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Viruses 2018, 10(11), 604; https://doi.org/10.3390/v10110604

Evolution of Codon Usage Bias in Henipaviruses Is Governed by Natural Selection and Is Host-Specific

1
National Institute of High Security Animal Diseases, Bhopal 462022, India
2
Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
3
Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, Delhi 110016, India
4
Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Kanagawa 2300045, Japan
5
The Pirbright Institute, Woking GU24 0NF, UK
*
Author to whom correspondence should be addressed.
Received: 27 September 2018 / Revised: 28 October 2018 / Accepted: 30 October 2018 / Published: 1 November 2018
(This article belongs to the Special Issue Viruses and Bats 2019)
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Abstract

Hendra virus (HeV) and Nipah virus (NiV) are among a group of emerging bat-borne paramyxoviruses that have crossed their species-barrier several times by infecting several hosts with a high fatality rate in human beings. Despite the fatal nature of their infection, a comprehensive study to explore their evolution and adaptation in different hosts is lacking. A study of codon usage patterns in henipaviruses may provide some fruitful insight into their evolutionary processes of synonymous codon usage and host-adapted evolution. Here, we performed a systematic evolutionary and codon usage bias analysis of henipaviruses. We found a low codon usage bias in the coding sequences of henipaviruses and that natural selection, mutation pressure, and nucleotide compositions shapes the codon usage patterns of henipaviruses, with natural selection being more important than the others. Also, henipaviruses showed the highest level of adaptation to bats of the genus Pteropus in the codon adaptation index (CAI), relative to the codon de-optimization index (RCDI), and similarity index (SiD) analyses. Furthermore, a comparison to recently identified henipa-like viruses indicated a high tRNA adaptation index of henipaviruses for human beings, mainly due to F, G and L proteins. Consequently, the study concedes the substantial emergence of henipaviruses in human beings, particularly when paired with frequent exposure to direct/indirect bat excretions. View Full-Text
Keywords: Henipaviruses; codon usage bias; host adaptation; natural selection; evolution Henipaviruses; codon usage bias; host adaptation; natural selection; evolution
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Kumar, N.; Kulkarni, D.D.; Lee, B.; Kaushik, R.; Bhatia, S.; Sood, R.; Pateriya, A.K.; Bhat, S.; Singh, V.P. Evolution of Codon Usage Bias in Henipaviruses Is Governed by Natural Selection and Is Host-Specific. Viruses 2018, 10, 604.

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