Author : Rekha khandia1 , shailja singhal1 , utsang kumar1 , afzal ansari2 , ruchi tiwari3 , kuldeep dhama4 , jayashankar das2 *, ashok munjal1 * and raj kumar singh5
Keyword : Nipah virus, codon usage, cai, rcdi, similarity index, selection pressure, compositional constraint
Subject : Microbiology
Article Type : Original article (research)
DOI : 10.3389/fmicb.2019.00886
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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.
Article by : Utsang Kumar
Article add date : 2020-12-14
How to cite : Rekha khandia1 , shailja singhal1 , utsang kumar1 , afzal ansari2 , ruchi tiwari3 , kuldeep dhama4 , jayashankar das2 *, ashok munjal1 * and raj kumar singh5. (2020-December-14). Analysis of nipah virus codon usage and adaptation to hosts. retrieved from https://www.openacessjournal.com/abstract/496