RT Journal Article
SR Electronic
T1 Short sequence motif dynamics in the SARS-CoV-2 genome suggest a role for cytosine deamination in CpG reduction
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.06.19.161687
DO 10.1101/2020.06.19.161687
A1 Sadykov, Mukhtar
A1 Mourier, Tobias
A1 Guan, Qingtian
A1 Pain, Arnab
YR 2021
UL http://biorxiv.org/content/early/2021/01/05/2020.06.19.161687.abstract
AB RNA viruses use CpG reduction to evade the host cell defense, but the driving mechanisms are still largely unknown. In an attempt to address this we used a rapidly growing genomic dataset of SARS-CoV-2 with relevant metadata information. Remarkably, by simply ordering SARS-CoV-2 genomes by their date of collection, we find a progressive increase of C-to-U substitutions resulting in 5'-UCG-3' motif reduction that in turn have reduced the CpG frequency over just a few months of observation. This is consistent with APOBEC-mediated RNA editing resulting in CpG reduction, thus allowing the virus to escape ZAP-mediated RNA degradation. Our results thus link the dynamics of target sequences in the viral genome for two known host molecular defense mechanisms, mediated by the APOBEC and ZAP proteins.Competing Interest StatementThe authors have declared no competing interest.C>Ustands for cytosine to uracil substitution, the same applies to other nucleotide substitutionsAPOBECApolipoprotein B Editing ComplexZAPzinc-finger antiviral protein