Dinucleotide and codon usage biases are universal in all organisms and occur due to the interplay between their nucleotide composition and selective pressures. Selective pressures include for instance translation efficiency, translation kinetics modulation and in the particular case of viruses also escaping from cellular antiviral responses. Furthermore, the genome composition of viruses plays an important role in the virus-cell interaction and consequently contributes to the viral evolution. Virus genomes with severe or subtle changes in the dinucleotide and/or codon composition, produced by means of synthetic biology or genomic selection, render virus populations with altered replication capacities useful in new vaccine designs.
The origin of codon and dinucleotide biases is still controversial. Some studies suggest that it’s mostly due to mutational biases, while others consider natural selection to play the main role. The truth probably lies in a combination of both. In the case of viruses, there is an additional factor emphasizing the critical role of selection in shaping the viral codon and dinucleotide usage: the virus-host interaction. Viruses need to adapt to the cell machinery, resources and responses for their own biological cycle, and this adaptation may involve genomic biases.
It is possible to manipulate the genome composition of viruses with a described relationship between their codon and/or dinucleotide composition and their cellular interaction. Such a modification may serve to attenuate or improve viral replication, with the final aim to design new vaccines.
With these principles in mind, we propose this Research Topic to cover three main areas, below:
1. Implications of the virus genome composition in the biology and evolution of various organisms.
2. Effects of the genome composition on virus evolution and the virus-host interaction.
3. Application of the genome composition findings in the development of vaccines against particular viruses.
Dinucleotide and codon usage biases are universal in all organisms and occur due to the interplay between their nucleotide composition and selective pressures. Selective pressures include for instance translation efficiency, translation kinetics modulation and in the particular case of viruses also escaping from cellular antiviral responses. Furthermore, the genome composition of viruses plays an important role in the virus-cell interaction and consequently contributes to the viral evolution. Virus genomes with severe or subtle changes in the dinucleotide and/or codon composition, produced by means of synthetic biology or genomic selection, render virus populations with altered replication capacities useful in new vaccine designs.
The origin of codon and dinucleotide biases is still controversial. Some studies suggest that it’s mostly due to mutational biases, while others consider natural selection to play the main role. The truth probably lies in a combination of both. In the case of viruses, there is an additional factor emphasizing the critical role of selection in shaping the viral codon and dinucleotide usage: the virus-host interaction. Viruses need to adapt to the cell machinery, resources and responses for their own biological cycle, and this adaptation may involve genomic biases.
It is possible to manipulate the genome composition of viruses with a described relationship between their codon and/or dinucleotide composition and their cellular interaction. Such a modification may serve to attenuate or improve viral replication, with the final aim to design new vaccines.
With these principles in mind, we propose this Research Topic to cover three main areas, below:
1. Implications of the virus genome composition in the biology and evolution of various organisms.
2. Effects of the genome composition on virus evolution and the virus-host interaction.
3. Application of the genome composition findings in the development of vaccines against particular viruses.
