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3. 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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4. Using artificial intelligence to document the hidden RNA virosphere

Author

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

Published
2024
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16. 2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author

Kuhn, Jens H., Adkins, Scott, Alkhovsky, Sergey V., Avšič-Županc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, Anne, Ballinger, Matthew J., Bandte, Martina, Beer, Martin, Bejerman, Nicolas, Bergeron, Éric, Biedenkopf, Nadine, Bigarré, Laurent, Blair, Carol D., Blasdell, Kim R., Bradfute, Steven B., Briese, Thomas, Brown, Paul A., Bruggmann, Rémy, Buchholz, Ursula J., Buchmeier, Michael J., Bukreyev, Alexander, Burt, Felicity, Büttner, Carmen, Calisher, Charles H., Candresse, Thierry, Carson, Jeremy, Casas, Inmaculada, Chandran, Kartik, Charrel, Rémi N., Chiaki, Yuya, Crane, Anya, Crane, Mark, Dacheux, Laurent, Bó, Elena Dal, de la Torre, Juan Carlos, de Lamballerie, Xavier, de Souza, William M., de Swart, Rik L., Dheilly, Nolwenn M., Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G., Digiaro, Michele, Drexler, J. Felix, Duprex, W. Paul, Dürrwald, Ralf, Easton, Andrew J., Elbeaino, Toufic, Ergünay, Koray, Feng, Guozhong, Feuvrier, Claudette, Firth, Andrew E., Fooks, Anthony R., Formenty, Pierre B. H., Freitas-Astúa, Juliana, Gago-Zachert, Selma, García, María Laura, García-Sastre, Adolfo, Garrison, Aura R., Godwin, Scott E., Gonzalez, Jean-Paul J., de Bellocq, Joëlle Goüy, Griffiths, Anthony, Groschup, Martin H., Günther, Stephan, Hammond, John, Hepojoki, Jussi, Hierweger, Melanie M., Hongō, Seiji, Horie, Masayuki, Horikawa, Hidenori, Hughes, Holly R., Hume, Adam J., Hyndman, Timothy H., Jiāng, Dàohóng, Jonson, Gilda B., Junglen, Sandra, Kadono, Fujio, Karlin, David G., Klempa, Boris, Klingström, Jonas, Koch, Michel C., Kondō, Hideki, Koonin, Eugene V., Krásová, Jarmila, Krupovic, Mart, Kubota, Kenji, Kuzmin, Ivan V., Laenen, Lies, Lambert, Amy J., Lǐ, Jiànróng, Li, Jun-Min, Lieffrig, François, Lukashevich, Igor S., Luo, Dongsheng, Maes, Piet, Marklewitz, Marco, Marshall, Sergio H., Marzano, Shin-Yi L., McCauley, John W., Mirazimi, Ali, Mohr, Peter G., Moody, Nick J. G., Morita, Yasuaki, Morrison, Richard N., Mühlberger, Elke, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, José A., Neriya, Yutaro, Netesov, Sergey V., Neumann, Gabriele, Nowotny, Norbert, Ochoa-Corona, Francisco M., Palacios, Gustavo, Pallandre, Laurane, Pallás, Vicente, Papa, Anna, Paraskevopoulou, Sofia, Parrish, Colin R., Pauvolid-Corrêa, Alex, Pawęska, Janusz T., Pérez, Daniel R., Pfaff, Florian, Plemper, Richard K., Postler, Thomas S., Pozet, Françoise, Radoshitzky, Sheli R., Ramos-González, Pedro L., Rehanek, Marius, Resende, Renato O., Reyes, Carina A., Romanowski, Víctor, Rubbenstroth, Dennis, Rubino, Luisa, Rumbou, Artemis, Runstadler, Jonathan A., Rupp, Melanie, Sabanadzovic, Sead, Sasaya, Takahide, Schmidt-Posthaus, Heike, Schwemmle, Martin, Seuberlich, Torsten, Sharpe, Stephen R., Shi, Mang, Sironi, Manuela, Smither, Sophie, Song, Jin-Won, Spann, Kirsten M., Spengler, Jessica R., Stenglein, Mark D., Takada, Ayato, Tesh, Robert B., Těšíková, Jana, Thornburg, Natalie J., Tischler, Nicole D., Tomitaka, Yasuhiro, Tomonaga, Keizō, Tordo, Noël, Tsunekawa, Kenta, Turina, Massimo, Tzanetakis, Ioannis E., Vaira, Anna Maria, van den Hoogen, Bernadette, Vanmechelen, Bert, Vasilakis, Nikos, Verbeek, Martin, von Bargen, Susanne, Wada, Jiro, Wahl, Victoria, Walker, Peter J., Whitfield, Anna E., Williams, John V., Wolf, Yuri I., Yamasaki, Junki, Yanagisawa, Hironobu, Ye, Gongyin, Zhang, Yong-Zhen, and Økland, Arnfinn Lodden

Published
2022
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17. Trafficked Malayan pangolins contain viral pathogens of humans

Author

Shi, Wenqiang, Shi, Mang, Que, Teng-Cheng, Cui, Xiao-Ming, Ye, Run-Ze, Xia, Luo-Yuan, Hou, Xin, Zheng, Jia-Jing, Jia, Na, Xie, Xing, Wu, Wei-Chen, He, Mei-Hong, Wang, Hui-Feng, Wei, Yong-Jie, Wu, Ai-Qiong, Zhang, Sheng-Feng, Pan, Yu-Sheng, Chen, Pan-Yu, Wang, Qian, Li, Shou-Sheng, Zhong, Yan-Li, Li, Ying-Jiao, Tan, Luo-Hao, Zhao, Lin, Jiang, Jia-Fu, Hu, Yan-Ling, and Cao, Wu-Chun

Published
2022
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19. VirID: Beyond Virus Discovery—An Integrated Platform for Comprehensive RNA Virus Characterization.

