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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.
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1 IRCCS, Multimodal Laboratory Research Unit, Bambino Gesù Children’s Hospital, Rome, Italy (GRID:grid.414125.7) (ISNI:0000 0001 0727 6809); University of Milan, Department of Oncology and Hemato-Oncology, Milan, Italy (GRID:grid.4708.b) (ISNI:0000 0004 1757 2822); Campus Bio-Medico University, Major School in Microbiology and Virology, Rome, Italy (GRID:grid.9657.d) (ISNI:0000 0004 1757 5329)
2 IRCCS, Multimodal Laboratory Research Unit, Bambino Gesù Children’s Hospital, Rome, Italy (GRID:grid.414125.7) (ISNI:0000 0001 0727 6809); University of Milan, Department of Oncology and Hemato-Oncology, Milan, Italy (GRID:grid.4708.b) (ISNI:0000 0004 1757 2822)
3 IRCCS, Multimodal Laboratory Research Unit, Bambino Gesù Children’s Hospital, Rome, Italy (GRID:grid.414125.7) (ISNI:0000 0001 0727 6809)
4 IRCCS, Academic Department of Pediatrics, Bambino Gesù Children’s Hospital, Rome, Italy (GRID:grid.414125.7) (ISNI:0000 0001 0727 6809)
5 IRCCS, Microbiology and Diagnostics in Immunology, Bambino Gesù Children’s Hospital, Rome, Italy (GRID:grid.414125.7) (ISNI:0000 0001 0727 6809)
6 IRCCS, Multimodal Laboratory Research Unit, Bambino Gesù Children’s Hospital, Rome, Italy (GRID:grid.414125.7) (ISNI:0000 0001 0727 6809); IRCCS, Microbiology and Diagnostics in Immunology, Bambino Gesù Children’s Hospital, Rome, Italy (GRID:grid.414125.7) (ISNI:0000 0001 0727 6809)