Flavivirus genome recoding by codon optimisation confers genetically stable in vivo attenuation in both mice and mosquitoes.
Virus genome recoding is an attenuation method that confers genetically stable attenuation by rewriting a virus genome with numerous silent mutations. Prior flavivirus genome recoding attempts utilised codon deoptimisation approaches. However, these codon deoptimisation approaches act in a species d...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2023-10-01
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| Series: | PLoS Pathogens |
| Online Access: | https://journals.plos.org/plospathogens/article/file?id=10.1371/journal.ppat.1011753&type=printable |
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| author | Wei-Xin Chin Hao Yuin Kong Isabelle Xin Yu Zhu Zi Yun Teo Regina Faruk Regina Ching Hua Lee Si Xian Ho Zhen Qin Aw Bowen Yi Xin Jun Hou Antson Kiat Yee Tan Thinesshwary Yogarajah Roland G Huber Yu Cai Yue Wan Justin Jang Hann Chu |
| author_facet | Wei-Xin Chin Hao Yuin Kong Isabelle Xin Yu Zhu Zi Yun Teo Regina Faruk Regina Ching Hua Lee Si Xian Ho Zhen Qin Aw Bowen Yi Xin Jun Hou Antson Kiat Yee Tan Thinesshwary Yogarajah Roland G Huber Yu Cai Yue Wan Justin Jang Hann Chu |
| author_sort | Wei-Xin Chin |
| collection | DOAJ |
| description | Virus genome recoding is an attenuation method that confers genetically stable attenuation by rewriting a virus genome with numerous silent mutations. Prior flavivirus genome recoding attempts utilised codon deoptimisation approaches. However, these codon deoptimisation approaches act in a species dependent manner and were unable to confer flavivirus attenuation in mosquito cells or in mosquito animal models. To overcome these limitations, we performed flavivirus genome recoding using the contrary approach of codon optimisation. The genomes of flaviviruses such as dengue virus type 2 (DENV2) and Zika virus (ZIKV) contain functional RNA elements that regulate viral replication. We hypothesised that flavivirus genome recoding by codon optimisation would introduce silent mutations that disrupt these RNA elements, leading to decreased replication efficiency and attenuation. We chose DENV2 and ZIKV as representative flaviviruses and recoded them by codon optimising their genomes for human expression. Our study confirms that this recoding approach of codon optimisation does translate into reduced replication efficiency in mammalian, human, and mosquito cells as well as in vivo attenuation in both mice and mosquitoes. In silico modelling and RNA SHAPE analysis confirmed that DENV2 recoding resulted in the extensive disruption of genomic structural elements. Serial passaging of recoded DENV2 resulted in the emergence of rescue or adaptation mutations, but no reversion mutations. These rescue mutations were unable to rescue the delayed replication kinetics and in vivo attenuation of recoded DENV2, demonstrating that recoding confers genetically stable attenuation. Therefore, our recoding approach is a reliable attenuation method with potential applications for developing flavivirus vaccines. |
| first_indexed | 2024-03-11T11:40:31Z |
| format | Article |
| id | doaj.art-6c7e5f7d18a143fe966098392d649a02 |
| institution | Directory Open Access Journal |
| issn | 1553-7366 1553-7374 |
| language | English |
| last_indexed | 2024-03-11T11:40:31Z |
| publishDate | 2023-10-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Pathogens |
| spelling | doaj.art-6c7e5f7d18a143fe966098392d649a022023-11-10T05:31:22ZengPublic Library of Science (PLoS)PLoS Pathogens1553-73661553-73742023-10-011910e101175310.1371/journal.ppat.1011753Flavivirus genome recoding by codon optimisation confers genetically stable in vivo attenuation in both mice and mosquitoes.Wei-Xin ChinHao Yuin KongIsabelle Xin Yu ZhuZi Yun TeoRegina FarukRegina Ching Hua LeeSi Xian HoZhen Qin AwBowen YiXin Jun HouAntson Kiat Yee TanThinesshwary YogarajahRoland G HuberYu CaiYue WanJustin Jang Hann ChuVirus genome recoding is an attenuation method that confers genetically stable attenuation by rewriting a virus genome with numerous silent mutations. Prior flavivirus genome recoding attempts utilised codon deoptimisation approaches. However, these codon deoptimisation approaches act in a species dependent manner and were unable to confer flavivirus attenuation in mosquito cells or in mosquito animal models. To overcome these limitations, we performed flavivirus genome recoding using the contrary approach of codon optimisation. The genomes of flaviviruses such as dengue virus type 2 (DENV2) and Zika virus (ZIKV) contain functional RNA elements that regulate viral replication. We hypothesised that flavivirus genome recoding by codon optimisation would introduce silent mutations that disrupt these RNA elements, leading to decreased replication efficiency and attenuation. We chose DENV2 and ZIKV as representative flaviviruses and recoded them by codon optimising their genomes for human expression. Our study confirms that this recoding approach of codon optimisation does translate into reduced replication efficiency in mammalian, human, and mosquito cells as well as in vivo attenuation in both mice and mosquitoes. In silico modelling and RNA SHAPE analysis confirmed that DENV2 recoding resulted in the extensive disruption of genomic structural elements. Serial passaging of recoded DENV2 resulted in the emergence of rescue or adaptation mutations, but no reversion mutations. These rescue mutations were unable to rescue the delayed replication kinetics and in vivo attenuation of recoded DENV2, demonstrating that recoding confers genetically stable attenuation. Therefore, our recoding approach is a reliable attenuation method with potential applications for developing flavivirus vaccines.https://journals.plos.org/plospathogens/article/file?id=10.1371/journal.ppat.1011753&type=printable |
| spellingShingle | Wei-Xin Chin Hao Yuin Kong Isabelle Xin Yu Zhu Zi Yun Teo Regina Faruk Regina Ching Hua Lee Si Xian Ho Zhen Qin Aw Bowen Yi Xin Jun Hou Antson Kiat Yee Tan Thinesshwary Yogarajah Roland G Huber Yu Cai Yue Wan Justin Jang Hann Chu Flavivirus genome recoding by codon optimisation confers genetically stable in vivo attenuation in both mice and mosquitoes. PLoS Pathogens |
| title | Flavivirus genome recoding by codon optimisation confers genetically stable in vivo attenuation in both mice and mosquitoes. |
| title_full | Flavivirus genome recoding by codon optimisation confers genetically stable in vivo attenuation in both mice and mosquitoes. |
| title_fullStr | Flavivirus genome recoding by codon optimisation confers genetically stable in vivo attenuation in both mice and mosquitoes. |
| title_full_unstemmed | Flavivirus genome recoding by codon optimisation confers genetically stable in vivo attenuation in both mice and mosquitoes. |
| title_short | Flavivirus genome recoding by codon optimisation confers genetically stable in vivo attenuation in both mice and mosquitoes. |
| title_sort | flavivirus genome recoding by codon optimisation confers genetically stable in vivo attenuation in both mice and mosquitoes |
| url | https://journals.plos.org/plospathogens/article/file?id=10.1371/journal.ppat.1011753&type=printable |
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