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

Oliveira, Francisca Andréa da Silva; Holanda, Maísa Viana de; Lima, Luína Benevides; Dantas, Mariana Brito; Duarte, Igor Oliveira; Castro, Luzia Gabrielle Zeferino de; Oliveira, Laís Lacerda Brasil de; Paier, Carlos Roberto Koscky; Moreira-Nunes, Caroline Aquino; Lima, Nicholas Costa Barroso; Moraes, Maria Elisabete Amaral de; Filho, Manoel Odorico de Moraes; Melo, Vânia Maria Maciel; Montenegro, Raquel Carvalho

doi:10.1016/j.virusres.2022.198908

Cited by 2 publications

(1 citation statement)

References 37 publications

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“…An example is that of Lombardy, the region of Italy where the COVID-19 pandemic originally spread [80]. Another example is brought by the Brazilian states of the Amazonas and Ceará [81], [82] 2) Low-resources settings. The WHO has recently analyzed the context of a number of African countries where attempts to monitor COVID-19 and SARS-CoV-2 evolution have been undermined by understaffed infrastructures and a lack of resources [83].…”

Section: A Different Geographical Scalesmentioning

confidence: 99%

The Opportunity of Data-Driven Services for Viral Genomic Surveillance

Bernasconi

2023

2023 IEEE International Conference on Service-Oriented System Engineering (SOSE)

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The recent COVID-19 pandemic has posed novel challenges to the big data and knowledge management community. The unprecedented availability of viral genomes on public databases has made possible the data-driven exploration of viruses' evolution (especially of SARS-CoV-2, the virus responsible for the disease). Properties of data and knowledge in the genomic and virological domain may fuel data science methods for the identification and possible prediction of critical phenomena, such as the emergence of variants with improved transmissibility/virulence and recombined strains. A number of tools have been produced to explore the variants' trends or suggest hypotheses on the evolutionary mechanisms of the virus. In this perspective, we elaborate on plausible directions of this field of research, which are still applicable to the SARS-CoV-2 virus but may become even more relevant in the context of new outbreaks (e.g., monkeypox, malaria, diphtheria). Expressly, we point to 1) data-driven identification of mutations or variants with potential impact; 2) data-driven identification of recombination events -creating opportunities to overcome selective pressure and adapt to new environments and hosts (e.g., livestock or humans). These directions can be framed within genomic surveillance measures, characterized by the possibility of tracking viruses by using their genome, which is collected, sequenced, and submitted to public databases by laboratories around the world. If successful, genomic surveillance substantially supports the understanding of novel viral pathogens and of their dangerousness in terms of prevalence, infectivity, and transmissibility; the implemented services can be of great utility to decision-makers in healthcare. Here, we draw current trends, challenges, and future directions of data-driven services for genomic surveillance.

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Section: A Different Geographical Scalesmentioning

confidence: 99%

The Opportunity of Data-Driven Services for Viral Genomic Surveillance

Bernasconi

2023

2023 IEEE International Conference on Service-Oriented System Engineering (SOSE)

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SARS-CoV-2 Genomic Surveillance in Brazil: A Systematic Review with Scientometric Analysis

Menezes

Fonseca

Araújo

et al. 2022

Viruses

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Several studies have monitored the SARS-CoV-2 variants in Brazil throughout the pandemic. Here, we systematically reviewed and conducted a scientometric analysis of the SARS-CoV-2 genomic surveillance studies using Brazilian samples. A Pubmed database search on October 2022 returned 492 articles, of which 106 were included. Ninety-six different strains were reported, with variant of concern (VOC) gamma (n = 35,398), VOC delta (n = 15,780), and the variant of interest zeta (n = 1983) being the most common. The top three states with the most samples in the published articles were São Paulo, Rio de Janeiro, and Minas Gerais. Whereas the first year of the pandemic presented primary circulation of B.1.1.28 and B.1.1.33 variants, consecutive replacements were observed between them and VOI zeta, VOC gamma, VOC delta, and VOC omicron. VOI mu, VOI lambda, VOC alpha, and VOC beta were also detected but failed to reach significant circulation. Co-infection, re-infection, and vaccine breakthrough reports were found. Article co-citation differed from the co-authorship structure. Despite the limitations, we expect to give an overview of Brazil’s genomic surveillance studies and contribute to future research execution.

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

Cited by 2 publications

References 37 publications

The Opportunity of Data-Driven Services for Viral Genomic Surveillance

The Opportunity of Data-Driven Services for Viral Genomic Surveillance

SARS-CoV-2 Genomic Surveillance in Brazil: A Systematic Review with Scientometric Analysis

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