Insights into the Evolution and Host Adaptation of the Monkeypox Virus from a Codon Usage Perspective: Focus on the Ongoing 2022 Outbreak
The exceptionally widespread outbreak of human monkeypox, an emerging zoonosis caused by the <i>monkeypox virus</i> (MPXV), with more than 69,000 confirmed cases in 100 non-endemic countries since 2022, is a major public health concern. Codon usage patterns reflect genetic variation and...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-07-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/14/11524 |
| _version_ | 1797589027901145088 |
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| author | Jianglin Zhou Xuejun Wang Zhe Zhou Shengqi Wang |
| author_facet | Jianglin Zhou Xuejun Wang Zhe Zhou Shengqi Wang |
| author_sort | Jianglin Zhou |
| collection | DOAJ |
| description | The exceptionally widespread outbreak of human monkeypox, an emerging zoonosis caused by the <i>monkeypox virus</i> (MPXV), with more than 69,000 confirmed cases in 100 non-endemic countries since 2022, is a major public health concern. Codon usage patterns reflect genetic variation and adaptation to new hosts and ecological niches. However, detailed analyses of codon usage bias in MPXV based on large-scale genomic data, especially for strains responsible for the 2022 outbreak, are lacking. In this study, we analyzed codon usage in MPXV and its relationship with host adaptation. We confirmed the ongoing outbreak of MPXVs belonging to the West Africa (WA) lineage by principal component analysis based on their codon usage patterns. The 2022 outbreak strains had a relatively low codon usage bias. Codon usage of MPXVs was shaped by mutation and natural selection; however, different from past strains, codon usage in the 2022 outbreak strains was predominantly determined by mutation pressure. Additionally, as revealed by the codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses, the codon usage patterns of MPXVs were also affected by their hosts. In particular, the 2022 outbreak strains showed slightly but significantly greater adaptation to many primates, including humans, and were subjected to stronger selection pressure induced by hosts. Our results suggest that MPXVs contributing to the 2022 outbreak have unique evolutionary features, emphasizing the importance of sustained monitoring of their transmission and evolution. |
| first_indexed | 2024-03-11T01:00:29Z |
| format | Article |
| id | doaj.art-3be7a2b9b37e412687438ea28a24b248 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-11T01:00:29Z |
| publishDate | 2023-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-3be7a2b9b37e412687438ea28a24b2482023-11-18T19:40:50ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-07-0124141152410.3390/ijms241411524Insights into the Evolution and Host Adaptation of the Monkeypox Virus from a Codon Usage Perspective: Focus on the Ongoing 2022 OutbreakJianglin Zhou0Xuejun Wang1Zhe Zhou2Shengqi Wang3Bioinformatics Center of AMMS, Beijing 100850, ChinaBioinformatics Center of AMMS, Beijing 100850, ChinaBioinformatics Center of AMMS, Beijing 100850, ChinaBioinformatics Center of AMMS, Beijing 100850, ChinaThe exceptionally widespread outbreak of human monkeypox, an emerging zoonosis caused by the <i>monkeypox virus</i> (MPXV), with more than 69,000 confirmed cases in 100 non-endemic countries since 2022, is a major public health concern. Codon usage patterns reflect genetic variation and adaptation to new hosts and ecological niches. However, detailed analyses of codon usage bias in MPXV based on large-scale genomic data, especially for strains responsible for the 2022 outbreak, are lacking. In this study, we analyzed codon usage in MPXV and its relationship with host adaptation. We confirmed the ongoing outbreak of MPXVs belonging to the West Africa (WA) lineage by principal component analysis based on their codon usage patterns. The 2022 outbreak strains had a relatively low codon usage bias. Codon usage of MPXVs was shaped by mutation and natural selection; however, different from past strains, codon usage in the 2022 outbreak strains was predominantly determined by mutation pressure. Additionally, as revealed by the codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses, the codon usage patterns of MPXVs were also affected by their hosts. In particular, the 2022 outbreak strains showed slightly but significantly greater adaptation to many primates, including humans, and were subjected to stronger selection pressure induced by hosts. Our results suggest that MPXVs contributing to the 2022 outbreak have unique evolutionary features, emphasizing the importance of sustained monitoring of their transmission and evolution.https://www.mdpi.com/1422-0067/24/14/11524monkeypox viruscodon usage biasmutation pressurenatural selectionevolutionhost adaptation |
| spellingShingle | Jianglin Zhou Xuejun Wang Zhe Zhou Shengqi Wang Insights into the Evolution and Host Adaptation of the Monkeypox Virus from a Codon Usage Perspective: Focus on the Ongoing 2022 Outbreak International Journal of Molecular Sciences monkeypox virus codon usage bias mutation pressure natural selection evolution host adaptation |
| title | Insights into the Evolution and Host Adaptation of the Monkeypox Virus from a Codon Usage Perspective: Focus on the Ongoing 2022 Outbreak |
| title_full | Insights into the Evolution and Host Adaptation of the Monkeypox Virus from a Codon Usage Perspective: Focus on the Ongoing 2022 Outbreak |
| title_fullStr | Insights into the Evolution and Host Adaptation of the Monkeypox Virus from a Codon Usage Perspective: Focus on the Ongoing 2022 Outbreak |
| title_full_unstemmed | Insights into the Evolution and Host Adaptation of the Monkeypox Virus from a Codon Usage Perspective: Focus on the Ongoing 2022 Outbreak |
| title_short | Insights into the Evolution and Host Adaptation of the Monkeypox Virus from a Codon Usage Perspective: Focus on the Ongoing 2022 Outbreak |
| title_sort | insights into the evolution and host adaptation of the monkeypox virus from a codon usage perspective focus on the ongoing 2022 outbreak |
| topic | monkeypox virus codon usage bias mutation pressure natural selection evolution host adaptation |
| url | https://www.mdpi.com/1422-0067/24/14/11524 |
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