Author

Yang, Ziyue, Shan, Yongtao, Liu, Xue, Chen, Guowei, Pan, Yuanfei, Gou, Qinyu, Zou, Jie, Chang, Zilong, Zeng, Qiang, Yang, Chunhui, Kong, Jianbin, Sun, Yanni, Li, Shaochuan, Zhang, Xu, Wu, Wei-chen, Li, Chunmei, Peng, Hong, Holmes, Edward C, Guo, Deyin, and Shi, Mang

Subjects
RNA replicase, RNA viruses, VIRUS diversity, SOFTWARE development tools, GENETIC variation
Abstract

RNA viruses exhibit vast phylogenetic diversity and can significantly impact public health and agriculture. However, current bioinformatics tools for viral discovery from metagenomic data frequently generate false positive virus results, overestimate viral diversity, and misclassify virus sequences. Additionally, current tools often fail to determine virus–host associations, which hampers investigation of the potential threat posed by a newly detected virus. To address these issues we developed VirID, a software tool specifically designed for the discovery and characterization of RNA viruses from metagenomic data. The basis of VirID is a comprehensive RNA-dependent RNA polymerase database to enhance a workflow that includes RNA virus discovery, phylogenetic analysis, and phylogeny-based virus characterization. Benchmark tests on a simulated data set demonstrated that VirID had high accuracy in profiling viruses and estimating viral richness. In evaluations with real-world samples, VirID was able to identify RNA viruses of all types, but also provided accurate estimations of viral genetic diversity and virus classification, as well as comprehensive insights into virus associations with humans, animals, and plants. VirID therefore offers a robust tool for virus discovery and serves as a valuable resource in basic virological studies, pathogen surveillance, and early warning systems for infectious disease outbreaks. [ABSTRACT FROM AUTHOR]

Published
2024
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23. 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author

