Evolution of Codon Usage Bias in Henipaviruses Is Governed by Natural Selection and Is Host-Specific
Hendra virus (HeV) and Nipah virus (NiV) are among a group of emerging <i>bat</i>-borne paramyxoviruses that have crossed their species-barrier several times by infecting several hosts with a high fatality rate in <i>human beings</i>. Despite the fatal nature of their infecti...
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doaj-4e4fff7d42d049ffacec58135bba9b952020-11-25T02:11:16ZengMDPI AGViruses1999-49152018-11-01101160410.3390/v10110604v10110604Evolution of Codon Usage Bias in Henipaviruses Is Governed by Natural Selection and Is Host-SpecificNaveen Kumar0Diwakar D. Kulkarni1Benhur Lee2Rahul Kaushik3Sandeep Bhatia4Richa Sood5Atul Kumar Pateriya6Sushant Bhat7Vijendra Pal Singh8National Institute of High Security Animal Diseases, Bhopal 462022, IndiaNational Institute of High Security Animal Diseases, Bhopal 462022, IndiaDepartment of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USASupercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, Delhi 110016, IndiaNational Institute of High Security Animal Diseases, Bhopal 462022, IndiaNational Institute of High Security Animal Diseases, Bhopal 462022, IndiaNational Institute of High Security Animal Diseases, Bhopal 462022, IndiaThe Pirbright Institute, Woking GU24 0NF, UKNational Institute of High Security Animal Diseases, Bhopal 462022, IndiaHendra virus (HeV) and Nipah virus (NiV) are among a group of emerging <i>bat</i>-borne paramyxoviruses that have crossed their species-barrier several times by infecting several hosts with a high fatality rate in <i>human beings</i>. 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 <i>bats</i> of the genus <i>Pteropus</i> 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 <i>human beings</i>, mainly due to F, G and L proteins. Consequently, the study concedes the substantial emergence of henipaviruses in <i>human beings</i>, particularly when paired with frequent exposure to direct/indirect <i>bat</i> excretions.https://www.mdpi.com/1999-4915/10/11/604Henipavirusescodon usage biashost adaptationnatural selectionevolution |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Naveen Kumar Diwakar D. Kulkarni Benhur Lee Rahul Kaushik Sandeep Bhatia Richa Sood Atul Kumar Pateriya Sushant Bhat Vijendra Pal Singh |
spellingShingle |
Naveen Kumar Diwakar D. Kulkarni Benhur Lee Rahul Kaushik Sandeep Bhatia Richa Sood Atul Kumar Pateriya Sushant Bhat Vijendra Pal Singh Evolution of Codon Usage Bias in Henipaviruses Is Governed by Natural Selection and Is Host-Specific Viruses Henipaviruses codon usage bias host adaptation natural selection evolution |
author_facet |
Naveen Kumar Diwakar D. Kulkarni Benhur Lee Rahul Kaushik Sandeep Bhatia Richa Sood Atul Kumar Pateriya Sushant Bhat Vijendra Pal Singh |
author_sort |
Naveen Kumar |
title |
Evolution of Codon Usage Bias in Henipaviruses Is Governed by Natural Selection and Is Host-Specific |
title_short |
Evolution of Codon Usage Bias in Henipaviruses Is Governed by Natural Selection and Is Host-Specific |
title_full |
Evolution of Codon Usage Bias in Henipaviruses Is Governed by Natural Selection and Is Host-Specific |
title_fullStr |
Evolution of Codon Usage Bias in Henipaviruses Is Governed by Natural Selection and Is Host-Specific |
title_full_unstemmed |
Evolution of Codon Usage Bias in Henipaviruses Is Governed by Natural Selection and Is Host-Specific |
title_sort |
evolution of codon usage bias in henipaviruses is governed by natural selection and is host-specific |
publisher |
MDPI AG |
series |
Viruses |
issn |
1999-4915 |
publishDate |
2018-11-01 |
description |
Hendra virus (HeV) and Nipah virus (NiV) are among a group of emerging <i>bat</i>-borne paramyxoviruses that have crossed their species-barrier several times by infecting several hosts with a high fatality rate in <i>human beings</i>. 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 <i>bats</i> of the genus <i>Pteropus</i> 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 <i>human beings</i>, mainly due to F, G and L proteins. Consequently, the study concedes the substantial emergence of henipaviruses in <i>human beings</i>, particularly when paired with frequent exposure to direct/indirect <i>bat</i> excretions. |
topic |
Henipaviruses codon usage bias host adaptation natural selection evolution |
url |
https://www.mdpi.com/1999-4915/10/11/604 |
work_keys_str_mv |
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