About: Evidence for strong mutation bias towards, and selection against, T/U content in SARS-CoV2: implications for attenuated vaccine design

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About: Evidence for strong mutation bias towards, and selection against, T/U content in SARS-CoV2: implications for attenuated vaccine design Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Evidence for strong mutation bias towards, and selection against, T/U content in SARS-CoV2: implications for attenuated vaccine design
Creator	Hurst, Laurence Cano, Laura Castillo Morales, Atahualpa Ho, Alexander Kudla, Grzegorz Mordstein, Christine Mühlhausen, Stefanie Rice, Alan Watson, Samir Young, Bethan
Source	BioRxiv
abstract	Large-scale re-engineering of synonymous sites is a promising strategy to generate attenuated viruses for vaccines. Attenuation typically relies on de-optimisation of codon pairs and maximization of CpG dinculeotide frequencies. So as to formulate evolutionarily-informed attenuation strategies, that aim to force nucleotide usage against the estimated direction favoured by selection, here we examine available whole-genome sequences of SARS-CoV2 to infer patterns of mutation and selection on synonymous sites. Analysis of mutational profiles indicates a strong mutation bias towards T with concomitant selection against T. Accounting for dinucleotide effects reinforces this conclusion, observed TT content being a quarter of that expected under neutrality. A significantly different mutational profile at CDS sites that are not 4-fold degenerate is consistent with contemporaneous selection against T mutations more widely. Although selection against CpG dinucleotides is expected to drive synonymous site G+C content below mutational equilibrium, observed G+C content is slightly above equilibrium, possibly because of selection for higher expression. Consistent with gene-specific selection against CpG dinucleotides, we observe systematic differences of CpG content between SARS-CoV2 genes. We propose an evolutionarily informed gene-bespoke approach to attenuation that, unusually, seeks to increase usage of the already most common synonymous codons. Comparable analysis of H1N1 and Ebola finds that GC3 deviated from neutral equilibrium is not a universal feature, cautioning against generalization of results.
has issue date	2020-05-11(xsd:dateTime)
bibo:doi	10.1101/2020.05.11.088112
has license	biorxiv
sha1sum (hex)	6e310214ee503c0c1bc1bc8b52276fba662a1a0e
schema:url	https://doi.org/10.1101/2020.05.11.088112
resource representing a document's title	Evidence for strong mutation bias towards, and selection against, T/U content in SARS-CoV2: implications for attenuated vaccine design
schema:publication	bioRxiv
resource representing a document's body	covid:6e310214ee503c0c1bc1bc8b52276fba662a1a0e#body_text
is schema:about of	named entity 'FREQUENCIES' named entity 'codon' named entity 'SARS-CoV2' named entity 'CpG' named entity 'viruses' named entity 'CpG' named entity 'synonymous mutations' named entity 'gene expression' named entity 'mutation' named entity 'non-parametric' named entity 'mutation' named entity 'viruses' named entity 'CpG' named entity 'deleterious mutations' named entity 'taxonomic' named entity 'CpG' named entity 'SARS-CoV-2' named entity 'correlation' named entity 'viruses' named entity 'virus' named entity 'viruses' named entity 'GC content' named entity 'gene' named entity 'positive correlation' named entity '2019' named entity 'protein' named entity 'viruses' named entity 'Euclidean distance' named entity 'G+C content' named entity 'random sampling' named entity 'gene' named entity 'mutation' named entity 'GISAID' named entity 'cytoplasmic' named entity 'Monte Carlo sampling' named entity 'low GC' named entity 'nucleotide' named entity 'CpG' named entity 'subgenomic RNAs' named entity 'viruses' named entity 'CpG' named entity 'CpG' named entity 'common ancestry' named entity 'codon' named entity 'sequencing errors' named entity 'mutation' named entity 'amino acid' named entity 'GC3' named entity 'nucleotides' named entity 'Experimental manipulation' named entity 'G+C' named entity 'CpG' named entity 'stop codon' named entity 'host adaptation' named entity 'SARS-CoV2' named entity 'correlation' named entity 'CpG' named entity 'genome' named entity 'gene' named entity 'gene' named entity 'CpG' named entity 'mononucleotides' named entity 'codon' named entity 'mutation' named entity 'recombination' named entity 'phylogeny' named entity 'codon' named entity 'gene conversion' named entity 'CpG' named entity 'viruses' named entity 'GC3' named entity 'correlation' named entity 'amino acid' named entity 'GC3' named entity 'homoplasies'

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