SARS-CoV-2 excretion and genetic evolution in nasopharyngeal and stool samples from primary immunodeficiency and immunocompetent pediatric patients

Haifa Khemiri; Ilhem Ben Fraj; Alessio Lorusso; Najla Mekki; Iolanda Mangone; Mariem Gdoura; Adriano Di Pasqual; Cesare Cammà; Valeria Di Lollo; Asma Cherni; Henda Touzi; Amel Sadraoui; Zina Meddeb; Nahed Hogga; Imen Ben Mustapha; Mohamed-Ridha Barbouche; Monia Ouederni; Henda Triki; Sondes Haddad-Boubaker

doi:10.1186/s12985-025-02628-7

SARS-CoV-2 excretion and genetic evolution in nasopharyngeal and stool samples from primary immunodeficiency and immunocompetent pediatric patients

Virol J. 2025 Jan 13;22(1):9. doi: 10.1186/s12985-025-02628-7.

Authors

Haifa Khemiri^{1

2}, Ilhem Ben Fraj³, Alessio Lorusso⁴, Najla Mekki^{5

6}, Iolanda Mangone⁴, Mariem Gdoura^{7

8}, Adriano Di Pasqual⁴, Cesare Cammà⁴, Valeria Di Lollo⁴, Asma Cherni^{7

8}, Henda Touzi^{7

8}, Amel Sadraoui^{7

8}, Zina Meddeb^{7

8}, Nahed Hogga^{7

8}, Imen Ben Mustapha^{5

6}, Mohamed-Ridha Barbouche^{5

6

9}, Monia Ouederni^{3

6}, Henda Triki^{7

8

6}, Sondes Haddad-Boubaker^{10

11}

Affiliations

¹ Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University of Tunis El Manar, 13 place Pasteur, BP74 1002 le Belvédère, Tunis, Tunisia. [email protected].
² Research Laboratory "Viruses, Vectors and Hosts" (LR20IPT02), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia. [email protected].
³ Pediatric Department of the National Center of Bone Marrow Transplantation, Tunis, Tunisia.
⁴ Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, 64100, Teramo, Italy.
⁵ Laboratory of Transmission, Control and Immunobiology of Infection (LR11IPT02), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.
⁶ Faculty of Medicine, University of Tunis El Manar, Tunis, Tunisia.
⁷ Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University of Tunis El Manar, 13 place Pasteur, BP74 1002 le Belvédère, Tunis, Tunisia.
⁸ Research Laboratory "Viruses, Vectors and Hosts" (LR20IPT02), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.
⁹ Department of Microbiology, Immunology and Infectious Diseases, College of Medicine and Health Sciences, Arabian Gulf University, Manama, Bahrain.
¹⁰ Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University of Tunis El Manar, 13 place Pasteur, BP74 1002 le Belvédère, Tunis, Tunisia. [email protected].
¹¹ Research Laboratory "Viruses, Vectors and Hosts" (LR20IPT02), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia. [email protected].

Abstract

Background: Primary Immunodeficiency disorders (PID) can increase the risk of severe COVID-19 and prolonged infection. This study investigates the duration of SARS-CoV-2 excretion and the genetic evolution of the virus in pediatric PID patients as compared to immunocompetent (IC) patients.

Materials and methods: A total of 40 nasopharyngeal and 24 stool samples were obtained from five PID and ten IC children. RNA detection was performed using RT-qPCR, and whole-genome sequencing was conducted with the NexSeq 1000 platform. Data analysis used the nextflow/viralrecon pipeline. Hotspot amino acid frequencies were investigated using GraphPad Prism v10. Phylodynamic analysis was conducted with BEAST software.

Results: In IC children, the viral excretion period lasted up to 14 days in nasopharyngeal swabs, with an average duration of 7 days, and ranged from 7 to 14 days in stool samples. In PID patients, the viral RNA was detected in nasopharyngeal for periods between 7 and 28 days, with an average duration of 15 days, and up to 28 days in stool samples. Two SARS-CoV-2 variants were detected in PID patients: Delta (AY.122) and Omicron (BA.1.1). Patients with antibody and combined deficiencies, exhibited the most prolonged shedding periods in both nasopharyngeal and stool samples and one patient presented complications and fatal outcome. Specific Hotspot amino acid changes were detected in PID: A2821V and R550H (ORF1ab).

Conclusion: Our findings underscore the prolonged excretion of SARS-CoV-2 RNA in patients with antibody and combined deficiencies. Thus, specialized care is essential for effectively managing PID patients.

Keywords: Amino acid; COVID-19; Duration; Immunocompetent; Primary immunodeficiency; SNPs.

MeSH terms

Adolescent
COVID-19* / immunology
COVID-19* / virology
Child
Child, Preschool
Evolution, Molecular
Feces* / virology
Female
Humans
Infant
Male
Nasopharynx* / virology
Phylogeny
Primary Immunodeficiency Diseases / genetics
RNA, Viral* / genetics
SARS-CoV-2* / genetics
SARS-CoV-2* / immunology
Virus Shedding*
Whole Genome Sequencing

Substances

RNA, Viral

Supplementary concepts

SARS-CoV-2 variants