkova Z. Sensitive SARS-CoV-2 detection, air travel Covid-19 testing, variant determination and fast direct PCR detection, using ddPCR and RT-qPCR methods. Acta Virol 2023;67:3-12.
  • 5. Tang YW, Schmitz JE, Persing DH, Stratton CW. Laboratory diagnosis of COVID-19: current issues and challenges. J Clin Microbiol 2020;58:e00512-20.
  • 6. Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DKW, et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR, Euro Surveill 2020;25:2000045.
  • 7. Gülbudak H, Karvar Ş, Soydan G, Tezcan Ülger S, Kandemir Ö, Tamer L, et al. [Comparison of real time PCR cycle threshold values in symptomatic and asymptomatic COVID-19 patients]. Mikrobiyol Bul 2021;55:435-44. [Article in Turkish]
  • 8. Xu K, Chen Y, Yuan J, Yi P, Ding C, Wu W, et al. Factors associated with prolonged viral RNA shedding in patients with COVID-19. Clin Infect Dis 2020;71:799-806.
  • 9. COVID-19 Tanı Kitleri Ürün Değerlendirme İşlemleri. [online] Available from: https://hsgm.saglik.gov.tr/tr/duyurular/covid-19-tani-kitleri-urun-degerlendirme-islemleri.html [cited 03 May 2023].(Turkish)
  • 10. Saxena KS, Kumar S, Ansari S, Paweska TJ, Maurya KV, Tripathi KA, et al. Characterization of the novel SARS-CoV-2 Omicron (B.1.1.529) variant of concern and its global perspective. J Med Virol 2022;94:1738-44.
  • 11. Davies NG, Abbott S, Barnard CR, Jarvis IC, Kucharsk JA, Munday JD, et al. Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science 2021;372:eabg3055149.
  • 12. Greaney JA, Loes NA, Crawford K, Starr TN, Malone KD, Chu YC, et al. Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies Cell Host Microbe 2021;29:463-76.e6
  • 13. Planas D, Bruel T, Grzelak L, Guivel-Benhassine F, Staropoli I, Porrot F, et al. Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies. Nat Med 2021;27:917-24.
  • 14. Deng X, Garcia-Knight MA, Khalid MM, Servellita V, Wang C, Morris MK, et al. Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant. Cell 2021;184:3426-37.
  • 15. Wu Y, Xu W, Zhu Z, Xia X. Laboratory verification of an RT-PCR assay for SARS-CoV-2. J Clin Lab Anal 2020;34:e23507.
  • 16. Sherif B, Hafez MH, Abdelhalim RM, Elwafa M, Wahba NS, Hamdy P. Evaluation of diagnostic performance of SARS-CoV-2 detection kits: a comparative study. Beni Suef Univ J Basic Appl Sci 2023;12:17.
  • 17. Mulahuseinovic N, Salihefendic L, Durgut S, Kandic E, Konjhodzic R. Comparative analysis of SARS-CoV-2 detection kits. Acta Inform Med 2022;30:110-114.
  • 18. Shen L, Cui S, Zhang D, Lin C, Chen L, Wang Q. Comparison of four commercial RT-PCR diagnostic kits for COVID-19 in China. J Clin Lab Anal 2021;35:e23605.
  • 19. Al-Hashimi OTM, AL-Ansari WIA, Abbas SA, Jumaa DS, Hammad SA, Hammoudi A, et al. The sensitivity and specificity of COVID-19 rapid anti-gene test in comparison to RT-PCR test as a gold standard test. J Clin Lab Anal 2023;37:e24844.
  • 20. van Kasteren PB, van der Veer B, van den Brink S, Wijsman L, de Jonge J, van den Brandt A, et al. Comparison of seven commercial RT-PCR diagnostic kits for COVID-19. J Clin Virol 2020;128:104412.
  • 21. 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:E41-5.
  • 22. Wu S, Liu X, Ye S, Liu J, Zheng W, Dong X, et al. Colorimetric isothermal nucleic acid detection of SARS‐CoV‐2 with dye combination. Heliyon 2021;7: e06886.
  • 23. WHO Laboratory testing for coronavirus disease (COVID-19) in suspected human cases: interim guidance. [online] Available from: https://apps.who.int/iris/bitstream/handle/10665/331501/WHO-COVID-19-laboratory-2020.5-eng.pdf [cited 13 Dec 2022]
  • 24. Temiz H, Özbek E, Zeyrek FY. Retrospective review of re-positive qPCR tests for SARS-CoV: do they indicate presence of reinfection? Eur Rev Med Pharmacol Sci 2022;26:5278-84.
  • 25. Sarıgul F, Doluca O, Akhan S, Sayan M. Investigation of compatibility of severe acute respiratory syndrome coronavirus 2 reverse transcriptase-PCR kits containing different gene targets during coronavirus disease 2019 pandemic. Future Virol 2020;15:515-24.

