Evidence map›Paper›PMID 37469288›Full record

ArticleEpidemiology and infection2023

Genomic epidemiology of SARS-CoV-2 in large university hospital cohort: the UnCoVER-Brazil project.

Felipe Santos de Carvalho, Sarah Danielle Slack, Francisco Barbosa-Júnior, Mateus Rennó de Campos, Guilherme Silveira Castro, Sabrina Baroni, Livia Mara Torres Bueno, Fernanda Borchers Coeli, Aparecida Yulie Yamamoto, Jorgete Maria Silva and 4 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Epidemiology and infection, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

14 authors.

Felipe Santos de CarvalhoSocial Medicine Department, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.ORCID 0000-0002-6062-7468
Sarah Danielle SlackInfectious Diseases Division, Internal Medicine Department, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.ORCID 0000-0002-0559-3138
Francisco Barbosa-JúniorSocial Medicine Department, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
Mateus Rennó de CamposSocial Medicine Department, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
Guilherme Silveira CastroSocial Medicine Department, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
Sabrina BaroniOncology and Imaging Department, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
Livia Mara Torres BuenoOncology and Imaging Department, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
Fernanda Borchers CoeliOncology and Imaging Department, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
Aparecida Yulie YamamotoVirology Laboratory, University Hospital of Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
Jorgete Maria SilvaSocial Medicine Department, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
Rodrigo do Tocantins CaladoOncology and Imaging Department, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
Benedito Antônio Lopes FonsecaInfectious Diseases Division, Internal Medicine Department, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
Leandro Machado ColliOncology and Imaging Department, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
Fernando Bellissimo-RodriguesSocial Medicine Department, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.ORCID 0000-0002-3736-7127

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

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.

Indexed as

COVID-19SARS-CoV-2BrazilGenomicsHospitals, UniversityHumansPandemicsCOVID-19epidemiologygenomeSARS-CoV-2variants

Identifiers

PMID37469288
PMCPMC10620948

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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.