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18 results on '"Li, Cixiu"'

4. The evolutionary and molecular history of a chikungunya virus outbreak lineage

Author

Krambrich, Janina, Mihalič, Filip, Gaunt, Michael W., Bohlin, Jon, Hesson, Jenny C., Lundkvist, Åke, de Lamballerie, Xavier, Li, Cixiu, Shi, Weifeng, Pettersson, John H.-O., Krambrich, Janina, Mihalič, Filip, Gaunt, Michael W., Bohlin, Jon, Hesson, Jenny C., Lundkvist, Åke, de Lamballerie, Xavier, Li, Cixiu, Shi, Weifeng, and Pettersson, John H.-O.

Abstract

In 2018–2019, Thailand experienced a nationwide spread of chikungunya virus (CHIKV), with approximately 15,000 confirmed cases of disease reported. Here, we investigated the evolutionary and molecular history of the East/Central/South African (ECSA) genotype to determine the origins of the 2018–2019 CHIKV outbreak in Thailand. This was done using newly sequenced clinical samples from travellers returning to Sweden from Thailand in late 2018 and early 2019 and previously published genome sequences. Our phylogeographic analysis showed that before the outbreak in Thailand, the Indian Ocean lineage (IOL) found within the ESCA, had evolved and circulated in East Africa, South Asia, and Southeast Asia for about 15 years. In the first half of 2017, an introduction occurred into Thailand from another South Asian country, most likely Bangladesh, which subsequently developed into a large outbreak in Thailand with export to neighbouring countries. Based on comparative phylogenetic analyses of the complete CHIKV genome and protein modelling, we identified several mutations in the E1/E2 spike complex, such as E1 K211E and E2 V264A, which are highly relevant as they may lead to changes in vector competence, transmission efficiency and pathogenicity of the virus. A number of mutations (E2 G205S, Nsp3 D372E, Nsp2 V793A), that emerged shortly before the outbreak of the virus in Thailand in 2018 may have altered antibody binding and recognition due to their position. This study not only improves our understanding of the factors contributing to the epidemic in Southeast Asia, but also has implications for the development of effective response strategies and the potential development of new vaccines.

Published
2024
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8. Metatranscriptomic Sequencing Reveals Host Species as an Important Factor Shaping the Mosquito Virome

Author

Li, Cixiu, primary, Liu, Shuqi, additional, Zhou, Hong, additional, Zhu, Wei, additional, Cui, Mingxue, additional, Li, Juan, additional, Wang, Jiao, additional, Liu, Jiangyun, additional, Zhu, Jin, additional, Li, Weiping, additional, Bi, Yuhai, additional, Carr, Michael J., additional, Holmes, Edward C., additional, and Shi, Weifeng, additional

Published
2023
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9. Additional file 2 of Nationwide genomic surveillance reveals the prevalence and evolution of honeybee viruses in China

Author

Li, Nannan, Li, Cixiu, Hu, Tao, Li, Juan, Zhou, Hong, Ji, Jingkai, Wu, Jiangli, Kang, Weipeng, Holmes, Edward C., Shi, Weifeng, and Xu, Shufa

Abstract

Additional file 2: Figure S1. Maximum likelihood phylogeny of DWV. Figure S2. Maximum likelihood phylogeny of SBV. Figure S3. Maximum likelihood phylogeny of LSV. Figure S4. Maximum likelihood phylogeny of BQCV. Figure S5. Maximum likelihood phylogeny of CBPV. Figure S6. Maximum likelihood phylogeny of IAPV. Figure S7. Maximum likelihood phylogeny of BMLV-AMFV. Figure S8. Maximum likelihood phylogeny of ABPV. Figure S9. Maximum likelihood phylogeny of ARV1-ARV2. Figure S10. Maximum likelihood phylogeny of VOV1-VDV3/5. Figure S11. Intra-species diversity and global distribution of DWV. Figure S12. Summary of genomic features of the novel viruses identified in this study. Figure S13. Maximum likelihood phylogeny of the rhabdoviruses. Figure S14. Tagged RT-PCR results on four viruses. Figure S15. Beta diversity analysis of the viromic composition among libraries.

Published
2023
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10. A Novel Bunyavirus Discovered in Oriental Shrimp (Penaeus chinensis)

Author

Dong, Xuan, primary, Hu, Tao, additional, Ren, Yanbei, additional, Meng, Fanzeng, additional, Li, Chen, additional, Zhang, Qingli, additional, Chen, Jiayuan, additional, Song, Jipeng, additional, Wang, Ruoyu, additional, Shi, Mang, additional, Li, Juan, additional, Zhao, Peng, additional, Li, Cixiu, additional, Tang, Kathy F. J., additional, Cowley, Jeff A., additional, Shi, Weifeng, additional, and Huang, Jie, additional

Published
2021
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13. A Novel Virus of Flaviviridae Associated with Sexual Precocity in Macrobrachium rosenbergii

Author

Dong, Xuan, primary, Wang, Guohao, additional, Hu, Tao, additional, Li, Juan, additional, Li, Chen, additional, Cao, Zhi, additional, Shi, Mang, additional, Wang, Yiting, additional, Zou, Peizhuo, additional, Song, Jipeng, additional, Gao, Wen, additional, Meng, Fanzeng, additional, Yang, Guoliang, additional, Tang, Kathy F. J., additional, Li, Cixiu, additional, Shi, Weifeng, additional, and Huang, Jie, additional

