Evaluation of alternative clinical samples for the detection of SARS-CoV-2 and influenza virus by automated multiplex RT-PCR

Authors

  • Muhammed A Özarslan Department of Medical Microbiology, Faculty of Medicine, Ege University, Izmir 35100, Turkey https://orcid.org/0000-0003-0470-5959
  • Ömür M Parkan Department of Medical Microbiology, Faculty of Medicine, Erciyes University, Kayseri 38039, Turkey https://orcid.org/0000-0002-1071-4985
  • Mehmet Soylu Department of Medical Microbiology, Faculty of Medicine, Ege University, Izmir 35100, Turkey https://orcid.org/0000-0002-9145-1506
  • Oğuzhan Acet Department of Infectious Diseases, Faculty of Medicine, Ege University, Izmir 35100, Turkey
  • Selma Gökahmetoğlu Department of Medical Microbiology, Faculty of Medicine, Erciyes University, Kayseri 38039, Turkey
  • Zeynep Türe Yüce Department of Infectious Diseases, Faculty of Medicine, Erciyes University, Kayseri 38039, Turkey https://orcid.org/0000-0001-6895-0318
  • Gamze Kalın Ünüvar Department of Infectious Diseases, Faculty of Medicine, Erciyes University, Kayseri 38039, Turkey
  • Seyfi Durmaz Department of Occupational Health and Safety Unit, Faculty of Medicine, Ege University, Izmir 35100, Turkey https://orcid.org/0000-0001-9756-7764
  • Deniz Akyol Department of Infectious Diseases, Faculty of Medicine, Ege University, Izmir 35100, Turkey
  • Feyza İzci Çetinkaya Department of Infectious Diseases, Faculty of Medicine, Erciyes University, Kayseri 38039, Turkey
  • Pınar Sağıroğlu Department of Medical Microbiology, Faculty of Medicine, Erciyes University, Kayseri 38039, Turkey https://orcid.org/0000-0001-6742-0200
  • Gözde Akkuş Kayalı Department of Medical Microbiology, Faculty of Medicine, Ege University, Izmir 35100, Turkey
  • Isabel R Durusoy Department of Public Health, Faculty of Medicine, Ege University, Izmir 35100, Turkey
  • Ayşin Zeytinoğlu Department of Medical Microbiology, Faculty of Medicine, Izmir Economy University, Izmir 35330, Turkey https://orcid.org/0000-0003-4174-9539
  • Mustafa A Atalay Department of Medical Microbiology, Faculty of Medicine, Erciyes University, Kayseri 38039, Turkey https://orcid.org/0000-0003-4169-0637
  • Meltem Taşbakan Department of Infectious Diseases, Faculty of Medicine, Ege University, Izmir 35100, Turkey
  • Candan Çiçek Department of Medical Microbiology, Faculty of Medicine, Ege University, Izmir 35100, Turkey https://orcid.org/0000-0002-3486-8305
  • Orhan Yıldız Department of Infectious Diseases, Faculty of Medicine, Erciyes University, Kayseri 38039, Turkey
  • Hüsnü Pullukçu Department of Infectious Diseases, Faculty of Medicine, Ege University, Izmir 35100, Turkey
  • Şaziye R Sertöz Department of Medical Microbiology, Faculty of Medicine, Ege University, Izmir 35100, Turkey
  • Selda Erensoy Department of Medical Microbiology, Faculty of Medicine, Ege University, Izmir 35100, Turkey https://orcid.org/0000-0002-7052-8359

DOI:

https://doi.org/10.3855/jidc.20801

Keywords:

SARS-CoV-2, influenza A, RT-PCR, saliva, nasal, nasopharyngeal

Abstract

Introduction: The aim of this study was to compare the performance of different clinical specimens—nasopharyngeal (NP) swabs collected by healthcare professionals (HCP-NP), self-collected nasal swabs (Sc-N), and saliva samples (S)—in diagnostic tests for investigating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA and influenza A/B RNA.

Methodology: These clinical samples were collected from 404 symptomatic cases and tested with the SARS-CoV-2 and influenza A/B RNA tests on the cobas 6800 System of Roche Molecular Systems (Roche Molecular Systems, Pleasanton, USA). The SARS-CoV-2 or influenza virus infection status was determined for all patients based on the predefined criteria and corresponding algorithms. Positive and negative predictive values (PPV, NPV), sensitivity, specificity, coefficient of variation (CV), interrater reliability, correlation, ,and days of sample collection of these three sample types were analyzed.

Results: There was almost perfect agreement between the these sample types for the diagnosis of SARS-CoV-2 and influenza A. The overall performance (PPV, NPV, sensitivity) and reproducibility (CV ≤ 6%) were favorable. Additionally, they showed similar trends for days of sample collection.

Conclusions: Diagnostic detection of SARS-CoV-2 and influenza RNA from Sc-N and S samples was comparable to HCP-NP samples. Using these samples would provide an advantage in diagnosing SARS-CoV-2 and influenza A infection, as they can be easily collected without the need for viral transport media.

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Published

2025-08-31

How to Cite

1.
Özarslan MA, Parkan Ömür M, Soylu M, Acet O, Gökahmetoğlu S, Türe Yüce Z, Kalın Ünüvar G, Durmaz S, Akyol D, İzci Çetinkaya F, Sağıroğlu P, Akkuş Kayalı G, Durusoy IR, Zeytinoğlu A, Atalay MA, Taşbakan M, Çiçek C, Yıldız O, Pullukçu H, Sertöz Şaziye R, Erensoy S (2025) Evaluation of alternative clinical samples for the detection of SARS-CoV-2 and influenza virus by automated multiplex RT-PCR. J Infect Dev Ctries 19:1159–1171. doi: 10.3855/jidc.20801

Issue

Vol. 19 No. 08: August 2025

Section

Coronavirus Pandemic

License

Copyright (c) 2025 Muhammed Alper Özarslan, Ömür Mustafa Parkan, Mehmet Soylu, Oğuzhan Acet, Selma Gökahmetoğlu, Zeynep Türe Yüce, Gamze Kalın Ünüvar, Seyfi Durmaz, Deniz Akyol, Feyza İzci Çetinkaya, Pınar Sağıroğlu, Gözde Akkuş Kayalı, Isabel Raika Durusoy, Ayşin Zeytinoğlu, Mustafa Altay Atalay, Meltem Taşbakan, Candan Çiçek, Orhan Yıldız, Hüsnü Pullukçu, Şaziye Rüçhan Sertöz, Selda Erensoy

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