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12 results on '"Gou, Qin-yu"'

1. Metagenomic analysis of individual mosquito viromes reveals the geographical patterns and drivers of viral diversity

Author

Pan, Yuan-Fei, Zhao, Hailong, Gou, Qin-Yu, Shi, Pei-Bo, Tian, Jun-Hua, Feng, Yun, Li, Kun, Yang, Wei-Hong, Wu, De, Tang, Guangpeng, Zhang, Bing, Ren, Zirui, Peng, Shiqin, Luo, Geng-Yan, Le, Shi-Jia, Xin, Gen-Yang, Wang, Jing, Hou, Xin, Peng, Min-Wu, Kong, Jian-Bin, Chen, Xin-Xin, Yang, Chun-Hui, Mei, Shi-Qiang, Liao, Yu-Qi, Cheng, Jing-Xia, Wang, Juan, Chaolemen, Wu, Yu-Hui, Wang, Jian-Bo, An, Tongqing, Huang, Xinyi, Eden, John-Sebastian, Li, Jun, Guo, Deyin, Liang, Guodong, Jin, Xin, Holmes, Edward C., Li, Bo, Wang, Daxi, Li, Junhua, Wu, Wei-Chen, and Shi, Mang

Published
2024
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3. Metagenomic analysis of individual mosquitos reveals the ecology of insect viruses

Author

Pan, Yuan-fei, primary, Zhao, Hailong, additional, Gou, Qin-yu, additional, Shi, Pei-bo, additional, Tian, Jun-hua, additional, Feng, Yun, additional, Li, Kun, additional, Yang, Wei-hong, additional, Wu, De, additional, Tang, Guangpeng, additional, Zhang, Bing, additional, Ren, Zirui, additional, Peng, Shiqin, additional, Luo, Geng-yan, additional, Le, Shi-jia, additional, Xin, Gen-yang, additional, Wang, Jing, additional, Hou, Xin, additional, Peng, Min-wu, additional, Kong, Jian-bin, additional, Chen, Xin-xin, additional, Yang, Chun-hui, additional, Mei, Shi-qiang, additional, Liao, Yu-qi, additional, Cheng, Jing-xia, additional, Wang, Juan, additional, n/a, Chaolemen, additional, Wu, Yu-hui, additional, Wang, Jian-bo, additional, An, Tongqing, additional, Huang, Xinyi, additional, Eden, John-Sebastian, additional, Li, Jun, additional, Guo, Deyin, additional, Liang, Guodong, additional, Jin, Xin, additional, Holmes, Edward C, additional, Li, Bo, additional, Wang, Daxi, additional, Li, Junhua, additional, Wu, Wei-chen, additional, and Shi, Mang, additional

Published
2023
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4. Artificial intelligence redefines RNA virus discovery

Author

Shi, Mang, primary, Hou, Xin, additional, He, Yong, additional, Fang, Pan, additional, Mei, Shi-Qiang, additional, Xu, Zan, additional, Wu, Wei-Chen, additional, Tian, Jun-hua, additional, Zhang, Shun, additional, Zeng, Zhen-Yu, additional, Gou, Qin-Yu, additional, Xin, Gen-Yang, additional, Le, Shi-Jia, additional, Xia, Yinyue, additional, Zhou, Yu-Lan, additional, Hui, Feng-Ming, additional, Pan, Yuan-Fei, additional, Eden, John-Sebastian, additional, Yang, Zhaohui, additional, Han, Chong, additional, Shu, Yuelong, additional, Guo, Deyin, additional, Li, Jun, additional, Holmes, Edward, additional, and Li, Zhaorong, additional

Published
2023
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5. Artificial intelligence redefines RNA virus discovery