Kuhn, Jens H., Adkins, Scott, Agwanda, Bernard R., Al Kubrusli, Rim, Alkhovsky, Sergey V., Amarasinghe, Gaya K., Avšič-Županc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, Anne, Ballinger, Matthew J., Basler, Christopher F., Bavari, Sina, Beer, Martin, Bejerman, Nicolas, Bennett, Andrew J., Bente, Dennis A., Bergeron, Éric, Bird, Brian H., Blair, Carol D., Blasdell, Kim R., Blystad, Dag-Ragnar, Bojko, Jamie, Borth, Wayne B., Bradfute, Steven, Breyta, Rachel, Briese, Thomas, Brown, Paul A., Brown, Judith K., Buchholz, Ursula J., Buchmeier, Michael J., Bukreyev, Alexander, Burt, Felicity, Büttner, Carmen, Calisher, Charles H., Cao, Mengji, Casas, Inmaculada, Chandran, Kartik, Charrel, Rémi N., Cheng, Qi, Chiaki, Yuya, Chiapello, Marco, Choi, Il-Ryong, Ciuffo, Marina, Clegg, J. Christopher S., Crozier, Ian, Dal Bó, Elena, de la Torre, Juan Carlos, de Lamballerie, Xavier, de Swart, Rik L., Debat, Humberto, Dheilly, Nolwenn M., Di Cicco, Emiliano, Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G., Digiaro, Michele, Dolnik, Olga, Drebot, Michael A., Drexler, J. Felix, Dundon, William G., Duprex, W. Paul, Dürrwald, Ralf, Dye, John M., Easton, Andrew J., Ebihara, Hideki, Elbeaino, Toufic, Ergünay, Koray, Ferguson, Hugh W., Fooks, Anthony R., Forgia, Marco, Formenty, Pierre B. H., Fránová, Jana, Freitas-Astúa, Juliana, Fu, Jingjing, Fürl, Stephanie, Gago-Zachert, Selma, Gāo, George Fú, García, María Laura, García-Sastre, Adolfo, Garrison, Aura R., Gaskin, Thomas, Gonzalez, Jean-Paul J., Griffiths, Anthony, Goldberg, Tony L., Groschup, Martin H., Günther, Stephan, Hall, Roy A., Hammond, John, Han, Tong, Hepojoki, Jussi, Hewson, Roger, Hong, Jiang, Hong, Ni, Hongo, Seiji, Horie, Masayuki, Hu, John S., Hu, Tao, Hughes, Holly R., Hüttner, Florian, Hyndman, Timothy H., Ilyas, M., Jalkanen, Risto, Jiāng, Dàohóng, Jonson, Gilda B., Junglen, Sandra, Kadono, Fujio, Kaukinen, Karia H., Kawate, Michael, Klempa, Boris, Klingström, Jonas, Kobinger, Gary, Koloniuk, Igor, Kondō, Hideki, Koonin, Eugene V., Krupovic, Mart, Kubota, Kenji, Kurath, Gael, Laenen, Lies, Lambert, Amy J., Langevin, Stanley L., Lee, Benhur, Lefkowitz, Elliot J., Leroy, Eric M., Li, Shaorong, Li, Longhui, Lǐ, Jiànróng, Liu, Huazhen, Lukashevich, Igor S., Maes, Piet, de Souza, William Marciel, Marklewitz, Marco, Marshall, Sergio H., Marzano, Shin-Yi L., Massart, Sebastien, McCauley, John W., Melzer, Michael, Mielke-Ehret, Nicole, Miller, Kristina M., Ming, Tobi J., Mirazimi, Ali, Mordecai, Gideon J., Mühlbach, Hans-Peter, Mühlberger, Elke, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, José A., Netesov, Sergey V., Neumann, Gabriele, Nowotny, Norbert, Nunes, Márcio R. T., Olmedo-Velarde, Alejandro, Palacios, Gustavo, Pallás, Vicente, Pályi, Bernadett, Papa, Anna, Paraskevopoulou, Sofia, Park, Adam C., Parrish, Colin R., Patterson, David A., Pauvolid-Corrêa, Alex, Pawęska, Janusz T., Payne, Susan, Peracchio, Carlotta, Pérez, Daniel R., Postler, Thomas S., Qi, Liying, Radoshitzky, Sheli R., Resende, Renato O., Reyes, Carina A., Rima, Bertus K., Luna, Gabriel Robles, Romanowski, Víctor, Rota, Paul, Rubbenstroth, Dennis, Rubino, Luisa, Runstadler, Jonathan A., Sabanadzovic, Sead, Sall, Amadou Alpha, Salvato, Maria S., Sang, Rosemary, Sasaya, Takahide, Schulze, Angela D., Schwemmle, Martin, Shi, Mang, Shí, Xiǎohóng, Shí, Zhènglì, Shimomoto, Yoshifumi, Shirako, Yukio, Siddell, Stuart G., Simmonds, Peter, Sironi, Manuela, Smagghe, Guy, Smither, Sophie, Song, Jin-Won, Spann, Kirsten, Spengler, Jessica R., Stenglein, Mark D., Stone, David M., Sugano, Jari, Suttle, Curtis A., Tabata, Amy, Takada, Ayato, Takeuchi, Shigeharu, Tchouassi, David P., Teffer, Amy, Tesh, Robert B., Thornburg, Natalie J., Tomitaka, Yasuhiro, Tomonaga, Keizō, Tordo, Noël, Torto, Baldwyn, Towner, Jonathan S., Tsuda, Shinya, Tu, Changchun, Turina, Massimo, Tzanetakis, Ioannis E., Uchida, Janice, Usugi, Tomio, Vaira, Anna Maria, Vallino, Marta, van den Hoogen, Bernadette, Varsani, Arvind, Vasilakis, Nikos, Verbeek, Martin, von Bargen, Susanne, Wada, Jiro, Wahl, Victoria, Walker, Peter J., Wang, Lin-Fa, Wang, Guoping, Wang, Yanxiang, Wang, Yaqin, Waqas, Muhammad, Wèi, Tàiyún, Wen, Shaohua, Whitfield, Anna E., Williams, John V., Wolf, Yuri I., Wu, Jiangxiang, Xu, Lei, Yanagisawa, Hironobu, Yang, Caixia, Yang, Zuokun, Zerbini, F. Murilo, Zhai, Lifeng, Zhang, Yong-Zhen, Zhang, Song, Zhang, Jinguo, Zhang, Zhe, and Zhou, Xueping

Published
2021
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24. Correction to: 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author

