Analysis of Nipah Virus Codon Usage and Adaptation to Hosts
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 co...
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| Language: | English |
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Frontiers Media S.A.
2019-05-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2019.00886/full |
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| author | Rekha Khandia Shailja Singhal Utsang Kumar Afzal Ansari Ruchi Tiwari Kuldeep Dhama Jayashankar Das Ashok Munjal Raj Kumar Singh |
| author_facet | Rekha Khandia Shailja Singhal Utsang Kumar Afzal Ansari Ruchi Tiwari Kuldeep Dhama Jayashankar Das Ashok Munjal Raj Kumar Singh |
| author_sort | Rekha Khandia |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-20T19:55:13Z |
| format | Article |
| id | doaj.art-98b5b7fd35444416bae476e07917f154 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-20T19:55:13Z |
| publishDate | 2019-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-98b5b7fd35444416bae476e07917f1542022-12-21T19:28:10ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2019-05-011010.3389/fmicb.2019.00886439603Analysis of Nipah Virus Codon Usage and Adaptation to HostsRekha Khandia0Shailja Singhal1Utsang Kumar2Afzal Ansari3Ruchi Tiwari4Kuldeep Dhama5Jayashankar Das6Ashok Munjal7Raj Kumar Singh8Department of Biochemistry and Genetics, Barkatullah University, Bhopal, IndiaDepartment of Biochemistry and Genetics, Barkatullah University, Bhopal, IndiaDepartment of Biochemistry and Genetics, Barkatullah University, Bhopal, IndiaGujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, IndiaDepartment of Veterinary Microbiology and Immunology, College of Veterinary Uttar Pradesh Pandit Deen Dayal Upadhyaya Pashu Chikitsa Vigyan Vishwavidyalaya Evam Go Anusandhan Sansthan (DUVASU), Mathura, IndiaDivision of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, IndiaGujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, IndiaDepartment of Biochemistry and Genetics, Barkatullah University, Bhopal, IndiaICAR-Indian Veterinary Research Institute, Bareilly, IndiaA 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.https://www.frontiersin.org/article/10.3389/fmicb.2019.00886/fullNipah viruscodon usageCAIRCDIsimilarity indexselection pressure |
| spellingShingle | Rekha Khandia Shailja Singhal Utsang Kumar Afzal Ansari Ruchi Tiwari Kuldeep Dhama Jayashankar Das Ashok Munjal Raj Kumar Singh Analysis of Nipah Virus Codon Usage and Adaptation to Hosts Frontiers in Microbiology Nipah virus codon usage CAI RCDI similarity index selection pressure |
| title | Analysis of Nipah Virus Codon Usage and Adaptation to Hosts |
| title_full | Analysis of Nipah Virus Codon Usage and Adaptation to Hosts |
| title_fullStr | Analysis of Nipah Virus Codon Usage and Adaptation to Hosts |
| title_full_unstemmed | Analysis of Nipah Virus Codon Usage and Adaptation to Hosts |
| title_short | Analysis of Nipah Virus Codon Usage and Adaptation to Hosts |
| title_sort | analysis of nipah virus codon usage and adaptation to hosts |
| topic | Nipah virus codon usage CAI RCDI similarity index selection pressure |
| url | https://www.frontiersin.org/article/10.3389/fmicb.2019.00886/full |
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