Association of N and E Genes with ORF1b Gene for Early Detection of COVID-19 in Pakistani Patients

Authors

  • Yar Mohammad Waryah
  • Shaista Ehsan
  • Roohi Nigar

Keywords:

SARS CoV-2, COVID-19 , E-gene, N-gene, ORF1b gene, RT-PCR

Abstract

Objective:  To investigate the role of the first line and additional confirmatory assay to detect coronavirus based on Ct RT-PCR values.

Methodology: A collaborative cross-sectional study was conducted using a systematic sampling type at Hyderabad's diagnostic and research laboratory and the SIOVS, Hyderabad, after getting ethical approval from the LUMHS ERC committee from July 2021 to June 2022. A total of 4822 patients have enrolled; 1200 patients were positive for COVID-19, and a nasopharyngeal swab was collected from patients for RNA extraction; the patients positive with COVID-19 RT-PCR test were included, and patients negative with COVID-19 RT-PCR were excluded out from this study. The RT-PCR was performed, and the Ct values of each potential target were recorded.

Results: The RT-PCR finding of potential targets revealed that the N and E genes are correlated and simultaneously positive with OFRb1 and RdRP genes and are crucial for detecting coronavirus. In 77.5% (310/400) of patients, the E gene was positive, and the N gene was positive in 85.8% (1030/1200) patients with ORF1b and Rdrp genes. 71% (850/1200) of males were infected in our cohort, and young patients carried the highest viral load than old age patients with asymptomatic features. Each target's obtained cycler threshold values by different kits were recorded and analyzed in SPSS-17.

Conclusion: The data showed N and E genes are simultaneously associated with the ORFb1 gene for detecting COVID-19 in our patients. 

References

Zhou P, Yang XL, Wang XG, 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. Epub 2020/ 02/06.

Jiatong S, Wenjun L. Epidemiological characteristics and prevention and control measures of Corona Virus Disease 2019 in children. J Trop Med. 2020; 20(2): 153-6.

Organization WH. WHO characterizes COVID-19 as a pandemic [EB/OL]. 2020.

Rodriguez-Morales AJ, Bonilla-Aldana DK, Balbin-Ramon GJ, Rabaan AA, Sah R, Paniz-Mondolfi A, et al. History is repeating itself: Probable zoonotic spillover as the cause of the 2019 novel Coronavirus Epidemic. Le infezioni in medicina. 2020; 28(1): 3-5. Epub 2020/02/06.

Wu JT, Leung K, Leung GM. Nowcasting and forecasting the potential domestic and international spread of the 2019-nCoV outbreak originating in Wuhan, China: a modelling study. Lancet. 2020; 395(10225): 689-97. Epub 2020/02/06.

Dhama K, Khan S, Tiwari R, Sircar S, Bhat S, Malik YS et al. Coronavirus Disease 2019-COVID-19. Clin Microbiol Rev. 2020; 33(4). Epub 2020/06/26.

Woo PC, Huang Y, Lau SK, Yuen KY. Coronavirus genomics and bioinformatics analysis. Viruses. 2010; 2(8): 1804-20. Epub 2010/08/01.

Lu R, Zhao X, Li J, Niu P, Yang B, Wu H et al. Genomic characterization and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet (Londs, Engl). 2020; 395(10224): 565-74. Epub 2020/02/03.

Younes N, Al-Sadeq DW, Al-Jighefee H, Younes S, Al-Jamal O, Daas HI et al. Challenges in Laboratory Diagnosis of the Novel Coronavirus SARS-CoV-2. Viruses. 2020; 12(6). Epub 2020/05/30.

Ward S, Lindsley A, Courter J, Assa'ad A. Clinical testing for COVID-19. J Allergy Clin Immun. 2020; 146(1): 23-34. Epub 2020/05/24.

Li X, Geng M, Peng Y, Meng L, Lu S. Molecular immune pathogenesis and diagnosis of COVID-19. J Pharmaceut Analysis. 2020; 10(2): 102-8. Epub 2020/04/14.

Kakhki RK, Kakhki MK, Neshani A. COVID-19 target: A specific target for novel coronavirus detection. Gene Reports. 2020; 20: 100740. Epub 2020/06/09.

Chu DKW, Pan Y, Cheng SMS, Hui KPY, Krishnan P, Liu Y et al. Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia. Clin Chem. 2020; 66(4): 549-55. Epub 2020/02/08.

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Published

27-09-2023

How to Cite

1.
Waryah YM, Ehsan S, Nigar R. Association of N and E Genes with ORF1b Gene for Early Detection of COVID-19 in Pakistani Patients. J Liaq Uni Med Health Sci [Internet]. 2023 Sep. 27 [cited 2024 Dec. 12];22(03):197-200. Available from: http://ojs.lumhs.edu.pk/index.php/jlumhs/article/view/1109

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