Prevalence of SARS-CoV-2 RNA in Fecal and Nasopharyngeal Specimens of Children with Gastroenteritis Complications: A Cross-Sectional Study

Introduction: Laboratory diagnosis of SARS-CoV-2 infection is primarily based on the detection of viral RNA using RT-PCR methods on respiratory specimens. This study aimed to detect SARS-CoV-2 in pediatric stool specimens and to compare the positivity rate of stool specimens with oropharyngeal/nasopharyngeal swabs in children with gastroenteritis complications referred to our laboratory. Materials and Methods: Stool samples and oropharyngeal/nasopharyngeal swabs (mixed specimens) were collected from 136 children with suspected COVID-19 infection, 2–3 days after symptom onset. Samples were tested using reverse transcription real-time polymerase chain reaction (rRT-PCR) targeting the RdRP and N genes. The Fisher’s exact probability test was used to compare the two groups. Results: After rRT-PCR assessment of samples, in the group without diarrhea (15 cases), there was no statistically significant difference between the positivity rate of oropharyngeal /nasopharyngeal swabs (46.7%) and stool samples (73.3%) (p = 0.137). In children with diarrhea, 53.7% of oropharyngeal/ nasopharyngeal swab samples and 71.9% of stool samples were positive, showing a statistically significant difference (p = 0.003). Discussion: The significantly higher viral load and prolonged shedding of SARS-CoV-2 in stool, particularly among children with diarrhea, suggest active viral replication in the gastrointestinal tract. These findings reinforce the potential role of fecal-oral transmission and highlight the diagnostic value of stool testing. Conclusion: Based on our findings, stool can serve as a suitable specimen for the detection of SARS-CoV-2 RNA, especially in children with diarrhea or in suspected COVID-19 cases with negative oropharyngeal/nasopharyngeal swab results.