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Updated: Jun 5, 2026
10:55
Rescue of Recombinant Newcastle Disease Virus from cDNA
Published on: October 11, 2013
Analysis of codon usage in Newcastle disease virus
Meng Wang1, Yong-Sheng Liu, Jian-Hua Zhou
1Key Laboratory of Animal Virology of Ministry of Agriculture, State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046 Gansu, People's Republic of China.
Virus Genes
|January 21, 2011
Summary
Newcastle disease virus (NDV) exhibits low codon usage bias, primarily driven by mutational pressure, not natural selection. Codon patterns are gene function and geography specific, with CpG under-representation aiding host adaptation.
Area of Science:
- Virology
- Molecular Biology
- Genomics
Background:
- Newcastle disease virus (NDV) is a significant avian pathogen.
- Understanding viral genome evolution and adaptation is crucial for disease control.
- Codon usage patterns can reveal insights into viral evolution and host interactions.
Purpose of the Study:
- To investigate the codon usage patterns in 31 Newcastle disease virus (NDV) isolates.
- To determine the factors influencing codon usage bias in NDV genomes.
- To explore the relationship between codon usage, gene function, geography, host, and NDV evolution.
Main Methods:
- Analysis of relative synonymous codon usage (RSCU) values.
- Calculation of effective number of codons (ENC) values.
- Assessment of nucleotide and dinucleotide contents.
- Comparative analysis of codon usage patterns across different NDV isolates.
Main Results:
- NDV shows a low extent of codon usage bias (mean ENC = 56.15).
- Mutational pressure, rather than natural selection, is the primary driver of codon usage bias and base composition.
- Synonymous codon usage patterns are specific to gene function and geography, but not host.
- Multiple NDV genotypes appear to circulate in US waterfowl.
- CpG under-representation is a characteristic feature of NDV adaptation to its host.
Conclusions:
- Codon usage bias in NDV is minimal and influenced by mutational forces.
- Gene function and geographical origin dictate codon usage patterns, suggesting localized evolutionary pressures.
- The findings provide insights into NDV genome variation and evolutionary mechanisms, including host adaptation strategies.
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