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Dynamic clade transitions and the influence of vaccination on the spatiotemporal circulation of SARS-CoV-2 variants.

Cecília Artico BanhoBeatriz de Carvalho MarquesLívia SacchettoAna Karoline Sepedro LimaMaisa Carla Pereira ParraAlex Ranieri Jeronimo LimaGabriela RibeiroAntonio Jorge MartinsClaudia Renata Dos Santos BarrosMaria Carolina EliasSandra Coccuzzo SampaioSvetoslav Nanev SlavovEvandra Strazza RodriguesElaine Vieira SantosDimas Tadeu CovasSimone KashimaRicardo Augusto BrassalotiBruna PetryLuan Gaspar ClementeLuiz Lehmann CoutinhoPatricia Akemi AssatoFelipe Allan da Silva da CostaRejane Maria Tommasini GrottoMirele Daiana PoletiJessika Cristina Chagas LesbonElisangela Chicaroni MattosHeidge FukumasuMarta GiovanettiLuiz Carlos Junior AlcantaraJayme A Souza-NetoPaula RahalJoão Pessoa Araújo JúniorFernando Rosado SpilkiBenjamin M AlthouseNikos VasilakisMauricio Lacerda Nogueira
Published in: NPJ vaccines (2024)
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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