Molecular characterization of SARS-CoV-2 Omicron clade and clinical presentation in children

• Published in: Scientific Reports
• Main Authors: Rossana Scutari, Valeria Fox, Vanessa Fini, Annarita Granaglia, Anna Chiara Vittucci, Andrea Smarrazzo, Laura Lancella, Francesca Calo’ Carducci, Lorenza Romani, Laura Cursi, Paola Bernaschi, Cristina Russo, Andrea Campana, Stefania Bernardi, Alberto Villani, Carlo Federico Perno, Claudia Alteri
• Format: Article
• Language: English
• Published: Nature Portfolio 2024-03-01
• Subjects: SARS-CoV-2 genomic evolution; Omicron clade; Minority variants; COVID-19 in children
• Online Access: https://doi.org/10.1038/s41598-024-55599-0

Abstract Since its emergence, SARS-CoV-2 Omicron clade has shown a marked degree of variability and different clinical presentation compared with previous clades. Here we demonstrate that at least four Omicron lineages circulated in children since December 2021, and studied until November 2022: BA.1 (33.6%), BA.2 (40.6%), BA.5 (23.7%) and BQ.1 (2.1%). At least 70% of infections concerned children under 1 year, most of them being infected with BA.2 lineages (n = 201, 75.6%). Looking at SARS-CoV-2 genetic variability, 69 SNPs were found to be significantly associated in pairs, (phi <  − 0.3 or > 0.3 and p-value < 0.001). 16 SNPs were involved in 4 distinct clusters (bootstrap > 0.75). One of these clusters (A23040G, A27259C, T23617G, T23620G) was also positively associated with moderate/severe COVID-19 presentation (AOR [95% CI] 2.49 [1.26–4.89] p-value: 0.008) together with comorbidities (AOR [95% CI] 2.67 [1.36–5.24] p-value: 0.004). Overall, these results highlight the extensive SARS-CoV-2 Omicron circulation in children, mostly aged < 1 year, and provide insights on viral diversification even considering low-abundant SNPs, finally suggesting the potential contribution of viral diversification in affecting disease severity.