Evidence for Strong Mutation Bias toward, and Selection against, U Content in SARS-CoV-2: Implications for Vaccine Design.

Alan M Rice,Christine Mordstein,Grzegorz Kudla,Laura Cano,Samir Watson,Alexander T Ho,Atahualpa Castillo Morales,Bethan Young,Stefanie Mühlhausen,Laurence D Hurst

doi:10.1093/molbev/msaa188

Alan M Rice, Christine Mordstein + Show 8 more

Open Access

https://doi.org/10.1093/molbev/msaa188

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Abstract

Large-scale re-engineering of synonymous sites is a promising strategy to generate vaccines either through synthesis of attenuated viruses or via codon-optimized genes in DNA vaccines. Attenuation typically relies on deoptimization of codon pairs and maximization of CpG dinucleotide frequencies. So as to formulate evolutionarily informed attenuation strategies that aim to force nucleotide usage against the direction favored by selection, here, we examine available whole-genome sequences of SARS-CoV-2 to infer patterns of mutation and selection on synonymous sites. Analysis of mutational profiles indicates a strong mutation bias toward U. In turn, analysis of observed synonymous site composition implicates selection against U. Accounting for dinucleotide effects reinforces this conclusion, observed UU content being a quarter of that expected under neutrality. Possible mechanisms of selection against U mutations include selection for higher expression, for high mRNA stability or lower immunogenicity of viral genes. Consistent with gene-specific selection against CpG dinucleotides, we observe systematic differences of CpG content between SARS-CoV-2 genes. We propose an evolutionarily informed 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.

Highlights

Large-scale re-engineering of synonymous sites is a promising strategy to generate vaccines either through synthesis of attenuated viruses or via codon optimized genes in DNA vaccines
As to formulate evolutionarily-informed attenuation strategies that aim to force nucleotide usage against the direction favoured by selection, here we examine available whole-genome sequences of SARS-CoV-2 to infer patterns of mutation and selection on synonymous sites
Viral attenuation can be achieved by alteration of synonymous sites as a means to modify the pattern of dinucleotides that bridge between successive codons while retaining the original protein (Karlin, et al 1994; Rima and McFerran 1997; Coleman, et al 2008)

Summary

Introduction

Large-scale re-engineering of synonymous sites is a promising strategy to generate vaccines either through synthesis of attenuated viruses or via codon optimized genes in DNA vaccines. ZAP is under positive selection owing to hostparasite coevolution (Kerns, et al 2008) This activity of ZAP suggests a simple attenuation strategy for SARS-CoV-2, i.e. to increase CpG content (Kames, et al 2020), this being consistent with the observed low CpG enrichment of the virus as sequenced in the wild (Xia 2020), seen in cytoplasmic viruses more generally (Simmonds, et al 2013). UpA depletion in SARS-CoV-2 is weaker than CpG depletion (see below)

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