Kuhn, Jens H., Adkins, Scott, Agwanda, Bernard R., Al Kubrusli, Rim, Alkhovsky, Sergey V., Amarasinghe, Gaya K., Avšič-Županc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, Anne, Ballinger, Matthew J., Basler, Christopher F., Bavari, Sina, Beer, Martin, Bejerman, Nicolas, Bennett, Andrew J., Bente, Dennis A., Bergeron, Éric, Bird, Brian H., Blair, Carol D., Blasdell, Kim R., Blystad, Dag-Ragnar, Bojko, Jamie, Borth, Wayne B., Bradfute, Steven, Breyta, Rachel, Briese, Thomas, Brown, Paul A., Brown, Judith K., Buchholz, Ursula J., Buchmeier, Michael J., Bukreyev, Alexander, Burt, Felicity, Büttner, Carmen, Calisher, Charles H., Cao, Mengji, Casas, Inmaculada, Chandran, Kartik, Charrel, Rémi N., Cheng, Qi, Chiaki, Yuya, Chiapello, Marco, Choi, Il-Ryong, Ciuffo, Marina, Clegg, J. Christopher S., Crozier, Ian, Dal Bó, Elena, de la Torre, Juan Carlos, de Lamballerie, Xavier, de Swart, Rik L., Debat, Humberto, Dheilly, Nolwenn M., Di Cicco, Emiliano, Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G., Digiaro, Michele, Dolnik, Olga, Drebot, Michael A., Drexler, J. Felix, Dundon, William G., Duprex, W. Paul, Dürrwald, Ralf, Dye, John M., Easton, Andrew J., Ebihara, Hideki, Elbeaino, Toufic, Ergünay, Koray, Ferguson, Hugh W., Fooks, Anthony R., Forgia, Marco, Formenty, Pierre B. H., Fránová, Jana, Freitas-Astúa, Juliana, Fu, Jingjing, Fürl, Stephanie, Gago-Zachert, Selma, Gāo, George Fú, García, María Laura, García-Sastre, Adolfo, Garrison, Aura R., Gaskin, Thomas, Gonzalez, Jean-Paul J., Griffiths, Anthony, Goldberg, Tony L., Groschup, Martin H., Günther, Stephan, Hall, Roy A., Hammond, John, Han, Tong, Hepojoki, Jussi, Hewson, Roger, Hong, Jiang, Hong, Ni, Hongo, Seiji, Horie, Masayuki, Hu, John S., Hu, Tao, Hughes, Holly R., Hüttner, Florian, Hyndman, Timothy H., Ilyas, M., Jalkanen, Risto, Jiāng, Dàohóng, Jonson, Gilda B., Junglen, Sandra, Kadono, Fujio, Kaukinen, Karia H., Kawate, Michael, Klempa, Boris, Klingström, Jonas, Kobinger, Gary, Koloniuk, Igor, Kondō, Hideki, Koonin, Eugene V., Krupovic, Mart, Kubota, Kenji, Kurath, Gael, Laenen, Lies, Lambert, Amy J., Langevin, Stanley L., Lee, Benhur, Lefkowitz, Elliot J., Leroy, Eric M., Li, Shaorong, Li, Longhui, Lǐ, Jiànróng, Liu, Huazhen, Lukashevich, Igor S., Maes, Piet, de Souza, William Marciel, Marklewitz, Marco, Marshall, Sergio H., Marzano, Shin-Yi L., Massart, Sebastien, McCauley, John W., Melzer, Michael, Mielke-Ehret, Nicole, Miller, Kristina M., Ming, Tobi J., Mirazimi, Ali, Mordecai, Gideon J., Mühlbach, Hans-Peter, Mühlberger, Elke, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, José A., Netesov, Sergey V., Neumann, Gabriele, Nowotny, Norbert, Nunes, Márcio R. T., Olmedo-Velarde, Alejandro, Palacios, Gustavo, Pallás, Vicente, Pályi, Bernadett, Papa, Anna, Paraskevopoulou, Sofia, Park, Adam C., Parrish, Colin R., Patterson, David A., Pauvolid-Corrêa, Alex, Pawęska, Janusz T., Payne, Susan, Peracchio, Carlotta, Pérez, Daniel R., Postler, Thomas S., Qi, Liying, Radoshitzky, Sheli R., Resende, Renato O., Reyes, Carina A., Rima, Bertus K., Luna, Gabriel Robles, Romanowski, Víctor, Rota, Paul, Rubbenstroth, Dennis, Rubino, Luisa, Runstadler, Jonathan A., Sabanadzovic, Sead, Sall, Amadou Alpha, Salvato, Maria S., Sang, Rosemary, Sasaya, Takahide, Schulze, Angela D., Schwemmle, Martin, Shi, Mang, Shí, Xiǎohóng, Shí, Zhènglì, Shimomoto, Yoshifumi, Shirako, Yukio, Siddell, Stuart G., Simmonds, Peter, Sironi, Manuela, Smagghe, Guy, Smither, Sophie, Song, Jin-Won, Spann, Kirsten, Spengler, Jessica R., Stenglein, Mark D., Stone, David M., Sugano, Jari, Suttle, Curtis A., Tabata, Amy, Takada, Ayato, Takeuchi, Shigeharu, Tchouassi, David P., Teffer, Amy, Tesh, Robert B., Thornburg, Natalie J., Tomitaka, Yasuhiro, Tomonaga, Keizō, Tordo, Noël, Torto, Baldwyn, Towner, Jonathan S., Tsuda, Shinya, Tu, Changchun, Turina, Massimo, Tzanetakis, Ioannis E., Uchida, Janice, Usugi, Tomio, Vaira, Anna Maria, Vallino, Marta, van den Hoogen, Bernadette, Varsani, Arvind, Vasilakis, Nikos, Verbeek, Martin, von Bargen, Susanne, Wada, Jiro, Wahl, Victoria, Walker, Peter J., Wang, Lin-Fa, Wang, Guoping, Wang, Yanxiang, Wang, Yaqin, Waqas, Muhammad, Wèi, Tàiyún, Wen, Shaohua, Whitfield, Anna E., Williams, John V., Wolf, Yuri I., Wu, Jiangxiang, Xu, Lei, Yanagisawa, Hironobu, Yang, Caixia, Yang, Zuokun, Zerbini, F. Murilo, Zhai, Lifeng, Zhang, Yong-Zhen, Zhang, Song, Zhang, Jinguo, Zhang, Zhe, and Zhou, Xueping

Published
2021
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27. The discovery of novel variants reveals the genetic diversity and potential origin of Seoul orthohantavirus.

