Analysis of Nipah Virus Codon Usage and Adaptation to Hosts - PubMed (original) (raw)
Analysis of Nipah Virus Codon Usage and Adaptation to Hosts
Rekha Khandia et al. Front Microbiol. 2019.
Abstract
A recent outbreak of Nipah virus (NiV) in India has caused 17 deaths in people living in districts of Kerala state. Its zoonotic nature, as well as high rate of human-to-human transmission, has led researchers worldwide to work toward understanding the different aspects of the NiV. We performed a codon usage analysis, based on publicly available nucleotide sequences of NiV and its host adaptation, along with other members of the Henipavirus genus in ten hosts. NiV genome encodes nine open reading frames; and overall, no significant bias in codon usage was observed. Aromaticity of proteins had no impact on codon usage. An analysis of preferred codons used by NiV and the tRNA pool in human cells indicated that NiV prefers codons from a suboptimal anticodon tRNA pool. We observed that codon usage by NiV is mainly constrained by compositional and selection pressures, not by mutational forces. Parameters that define NiV and host relatedness in terms of codon usage were analyzed, with a codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index calculations; which indicated that, of all hosts analyzed, NiV was best adapted to African green monkeys. A comparative analysis based on the relative codon deoptimization index (RCDI) for host adaptation of NiV, Hendra virus (HeV), Cedar virus (CedV), and Hendra like Mojiang virus (MojV) revealed that except for dogs and ferrets, all evaluated hosts were more susceptible to HeV than NiV.
Keywords: CAI; Nipah virus; RCDI; codon usage; compositional constraint; selection pressure; similarity index.
Figures
FIGURE 1
(A) Heat map of RSCU values (averages) of NiV and its plausible hosts. (B) Heat map comparing average RSCU values for different CDSs of NiV. The map indicates that, within genes themselves, codon preferences differ (higher RSCU values representing more frequent codon usage depicted in dark red, and lower RSCU values depicted in dark blue).
FIGURE 2
Nc–GC3 plots of different genes of NiV. The Nc curve is indicating the expected codon usage, if GC compositional constraints only account for the codon usage bias. Panel (A) for all coding sequences; (B–J) for coding sequence C, F, G, M, N, P, L, W, and V, respectively.
FIGURE 3
The neutrality plot to analyze the influences of mutation bias and translation selection on codon usage. GC12 stands for the average value of GC content at first and second position of codon. GC3 stands for GC content at third position of codon. The slope value indicates the mutational pressure.
FIGURE 4
Parity plot showing the presence of AT bias [A3%/(A3% + T3%)] and GC bias [G3%/(G3% + C3%)]. The center of the plot, where value of both the coordinates is 0.5, indicates the place where there is no bias in mutation or selection rates.
FIGURE 5
Tree plot for intragenic RCDI analysis. The plot indicates an average RCDI values with reference to different hosts and the 9 coding sequences of NiV. For adaptation of NiV genome, with least RCDI values African green monkey and with highest RCDI values Ferrets are best and least adapted, respectively, for growth NiV, where exhibiting the RCDI and hence east adapted. (For a single gene, an average RCDI has been taken).
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