The open reading frame 4 (ORF4) constitutes an important component
of the genome of the Hepatitis E virus (HEV) Genotype 1 (GT 1). The codon usage
is involved in establishing a host-pathogen relationship, therefore, in this
context, different factors influencing the codon usage patterns were analyzed
in the ORF4 coding sequences of HEV. The overall nucleotide composition showed
C as the most-represented nucleotide and A as the least in the ORF4 coding
sequences. Relative synonymous codon usage (RSCU) revealed biasness towards C
and G-ended codons over U and A-ended codons. GC content was significantly
higher in ORF4 coding genes. The comparative codon frequency analysis among
HEV-hosts showed both similarities and differences in preferred codon usage
signifying that ORF4 codon usage patterns were a mixture of coincidence and
antagonism. Further, our results emphasized the influence of both selection
forces, i.e., mutational pressure and natural selection, on the codon usage
patterns of ORF4, from virus and host respectively. The present study
highlighted the influence of compositional constraints, codon usage biasness,
in conjunction with the selective forces in shaping the ORF4 codon usage
patterns. These findings are expected to increase our understanding of factors
involved in viral evolution, and fitness towards hosts and the environment.
Author(s) Details
Zoya Shafat
Centre for Interdisciplinary Research in Basic Sciences,
Jamia Millia Islamia, New Delhi 110025, India.
Please see the link:- https://doi.org/10.9734/bpi/mono/978-81-976007-3-9/CH2
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