Author

Kuang, Guopeng, Wang, Jing, Feng, Yun, Wu, Weichen, Han, Xi, Xin, Genyang, Yang, Weihong, Pan, Hong, Yang, Lifen, Wang, Juan, Shi, Mang, and Gao, Zihou

Subjects
HEMORRHAGIC fever with renal syndrome, RATTUS norvegicus, RODENT populations, GENETIC variation, VIRAL transmission
Abstract

Seoul orthohantavirus (SEOV) has been identified as one of the main causative agents of hemorrhagic fever with renal syndrome (HFRS) in China. The virus was found circulating in rodent populations in almost all provinces of the country, reflecting the wide distribution of HFRS. Here, using the direct immunofluorescence assay (DFA) and real-time quantitative reverse transcription PCR (qRT-PCR) approach, we performed screening in 1784 small mammals belonging to 14 species of three orders captured in the main areas of HFRS endemicity in Yunnan province (southwestern China) and identified 37 SEOV-positive rats (36 Rattus norvegicus and 1 Rattus tanezumi). A 3-year surveillance of HFRS epidemics and dynamics of rodent reservoir density and virus prevalence implied a potential correlation between them. The subsequent meta-transcriptomic sequencing and phylogenetic analyses revealed three SEOV variants, among which two are completely novel. The ancestral character state reconstruction (ACSR) analysis based on both novel variants and documented strains from 5 continents demonstrated that SEOV appeared to originate near the southwestern area (Yunnan-Kweichow Plateau) of China, then could spread to other regions and countries by their rodent carriers, resulting in a global distribution today. In summary, these data furthered the understanding regards genetic diversity and the potential origin for SEOV. However, the expanding endemic foci in the province suggest that the virus is spreading over a wider region and is much more diverse than previous depicted, which means that increased sampling is necessary. Author summary: Hantaviruses are primarily hosted by small mammals such as rodents, shrews, moles, and bats. In recent years, the diseases caused by rodent-associated hantaviruses become more frequent among humans in Yunnan province. In order to curb human infections, it is necessary to monitor the dynamics of virus prevalence in their natural reservoir populations. As expected, we detected 37 SEOV strains harbored by rats in the main endemic areas of the province, and the subsequent meta-transcriptomic and phylogenetic analyses revealed two SEOV variants that diverged early from the rest of the viruses, based on which Yunnan-Kweichow Plateau appears to be the region where earlier SEOV was originated. Further studies and more samples are needed to clarify how the virus migrates worldwide, and the pathogenicity of newly discovered viruses. [ABSTRACT FROM AUTHOR]

Published
2024
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28. SegVir: Reconstruction of Complete Segmented RNA Viral Genomes from Metatranscriptomes.

Author

Tang, Xubo, Shang, Jiayu, Chen, Guowei, Chan, Kei Hang Katie, Shi, Mang, and Sun, Yanni

Subjects
RNA viruses, GENETIC variation, SOURCE code, DATABASES, GENOMES
Abstract

Segmented RNA viruses are a complex group of RNA viruses with multisegment genomes. Reconstructing complete segmented viruses is crucial for advancing our understanding of viral diversity, evolution, and public health impact. Using metatranscriptomic data to identify known and novel segmented viruses has sped up the survey of segmented viruses in various ecosystems. However, the high genetic diversity and the difficulty in binning complete segmented genomes present significant challenges in segmented virus reconstruction. Current virus detection tools are primarily used to identify nonsegmented viral genomes. This study presents SegVir, a novel tool designed to identify segmented RNA viruses and reconstruct their complete genomes from complex metatranscriptomes. SegVir leverages both close and remote homology searches to accurately detect conserved and divergent viral segments. Additionally, we introduce a new method that can evaluate the genome completeness and conservation based on gene content. Our evaluations on simulated datasets demonstrate SegVir's superior sensitivity and precision compared to existing tools. Moreover, in experiments using real data, we identified some virus segments missing in the NCBI database, underscoring SegVir's potential to enhance viral metagenome analysis. The source code and supporting data of SegVir are available via https://github.com/HubertTang/SegVir. [ABSTRACT FROM AUTHOR]

Published
2024
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29. c-FLIP facilitates ZIKV infection by mediating caspase-8/3-dependent apoptosis.

Author

Zhang, Shengze, Li, Nina, Wu, Shu, Xie, Ting, Chen, Qiqi, Wu, Jiani, Zeng, Shike, Zhu, Lin, Bai, Shaohui, Zha, Haolu, Tian, Weijian, Wu, Nan, Zou, Xuan, Fang, Shisong, Luo, Chuming, Shi, Mang, Sun, Caijun, Shu, Yuelong, and Luo, Huanle

