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

Haifa Khemiri1,2, Ilhem Ben Fraj3, Alessio Lorusso4

  • 1Laboratory 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. haifa.khemiri@pasteur.utm.tn.

Virology Journal
|January 13, 2025
PubMed

Insights

Primary Immunodeficiency disorders (PID) lead to prolonged SARS-CoV-2 excretion in children. Antibody and combined deficiencies showed the longest viral shedding, highlighting the need for specialized care in these patients.

Area of Science:

  • Immunology
  • Virology
  • Pediatrics

Background:

  • Primary Immunodeficiency disorders (PID) increase the risk of severe COVID-19 and prolonged SARS-CoV-2 infection.
  • This study compares viral excretion duration and genetic evolution in pediatric PID patients versus immunocompetent (IC) children.

Purpose of the Study:

  • To investigate the duration of SARS-CoV-2 excretion in pediatric PID patients.
  • To analyze the genetic evolution of SARS-CoV-2 in pediatric PID patients.
  • To compare viral shedding and evolution between PID and IC pediatric patients.

Main Methods:

  • Collected nasopharyngeal and stool samples from five PID and ten IC children.
  • Utilized RT-qPCR for RNA detection and whole-genome sequencing (NexSeq 1000).
  • Analyzed data using nextflow/viralrecon, GraphPad Prism v10, and BEAST software for phylodynamic analysis.

Main Results:

  • Viral RNA detected up to 14 days in IC children (nasopharyngeal) and up to 28 days in PID patients.
  • PID patients exhibited prolonged shedding (average 15 days nasopharyngeal, up to 28 days stool).
  • Delta (AY.122) and Omicron (BA.1.1) variants found in PID patients; specific amino acid changes (A2821V, R550H) noted.

Conclusions:

  • Prolonged SARS-CoV-2 RNA excretion observed in PID patients, particularly those with antibody and combined deficiencies.
  • One PID patient experienced complications and a fatal outcome.
  • Specialized care is crucial for managing PID patients with COVID-19.
Abstract

Keywords:
Amino acidCOVID-19DurationImmunocompetentPrimary immunodeficiencySNPs

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