rSWeeP: A R/Bioconductor package deal with SWeeP sequences representation

Fernandes, Danrley R.; Kulik, Mariane Gonçalves; Machado, Diogo; Marchaukoski, Jeroniza Nunes; Fo, Pedrosa; Pierri, Camilla Reginatto De; Raittz, Roberto Tadeu

doi:10.1101/2020.09.09.290247

Cited by 2 publications

(2 citation statements)

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“…Protein sequences were concatenated (with border delimiters) into proteomes which were represented in vectors using the SWeeP tool (Spaced Words Projection) (De Pierri et al, 2020 ). The R version of the SWeeP tool, used for the proteome vectorization, is available in the Bioconductor Platform 4 for R version 3.12 (Fernandes et al, 2020 ). Finally, we made the vector projection of the Brazilian genomes (coded in DNA) in the SWeeP tool in Matlab® (De Pierri et al, 2020 ) with its default parameters.…”

Section: Methodsmentioning

confidence: 99%

Genomic landscape of the SARS-CoV-2 pandemic in Brazil suggests an external P.1 variant origin

Perico

Pierri²,

Neto³

et al. 2022

Front. Microbiol.

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Brazil was the epicenter of worldwide pandemics at the peak of its second wave. The genomic/proteomic perspective of the COVID-19 pandemic in Brazil could provide insights to understand the global pandemics behavior. In this study, we track SARS-CoV-2 molecular information in Brazil using real-time bioinformatics and data science strategies to provide a comparative and evolutive panorama of the lineages in the country. SWeeP vectors represented the Brazilian and worldwide genomic/proteomic data from Global Initiative on Sharing Avian Influenza Data (GISAID) between February 2020 and August 2021. Clusters were analyzed and compared with PANGO lineages. Hierarchical clustering provided phylogenetic and evolutionary analyses of the lineages, and we tracked the P.1 (Gamma) variant origin. The genomic diversity based on Chao's estimation allowed us to compare richness and coverage among Brazilian states and other representative countries. We found that epidemics in Brazil occurred in two moments with different genetic profiles. The P.1 lineages emerged in the second wave, which was more aggressive. We could not trace the origin of P.1 from the variants present in Brazil. Instead, we found evidence pointing to its external source and a possible recombinant event that may relate P.1 to a B.1.1.28 variant subset. We discussed the potential application of the pipeline for emerging variants detection and the PANGO terminology stability over time. The diversity analysis showed that the low coverage and unbalanced sequencing among states in Brazil could have allowed the silent entry and dissemination of P.1 and other dangerous variants. This study may help to understand the development and consequences of variants of concern (VOC) entry.

show abstract

Section: Methodsmentioning

confidence: 99%

Genomic landscape of the SARS-CoV-2 pandemic in Brazil suggests an external P.1 variant origin

Perico

Pierri²,

Neto³

et al. 2022

Front. Microbiol.

Self Cite

View full text Add to dashboard Cite

show abstract

“…Protein sequences were concatenated (with border delimiters) into proteomes which were represented in vectors using the SWeeP tool (Spaced Words Projection) (14). The R version of SWeeP tool, used for the proteome vectorization, is available in the Bioconductor Platform 4 for R version 3.12 (25). Finally, we made the vector projection of the Brazilian genomes (coded in DNA) in the SWeeP tool in Matlab (14) with its default parameters.…”

Section: Sequences Vectorial Representationmentioning

confidence: 99%

Genomic landscape of SARS-CoV-2 pandemic in Brazil suggests an external P.1 variant origin

Perico

Pierri

Neto

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

Brazil was the epicenter of worldwide pandemics at the peak of its second wave. The genomic/proteomic perspective of the COVID-19 pandemic in Brazil can bring new light to understand the global pandemics behavior. In this study, we track SARS-CoV-2 molecular information in Brazil using real-time bioinformatics and data science strategies to provide a comparative and evolutive panorama of the lineages in the country. SWeeP vectors represented the Brazilian and worldwide genomic/proteomic data from GISAID between 02/2020 – 08/2021. Clusters were analyzed and compared with PANGO lineages. Hierarchical clustering provided phylogenetic and evolutionary analysis of the lineages, and we tracked the P.1 (Gamma) variant origin. The genomic diversity based on Chao’s estimation allowed us to compare richness and coverage among Brazilian states and other representative countries. We found that epidemics in Brazil occurred in two distinct moments, with different genetic profiles. The P.1 lineages emerged in the second wave, which was more aggressive. We could not trace the origin of P.1 from the variants present in Brazil in 2020. Instead, we found evidence pointing to its external source and a possible recombinant event that may relate P.1 to the B.1.1.28 variant subset. We discussed the potential application of the pipeline for emerging variants detection and the stability of the PANGO terminology over time. The diversity analysis showed that the low coverage and unbalanced sequencing among states in Brazil could have allowed the silenty entry and dissemination of P.1 and other dangerous variants. This comparative and evolutionary analysis may help to understand the development and the consequences of the entry of variants of concern (VOC).

show abstract

rSWeeP: A R/Bioconductor package deal with SWeeP sequences representation

Cited by 2 publications

References 9 publications

Genomic landscape of the SARS-CoV-2 pandemic in Brazil suggests an external P.1 variant origin

Genomic landscape of the SARS-CoV-2 pandemic in Brazil suggests an external P.1 variant origin

Genomic landscape of SARS-CoV-2 pandemic in Brazil suggests an external P.1 variant origin

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