SARS-CoV-2 Disease Severity and Cycle Threshold Values in Children Infected during Pre-Delta, Delta, and Omicron Periods, Colorado, USA, 2021-2022

Abstract

In adults, viral load and disease severity can differ by SARS-CoV-2 variant, patterns less understood in children. We evaluated symptomatology, cycle threshold (Ct) values, and SARS-CoV-2 variants among 2,299 pediatric SARS-CoV-2 patients (0-21 years of age) in Colorado, USA, to determine whether children infected with Delta or Omicron had different symptom severity or Ct values than during earlier variants. Children infected during the Delta and Omicron periods had lower Ct values than those infected during pre-Delta, and children <1 year of age had lower Ct values than older children. Hospitalized symptomatic children had lower Ct values than asymptomatic patients. Compared with pre-Delta, more children infected during Delta and Omicron were symptomatic (75.4% pre-Delta, 95.3% Delta, 99.5% Omicron), admitted to intensive care (18.8% pre-Delta, 39.5% Delta, 22.9% Omicron), or received oxygen support (42.0% pre-Delta, 66.3% Delta, 62.3% Omicron). Our data reinforce the need to include children, especially younger children, in pathogen surveillance efforts.

Keywords: COVID-19; COVID-19 pandemic; COVID-19 testing; Colorado; Ct values; Delta; Omicron; SARS-CoV-2; United States; children; coronavirus disease; respiratory infections; severe acute respiratory syndrome coronavirus 2; viruses; whole-genome sequencing; zoonoses.

Figure 1

Variant counts of sequencing-confirmed lineages by week of sample collection in study of SARS-CoV-2 disease severity in children during pre-Delta, Delta, and Omicron periods, Colorado, USA, January 2021–January 2022. Gray boxes indicate time periods of potentially mixed lineage that were excluded from time period analyses.

Figure 2

Ct value patterns across all variants in study of SARS-CoV-2 disease severity in children during pre-Delta, Delta, and Omicron periods, Colorado, USA, January 2021–January 2022. Boxplots indicate overall Ct value patterns across categories of patient characteristics, regardless of variant period. A) Age group; B) vaccination status (unvaccinated vs. vaccinated with any number of doses); C) vaccination status (unvaccinated versus vaccinated by number of doses); D) patient type (outpatient/not hospitalized, hospitalized because of COVID-19, hospitalized but not because of COVID-19); E) symptomatic versus asymptomatic; F) number of days between symptom onset and positive test (symptom onset groups); G) hospitalized but not admitted to PICU versus admitted to PICU; H) any type of supplemental oxygen support versus no oxygen support received; I) highest level of supplemental oxygen support received (none, noninvasive oxygen support, invasive oxygen support). Significance was determined using 1-way analysis of variance with Tukey test. Brackets indicate which comparisons correspond to the significance codes, and connected brackets indicate comparisons that have the same significance code. Ct, cycle threshold; PICU, pediatric intensive care unit.

Figure 3

Ct value patterns of patient characteristics across variant periods in study of SARS-CoV-2 disease severity in children during pre-Delta, Delta, and Omicron periods, Colorado, USA, January 2021–January 2022. Boxplots indicate overall Ct value patterns among patient characteristics across variant periods. A) Variant period; B) age group; C) vaccination status (unvaccinated vs. vaccinated with any number of doses); D) vaccination status (unvaccinated vs. vaccinated by number of doses). Red = pre-Delta, Blue = Delta, Orange = Omicron. Significance was determined using 1-way analysis of variance (A) or 2-way (B–D) with Tukey test. Brackets indicate which comparisons correspond to the significance codes, and connected brackets indicate comparisons that have the same significance code. Ct, cycle threshold.

Figure 4

Ct value patterns among markers of disease severity across variant periods in study of SARS-CoV-2 disease severity in children during pre-Delta, Delta, and Omicron periods, Colorado, USA, January 2021–January 2022. Boxplots indicate overall Ct value patterns across disease severity markers by variant period. A) Patient type (outpatient/not hospitalized, hospitalized because of COVID-19); B) symptomatic versus asymptomatic; C) number of days between symptom onset and positive test (symptom onset groups); D) hospitalized but not admitted to PICU versus admitted to PICU; E) any type of supplemental oxygen support versus no oxygen support received; F) highest level of supplemental oxygen support received (none, noninvasive oxygen support, invasive oxygen support). Red = pre-Delta, Blue = Delta, Orange = Omicron. Significance was determined using 2-way analysis of variance with Tukey test. Brackets indicate which comparisons correspond to the significance codes, and connected brackets indicate comparisons that have the same significance code. Ct, cycle threshold; PICU, pediatric intensive care unit.