Subjects
ZIKA virus infections, RECURRENT miscarriage, APOPTOSIS, FETAL growth retardation, TROPHOBLAST, PYROPTOSIS, SPERMATOGENESIS, ZIKA virus
Abstract

c-FLIP functions as a dual regulator of apoptosis and inflammation, yet its implications in Zika virus (ZIKV) infection remain partially understood, especially in the context of ZIKV-induced congenital Zika syndrome (CZS) where both apoptosis and inflammation play pivotal roles. Our findings demonstrate that c-FLIP promotes ZIKV infection in placental cells and myeloid-derived macrophages, involving inflammation and caspase-8/3-mediated apoptosis. Moreover, our observations reveal that c-FLIP augments ZIKV infection in multiple tissues, including blood cell, spleen, uterus, testis, and the brain of mice. Notably, the partial deficiency of c-FLIP provides protection to embryos against ZIKV-induced CZS, accompanied by a reduction in caspase-3-mediated apoptosis. Additionally, we have found a distinctive parental effect of c-FLIP influencing ZIKV replication in fetal heads. In summary, our study reveals the critical role of c-FLIP as a positive regulator in caspase-8/3-mediated apoptosis during ZIKV infection, significantly contributing to the development of CZS. Author summary: Zika virus (ZIKV) infection in pregnant women can lead to the development of Congenital Zika Syndrome (CZS) in infants, resulting in complications such as microcephaly, intrauterine growth restriction (IUGR), and miscarriages. Although the mechanisms of apoptosis and inflammatory responses in ZIKV-induced CZS are not fully understood, our study investigated the role of c-FLIP, a critical regulator of apoptosis and inflammation during ZIKV infection and its associated CZS. In both human trophoblast cells and murine-derived macrophages, we observed that c-FLIP facilitated ZIKV infection by modulating caspase-8/3-mediated apoptosis. Mice deficient in c-FLIP exhibited reduced ZIKV replication and a decrease in inflammatory cytokine production. Importantly, c-FLIP deficiency demonstrated an inhibitory effect on CZS in ZIKV-infected pregnant mice. Additionally, c-FLIP displayed a parental influence on ZIKV replication in the fetal head by triggering caspase-3 activation. This research emphasizes the significance of c-FLIP in regulating caspase-8/3 and its profound impact on ZIKV-induced CZS, providing valuable insights into the role of apoptosis in ZIKV vertical transmission and fetal development. [ABSTRACT FROM AUTHOR]

Published
2024
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30. Emerging Sand Fly--Borne Phlebovirus in China

Author

Wang, Jing, Fu, Shihong, Xu, Ziqian, Cheng, Jingxia, Shi, Mang, Fan, Na, Song, Jingdong, Tian, Xiaodong, Cheng, Jianshu, Ni, Shuqing, He, Ying, Lei, Wenwen, Li, Fan, Peng, Heng, Wang, Bin, Wang, Huanyu, Lu, Xiaoqing, Ma, Yajun, and Liang, Guodong

Subjects
Cells (Biology) -- Analysis, Phylogeny -- Analysis, Health
Abstract

The genus Phlebovirus belongs to the order Bunyavirales, family Phenuiviridae (1). Many phleboviruses are sand fly-borne, including sandfly fever Sicilian virus (SFSV), sandfly fever Naples virus (SFNV), and sandfly fever [...]

Published
2020
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33. Rapid isolation and immune profiling of SARS-CoV-2 specific memory B cell in convalescent COVID-19 patients via LIBRA-seq

Author

He, Bing, Liu, Shuning, Wang, Yuanyuan, Xu, Mengxin, Cai, Wei, Liu, Jia, Bai, Wendi, Ye, Shupei, Ma, Yong, Hu, Hengrui, Meng, Huicui, Sun, Tao, Li, Yanling, Luo, Huanle, Shi, Mang, Du, Xiangjun, Zhao, Wenjing, Chen, Shoudeng, Yang, Jingyi, Zhu, Haipeng, Jie, Yusheng, Yang, Yuedong, Guo, Deyin, Wang, Qiao, Liu, Yuwen, Yan, Huimin, Wang, Manli, and Chen, Yao-Qing

Published
2021
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34. Transcriptomic Investigation of the Virus Spectrum Carried by Midges in Border Areas of Yunnan Province.

Author

Yang, Lifen, Wu, Weichen, Cai, Sa, Wang, Jing, Kuang, Guopeng, Yang, Weihong, Wang, Juan, Han, Xi, Pan, Hong, Shi, Mang, and Feng, Yun

Subjects
CULICOIDES, DIPTERA, CYTOCHROME oxidase, JAPANESE encephalitis viruses, DOUBLE-stranded RNA, ARTHROPOD vectors
Abstract

