Analysis of Nipah Virus Codon Usage and Adaptation to Hosts.

Rekha Khandia,Jayashankar Das,Utsang Kumar,Afzal Ansari,Shailja Singhal,Ashok Munjal,Raj Kumar Singh,Ruchi Tiwari,Kuldeep Dhama

doi:10.3389/fmicb.2019.00886

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.

Highlights

The Nipah virus (NiV) is an RNA virus in the Henipavirus genus, Paramyxoviridae family, that infects both wild animals and humans (Gurley et al, 2017)
The African green monkey was found to be the best suited for animal experiments, with the highest codon adaptation index (CAI) and similarity index; and the lowest relative codon deoptimization index (RCDI) value
The NiV sequences were found to be highly adapted to the bat and human sequences based on CAI values

Summary

Introduction

The Nipah virus (NiV) is an RNA virus in the Henipavirus genus, Paramyxoviridae family, that infects both wild animals and humans (Gurley et al, 2017). (Epstein et al, 2006b) such as P. vampyrus, P. hypomelanus, P. lylei, and P. giganteus These bats have been associated with outbreaks of NiV (Wacharapluesadee et al, 2010; Hasebe et al, 2012; Yadav et al, 2012; de Wit and Munster, 2015). The virus is regarded as a biosafety level-4 pathogen, presenting a great threat to human health as well as security, because of the high rate of mortality associated with its infection, along with the lack of an efficacious treatment regimen and vaccine (Epstein et al, 2006a; Rahman and Chakraborty, 2012). The clinical signs and symptoms of its infection include fever with labored breathing, cough, headache, encephalitis and seizures (Ang et al, 2018)

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