Evaluation of Currently Available Molecular Assays and Performance of Sampling Approaches for Detection of Sars-Cov-2 RNA

Authors

  • Muhammad Taimur Asad The University of Lahore
  • Aamer Ali Khattak The University of Haripur
  • Usman Ayub Awan The University of Lahore
  • Waseem Iqbal The University of Haripur
  • Zakir Ahmad Abdul Wali Khan University, Mardan
  • Muhammad Abbas Abdul Wali Khan University, Mardan

DOI:

https://doi.org/10.37762/jgmds.11-1.500

Keywords:

Molecular Assays, Sars-Cov-2 RNA, Sampling Approaches COVID-19

Abstract

OBJECTIVES

This study aims to identify the essential characteristics of diagnostic tests for SARS-CoV-2 and to discuss the limitations of currently available tests and their impact on the test selection process.

METHODOLOGY

The current study was conducted at Mardan Medical Complex (MMC). One hundred nasopharyngeal-positive samples were collected from February to March 2021. Oropharyngeal swab OPS, sputum, and blood samples were collected from the participants to detect SARS-CoV-2 RNA. RNA extraction of SARS-CoV-2 was done using a BigFish auto extractor. A Qiagen Thermal Cycler was used for genome amplification. Five different molecular assays, namely COVSIGN (N gene) Spain, BGI (ORF1ab gene) China, Maccura(ORF1ab, E and N gene) China, R-GENE (RdRp and N genes) France and Genuru (N gene, S gene and ORF ab/1) were used.

RESULTS
100 % positivity was recorded in the sputum of all individuals, followed by 91 % OPS and 21% blood. The highest positivity rate for different genes was observed. ROC (Receiver operating characteristic curve) was developed through SPPS version 26.00 to compare the sensitivity and specificity.

CONCLUSION

By comparing the results of different diagnostic kits, it was found that BGI and Maccura are the most sensitive and specific for diagnostic purposes against COVID-19.

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Author Biographies

Muhammad Taimur Asad, The University of Lahore

Lecturer, University Institute of Medical Laboratory Technology,
The University of Lahore,

Aamer Ali Khattak, The University of Haripur

Assistant Professor,
Department of Medical Lab Technology,
The University of Haripur

Usman Ayub Awan, The University of Lahore

Assistant Professor,
University Institute of Medical Laboratory Technology,
The University of Lahore

Waseem Iqbal, The University of Haripur

MLT Technologist,
Department of Medical lab Technology,
The University of Haripur

Zakir Ahmad, Abdul Wali Khan University, Mardan

MLT Technologist,
Institute of Chemical and Life Sciences,
Department of Biochemistry,
Abdul Wali Khan University, Mardan

Muhammad Abbas, Abdul Wali Khan University, Mardan

Lecturer,
Department of Microbiology,
Abdul Wali Khan University, Mardan

References

Banko A, Petrovic G, Miljanovic D, Loncar A, Vukcevic M, Despot D, et al. Comparison and sensitivity evaluation of three different commercial real-time quantitative PCR kits for SARS-CoV-2 detection. Viruses. 2021 Jul 1;13(7)

Cauchemez S, Boëlle PY, Donnelly CA, Ferguson NM, Thomas G, Leung GM, et al. Real-time estimates in early detection of SARS. Emerg Infect Dis. 2006;12(1):110-3

Ndaïrou F, Area I, Nieto JJ, Torres DFM. Mathematical modeling of COVID-19 transmission dynamics with a case study of Wuhan. Chaos Solitons Fractals. 2020 Jun 1;135:109846

Coronaviridae Study Group of the International Committee on Taxonomy of Viruses. The species severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol. 2020 Apr 1;5(4):536-44

Sola I, Almazán F, Zúñiga S, Enjuanes L. Continuous and discontinuous RNA synthesis in coronaviruses. Annu Rev Virol. 2015 Nov 9;2(1):265-88

Xiang Y, Jia Y, Chen L, Guo L, Shu B, Long E. COVID-19 epidemic prediction and the impact of public health interventions: a review of COVID-19 epidemic models. Infect Dis Modell. 2021 Jan 1;6:324-42

Kumar K, Mhetre A, Ratnaparkhi GS, Kamat SS. A superfamily-wide activity atlas of serine hydrolases in Drosophila melanogaster. Biochemistry. 2021 Apr 27;60(16):1312-24

Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, et al. A new coronavirus associated with human respiratory disease in China. Nature. 2020 Mar 12;579(7798):265-9

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 Feb 22;395(10224):565-74

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 Jan 23;25(3):2000045

Lam TTY, Jia N, Zhang YW, Shum MHH, Jiang JF, Zhu HC, et al. Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature. 2020 Jul 9;583(7815):282-5

Ji W, Wang W, Zhao X, Zai J, Li X. Cross-species transmission of the newly identified coronavirus 2019-nCoV. J Med Virol. 2020 Apr 1;92(4):433-40

Benvenuto D, Giovanetti M, Salemi M, Prosperi M, De Flora C, Junior Alcantara LC, et al. The global spread of 2019-nCoV: a molecular evolutionary analysis. Pathog Glob Health. 2020 Feb 17;114(2):64-7

Al-Saud H, Al-Romaih K, Bakheet R, Mahmoud L, Al-Harbi N, Alshareef I, et al. Automated SARS-COV-2 RNA extraction from patient nasopharyngeal samples using a modified DNA extraction kit for high throughput testing. Ann Saudi Med. 2020 Sep 1;40(5):373-81

Yang H, Lu S. COVID-19 and tuberculosis. Journal of Translational Internal Medicine. 2020 Jun 1;8(2):59-65

Bwire G, Ario AR, Eyu P, Ocom F, Wamala JF, Kusi KA, et al. The COVID-19 pandemic in the African continent. BMC Med. 2022 Dec 1;20(1):167

Al-Mufti ON. Discussion of Li et al. Sedimentology. 2022 Oct 1. 2021 – On the origin and significance of composite particles in mudstones: Examples from the Cenomanian Dunvegan Formation, Sedimentology, 68;69(6):2676–81:737-54

Eberle C, Stichling S. Impact of COVID-19 lockdown on glycemic control in patients with type 1 and type 2 diabetes mellitus: a systematic review. Diabetol Metab Syndr. 2021 Dec 1;13(1):95

Marin Bosch B, Bringard A, Logrieco MG, Lauer E, Imobersteg N, Thomas A, et al. Effect of acute physical exercise on motor sequence memory. Sci Rep. 2020 Dec 1;10(1):15322

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Published

2023-12-31

How to Cite

Asad, M. T. ., Khattak, A. A. ., Awan, U. A. ., Iqbal, W. ., Zakir Ahmad, & Abbas, M. . (2023). Evaluation of Currently Available Molecular Assays and Performance of Sampling Approaches for Detection of Sars-Cov-2 RNA. Journal of Gandhara Medical and Dental Science, 11(1), 21–25. https://doi.org/10.37762/jgmds.11-1.500