Iranian Journal of Pathology

Endogenous Biomarkers Analysis and False-Negative Results for SARSCov2 Using two Commercial RT-PCR Diagnostic Kits

Document Type : Original Research

Authors

Mahdieh Khoshakhlagh 1, 2
Toktam Dehghani 3
Alaleh Alizadeh 4
Mojtaba Meshkat 5
Samaneh Abolbashari 6
Aida Gholoobi 1, 7
Fatemeh Ghaemi 2
Zahra Meshkat 6

1 Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran

2 Department of Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran

3 Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran

4 Student Research Committee, Faculty of Medicine, Mashhad Branch, Islamic Azad University, Mashhad, Iran

5 Department of Community Medicine, Faculty of Medicine, Mashhad Medical Sciences, Islamic Azad University, Mashhad, Iran

6 Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran

7 Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran

https://doi.org/10.30699/ijp.2025.2053609.3417
Abstract
Background & Objective: Real-time PCR is widely used to detect SARS-CoV-2, the virus responsible for COVID-19, but false-negative results can occur even with internal controls. This study aimed to investigate the impact of using alternative internal control materials on the accuracy of SARS-CoV-2 detection kits.
Methods: Between December 2021 and January 2022, 162 respiratory tract samples were collected from patients with suspected COVID-19 at Ghaem Hospital in Mashhad, IR Iran. Samples were initially tested with the Pishtaz Teb kit, which uses DNA internal control, and then negative samples were retested with the Geneova kit, which uses a RNA internal control. Positive and negative controls were consistently used to validate the results.
Results: After retesting with the Geneova kit, only one patient out of 162 negative samples was positive for SARS-CoV-2. The Pishtaz Teb and Geneova controls consistently produced the expected results, but the Geneova internal control matched the Pishtaz Teb control in only 44% of cases. The higher threshold cycle value for Geneova internal control suggested RNA degradation during the experimental period.
Conclusion: Proper quality control measures are crucial for accurate SARS-CoV-2 detection. The study highlights the importance of selecting reliable diagnostic kits with high sensitivity and specificity to reduce false-negative results, particularly in cases with a low viral load or early stages of the disease. The internal RNA control can detect RNA degradation and help identify false-negative diagnoses, leading to better disease control and management. Further research is needed to improve the accuracy of COVID-19 diagnostic tests.

Keywords

COVID-19
Real-time PCR
internal control
false-negative diagnoses
respiratory tract samples

Subjects

Copyright © 2026. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The license also allows users to adapt, remix, transform, and build upon the material for any purpose, including commercial use.

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Iranian Journal of Pathology
Volume 21, Issue 1
Winter 2026
Pages 59-67

  • Receive Date 18 February 2025
  • Revise Date 06 May 2025
  • Accept Date 02 June 2025

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