Social Medicine Department, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
Infectious Diseases Division, Internal Medicine Department, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
Epidemiol Infect. 2023 Jul 20;151:e126. doi: 10.1017/S095026882300119X.
This work aimed to study the role of different SARS-CoV-2 lineages in the epidemiology of multiple waves of the COVID-19 pandemic in Ribeirão Preto (São Paulo state), with comparison within Brazil and globally. Viral genomic sequencing was combined with clinical and sociodemographic information of 2,379 subjects at a large Brazilian hospital. On the whole 2,395 complete SARS-CoV-2 genomes were obtained from April 2020 to January 2022. We report variants of concern (VOC) and interest (VOI) dynamics and the role of Brazilian lineages. We identified three World Health Organization VOCs (Gamma, Delta, Omicron) and one VOI (Zeta), which caused distinct waves in this cohort. We also identified 47 distinct Pango lineages. Consistent with the high prevalence of Gamma in Brazil, Pango lineage P.1 dominated infections in this cohort for half of 2021. Each wave of infection largely consisted of a single variant group, with each new group quickly and completely rising to dominance. Despite increasing vaccination in Brazil starting in 2021, this pattern was observed throughout the study and is consistent with the hypothesis that herd immunity tends to be SARS-CoV-2 variant-specific and does not broadly protect against COVID-19.
这项工作旨在研究不同的 SARS-CoV-2 谱系在里贝朗普雷图（圣保罗州）COVID-19 大流行多波次中的作用，并与巴西国内和全球范围内进行比较。对大型巴西医院的 2379 名患者的临床和社会人口学信息与病毒基因组测序相结合。总共从 2020 年 4 月到 2022 年 1 月获得了 2395 个完整的 SARS-CoV-2 基因组。我们报告了关注变异株（VOC）和感兴趣变异株（VOI）的动态以及巴西谱系的作用。我们鉴定了三个世界卫生组织 VOC（Gamma、Delta、Omicron）和一个 VOI（Zeta），它们在该队列中引起了不同的波次。我们还鉴定了 47 个不同的 Pango 谱系。与巴西 Gamma 高流行率一致，Pango 谱系 P.1 在 2021 年上半年主导了该队列的感染。每次感染波次主要由单一变异群组成，每个新的变异群迅速且完全占据主导地位。尽管巴西从 2021 年开始增加疫苗接种，但在整个研究过程中都观察到这种模式，这与假设一致，即群体免疫倾向于 SARS-CoV-2 变异株特异性，而不能广泛预防 COVID-19。