Published
2021
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14. Diversity and connectedness of brine shrimp viruses in global hypersaline ecosystems

Author

Dong, Xuan, Li, Cixiu, Wang, Yiting, Hu, Tao, Zhang, Fan, Meng, Fanzeng, Gao, Meirong, Han, Xuekai, Wang, Guohao, Qin, Jiahao, Nauwynck, Hans, Holmes, Edward C., Sorgeloos, Patrick, Sui, Liying, Huang, Jie, and Shi, Weifeng

Abstract

Brine shrimp (Artemia) has existed on Earth for 400 million years and has major ecological importance in hypersaline ecosystems. As a crucial live food in aquaculture, brine shrimp cysts have become one of the most important aquatic products traded worldwide. However, our understanding of the biodiversity, prevalence and global connectedness of viruses in brine shrimp is still very limited. A total of 143 batches of brine shrimp (belonging to seven species) cysts were collected from six continents including 21 countries and more than 100 geographic locations worldwide during 1977–2019. In total, 55 novel RNA viruses were identified, which could be assigned to 18 different viral families and related clades. Eleven viruses were dsRNA viruses, 16 were +ssRNA viruses, and 28 were–ssRNA viruses. Phylogenetic analyses of the RNA-directed RNA polymerase (RdRp) showed that brine shrimp viruses were often grouped with viruses isolated from other invertebrates and fungi. Remarkably, most brine shrimp viruses were related to those from different hosts that might feed on brine shrimp or share the same ecological niche. A notable case was the novel brine shrimp noda-like virus 3, which shared 79.25% (RdRp) and 63.88% (capsid proteins) amino acid identity with covert mortality nodavirus (CMNV) that may cause losses in aquaculture. In addition, both virome composition and phylogenetic analyses revealed global connectedness in certain brine shrimp viruses, particularly among Asia and Northern America. This highlights the incredible species diversity of viruses in these ancient species and provides essential data for the prevalence of RNA viruses in the global aquaculture industry. More broadly, these findings provide novel insights into the previously unrecognized RNA virosphere in hypersaline ecosystems worldwide and demonstrate that human activity might have driven the global connectedness of brine shrimp viruses.

Published
2023
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16. Total infectomes of 162 SARS-CoV-2 cases using meta-transcriptomic sequencing

Author

Zhou, Hong, primary, Li, Cixiu, additional, Hu, Tao, additional, Liu, Ti, additional, Ni, Nan, additional, Chen, Weijun, additional, Zhao, Huailong, additional, Ruan, Shiman, additional, Li, Juan, additional, Wu, Honglong, additional, François, Sarah, additional, Pybus, Oliver G., additional, Holmes, Edward C., additional, Kang, Dianmin, additional, Hou, Peiqiang, additional, and Shi, Weifeng, additional

Published
2021
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18. The evolutionary and molecular history of a chikungunya virus outbreak lineage.

Author

Krambrich J, Mihalič F, Gaunt MW, Bohlin J, Hesson JC, Lundkvist Å, de Lamballerie X, Li C, Shi W, and Pettersson JH

Subjects
Humans, Thailand epidemiology, Genome, Viral, Sweden epidemiology, Phylogeography, Mutation, Viral Envelope Proteins genetics, Chikungunya virus genetics, Chikungunya virus classification, Chikungunya virus isolation & purification, Chikungunya Fever epidemiology, Chikungunya Fever virology, Disease Outbreaks, Phylogeny, Evolution, Molecular, Genotype
Abstract

In 2018-2019, Thailand experienced a nationwide spread of chikungunya virus (CHIKV), with approximately 15,000 confirmed cases of disease reported. Here, we investigated the evolutionary and molecular history of the East/Central/South African (ECSA) genotype to determine the origins of the 2018-2019 CHIKV outbreak in Thailand. This was done using newly sequenced clinical samples from travellers returning to Sweden from Thailand in late 2018 and early 2019 and previously published genome sequences. Our phylogeographic analysis showed that before the outbreak in Thailand, the Indian Ocean lineage (IOL) found within the ESCA, had evolved and circulated in East Africa, South Asia, and Southeast Asia for about 15 years. In the first half of 2017, an introduction occurred into Thailand from another South Asian country, most likely Bangladesh, which subsequently developed into a large outbreak in Thailand with export to neighbouring countries. Based on comparative phylogenetic analyses of the complete CHIKV genome and protein modelling, we identified several mutations in the E1/E2 spike complex, such as E1 K211E and E2 V264A, which are highly relevant as they may lead to changes in vector competence, transmission efficiency and pathogenicity of the virus. A number of mutations (E2 G205S, Nsp3 D372E, Nsp2 V793A), that emerged shortly before the outbreak of the virus in Thailand in 2018 may have altered antibody binding and recognition due to their position. This study not only improves our understanding of the factors contributing to the epidemic in Southeast Asia, but also has implications for the development of effective response strategies and the potential development of new vaccines., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Krambrich et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Published
2024
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