Virus Attenuation by Genome-Scale Changes in Codon Pair Bias

TLDR

The genetic code’s redundancy allows many synonymous codon pairs, and species‑specific codon pair bias means some pairs are used more or less frequently than expected. The authors synthesized large DNA constructs encoding the poliovirus capsid protein with hundreds of over‑ or underrepresented synonymous codon pairs. Viruses with underrepresented codon pairs showed reduced protein translation, were attenuated in mice, conferred protective immunity upon immunization, and suggest a broadly applicable attenuation strategy.

Abstract

As a result of the redundancy of the genetic code, adjacent pairs of amino acids can be encoded by as many as 36 different pairs of synonymous codons. A species-specific "codon pair bias" provides that some synonymous codon pairs are used more or less frequently than statistically predicted. We synthesized de novo large DNA molecules using hundreds of over-or underrepresented synonymous codon pairs to encode the poliovirus capsid protein. Underrepresented codon pairs caused decreased rates of protein translation, and polioviruses containing such amino acid-independent changes were attenuated in mice. Polioviruses thus customized were used to immunize mice and provided protective immunity after challenge. This "death by a thousand cuts" strategy could be generally applicable to attenuating many kinds of viruses.