Evidence map›Paper›PMID 36057416›Full record

ArticleVirus research2022

Genomic surveillance: Circulating lineages and genomic variation of SARS-CoV-2 in early pandemic in Ceará state, Northeast Brazil.

Francisca Andréa da Silva Oliveira, Maísa Viana de Holanda, Luína Benevides Lima, Mariana Brito Dantas, Igor Oliveira Duarte, Luzia Gabrielle Zeferino de Castro, Laís Lacerda Brasil de Oliveira, Carlos Roberto Koscky Paier, Caroline de Fátima Aquino Moreira-Nunes, Nicholas Costa Barroso Lima and 4 more

Abstract read
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In one paragraph

Article in Virus research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed, 1 pooled it
–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

2 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
  2. 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.

Francisca Andréa da Silva OliveiraLaboratório de Farmacogenética, Núcleo de Pesquisa e Desenvolvimento de Medicamentos, Universidade Federal do Ceará, Rua Coronel Nunes de Melo, n° 1000, 60430-270, Fortaleza, CE, Brazil; Central de Genômica e Bioinformática, Núcleo de Pesquisa e Desenvolvimento de Medicamentos, Universidade Federal do Ceará, Rua Coronel Nunes de Melo, n° 1000, 60430-270, Fortaleza, CE, Brazil; Laboratório de Ecologia Microbiana e Biotecnologia, Departamento de Biologia, Universidade Federal do Ceará, Campus do Pici, s/n, Bloco 909, Pici, 60455-760, Fortaleza, CE, Brazil. Electronic address: andreaoliveira@ufc.br.
Maísa Viana de HolandaCentral de Genômica e Bioinformática, Núcleo de Pesquisa e Desenvolvimento de Medicamentos, Universidade Federal do Ceará, Rua Coronel Nunes de Melo, n° 1000, 60430-270, Fortaleza, CE, Brazil.
Luína Benevides LimaLaboratório de Farmacogenética, Núcleo de Pesquisa e Desenvolvimento de Medicamentos, Universidade Federal do Ceará, Rua Coronel Nunes de Melo, n° 1000, 60430-270, Fortaleza, CE, Brazil.
Mariana Brito DantasCentral de Genômica e Bioinformática, Núcleo de Pesquisa e Desenvolvimento de Medicamentos, Universidade Federal do Ceará, Rua Coronel Nunes de Melo, n° 1000, 60430-270, Fortaleza, CE, Brazil.
Igor Oliveira DuarteLaboratório de Ecologia Microbiana e Biotecnologia, Departamento de Biologia, Universidade Federal do Ceará, Campus do Pici, s/n, Bloco 909, Pici, 60455-760, Fortaleza, CE, Brazil.
Luzia Gabrielle Zeferino de CastroLaboratório de Ecologia Microbiana e Biotecnologia, Departamento de Biologia, Universidade Federal do Ceará, Campus do Pici, s/n, Bloco 909, Pici, 60455-760, Fortaleza, CE, Brazil.
Laís Lacerda Brasil de OliveiraLaboratório de Farmacogenética, Núcleo de Pesquisa e Desenvolvimento de Medicamentos, Universidade Federal do Ceará, Rua Coronel Nunes de Melo, n° 1000, 60430-270, Fortaleza, CE, Brazil.
Carlos Roberto Koscky PaierLaboratório de Farmacogenética, Núcleo de Pesquisa e Desenvolvimento de Medicamentos, Universidade Federal do Ceará, Rua Coronel Nunes de Melo, n° 1000, 60430-270, Fortaleza, CE, Brazil.
Caroline de Fátima Aquino Moreira-NunesLaboratório de Farmacogenética, Núcleo de Pesquisa e Desenvolvimento de Medicamentos, Universidade Federal do Ceará, Rua Coronel Nunes de Melo, n° 1000, 60430-270, Fortaleza, CE, Brazil.
Nicholas Costa Barroso LimaDepartamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, s/n, Bloco 907, Pici, 60440-900, Fortaleza, CE, Brazil.
Maria Elisabete Amaral de MoraesLaboratório de Farmacogenética, Núcleo de Pesquisa e Desenvolvimento de Medicamentos, Universidade Federal do Ceará, Rua Coronel Nunes de Melo, n° 1000, 60430-270, Fortaleza, CE, Brazil. Electronic address: betemora@ufc.br.
Manoel Odorico de Moraes FilhoCentral de Genômica e Bioinformática, Núcleo de Pesquisa e Desenvolvimento de Medicamentos, Universidade Federal do Ceará, Rua Coronel Nunes de Melo, n° 1000, 60430-270, Fortaleza, CE, Brazil. Electronic address: odorico@ufc.br.
Vânia Maria Maciel MeloCentral de Genômica e Bioinformática, Núcleo de Pesquisa e Desenvolvimento de Medicamentos, Universidade Federal do Ceará, Rua Coronel Nunes de Melo, n° 1000, 60430-270, Fortaleza, CE, Brazil; Laboratório de Ecologia Microbiana e Biotecnologia, Departamento de Biologia, Universidade Federal do Ceará, Campus do Pici, s/n, Bloco 909, Pici, 60455-760, Fortaleza, CE, Brazil.
Raquel Carvalho MontenegroLaboratório de Farmacogenética, Núcleo de Pesquisa e Desenvolvimento de Medicamentos, Universidade Federal do Ceará, Rua Coronel Nunes de Melo, n° 1000, 60430-270, Fortaleza, CE, Brazil; Central de Genômica e Bioinformática, Núcleo de Pesquisa e Desenvolvimento de Medicamentos, Universidade Federal do Ceará, Rua Coronel Nunes de Melo, n° 1000, 60430-270, Fortaleza, CE, Brazil.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

In the Northeast of Brazil, Ceará was the second state most impacted by COVID-19 in number of cases and death rate. Despite that, the early dynamics of the pandemic in Ceará was not yet well understood due the low genomic surveillance of SARS-CoV-2 in 2020. In this study, we analyze the circulating lineages and the genomic variation of the virus in Ceará state. Thirty-four genomes were sequenced and combined with sequences available in GISAID database from March 2020 to June 2021 to compose the study dataset. The most prevalent lineages detected were B.1.1.33, in 2020, and P.1, in 2021. Other lineages were found, such as P.2, sublineages of P.1, B.1, B.1.1, B.1.1.28 and B.1.212. Analyzing the mutations, a total of 202 single-nucleotide polymorphisms (SNPs) were identified among the 34 genomes sequenced, of which 127 were missense, 74 synonymous, and one was a nonsense mutation. Among the missense mutations, C14408T, A23403G, T27299C, G28881A G28883C, and T29148C were the most prevalent within the dataset. Although SARS-CoV-2 sequencing data was limited in 2020, our results could provide insights to better understand the genetic diversity of the circulating lineages in Ceará.

Indexed as

COVID-19SARS-CoV-2BrazilCodon, NonsenseGenome, ViralGenomicsHumansMutationPandemicsPhylogenyCodon, NonsenseCOVID-19Genome sequencesMutations

Identifiers

PMID36057416
PMCPMC9429123

What OpenQuestion holds

Textmetadata
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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.