Vaccines are a remarkably effective way to stem the threat posed by infectious diseases. Methods that allow rapid development of vaccines are vital. Synonymous recoding of viral genomes is a recently developed, general, and highly promising strategy for producing live attenuated vaccines. From an antigenic perspective, the method is ideal because it leaves the amino acid sequence of the viral proteins identical to the circulating pathogenic form. A number of viruses have been attenuated by recoding with non-preferred codons or codon pairs, and at least eight studies have shown protective immunization of mice. Despite its demonstrated success, there are fundamental gaps in our knowledge: 1) no effort has been made to compare alternative recoding strategies within the same virus in the same study; 2) several potential methods of synonymous recoding have not been tested at all; 3) the way in which attenuation is affected by the combination of multiple recoded genes is not known; and 4) most importantly, it is unresolved whether viruses attenuated by synonymous recoding are robust to evolutionary recovery. This proposal tackles these gaps through three Specific Aims.
Aim 1 : Identify methods of synonymous recoding and associated sequence features that can be used to generate viral genomes with a targeted level of attenuation.
This aim i ncludes developing empirical measures of individual codon and codon pair effects on translation rate to guide attenuation. It will also test metrics that have not previously been used for synonymous recoding.
Aim 2 : Extend models of adaptive evolution to determine if the attenuating effects, within and among genes and transcripts, combine in additive or non-additive ways.
Aim 3 : Determine if some strategies of attenuation are more robust to recovery than others.
This aim will focus on viruses attenuated in multiple regions and by multiple methods, and also determine if some recovery pathways are broadly beneficial. The project takes advantage of a bacteriophage model system with well-developed tools for genome manipulation and methods for rapid experimental evolution relative to eukaryotic viral systems (i.e., a hundred generations per day at very large population sizes). Achieving these three aims will yield approaches that can be applied to other systems for designing viruses with targeted levels of attenuation that are robust to evolutionary recovery. This research is a critical step toward the long-term goal of achieving a general strategy for fighting infectious diseases by precision design of live vaccines that do not re-evolve virulence when used in humans.

Public Health Relevance

A new and promising form of vaccine design is to attenuate by recoding the genome without changing the protein sequence of the virus, thus providing a perfect antigenic match. Fundamental gaps in our understanding need to be addressed using a nonpathogenic virus. This proposal seeks to establish the best way to attenuate viruses by comparing methods of recoding, assessing how recoded genes interact, and, most importantly, by designing attenuated viruses that are robust to evolutionary recovery.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Genetic Variation and Evolution Study Section (GVE)
Program Officer
Janes, Daniel E
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Idaho
Schools of Arts and Sciences
United States
Zip Code
Miller, Craig R; Van Leuven, James T; Wichman, Holly A et al. (2018) Selecting among three basic fitness landscape models: Additive, multiplicative and stickbreaking. Theor Popul Biol 122:97-109
Miller, Craig R; Nagel, Anna C; Scott, LuAnn et al. (2016) Love the one you're with: replicate viral adaptations converge on the same phenotypic change. PeerJ 4:e2227
Baker, Christopher W; Miller, Craig R; Thaweethai, Tanayott et al. (2016) Genetically Determined Variation in Lysis Time Variance in the Bacteriophage ?X174. G3 (Bethesda) 6:939-55
Wojtowicz, Andrzej J; Miller, Craig R; Joyce, Paul (2015) Inference for one-step beneficial mutations using next generation sequencing. Stat Appl Genet Mol Biol 14:65-81
Miller, Craig R; Lee, Kuo Hao; Wichman, Holly A et al. (2014) Changing folding and binding stability in a viral coat protein: a comparison between substitutions accessible through mutation and those fixed by natural selection. PLoS One 9:e112988
Caudle, S Brian; Miller, Craig R; Rokyta, Darin R (2014) Environment determines epistatic patterns for a ssDNA virus. Genetics 196:267-79
Tyerman, Jabus G; Ponciano, José M; Joyce, Paul et al. (2013) The evolution of antibiotic susceptibility and resistance during the formation of Escherichia coli biofilms in the absence of antibiotics. BMC Evol Biol 13:22
Bull, James J; Joyce, Paul; Gladstone, Eric et al. (2013) Empirical complexities in the genetic foundations of lethal mutagenesis. Genetics 195:541-52
Bataillon, Thomas; Joyce, Paul; Sniegowski, Paul (2013) As it happens: current directions in experimental evolution. Biol Lett 9:20120945
Nagel, Anna C; Joyce, Paul; Wichman, Holly A et al. (2012) Stickbreaking: a novel fitness landscape model that harbors epistasis and is consistent with commonly observed patterns of adaptive evolution. Genetics 190:655-67

Showing the most recent 10 out of 27 publications