http://orcid.org/0000-0001-5078-6492
![Sample our Bioscience journals, sign in here to start your access, Latest two full volumes FREE to you for 14 days]({"type":"image" , "src" : "/sda/5925/TOC-Subject-Sample-2021-Bioscience.jpg"})
Abstract
Norovirus GII.4 variants, a genotype in genogroup II belonging to the genus Norovirus, is a single-strand positive sense RNA containing three open reading frames (ORF1, ORF2 and ORF3) and is the most important pathogen causing nonbacterial gastroenteritis outbreaks. By using bioinformatic softwares such as Codon W, SPSS and so on, a total of 292 strains of the viruses isolated from 1974 to 2016 were analyzed for nucleotide composition and synonymous codon usage in each ORF. The result shows that it is enriched for A over the other bases in nucleotide composition, G behind the other bases in the 3rd site of all synonymous codons in the three ORFs. The patterns of nucleotide composition and codon bias of ORF2 are similar to those of ORF3 and different from those of ORF1. There are generally UpA motif and CpG motif in the codons with the lowest proportion. Correspondence analysis indicates that the codon usage may be changing over a certain time period for ORF1 in 2006 and 2012, ORF2 in 2012, and ORF3 in 2013. ENC (effective number of codons) plot and other analyses indicate that both natural selection and mutational pressure play partly roles in the ORFs, but natural selection is more important for ORF2 and ORF3. Besides, we also found all optimal codons in the ORFs. The study provides a basic understanding of the mechanism for norovirus GII.4 codon usage bias.
| Abbreviations | ||
| ORF | = | Open Reading Frame |
| ENC | = | Effective Number of Codons |
| COA | = | correspondence analysis |
| RSCU | = | Relative Synonymous Codon Usage |
| CAI | = | Codon Adaptation Index |
| CBI | = | Codon Bias Index |
| Fop | = | frequency of optimal codons |
| L_sym | = | number of synonymous codons |
| L_aa | = | length amino acids |
| GRAVY | = | grand average of hydropathicity |
| Aroma | = | aromaticity |
Communicated by Ramaswamy H. Sarma
Disclosure statement
No potential conflict of interest was reported by the authors.
