Daniel Henrique Tsuha

Genomic surveillance has emerged as a crucial tool in monitoring and understanding the dynamics of viral variants during the COVID-19 pandemic. In the Midwest region of Brazil, Mato Grosso do Sul has faced a significant burden from the SARS-CoV-2 epidemic, with a total of 613,000 confirmed cases as of June 2023. In collaboration with the Central Public Health Laboratory in the capital city of Campo Grande, we conducted a portable whole-genome sequencing and phylodynamic analysis to investigate the circulation of the Omicron variant in the region. The study aimed to uncover the genomic landscape and provide valuable insights into the prevalence and transmission patterns of this highly transmissible variant. Our findings revealed an increase in the number of cases within the region during 2022, followed by a gradual decline as a result of the successful impact of the vaccination program together with the capacity of this unpredictable and very transmissible variant to quickly affect the proportion of susceptible population. Genomic data indicated multiple introduction events, suggesting that human mobility played a differential role in the variant’s dispersion dynamics throughout the state. These findings emphasize the significance of implementing public health interventions to mitigate further spread and highlight the powerful role of genomic monitoring in promptly tracking and uncovering the circulation of viral strains. Together those results underscore the importance of proactive surveillance, rapid genomic sequencing, and data sharing to facilitate timely public health responses.

São Paulo is a state in Brazil with one of the highest numbers of confirmed and severe cases of coronavirus disease (COVID-19), with an incidence of 294 hospitalizations per 100,000 inhabitants. We report the clinical characteristics and outcomes of 120,804 hospitalized patients with confirmed COVID-19 from February 26 to October 10, 2020, in São Paulo. Characteristics of patients who died and survived were compared using a survival analysis. The median age was 60 years (interquartile range [IQR], 47–72), 67,821 (56.1%) were men, and 61,659 (51.0%) were white. Most hospitalized patients (79,812; 66.1%) reported one or more comorbidities, 41,708 (34.5%) hospitalized patients were admitted to intensive care units, and 33,079 (27.4%) died. Men (hazard ratio [HR], 1.22; 95% confidence interval [CI], 1.18–1.25), elderly individuals (HR, 3.85; 95% CI, 3.68–4.02), and patients with chronic cardiovascular disease including hypertension (HR, 1.05; 95% CI, 1.02–1.08), chronic lung disease (HR, 1.38; 95% CI, 1.31–1.45), diabetes mellitus (HR, 1.14; 95% CI, 1.11–1.18), and chronic neurological disease (HR, 1.48; 95% CI, 1.41–1.55) were at higher risk for death from COVID-19.