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

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.

SUBMITTER: Banho CA

PROVIDER: S-EPMC11316783 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature

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

Banho Cecília Artico CA de Carvalho Marques Beatriz B Sacchetto Lívia L Lima Ana Karoline Sepedro AKS Parra Maisa Carla Pereira MCP Lima Alex Ranieri Jeronimo ARJ Ribeiro Gabriela G Martins Antonio Jorge AJ Barros Claudia Renata Dos Santos CRDS Elias Maria Carolina MC Sampaio Sandra Coccuzzo SC Slavov Svetoslav Nanev SN Rodrigues Evandra Strazza ES Santos Elaine Vieira EV Covas Dimas Tadeu DT Kashima Simone S Brassaloti Ricardo Augusto RA Petry Bruna B Clemente Luan Gaspar LG Coutinho Luiz Lehmann LL Assato Patricia Akemi PA da Silva da Costa Felipe Allan FA Grotto Rejane Maria Tommasini RMT Poleti Mirele Daiana MD Lesbon Jessika Cristina Chagas JCC Mattos Elisangela Chicaroni EC Fukumasu Heidge H Giovanetti Marta M Alcantara Luiz Carlos Junior LCJ Souza-Neto Jayme A JA Rahal Paula P Araújo João Pessoa JP Spilki Fernando Rosado FR Althouse Benjamin M BM Vasilakis Nikos N Nogueira Maurício Lacerda ML

NPJ vaccines 20240810 1

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 epid ...[more]

PMID: 39127725

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Project description:IntroductionThe coronavirus disease 2019 (COVID-19) pandemic has caused significant public health and socioeconomic crises across Africa; however, the prevalent patterns of COVID-19 and the circulating characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in the continent remain insufficiently documented.MethodsIn this study, national data on case numbers, infection incidences, mortality rates, the circulation of SARS-CoV-2 variants, and key health indexes were collected from various official and professional sources between January 2020 and December 2023 were analyzed with SaTScan and geographically weighted regression (GWR).ResultsThe prevalent profiles and circulating features of SARS-CoV-2 across the African continent, including its five regions and all African countries, were analyzed. Four major waves of the epidemic were observed. The first wave was closely associated with the introduction of the early SARS-CoV-2 strain while the subsequent waves were linked to the emergence of specific variants, including variants of concern (VOCs) Alpha, Beta, variants of interest (VOIs) Eta (second wave), VOC Delta (third wave), and VOC Omicron (fourth wave). SaTScan analysis identified four large spatiotemporal clusters that affected various countries. A significant number of countries (50 out of 56) reported their first cases during February 2020 and March 2020, predominantly involving individuals with confirmed cross-continental travel histories, mainly from Europe. In total, 12 distinct SARS-CoV-2 VOCs and VOIs were identified, with the most prevalent being VOCs Omicron, Delta, Beta, Alpha, and VOI Eta. Unlike the dominance of VOC Delta during the third wave and Omicron during the fourth wave, VOC Alpha was relatively rare in the Southern regions but more common in the other four regions. At the same time, Beta predominated in the Southern region and Eta in the Western region during the second wave. Additionally, relatively higher COVID-19 case incidences and mortalities were reported in the Southern and Northern African regions. Spearman rank correlation and geographically weighted regression (GWR) analyses of COVID-19 incidences against health indexes in 52 African countries indicate that countries with higher national health expenditures and better personnel indexes tended to report higher case incidences.DiscussionThis study offers a detailed overview of the COVID-19 pandemic in Africa. Strengthening the capacity of health institutions across African countries is essential for the timely detection of new SARS-CoV-2 variants and, consequently, for preparedness against future COVID-19 pandemics and other potentially infectious disease outbreaks.

Dataset Information

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

Publications

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

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