Intra-host diversity of SARS-CoV-2 in children with long-term and short-term excretion in nasopharyngeal samples

Abstract

BACKGROUND: The intra-host diversity of SARS-CoV-2 in pediatric populations remains insufficiently studied. To address this significant knowledge gap, the present study investigates the intra-host variability of SARS-CoV-2 in both immunocompetent and immunodeficient children, including those with severe cases. The research encompasses both short-term and long-term infections, aiming to provide a comprehensive understanding of viral dynamics in these vulnerable groups. MATERIALS AND METHODS: This study analyzed 47 pediatric COVID-19 patients: 37 with short-term infections and 10 with long-term infections including 3 immunodeficient cases. Viral RNA was extracted and detected using RT-qPCR, followed by whole-genome sequencing (WGS) using the Illumina COVIDSeq assay. Bioinformatics analysis was performed with the nextflow/viralrecon pipeline. The number of single nucleotide polymorphisms (SNPs) and the frequency of Major (M-SNPs) and minor (m-SNPs) missense SNPs were analyzed using the ggplot2 R package and GraphPad Prism software, respectively. RESULTS: A total of 96 SARS-CoV-2 sequences from 45 patients (35 short-term and 10 long-term shedders), were classified into four variants: Alpha, B.1.160, Delta, and Omicron. SNPs were common across SARS-CoV-2 variants (88.21%-100%), with frequent cytosine-to-thymidine (C > T) substitutions (44.05%-52.85%). Missense mutations were also prominent (57.52% to 80.32%). Variability in SNPs numbers was observed over time in Delta and Omicron variants, particularly in severe and immunodeficient cases. Missense m-SNPs exhibited variation in long-term shedders, especially among severe immunocompetent and immunodeficient patients. CONCLUSION: Our findings revealed significant intra-host variability in SARS-CoV-2 among severe and immunodeficient pediatric patients. These results underscore the critical importance of continuous surveillance of viral variants within pediatric populations to enhance our understanding of their impact on disease progression and clinical outcomes.