Evidence map›Paper›PMID 38343798›Full record

ArticleResearch square2024

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

Cecília Artico Banho, Beatriz de Carvalho Marques, Lívia Sacchetto, Ana Karoline Sepedro Lima, Maisa Carla Pereira Parra, Alex Ranieri Jeronimo Lima, Gabriela Ribeiro, Antonio Jorge Martins, Claudia Renata Dos Santos Barros, Maria Carolina Elias and 25 more

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in Research square, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed, 0 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

35 authors at 12 institutions in 3 countries.

Cecília Artico BanhoLaboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil.
Beatriz de Carvalho MarquesLaboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil.
Lívia SacchettoLaboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil.
Ana Karoline Sepedro LimaLaboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil.
Maisa Carla Pereira ParraLaboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil.
Alex Ranieri Jeronimo LimaCenter for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil.
Gabriela RibeiroCenter for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil.
Antonio Jorge MartinsCenter for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil.
Claudia Renata Dos Santos BarrosCenter for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil.
Maria Carolina EliasCenter for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil.
Sandra Coccuzzo SampaioCenter for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil.
Svetoslav Nanev SlavovCenter for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil.
Evandra Strazza RodriguesUniversity of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil.
Elaine Vieira SantosUniversity of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil.
Dimas Tadeu CovasCenter for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil.
Simone KashimaUniversity of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil.
Ricardo Augusto BrassalotiUniversity of São Paulo, Centro de Genômica Funcional da ESALQ, Piracicaba, SP, Brazil.
Bruna PetryUniversity of São Paulo, Centro de Genômica Funcional da ESALQ, Piracicaba, SP, Brazil.
Luan Gaspar ClementeUniversity of São Paulo, Centro de Genômica Funcional da ESALQ, Piracicaba, SP, Brazil.
Luiz Lehmann CoutinhoUniversity of São Paulo, Centro de Genômica Funcional da ESALQ, Piracicaba, SP, Brazil.
Patricia Akemi AssatoSão Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil.
Felipe Allan da Silva da CostaSão Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil.
Jayme A Souza-NetoSão Paulo State University (UNESP), School of Agricultural Sciences, Botucatu, Brazil.
Rejane Maria Tommasini GrottoSão Paulo State University (UNESP), School of Agricultural Sciences, Botucatu, Brazil.
Mirele Daiana PoletiDepartment of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil.
Jessika Cristina Chagas LesbonDepartment of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil.
Elisangela Chicaroni MattosDepartment of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil.
Heidge FukumasuDepartment of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil.
Marta GiovanettiOswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro, Brazil.
Luiz Carlos Junior AlcantaraOswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro, Brazil.
Paula RahalLaboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista (Unesp), São José do Rio Preto, Brazil.
João Fernando Pessoa AraújoInstituto de Biotecnologia, Universidade Estadual Paulista (Unesp), Botucatu, Brazil.
Benjamin M AlthouseDepartment of Biology, New Mexico State University, Las Cruces, NM.
Nikos VasilakisDepartment of Pathology, University of Texas Medical Branch; Galveston, Texas, United States of America.
Maurício Lacerda NogueiraLaboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil.ORCID https://orcid.org/0000-0003-1102-2419
Universidade de São Paulo · BRFaculdade de Medicina de São José do Rio Preto · BRInstituto Butantan · BRUniversidade Estadual Paulista (Unesp) · BRClinics Hospital of Ribeirão Preto · BRBiotech (Brazil) · BRFundação Oswaldo Cruz · BRNew Mexico State University · USTexas Medical Board · USThe University of Texas Medical Branch at Galveston · USUniversidade Feevale · BRUniversità Campus Bio-Medico · IT

Funding

University of Washington Arboviral Research Network (UWARN)U01AI151698 · NIAID · UNIVERSITY OF WASHINGTON · PI Michael Gale, PETER MACGARR RABINOWITZ · 2020 to 2026
$13.3M
Coordinating Research on Emerging Arboviral Threats Encompassing the Neotropics II (CREATE-NEO II)U01AI151807 · NIAID · UNIVERSITY OF TEXAS MED BR GALVESTON · PI Kathryn Alyce Hanley, MAURICIO Lacerda NOGUEIRA · 2020 to 2026
$9.8M
NIAID NIH HHS U01 AI151698NIAID NIH HHS U01 AI151807
6 · The paper itself

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.

Indexed as

COVID-19EpidemiologyGenomic surveillanceVaccine effectivenessVariant of Concern

Identifiers

PMID38343798
PMCPMC10854302
OpenAlexW4391078349

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.