Insight into the codon usage patterns and adaptation of Tembusu Virus
Since its emergence in 2010, Tembusu virus (TMUV) has rapidly spread across poultry populations in Asia, leading to substantial economic losses in these areas. Here, we investigate the codon usage patterns (CUPs) underlying TMUV's adaptation and evolutionary dynamics within host environments. P...
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| Language: | English |
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Elsevier
2025-01-01
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| Series: | Poultry Science |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S003257912401229X |
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| author | Fucheng Guo Huiming Tan Jinjin Yang Rumin Jia Ruichen Wang Lie Wu Fengzhi Pan Kai Kang Weitian Xie Youquan Li Kewei Fan |
| author_facet | Fucheng Guo Huiming Tan Jinjin Yang Rumin Jia Ruichen Wang Lie Wu Fengzhi Pan Kai Kang Weitian Xie Youquan Li Kewei Fan |
| author_sort | Fucheng Guo |
| collection | DOAJ |
| description | Since its emergence in 2010, Tembusu virus (TMUV) has rapidly spread across poultry populations in Asia, leading to substantial economic losses in these areas. Here, we investigate the codon usage patterns (CUPs) underlying TMUV's adaptation and evolutionary dynamics within host environments. Phylogenetic and compositional analyses consistently classify TMUV into four evolutionary lineages—Clusters 1, 2, 3, and ancestral TMUV—with Cluster 2 emerging as the dominant lineage. Codon adaptation index (CAI) analysis reveals that this lineage of TMUV show best adapted to the CUPs of duck than other lineages, underscoring the role of natural selection in shaping viral evolution, a finding in line with evidence that CUPs in the TMUV genome is predominantly shaped by natural selection. Furthermore, TMUV exhibits markedly higher adaptation to the CUPs of poultry hosts (duck, goose, and chicken) compared to potential host humans or vector mosquito. Thus, species-specific adaptability to the host environment may be a reason account for the distinct infectivity and clinic outcome of TMUV acted on hosts. Analysis of dinucleotide distribution reveals significant suppression of CpG and UpA dinucleotides in the TMUV genome, reflecting adaptive pressures to evade vertebrate immune responses. During transmission, TMUV shows increasing alignment with host CUPs and a continuous reduction in CpG dinucleotides, potentially enhancing its fitness within host microenvironments. This work advances our understanding of the basic biology underlying TMUV epidemiology, pathogenicity, and species-specific adaptation. |
| format | Article |
| id | doaj-art-3a49b29ff61f460ea2a5fe6d85df3026 |
| institution | Kabale University |
| issn | 0032-5791 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Poultry Science |
| spelling | doaj-art-3a49b29ff61f460ea2a5fe6d85df30262025-01-22T05:40:50ZengElsevierPoultry Science0032-57912025-01-011041104651Insight into the codon usage patterns and adaptation of Tembusu VirusFucheng Guo0Huiming Tan1Jinjin Yang2Rumin Jia3Ruichen Wang4Lie Wu5Fengzhi Pan6Kai Kang7Weitian Xie8Youquan Li9Kewei Fan10College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, China; Fujian Provincial Key Laboratory for Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan University, Longyan, 364012, Fujian, ChinaCollege of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, ChinaTechnology Center of Zhanjiang Customs District, Zhanjiang, 524000, Guangdong, ChinaCollege of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, ChinaNational Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, ChinaCollege of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, ChinaCollege of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, ChinaCollege of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, ChinaCollege of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, ChinaCollege of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, ChinaFujian Provincial Key Laboratory for Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan University, Longyan, 364012, Fujian, China; Corresponding authors.Since its emergence in 2010, Tembusu virus (TMUV) has rapidly spread across poultry populations in Asia, leading to substantial economic losses in these areas. Here, we investigate the codon usage patterns (CUPs) underlying TMUV's adaptation and evolutionary dynamics within host environments. Phylogenetic and compositional analyses consistently classify TMUV into four evolutionary lineages—Clusters 1, 2, 3, and ancestral TMUV—with Cluster 2 emerging as the dominant lineage. Codon adaptation index (CAI) analysis reveals that this lineage of TMUV show best adapted to the CUPs of duck than other lineages, underscoring the role of natural selection in shaping viral evolution, a finding in line with evidence that CUPs in the TMUV genome is predominantly shaped by natural selection. Furthermore, TMUV exhibits markedly higher adaptation to the CUPs of poultry hosts (duck, goose, and chicken) compared to potential host humans or vector mosquito. Thus, species-specific adaptability to the host environment may be a reason account for the distinct infectivity and clinic outcome of TMUV acted on hosts. Analysis of dinucleotide distribution reveals significant suppression of CpG and UpA dinucleotides in the TMUV genome, reflecting adaptive pressures to evade vertebrate immune responses. During transmission, TMUV shows increasing alignment with host CUPs and a continuous reduction in CpG dinucleotides, potentially enhancing its fitness within host microenvironments. This work advances our understanding of the basic biology underlying TMUV epidemiology, pathogenicity, and species-specific adaptation.http://www.sciencedirect.com/science/article/pii/S003257912401229XTembusu virusadaptationevolutioncodon usagedinucleotide |
| spellingShingle | Fucheng Guo Huiming Tan Jinjin Yang Rumin Jia Ruichen Wang Lie Wu Fengzhi Pan Kai Kang Weitian Xie Youquan Li Kewei Fan Insight into the codon usage patterns and adaptation of Tembusu Virus Poultry Science Tembusu virus adaptation evolution codon usage dinucleotide |
| title | Insight into the codon usage patterns and adaptation of Tembusu Virus |
| title_full | Insight into the codon usage patterns and adaptation of Tembusu Virus |
| title_fullStr | Insight into the codon usage patterns and adaptation of Tembusu Virus |
| title_full_unstemmed | Insight into the codon usage patterns and adaptation of Tembusu Virus |
| title_short | Insight into the codon usage patterns and adaptation of Tembusu Virus |
| title_sort | insight into the codon usage patterns and adaptation of tembusu virus |
| topic | Tembusu virus adaptation evolution codon usage dinucleotide |
| url | http://www.sciencedirect.com/science/article/pii/S003257912401229X |
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