Dynamic clade transitions and the influence of vaccine rollout on the spatiotemporal circulation of SARS-CoV-2 variants in São Paulo, Brazil

TL;DR

This study examines how SARS-CoV-2 variants spread in São Paulo, Brazil, and how vaccination impacted their circulation and the pandemic's progression.

Contribution

The study shows that local genomic surveillance can reflect national trends in SARS-CoV-2 variant spread and vaccine effectiveness.

Findings

Three SARS-CoV-2 variant replacements occurred from 2021 to early 2022: Gamma, Delta, and Omicron.

Vaccination was six and eleven times more effective in preventing cases during Delta and Omicron waves compared to Gamma.

Genomic monitoring at a local level accurately reflected national trends in variant spread and evolution.

Abstract

Since 2021, the emergence of variants of concern (VOC) has led Brazil to experience record numbers of in COVID-19 cases and deaths. The expanded spread of the SARS-CoV-2 combined with a low vaccination rate has contributed to the emergence of new mutations that may enhance viral fitness, leading to the persistence of the disease. Due to limitations in the real-time genomic monitoring of new variants in some Brazilian states, we aimed to investigate whether genomic surveillance, coupled with epidemiological data and SARS-CoV-2 variants spatiotemporal spread in a smaller region, can reflect the pandemic progression at a national level. Our findings revealed three SARS-CoV-2 variant replacements from 2021 to early 2022, corresponding to the introduction and increase in the frequency of Gamma, Delta, and Omicron variants, as indicated by peaks of the Effective Reproductive Number (Reff). These distinct clade replacements triggered two waves of COVID-19 cases, influenced by the increasing vaccine uptake over time. Our results indicated that the effectiveness of vaccination in preventing new cases during the Delta and Omicron circulations was six and eleven times higher, respectively, than during the period when Gamma was predominant, and it was highly efficient in reducing the number of deaths. Furthermore, we demonstrated that genomic monitoring at a local level can reflect the national trends in the spread and evolution of SARS-CoV-2.

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