Comparison of L452R mutation variant diagnosis in SARS-COV-2 PCR positive samples with two different qPCR kits

Year 2023, Volume: 9 Issue: 5 - September 2023, 1142 - 1148, 04.09.2023
https://doi.org/10.18621/eurj.1341822

Abstract

Objectives: Quantitative reverse transcription‐polymerase chain reaction (qPCR) is used as the gold standard method to diagnose COVID-19 infection caused by SARS-CoV-2 which is the cause of the most important epidemic in world history. It was aimed to compare the results of two of the most commonly used commercial kits for the diagnosis of SARS-CoV-2 mutation in our laboratory during the pandemic.

Methods: Our study included 5000 SARS-CoV-2 PCR positive nasopharyngeal swab samples (2500 L452R mutation positive samples, 2500 L452R mutation negative samples). PCR positivity and negativity of the L452R mutation of the positive SARS-CoV-2 positive samples were identified with the Diagnovital® (DIAGNO5plex NS SARS-CoV-2 Real Time PCR Kit [A1 Life Sciences Istanbul]) kit. The mentioned samples were also studied with a different commercial PCR kit, Bio-Speedy® (SARS-CoV-2 Emerging Plus Real Time PCR Kit [Bioeksen R&D Technologies Istanbul]).

Results: A total of 5000 samples included in the study were concluded as SARS-CoV-2 positive with both tests. One hundred and fifty of 2500 samples that were found positive for SARS-CoV-2 but negative for L452R mutations with the Diagnovital® kit were found positive with the Bio-Speedy® kit for SARS-CoV-2. The compatability between the two kits was found to be high (Kappa= 0.940). The mean Ct values of the samples found positive with the Diagnovital® kit and Bio-Speedy® kit were 24.15 ± 6.75 and 20.72 ± 7.17, respectively and the difference was statistically significant.

Conclusions: It was determined the two commercial kits included in the study were extremely compatible based on their analysis. Therefore both kits can be used safely for COVID-19 symptomatic patients.

