SARS-CoV-2 excretion and genetic evolution in nasopharyngeal and stool samples from primary immunodeficiency and immunocompetent pediatric patients
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. M...
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| Language: | English |
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BMC
2025-01-01
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| Series: | Virology Journal |
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| Online Access: | https://doi.org/10.1186/s12985-025-02628-7 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Haifa Khemiri |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-9f60c82794a04127aafbe2927c78d8d3 |
| institution | Kabale University |
| issn | 1743-422X |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Virology Journal |
| spelling | doaj-art-9f60c82794a04127aafbe2927c78d8d32025-01-19T12:10:17ZengBMCVirology Journal1743-422X2025-01-0122111210.1186/s12985-025-02628-7SARS-CoV-2 excretion and genetic evolution in nasopharyngeal and stool samples from primary immunodeficiency and immunocompetent pediatric patientsHaifa Khemiri0Ilhem Ben Fraj1Alessio Lorusso2Najla Mekki3Iolanda Mangone4Mariem Gdoura5Adriano Di Pasqual6Cesare Cammà7Valeria Di Lollo8Asma Cherni9Henda Touzi10Amel Sadraoui11Zina Meddeb12Nahed Hogga13Imen Ben Mustapha14Mohamed-Ridha Barbouche15Monia Ouederni16Henda Triki17Sondes Haddad-Boubaker18Laboratory 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 ManarPediatric Department of the National Center of Bone Marrow TransplantationIstituto Zooprofilattico Sperimentale dell’Abruzzo e del MoliseLaboratory of Transmission, Control and Immunobiology of Infection (LR11IPT02), Institut Pasteur de Tunis, University of Tunis El ManarIstituto Zooprofilattico Sperimentale dell’Abruzzo e del MoliseLaboratory 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 ManarIstituto Zooprofilattico Sperimentale dell’Abruzzo e del MoliseIstituto Zooprofilattico Sperimentale dell’Abruzzo e del MoliseIstituto Zooprofilattico Sperimentale dell’Abruzzo e del MoliseLaboratory 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 ManarLaboratory 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 ManarLaboratory 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 ManarLaboratory 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 ManarLaboratory 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 ManarLaboratory of Transmission, Control and Immunobiology of Infection (LR11IPT02), Institut Pasteur de Tunis, University of Tunis El ManarLaboratory of Transmission, Control and Immunobiology of Infection (LR11IPT02), Institut Pasteur de Tunis, University of Tunis El ManarPediatric Department of the National Center of Bone Marrow TransplantationLaboratory 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 ManarLaboratory 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 ManarAbstract 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.https://doi.org/10.1186/s12985-025-02628-7Primary immunodeficiencySNPsAmino acidDurationCOVID-19Immunocompetent |
| spellingShingle | 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 SARS-CoV-2 excretion and genetic evolution in nasopharyngeal and stool samples from primary immunodeficiency and immunocompetent pediatric patients Virology Journal Primary immunodeficiency SNPs Amino acid Duration COVID-19 Immunocompetent |
| title | SARS-CoV-2 excretion and genetic evolution in nasopharyngeal and stool samples from primary immunodeficiency and immunocompetent pediatric patients |
| title_full | SARS-CoV-2 excretion and genetic evolution in nasopharyngeal and stool samples from primary immunodeficiency and immunocompetent pediatric patients |
| title_fullStr | SARS-CoV-2 excretion and genetic evolution in nasopharyngeal and stool samples from primary immunodeficiency and immunocompetent pediatric patients |
| title_full_unstemmed | SARS-CoV-2 excretion and genetic evolution in nasopharyngeal and stool samples from primary immunodeficiency and immunocompetent pediatric patients |
| title_short | SARS-CoV-2 excretion and genetic evolution in nasopharyngeal and stool samples from primary immunodeficiency and immunocompetent pediatric patients |
| title_sort | sars cov 2 excretion and genetic evolution in nasopharyngeal and stool samples from primary immunodeficiency and immunocompetent pediatric patients |
| topic | Primary immunodeficiency SNPs Amino acid Duration COVID-19 Immunocompetent |
| url | https://doi.org/10.1186/s12985-025-02628-7 |
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