Yunnan province in China shares its borders with three neighboring countries: Myanmar, Vietnam, and Laos. The region is characterized by a diverse climate and is known to be a suitable habitat for various arthropods, including midges which are notorious for transmitting diseases which pose significant health burdens affecting both human and animal health. A total of 431,100 midges were collected from 15 different locations in the border region of Yunnan province from 2015 to 2020. These midges were divided into 37 groups according to the collection year and sampling site. These 37 groups of midges were then homogenized to extract nucleic acid. Metatranscriptomics were used to analyze their viromes. Based on the obtained cytochrome C oxidase I gene (COI) sequences, three genera were identified, including one species of Forcipomyia, one species of Dasyhelea, and twenty-five species of Culicoides. We identified a total of 3199 viruses in five orders and 12 families, including 1305 single-stranded positive-stranded RNA viruses (+ssRNA) in two orders and seven families, 175 single-stranded negative-stranded RNA viruses (−ssRNA) in two orders and one family, and 1719 double-stranded RNA viruses in five families. Six arboviruses of economic importance were identified, namely Banna virus (BAV), Japanese encephalitis virus (JEV), Akabane virus (AKV), Bluetongue virus (BTV), Tibetan circovirus (TIBOV), and Epizootic hemorrhagic disease virus (EHDV), all of which are capable, to varying extents, of causing disease in humans and/or animals. The survey sites in this study basically covered the current distribution area of midges in Yunnan province, which helps to predict the geographic expansion of midge species. The complexity and diversity of the viral spectrum carried by midges identified in the study calls for more in-depth research, which can be utilized to monitor arthropod vectors and to predict the emergence and spread of zoonoses and animal epidemics, which is of great significance for the control of vector-borne diseases. [ABSTRACT FROM AUTHOR]

Published
2024
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40. Total Infectome Characterization of Respiratory Infections during the 2022–23 COVID-19 Outbreak in China Revealed Extensive Coinfections with Links to SARS-CoV-2 Status, Age, and Disease Severity.

Author

Yang, Zhongzhou, Cai, Kanru, Liao, Yuqi, Wu, Wei-Chen, Xing, Li, Hu, Minxuan, Ren, Jiali, Zhang, Jieyun, Zhu, Xiuyun, Yuan, Ke, Wang, Shunyao, Huang, Hui, Yang, Chunhui, Zhang, Mingxia, Shi, Mang, and Lu, Hongzhou

Subjects
COVID-19 pandemic, RESPIRATORY infections, SARS-CoV-2, MIXED infections, NUCLEOTIDE sequencing
Abstract

Between 7 December 2022 and 28 February 2023, China experienced a new wave of COVID-19 that swept across the entire country and resulted in an increasing amount of respiratory infections and hospitalizations. The purpose of this study is to reveal the intensity and composition of coinfecting microbial agents. In total, 196 inpatients were recruited from The Third People's Hospital of Shenzhen, and 169 respiratory and 73 blood samples were collected for metagenomic next-generation sequencing. The total "Infectome" was characterized and compared across different groups defined by the SARS-CoV-2 detection status, age groups, and severity of disease. Our results revealed a total of 22 species of pathogenic microbes (4 viruses, 13 bacteria, and 5 fungi), and more were discovered in the respiratory tract than in blood. The diversity of the total infectome was highly distinguished between respiratory and blood samples, and it was generally higher in patients that were SARS-CoV-2-positive, older in age, and with more severe disease. At the individual pathogen level, HSV-1 seemed to be the major contributor to these differences observed in the overall comparisons. Collectively, this study reveals the highly complex respiratory infectome and high-intensity coinfection in patients admitted to the hospital during the period of the 2023 COVID-19 pandemic in China. [ABSTRACT FROM AUTHOR]

Published
2024
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42. Tamdy Virus in Ixodid Ticks Infesting Bactrian Camels, Xinjiang, China, 2018

Author

Zhou, Hong, Ma, Zhenghai, Hu, Tao, Bi, Yuhai, Mamuti, Amutikari, Yu, Runyuan, Carr, Michael J., Shi, Mang, Li, Juan, Sharshov, Kirill, Gao, George F., and Shi, Weifeng

Subjects
Phylogeny -- Analysis, Genomes -- Analysis, Genomics -- Analysis, Intelligence gathering, Newborn infants, Public health, Public health movements, Health
Abstract

Tamdy virus (TAMV) was first isolated from the tick species Hyalomma asiaticum asiaticum collected from sheep in the Tamdinsky district of the Bukhara region, Uzbekistan, in 1971 (1). Subsequently, large-scale [...]

Published
2019
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45. Emergence of an ancient and pathogenic mammarenavirus.

Author

Luo, Xue-Lian, Lu, Shan, Qin, Chuan, Shi, Mang, Lu, Xiao-Bo, Wang, Lu, Ga, Sang, Jin, Dong, Ma, Xin-Li, Yang, Jing, Dai, Yan, Bao, Lin-Lin, Cheng, Yan-Peng, Ge, Ya-Jun, Bai, Yi-Bo, Zhu, Wen-Tao, Pu, Ji, Sun, Hui, Huang, Yu-Yuan, and Xu, Ming-Chao

Published
2023
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46. Francisella tularensis subsp. holarctica in Ringtail Possums, Australia

Author

Eden, John-Sebastian, Rose, Karrie, Ng, Jimmy, Shi, Mang, Wang, Qinning, Sintchenko, Vitali, and Holmes, Edward C.

Subjects
Francisella tularensis -- Research, Pseudocheiridae -- Research, Health
Abstract

Tularemia is a highly infectious zoonotic disease caused by the bacterium Francisella tularensis that affects humans and other animals (1,2). Globally, tularemia has been identified in a wide range of [...]

Published
2017
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48. Hierarchical metacommunity structure of fungal endophytes.