References

  • 1. Dioni L, Orlandi A, Renteria SU, Favero C, Solazzo G, Oggioni M. Digital RT-PCR Chip method for detection of SARS-CoV-2 virus. J Immunol Methods 2022;509: 113339.
  • 2. Ciottia M, Ciccozzi M, Pieric M, Bernardini S. The COVID-19 pandemic: viral variants and vaccine efficacy. Crit Rev Clin Lab Sci 2022;59:66-75.
  • 3. Ontiveros N, Adol Bosque Aguirre DA, Gonzalez Urquijo M, Gonzalez DEH, Martinez Resendez FM, Schang L. Nasopharyngeal viral load at admission is not an independent predictor of thromboembolic complications in unvaccinated COVID 19 hospitalized patients. J Thromb Thrombolysis 2023;55:282-8.
  • 4. Burjanivova T, Lukacova E, Lucansky V, Samec M, Podlesniy P, Kolkova Z. Sensitive SARS-CoV-2 detection, air travel Covid-19 testing, variant determination and fast direct PCR detection, using ddPCR and RT-qPCR methods. Acta Virol 2023;67:3-12.
  • 5. Tang YW, Schmitz JE, Persing DH, Stratton CW. Laboratory diagnosis of COVID-19: current issues and challenges. J Clin Microbiol 2020;58:e00512-20.
  • 6. Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DKW, et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR, Euro Surveill 2020;25:2000045.
  • 7. Gülbudak H, Karvar Ş, Soydan G, Tezcan Ülger S, Kandemir Ö, Tamer L, et al. [Comparison of real time PCR cycle threshold values in symptomatic and asymptomatic COVID-19 patients]. Mikrobiyol Bul 2021;55:435-44. [Article in Turkish]
  • 8. Xu K, Chen Y, Yuan J, Yi P, Ding C, Wu W, et al. Factors associated with prolonged viral RNA shedding in patients with COVID-19. Clin Infect Dis 2020;71:799-806.
  • 9. COVID-19 Tanı Kitleri Ürün Değerlendirme İşlemleri. [online] Available from: https://hsgm.saglik.gov.tr/tr/duyurular/covid-19-tani-kitleri-urun-degerlendirme-islemleri.html [cited 03 May 2023].(Turkish)
  • 10. Saxena KS, Kumar S, Ansari S, Paweska TJ, Maurya KV, Tripathi KA, et al. Characterization of the novel SARS-CoV-2 Omicron (B.1.1.529) variant of concern and its global perspective. J Med Virol 2022;94:1738-44.
  • 11. Davies NG, Abbott S, Barnard CR, Jarvis IC, Kucharsk JA, Munday JD, et al. Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science 2021;372:eabg3055149.
  • 12. Greaney JA, Loes NA, Crawford K, Starr TN, Malone KD, Chu YC, et al. Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies Cell Host Microbe 2021;29:463-76.e6
  • 13. Planas D, Bruel T, Grzelak L, Guivel-Benhassine F, Staropoli I, Porrot F, et al. Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies. Nat Med 2021;27:917-24.
  • 14. Deng X, Garcia-Knight MA, Khalid MM, Servellita V, Wang C, Morris MK, et al. Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant. Cell 2021;184:3426-37.
  • 15. Wu Y, Xu W, Zhu Z, Xia X. Laboratory verification of an RT-PCR assay for SARS-CoV-2. J Clin Lab Anal 2020;34:e23507.
  • 16. Sherif B, Hafez MH, Abdelhalim RM, Elwafa M, Wahba NS, Hamdy P. Evaluation of diagnostic performance of SARS-CoV-2 detection kits: a comparative study. Beni Suef Univ J Basic Appl Sci 2023;12:17.
  • 17. Mulahuseinovic N, Salihefendic L, Durgut S, Kandic E, Konjhodzic R. Comparative analysis of SARS-CoV-2 detection kits. Acta Inform Med 2022;30:110-114.
  • 18. Shen L, Cui S, Zhang D, Lin C, Chen L, Wang Q. Comparison of four commercial RT-PCR diagnostic kits for COVID-19 in China. J Clin Lab Anal 2021;35:e23605.
  • 19. Al-Hashimi OTM, AL-Ansari WIA, Abbas SA, Jumaa DS, Hammad SA, Hammoudi A, et al. The sensitivity and specificity of COVID-19 rapid anti-gene test in comparison to RT-PCR test as a gold standard test. J Clin Lab Anal 2023;37:e24844.
  • 20. van Kasteren PB, van der Veer B, van den Brink S, Wijsman L, de Jonge J, van den Brandt A, et al. Comparison of seven commercial RT-PCR diagnostic kits for COVID-19. J Clin Virol 2020;128:104412.
  • 21. 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:E41-5.
  • 22. Wu S, Liu X, Ye S, Liu J, Zheng W, Dong X, et al. Colorimetric isothermal nucleic acid detection of SARS‐CoV‐2 with dye combination. Heliyon 2021;7: e06886.
  • 23. WHO Laboratory testing for coronavirus disease (COVID-19) in suspected human cases: interim guidance. [online] Available from: https://apps.who.int/iris/bitstream/handle/10665/331501/WHO-COVID-19-laboratory-2020.5-eng.pdf [cited 13 Dec 2022]
  • 24. Temiz H, Özbek E, Zeyrek FY. Retrospective review of re-positive qPCR tests for SARS-CoV: do they indicate presence of reinfection? Eur Rev Med Pharmacol Sci 2022;26:5278-84.
  • 25. Sarıgul F, Doluca O, Akhan S, Sayan M. Investigation of compatibility of severe acute respiratory syndrome coronavirus 2 reverse transcriptase-PCR kits containing different gene targets during coronavirus disease 2019 pandemic. Future Virol 2020;15:515-24.
There are 25 citations in total.

Details

Primary Language English
Subjects Medical Virology, Medical Microbiology (Other)
Journal Section Original Articles
Authors

Burcu Gürer Giray 0000-0003-3165-8924

Gökçe Güven Açık 0000-0001-9788-9480

Early Pub Date August 23, 2023
Publication Date September 4, 2023
Submission Date August 12, 2023
Acceptance Date August 16, 2023
Published in Issue Year 2023 Volume: 9 Issue: 5 - September 2023

Cite

AMA Gürer Giray B, Güven Açık G. Comparison of L452R mutation variant diagnosis in SARS-COV-2 PCR positive samples with two different qPCR kits. Eur Res J. September 2023;9(5):1142-1148. doi:10.18621/eurj.1341822

e-ISSN: 2149-3189 


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