Epidemiological characterization of SARS-CoV-2 variants in children over the four COVID-19 waves and correlation with clinical presentation

Abstract

Since the start of SARS-CoV-2 pandemic, children aged ≤ 12 years have always been defined as underrepresented in terms of SARS-CoV-2 infections' frequency and severity. By correlating SARS-CoV-2 transmission dynamics with clinical and virological features in 612 SARS-CoV-2 positive patients aged ≤ 12 years, we demonstrated a sizeable circulation of different SARS-CoV-2 lineages over the four pandemic waves in paediatric population, sustained by local transmission chains. Age < 5 years, highest viral load, gamma and delta clades positively influence this local transmission. No correlations between COVID-19 manifestations and lineages or transmission chains are seen, except for a negative correlation between B.1.1.7 and hospitalization.

Figure 1

Estimated maximum likelihood phylogeny of SARS-CoV-2 genomes from population aged ≤ 12 years diagnosed at OPBG (n = 612, red taxa). Representative SARS-CoV-2 genomes retrieved by GISAID (n = 1233) and adolescent and adult SARS-CoV-2 infected population diagnosed in the same geographical area (n = 410) (gray taxa) were also included. The phylogeny was estimated with Iqtree with 1000 replicates fast bootstrapping. Major lineages were highlighted by black (B + B-1 + B.1.1), in light green (B.1.177), in light blue (B.1.1.7), in brown (P.1 and P.1.1), in gray (B.1.525), in dark green (B.1.617.2 + AY), and in yellow (other) circles.

Figure 2

Bayesian phylogeographic reconstruction incorporating date of diagnosis of the 612 SARS-CoV-2 sequences obtained by population aged ≤ 12 years (A). SARS-CoV-2 genomes were highlighted in different colors against lineage. Information regarding Hospitalization, viral load and symptoms were also reported. Four independent chains were run for 50 million states. Parameters and trees were sampled every 1000 states. (B) Sampling of representative SARS-CoV-2 genomes retrieved by GISAID (n = 294), by adolescent and adult SARS-CoV-2 infected population diagnosed in the same geographical area (n = 207) (gray taxa), and by population aged ≤ 12 (N = 318) were included. Two independent chains were run for 50 million states. Parameters and trees were sampled every 1,000 states. Local clusters of SARS-CoV-2 sequences supported by an intra-genetic distance < 0.0002 and a posterior probability ≥ 0.99 were highlighted in different colors.