Author

Pan, Yuanfei, Liu, Mu, Sosa, Alejandro, Li, Bo, Shi, Mang, and Pan, Xiaoyun

Subjects
ENDOPHYTIC fungi, FUNGAL communities, HOST plants, INVASIVE plants, SPECIES distribution, PLANT invasions
Abstract

Summary: The ecological and evolutionary processes shaping community structure and functions of microbial symbionts are known to be scale‐dependent. Nonetheless, understanding how the relative importance of these processes changes across spatial scales, and deciphering the hierarchical metacommunity structure of fungal endophytes has proven challenging.We investigated metacommunities of endophytic fungi within leaves of an invasive plant (Alternanthera philoxeroides) across wide latitudinal transects both in its native (Argentina) and introduced (China) ranges to test whether metacommunities of fungal endophytes were structured by different drivers at different spatial scales.We found Clementsian structures with seven discrete compartments (distinctive groups of fungal species with coincident distribution ranges), which coincided with the distribution of major watersheds. Metacommunity compartments were explicitly demarcated at three spatial scales, that is, the between‐continent, between‐compartment, and within‐compartment scales. At larger spatial scales, local environmental conditions (climate, soil, and host plant traits) were replaced by other geographical factors as principal determinants of metacommunity structure of fungal endophytes and community diversity–function relationships.Our results reveal novel insights into the scale dependency of diversity and functions of fungal endophytes, which are likely similar for plant symbionts. These findings can potentially improve our understanding of the global patterns of fungal diversity. [ABSTRACT FROM AUTHOR]

Published
2023
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49. Origin, genomic diversity and evolution of African swine fever virus in East Asia.

Author

Xin, Genyang, Kuang, Qiyuan, Le, Shijia, Wu, Weichen, Gao, Qi, Gao, Han, Xu, Zhiying, Zheng, Zezhong, Lu, Gang, Gong, Lang, Wang, Heng, Zhang, Guihong, Shi, Mang, and Sun, Yankuo

Subjects
AFRICAN swine fever virus, AFRICAN swine fever, HUMAN origins, GENETIC distance, GENEALOGY
Abstract

Since 2018, the outbreaks of genotype II African swine fever virus (ASFV) in China and several eastern Asian countries have caused a huge impact on the local swine industry, resulting in huge economic losses. However, little is known about the origin, genomic diversity, evolutionary features, and epidemiological history of the genotype II ASFV. Here, 14 high-quality complete genomes of ASFVs were generated via sequencing of samples collected from China over the course of 3 years, followed by phylogenetic and phylodynamic analyses. The strains identified were relatively homogeneous, with a total of 52 SNPs and 11 indels compared with the prototype strain HLJ/2018, among which there were four exceptionally large deletions (620–18,023 nt). Evolutionary analyses revealed that ASFV strains distributed in eastern Asia formed a monophyly and a 'star-like' structure centered around the prototype strain, suggesting a single origin. Additionally, phylogenetic network analysis and ancestral reconstruction of geographic state indicated that genotype II ASFV strains in eastern Asia likely originated from Western Europe. Overall, these results contribute to the understanding of the history and current status of genotype II ASFV strains in eastern Asian, which could be of considerable importance in disease control and prevention. [ABSTRACT FROM AUTHOR]

Published
2023
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50. Viral community composition of hypersaline lakes.

Author

Lay, Callum Le, Hamm, Joshua N, Williams, Timothy J, Shi, Mang, Cavicchioli, Ricardo, and Holmes, Edward C

Subjects
RNA replicase, HIDDEN Markov models, DNA viruses, LAKES, RNA viruses
Abstract

Despite their widespread distribution and remarkable antiquity no RNA viruses definitively associated with the domain Archaea have been identified. In contrast, 17 families of DNA viruses are known to infect archaea. In an attempt to uncover more of the elusive archaeal virosphere, we investigated the metatranscriptomes of hypersaline lakes that are a rich source of archaea. We sequenced RNA extracted from water filter samples of Lake Tyrrell (Victoria, Australia) and cultures seeded from four lakes in Antarctica. To identify highly divergent viruses in these data, we employed a variety of search tools, including Hidden Markov models (HMMs) and position-specific scoring matrices (PSSMs). From this, we identified 12 highly divergent, RNA virus-like candidate sequences from the virus phyla Artverviricota , Duplornaviricota , Kitrinoviricota, Negarnaviricota , and Pisuviricota , including those with similarity to the RNA-dependent RNA polymerase (RdRp). An additional analysis with an artificial intelligence (AI)-based approach that utilises both sequence and structural information identified seven putative and highly divergent RdRp sequences of uncertain phylogenetic position. A sequence matching the Pisuviricota from Deep Lake in Antarctica had the strongest RNA virus signal. Analyses of the dinucleotide representation of the virus-like candidates in comparison to that of potential host species were in some cases compatible with an association to archaeal or bacterial hosts. Notably, however, the use of archaeal CRISPR spacers as a BLAST database failed to detect any RNA viruses. We also described DNA viruses from the families Pleolipoviridae , Sphaerolipoviridae , Halspiviridae , and the class Caudoviricetes. Although we were unable to provide definitive evidence the existence of an RNA virus of archaea in these hypersaline lakes, this study lays the foundations for further investigations of highly divergent RNA viruses in natural environments. [ABSTRACT FROM AUTHOR]

Published
2023
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