Host Adaptation and Evolutionary Analysis of Zaire ebolavirus: Insights From Codon Usage Based Investigations
Ebola virus (EBOV) has caused several outbreaks as the consequence of spillover events from zoonotic sources and has resulted in huge death tolls. In spite of considerable progress, a thorough know-how regarding EBOV adaptation in various host species and detailed information about the potential res...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-11-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2020.570131/full |
| _version_ | 1818268362072915968 |
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| author | Wen Luo Wen Luo Ayan Roy Fucheng Guo David M. Irwin David M. Irwin Xuejuan Shen Junbin Pan Yongyi Shen Yongyi Shen Yongyi Shen |
| author_facet | Wen Luo Wen Luo Ayan Roy Fucheng Guo David M. Irwin David M. Irwin Xuejuan Shen Junbin Pan Yongyi Shen Yongyi Shen Yongyi Shen |
| author_sort | Wen Luo |
| collection | DOAJ |
| description | Ebola virus (EBOV) has caused several outbreaks as the consequence of spillover events from zoonotic sources and has resulted in huge death tolls. In spite of considerable progress, a thorough know-how regarding EBOV adaptation in various host species and detailed information about the potential reservoirs of EBOV still remains obscure. The present study was executed to examine the patterns of codon usage and its associated influence in the adaptation of EBOV to potential hosts that dwell in Africa, the origin of the viral outbreaks. Correspondence analysis (CA) revealed that the codon usage signature in EBOV is a complex interplay of factors including compositional bias and natural selection, with the latter having a more pronounced impact. Low codon usage bias in EBOV indicates a flexibility of the viruses in adapting to diverse range of hosts with different codon usage architectures. EBOV adaptation in potential hosts, as estimated by codon adaptation index (CAI) and relative codon deoptimization index (RCDI), revealed that the viruses were relatively better adapted to African primates than other mammals examined, which might account for the high fatality rate of primates owing to EBOV infection. Bats have been speculated as natural reservoirs of EBOV. In the present analysis it was interesting to note that EBOV displayed lower degrees of adaptation, as estimated by CAI and RCDI, with bats in comparison to the primate hosts. Lower degrees of adaptation might contribute to long-term co-existence and circulation of the viral pathogens in bat populations. Codon usage patterns of EBOV isolates associated with different outbreaks varied significantly, with discrete patterns between the West and Central African isolates. Additional evolutionary analyses indicated that the West African Epidemic began with an initial spillover infection and there was more than one population of EBOV circulating in the natural reservoir in the Democratic Republic of the Congo. The present study yields valuable information regarding the possible circulation of EBOV in various African mammals. |
| first_indexed | 2024-12-12T20:37:17Z |
| format | Article |
| id | doaj.art-7e7a9605f82349b881b727ac1d23466d |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-12T20:37:17Z |
| publishDate | 2020-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-7e7a9605f82349b881b727ac1d23466d2022-12-22T00:12:51ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2020-11-011110.3389/fmicb.2020.570131570131Host Adaptation and Evolutionary Analysis of Zaire ebolavirus: Insights From Codon Usage Based InvestigationsWen Luo0Wen Luo1Ayan Roy2Fucheng Guo3David M. Irwin4David M. Irwin5Xuejuan Shen6Junbin Pan7Yongyi Shen8Yongyi Shen9Yongyi Shen10Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, ChinaGuangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, ChinaDepartment of Biotechnology, Lovely Professional University, Phagwara, IndiaCenter for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, ChinaDepartment of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, CanadaBanting and Best Diabetes Centre, University of Toronto, Toronto, ON, CanadaCenter for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, ChinaCenter for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, ChinaCenter for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, ChinaGuangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, ChinaKey Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, ChinaEbola virus (EBOV) has caused several outbreaks as the consequence of spillover events from zoonotic sources and has resulted in huge death tolls. In spite of considerable progress, a thorough know-how regarding EBOV adaptation in various host species and detailed information about the potential reservoirs of EBOV still remains obscure. The present study was executed to examine the patterns of codon usage and its associated influence in the adaptation of EBOV to potential hosts that dwell in Africa, the origin of the viral outbreaks. Correspondence analysis (CA) revealed that the codon usage signature in EBOV is a complex interplay of factors including compositional bias and natural selection, with the latter having a more pronounced impact. Low codon usage bias in EBOV indicates a flexibility of the viruses in adapting to diverse range of hosts with different codon usage architectures. EBOV adaptation in potential hosts, as estimated by codon adaptation index (CAI) and relative codon deoptimization index (RCDI), revealed that the viruses were relatively better adapted to African primates than other mammals examined, which might account for the high fatality rate of primates owing to EBOV infection. Bats have been speculated as natural reservoirs of EBOV. In the present analysis it was interesting to note that EBOV displayed lower degrees of adaptation, as estimated by CAI and RCDI, with bats in comparison to the primate hosts. Lower degrees of adaptation might contribute to long-term co-existence and circulation of the viral pathogens in bat populations. Codon usage patterns of EBOV isolates associated with different outbreaks varied significantly, with discrete patterns between the West and Central African isolates. Additional evolutionary analyses indicated that the West African Epidemic began with an initial spillover infection and there was more than one population of EBOV circulating in the natural reservoir in the Democratic Republic of the Congo. The present study yields valuable information regarding the possible circulation of EBOV in various African mammals.https://www.frontiersin.org/articles/10.3389/fmicb.2020.570131/fullcodon usageebolavirushost reservoircodon adaptation indexgenetic diversity |
| spellingShingle | Wen Luo Wen Luo Ayan Roy Fucheng Guo David M. Irwin David M. Irwin Xuejuan Shen Junbin Pan Yongyi Shen Yongyi Shen Yongyi Shen Host Adaptation and Evolutionary Analysis of Zaire ebolavirus: Insights From Codon Usage Based Investigations Frontiers in Microbiology codon usage ebolavirus host reservoir codon adaptation index genetic diversity |
| title | Host Adaptation and Evolutionary Analysis of Zaire ebolavirus: Insights From Codon Usage Based Investigations |
| title_full | Host Adaptation and Evolutionary Analysis of Zaire ebolavirus: Insights From Codon Usage Based Investigations |
| title_fullStr | Host Adaptation and Evolutionary Analysis of Zaire ebolavirus: Insights From Codon Usage Based Investigations |
| title_full_unstemmed | Host Adaptation and Evolutionary Analysis of Zaire ebolavirus: Insights From Codon Usage Based Investigations |
| title_short | Host Adaptation and Evolutionary Analysis of Zaire ebolavirus: Insights From Codon Usage Based Investigations |
| title_sort | host adaptation and evolutionary analysis of zaire ebolavirus insights from codon usage based investigations |
| topic | codon usage ebolavirus host reservoir codon adaptation index genetic diversity |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2020.570131/full |
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