The Concurrent Identification of SARS-Cov-2 and Influenza A/B Viruses in Nasopharyngeal Swabs Using Multiplex Real-time PCR

Khodaei, Hannan; Yari, Mohammad Ehsan; Ardehali, Seyed Hossein; Alebouyeh, Masoud; Abdollahi, Nafiseh; Fallah, Fatemeh; Azimi, Leila; Armin, Shahnaz; Karimi, Abdollah; Rokni, Hirad

doi:10.22092/ari.2025.368120.3482

The Concurrent Identification of SARS-Cov-2 and Influenza A/B Viruses in Nasopharyngeal Swabs Using Multiplex Real-time PCR

Document Type : Original Articles

Authors

¹ Pediatric Infections Research Center, Research Institute for Children’s Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran.

² School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.

³ Department of Anesthesiology and Critical Care, Shohadaye Tajrish Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.

⁴ Faculty of Density, Shahed University, Tehran Iran.

10.22092/ari.2025.368120.3482

Abstract

Introduction: Respiratory viral infections vary in their clinical presentation, treatment approaches and outcomes. Therefore, accurate, timely and cost-effective detection of key pathogens, particularly SARS-CoV-2 and influenza A/B, which are among the most common causes of respiratory infections, is crucial. This study aimed to identify the presence of COVID-19 and influenza A/B, as well as their co-occurrence, in hospitalized pediatric patients presenting with respiratory viral infections symptoms.
Materials & Methods: Nasopharyngeal specimens were collected from pediatric patients admitted to Mofid Children’s Hospital in Tehran, Iran who exhibited symptoms of viral respiratory infections. Detection of SARS-CoV-2 and influenza A/B was achieved using multiplex real-time polymerase chain reaction (PCR) following total RNA extraction of samples. Data regarding symptoms and other pertinent information about the patients were collected via a questionnaire.
Results: A total of 2,353 hospitalized children in this study, ranging from under one year old to 18 years old. Of these 43% were female and 57% male. Fever was the most commonly reported symptom. The results of the multiplex real-time PCR were positive in 8% of cases, including 55% for COVID-19, 8.5% forinfluenza A, 26% for influenza B, and 10.5% for co-infections.
Conclusion: The results of this study suggest a decline in seasonal influenza incidence compared to previous years, potentially due to the improved personal protection measures during to the COVID-19 pandemic. On the other hand, the presence of co-infection in this study is important and this co-infection should be considered in treatment and diagnostic systems in respiratory infection by physicians. Importantly, the presence of co-infections highlights the need for clinicians to consider dual pathogen involvement in diagnosis and treatment strategies for respiratory infections.

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