Author

Hou, Xin, primary, He, Yong, additional, Fang, Pan, additional, Mei, Shi-Qiang, additional, Xu, Zan, additional, Wu, Wei-Chen, additional, Tian, Jun-Hua, additional, Zhang, Shun, additional, Zeng, Zhen-Yu, additional, Gou, Qin-Yu, additional, Xin, Gen-Yang, additional, Le, Shi-Jia, additional, Xia, Yin-Yue, additional, Zhou, Yu-Lan, additional, Hui, Feng-Ming, additional, Pan, Yuan-Fei, additional, Eden, John-Sebastian, additional, Yang, Zhao-Hui, additional, Han, Chong, additional, Shu, Yue-Long, additional, Guo, Deyin, additional, Li, Jun, additional, Holmes, Edward C., additional, Li, Zhao-Rong, additional, and Shi, Mang, additional

Published
2023
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6. Individual bat viromes reveal the co-infection, spillover and emergence risk of potential zoonotic viruses

Author

Wang, Jing, primary, Pan, Yuanfei, additional, Yang, Li-fen, additional, Yang, Wei-hong, additional, Luo, Chuming, additional, Wang, Juan, additional, Kuang, Guo-peng, additional, Wu, Weichen, additional, Gou, Qin-yu, additional, Xin, Gen-yang, additional, Li, Bo, additional, Luo, Huanle, additional, chen, Yao-Qing, additional, Shu, Yuelong, additional, Guo, Deyin, additional, Gao, Zihou, additional, Liang, Guodong, additional, Li, Jun, additional, Holmes, Edward, additional, Feng, Yun, additional, and Shi, Mang, additional

Published
2022
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9. time-series meta-transcriptomic analysis reveals the seasonal, host, and gender structure of mosquito viromes.

Author

Feng, Yun, Gou, Qin-yu, Yang, Wei-hong, Wu, Wei-chen, Wang, Juan, Holmes, Edward C, Liang, Guodong, and Shi, Mang

Subjects
TIME series analysis, MOSQUITOES, JAPANESE encephalitis viruses, BAT conservation, DNA viruses, GENDER
Abstract

Although metagenomic sequencing has revealed high numbers of viruses in mosquitoes sampled globally, our understanding of how their diversity and abundance varies in time and space as well as by host species and gender remains unclear. To address this, we collected 23,109 mosquitoes over the course of 12 months from a bat-dwelling cave and a nearby village in Yunnan province, China. These samples were organized by mosquito species, mosquito gender, and sampling time for meta-transcriptomic sequencing. A total of 162 eukaryotic virus species were identified, of which 101 were novel, including representatives of seventeen RNA virus multi-family supergroups and four species of DNA virus from the families Parvoviridae, Circoviridae , and Nudiviridae. In addition, two known vector-borne viruses—Japanese encephalitis virus and Banna virus—were found. Analyses of the entire virome revealed strikingly different viral compositions and abundance levels in warmer compared to colder months, a strong host structure at the level of mosquito species, and no substantial differences between those viruses harbored by male and female mosquitoes. At the scale of individual viruses, some were found to be ubiquitous throughout the year and across four mosquito species, while most of the other viruses were season and/or host specific. Collectively, this study reveals the diversity, dynamics, and evolution of the mosquito virome at a single location and sheds new lights on the ecology of these important vector animals. [ABSTRACT FROM AUTHOR]

Published
2022
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10. Using artificial intelligence to document the hidden RNA virosphere.

Author

Hou X, He Y, Fang P, Mei SQ, Xu Z, Wu WC, Tian JH, Zhang S, Zeng ZY, Gou QY, Xin GY, Le SJ, Xia YY, Zhou YL, Hui FM, Pan YF, Eden JS, Yang ZH, Han C, Shu YL, Guo D, Li J, Holmes EC, Li ZR, and Shi M

