Abstract
We analyzed 364 children symptomatic or asymptomatic for respiratory symptoms, aged 0.1 month-17 years, selected from primary healthcare units of different municipalities of Rondônia from June 2021 to September 2022. Data were collected from medical and electronic records for epidemiological characterization. The positive cohort (n = 96) was quantified using a real-time (RT) qPCR and sequenced by next-generation sequencing. Whole-genome sequences were obtained, SARS-CoV-2 strains were classified using the Pango system, and the maximum likelihood method was used for phylogenetic analyses. Among the patients, 59.34% (216/364) were male and 40.66% (148/364) were female. Children aged 10-14 years showed the highest rate of SARS-CoV-2 positivity. At the time of collection, 54.12% (197/364) of the patients were not age-eligible for immunization against COVID-19. The unvaccinated group accounted for 34.07% (124/364), with the highest proportion in the age groups of 5-9 and 10-14 years. Most patients exhibited mild symptoms. Seventy-nine high-quality genomes were obtained: Delta variant of concern (VOC) was the most prevalent (most abundant strain: AY.99.2), Omicron VOC was reported in 26 individuals (most frequent subvariant: BA.1.1), and Gamma VOC with 22 cases (12 cases of P.1 strain). The viral load showed a median of 7.26 log10 copies/mL, with a mean symptom duration of 4 days. Most of the cases were from children who were unvaccinated and age-ineligible for immunization and were associated with Delta and Omicron VOCs with an increase in subvariants during the study period.