SARS-CoV-2 excretion kinetics in nasopharyngeal and stool samples from the pediatric population

Haifa Khemiri; Mariem Gdoura; Samar Ben Halima; Henda Krichen; Cesare Cammà; Alessio Lorusso; Massimo Ancora; Adriano Di Pasquale; Asma Cherni; Henda Touzi; Amel Sadraoui; Zina Meddeb; Nahed Hogga; Radhia Ammi; Henda Triki; Sondes Haddad-Boubaker

doi:10.3389/fmed.2023.1226207

SARS-CoV-2 excretion kinetics in nasopharyngeal and stool samples from the pediatric population

Front Med (Lausanne). 2023 Oct 30:10:1226207. doi: 10.3389/fmed.2023.1226207. eCollection 2023.

Authors

Haifa Khemiri^{1

2}, Mariem Gdoura^{1

2}, Samar Ben Halima^{1

2}, Henda Krichen^{1

2}, Cesare Cammà³, Alessio Lorusso³, Massimo Ancora³, Adriano Di Pasquale³, Asma Cherni^{1

2}, Henda Touzi^{1

2}, Amel Sadraoui^{1

2}, Zina Meddeb^{1

2}, Nahed Hogga^{1

2}, Radhia Ammi⁴, Henda Triki^{1

2}, Sondes Haddad-Boubaker^{1

2}

Affiliations

¹ Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.
² LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.
³ Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy.
⁴ Service of External Consultants, Institut Pasteur de Tunis, Tunis, Tunisia.

Abstract

Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for serious respiratory infections in humans. Even in the absence of respiratory symptoms, gastrointestinal (GI) signs were commonly reported in adults and children. Thus, oral-fecal transmission was suspected as a possible route of infection. The objective of this study was to describe RNA shedding in nasopharyngeal and stool samples obtained from asymptomatic and symptomatic children and to investigate virus viability.

Methods: This study included 179 stool and 191 nasopharyngeal samples obtained from 71 children, which included symptomatic (n = 64) and asymptomatic (n = 7) ones. They were collected every 7 days from the onset of the infection until negativation. Viral RNA was detected by real-time RT-PCR, targeting the N and ORF1 genes. Whole-genome sequencing was performed for positive cases. Viral isolation was assessed on Vero cells, followed by molecular detection confirmation.

Results: All cases included in this study (n = 71) were positive in their nasopharyngeal samples. SARS-CoV-2 RNA was detected in 36 stool samples obtained from 15 out of 71 (21.1%) children; 13 were symptomatic and two were asymptomatic. Excretion periods varied from 7 to 21 days and 7 to 14 days in nasopharyngeal and fecal samples, respectively. Four variants were detected: Alpha (n = 3), B.1.160 (n = 3), Delta (n = 7), and Omicron (n = 1). Inoculation of stool samples on cell culture showed no specific cytopathic effect. All cell culture supernatants were negative for RT-qPCR.

Conclusion: Our study demonstrated nasopharyngeal and fecal shedding of SARS-CoV-2 RNA by children up to 21 and 14 days, respectively. Fecal shedding was recorded in symptomatic and asymptomatic children. Nevertheless, SARS-CoV-2 was not isolated from positive stool samples.

Keywords: SARS-CoV-2; asymptomatic; infectious; pediatric population; stool; symptomatic; variants.

Grants and funding

This study was co-funded by the Italian Ministry of Health (IZSAM05/20 Ricerca Corrente 2020 PanCO: epidemiologia e patogenesi dei coronavirus umani e animali) via the project MEDNET coordinated by the World Health Organization Tunisia office, the Pasteur Institute of Tunis, the Tunisian Ministry of Health, and the Tunisian Ministry of Higher Education and Research (LR20IPT02). This research was also partially supported by EU funding within the NextGenerationEU-MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases (Project no. PE00000007, INF-ACT).