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Direct RNA Sequencing Reveals SARS-CoV-2 m6A Sites and Possible Differential DRACH Motif Methylation among Variants

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Center for Medical Bioinformatics, Escola Paulista de Medicina, Federal University of São Paulo (UNIFESP), São Paulo 04039032, Brazil
2
Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil
*
Author to whom correspondence should be addressed.
Academic Editor: Kenneth Lundstrom
Viruses 2021, 13(11), 2108; https://doi.org/10.3390/v13112108
Received: 3 September 2021 / Revised: 4 October 2021 / Accepted: 13 October 2021 / Published: 20 October 2021
(This article belongs to the Section SARS-CoV-2 and COVID-19)
The causative agent of COVID-19 pandemic, SARS-CoV-2, has a 29,903 bases positive-sense single-stranded RNA genome. RNAs exhibit about 150 modified bases that are essential for proper function. Among internal modified bases, the N6-methyladenosine, or m6A, is the most frequent, and is implicated in SARS-CoV-2 immune response evasion. Although the SARS-CoV-2 genome is RNA, almost all genomes sequenced thus far are, in fact, reverse transcribed complementary DNAs. This process reduces the true complexity of these viral genomes because the incorporation of dNTPs hides RNA base modifications. Here, we present an initial exploration of Nanopore direct RNA sequencing to assess the m6A residues in the SARS-CoV-2 sequences of ORF3a, E, M, ORF6, ORF7a, ORF7b, ORF8, N, ORF10 and the 3′-untranslated region. We identified fifteen m6A methylated positions, of which, six are in ORF N. Additionally, because m6A is associated with the DRACH motif, we compared its distribution in major SARS-CoV-2 variants. Although DRACH is highly conserved among variants, we show that variants Beta and Eta have a fourth position C > U change in DRACH at 28,884b that could affect methylation. This is the first report of direct RNA sequencing of a Brazilian SARS-CoV-2 sample coupled with the identification of modified bases. View Full-Text
Keywords: SARS-CoV-2; COVID-19; m6A; direct RNA sequencing; RNA methylation; Epitranscriptomics SARS-CoV-2; COVID-19; m6A; direct RNA sequencing; RNA methylation; Epitranscriptomics
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MDPI and ACS Style

Campos, J.H.C.; Maricato, J.T.; Braconi, C.T.; Antoneli, F.; Janini, L.M.R.; Briones, M.R.S. Direct RNA Sequencing Reveals SARS-CoV-2 m6A Sites and Possible Differential DRACH Motif Methylation among Variants. Viruses 2021, 13, 2108. https://doi.org/10.3390/v13112108

AMA Style

Campos JHC, Maricato JT, Braconi CT, Antoneli F, Janini LMR, Briones MRS. Direct RNA Sequencing Reveals SARS-CoV-2 m6A Sites and Possible Differential DRACH Motif Methylation among Variants. Viruses. 2021; 13(11):2108. https://doi.org/10.3390/v13112108

Chicago/Turabian Style

Campos, João H.C., Juliana T. Maricato, Carla T. Braconi, Fernando Antoneli, Luiz M.R. Janini, and Marcelo R.S. Briones. 2021. "Direct RNA Sequencing Reveals SARS-CoV-2 m6A Sites and Possible Differential DRACH Motif Methylation among Variants" Viruses 13, no. 11: 2108. https://doi.org/10.3390/v13112108

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