Abstract

Current metagenomic tools can fail to identify highly divergent RNA viruses. We developed a deep learning algorithm, termed LucaProt, to discover highly divergent RNA-dependent RNA polymerase (RdRP) sequences in 10,487 metatranscriptomes generated from diverse global ecosystems. LucaProt integrates both sequence and predicted structural information, enabling the accurate detection of RdRP sequences. Using this approach, we identified 161,979 potential RNA virus species and 180 RNA virus supergroups, including many previously poorly studied groups, as well as RNA virus genomes of exceptional length (up to 47,250 nucleotides) and genomic complexity. A subset of these novel RNA viruses was confirmed by RT-PCR and RNA/DNA sequencing. Newly discovered RNA viruses were present in diverse environments, including air, hot springs, and hydrothermal vents, with virus diversity and abundance varying substantially among ecosystems. This study advances virus discovery, highlights the scale of the virosphere, and provides computational tools to better document the global RNA virome., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Published
2024
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11. Metagenomic analysis of individual mosquitos reveals the ecology of insect viruses.

Author

Pan YF, Zhao H, Gou QY, Shi PB, Tian JH, Feng Y, Li K, Yang WH, Wu, Tang G, Zhang B, Ren Z, Peng S, Luo GY, Le SJ, Xin GY, Wang J, Hou X, Peng MW, Kong JB, Chen XX, Yang CH, Mei SQ, Liao YQ, Cheng JX, Wang J, Chaolemen, Wu YH, Wang JB, An T, Huang X, Eden JS, Li J, Guo D, Liang G, Jin X, Holmes EC, Li B, Wang D, Li J, Wu WC, and Shi M

Abstract

Mosquito transmitted viruses are responsible for an increasing burden of human disease. Despite this, little is known about the diversity and ecology of viruses within individual mosquito hosts. Using a meta-transcriptomic approach, we analysed the virome of 2,438 individual mosquitos (79 species), spanning ~4000 km along latitudes and longitudes in China. From these data we identified 393 core viral species associated with mosquitos, including seven (putative) arbovirus species. We identified potential species and geographic hotspots of viral richness and arbovirus occurrence, and demonstrated that host phylogeny had a strong impact on the composition of individual mosquito viromes. Our data revealed a large number of viruses shared among mosquito species or genera, expanding our knowledge of host specificity of insect-associated viruses. We also detected multiple virus species that were widespread throughout the country, possibly facilitated by long-distance mosquito migrations. Together, our results greatly expand the known mosquito virome, linked the viral diversity at the scale of individual insects to that at a country-wide scale, and offered unique insights into the ecology of viruses of insect vectors., Competing Interests: COMPETING INTERESTS The authors declare no competing interests.

Published
2023
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12. Individual bat viromes reveal the co-infection, spillover and emergence risk of potential zoonotic viruses.

Author

Wang J, Pan YF, Yang LF, Yang WH, Luo CM, Wang J, Kuang GP, Wu WC, Gou QY, Xin GY, Li B, Luo HL, Chen YQ, Shu YL, Guo D, Gao ZH, Liang G, Li J, Holmes EC, Feng Y, and Shi M

Abstract

Bats are reservoir hosts for many zoonotic viruses. Despite this, relatively little is known about the diversity and abundance of viruses within bats at the level of individual animals, and hence the frequency of virus co-infection and inter-species transmission. Using an unbiased meta-transcriptomics approach we characterised the mammalian associated viruses present in 149 individual bats sampled from Yunnan province, China. This revealed a high frequency of virus co-infection and species spillover among the animals studied, with 12 viruses shared among different bat species, which in turn facilitates virus recombination and reassortment. Of note, we identified five viral species that are likely to be pathogenic to humans or livestock, including a novel recombinant SARS-like coronavirus that is closely related to both SARS-CoV-2 and SARS-CoV, with only five amino acid differences between its receptor-binding domain sequence and that of the earliest sequences of SARS-CoV-2. Functional analysis predicts that this recombinant coronavirus can utilize the human ACE2 receptor such that it is likely to be of high zoonotic risk. Our study highlights the common occurrence of inter-species transmission and co-infection of bat viruses, as well as their implications for virus emergence.

Published
2022
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