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1. African army ants at the forefront of virome surveillance in a remote tropical forest

Author

Fritz, Matthieu, Reggiardo, Bérénice, Filloux, Denis, Claude, Lisa, Fernandez, Emmanuel, Mahé, Frédéric, Kraberger, Simona, Custer, Joy M., Becquart, Pierre, Mebaley, Telstar Ndong, Kombila, Linda Bohou, Lenguiya, Léadisaelle H., Boundenga, Larson, Mombo, Illich M., Maganga, Gael D., Niama, Fabien R., Koumba, Jean-Sylvain, Ogliastro, Mylène, Yvon, Michel, Martin, Darren P., Blanc, Stéphane, Varsani, Arvind, Leroy, Eric, and Roumagnac, Philippe

Subjects
Archaeology, CC1-960, Science
Abstract

In this study, we used a predator-enabled metagenomics strategy to sample the virome of a remote and difficult-to-access densely forested African tropical region. Specifically, we focused our study on the use of army ants of the genus Dorylus that are obligate collective foragers and group predators that attack and overwhelm a broad array of animal prey. Using 209 army ant samples collected from 29 colonies and the virion-associated nucleic acid-based metagenomics approach, we showed that a broad diversity of bacterial, plant, invertebrate and vertebrate viral sequences were accumulated by army ants: including sequences from 157 different viral genera in 56 viral families. This suggests that using predators and scavengers such as army ants to sample broad swathes of tropical forest viromes can shed light on the composition and the structure of viral populations of these complex and inaccessible ecosystems.

Published
2023
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9. Impact of Surface Chemistry of Silicon Nanoparticles on the Structural and Electrochemical Properties of Si/Ni3.4Sn4 Com-posite Anode for Li-Ion Batteries

Author

Azib, Tahar, Thaury, Claire, Cuevas, Fermin, Leroy, Eric, Jordy, Christian, Marx, Nicolas, and Latroche, Michel

Subjects
Condensed Matter - Materials Science
Abstract

Embedding silicon nanoparticles in an intermetallic matrix is a promising strategy to produce remarkable bulk anode materials for lithium-ion (Li-ion) batteries with low potential, high electrochemical capacity and good cycling stability. These composite materials can be synthetized at a large scale using mechanical milling. However, for Si-Ni3Sn4 composites, milling also induces a chemical reaction between the two components leading to the formation of free Sn and NiSi2, which is detrimental to the performance of the electrode. To prevent this reaction, a modification of the surface chemistry of the silicon has been undertaken. Si nanoparticles coated with a surface layer of either carbon or oxide were used instead of pure silicon. The influence of the coating on the composition, (micro)structure and electrochemical properties of Si-Ni3Sn4 composites is studied and compared with that of pure Si. Si coating strongly reduces the reaction between Si and Ni3Sn4 during milling. Moreover, contrary to pure silicon, Si-coated composites have a plate-like mor-phology in which the surface-modified silicon particles are surrounded by a nanostructured, Ni3Sn4-based matrix leading to smooth potential profiles during electrochemical cycling. The chemical homogeneity of the matrix is more uniform for carbon-coated than for oxygen-coated silicon. As a consequence, different electrochemical behaviors are obtained depending on the surface chemistry, with better lithiation properties for the carbon-covered silicon able to deliver over 500 mAh/g for at least 400 cycles.

Published
2021
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20. Toxoplasma gondii from Gabonese forest, Central Africa: First report of an African wild strain.

Author

Galal, Lokman, Fritz, Matthieu, Becquart, Pierre, Passebosc-Faure, Karine, Plault, Nicolas, Boundenga, Larson, Mombo, Illich Manfred, Kombila, Linda Bohou, Mebaley, Telstar Ndong, Lenguiya, Léadisaelle Hosanna, Ngoubangoye, Barthélémy, N'Dilimabaka, Nadine, Prugnolle, Franck, Forestier, Lionel, Gebremedhin, Endrias Zewdu, Leroy, Eric M., Maganga, Gael Darren, and Mercier, Aurélien

Abstract

The protozoan Toxoplasma gondii is a ubiquitous and highly prevalent parasite that can theoretically infect all warm-blooded vertebrates. In humans, toxoplasmosis causes infections in both immunodeficient and immunocompetent patients, congenital toxoplasmosis, and ocular lesions. These manifestations have different degrees of severity. Clinical severity is determined by multiple factors, including the genotype of the T. gondii strain involved in the infection. T. gondii exhibits remarkable genetic diversity, which varies according to geography and ecotype (domestic or wild). Previous studies have demonstrated that wild strains of T. gondii are of particular epidemiological interest, as they have been associated with more severe forms of toxoplasmosis in different regions of the world. However, no data on wild strains of T. gondii are available from Africa. In this study, we describe for the first time a wild T. gondii strain from Africa. Wild animals from the forest environment of Gabon, Central Africa, were screened for chronic infection with T. gondii using quantitative PCR. The infecting T. gondii strains were genotyped whenever possible by the analysis of 15 microsatellite markers and by whole-genome sequencing. A new T. gondii genotype was identified in the DNA extract from a heart sample of a duiker (Cephalophus sp.) and was found to be highly divergent from previously described T. gondii populations worldwide, including those from domestic environments in Gabon. This discovery suggests the existence of a wild T. gondii population in Africa. The role of wild T. gondii strains in the incidence of severe toxoplasmosis in Africa remains unclear and requires further investigation. Author summary: The emergence of new pathogens from wildlife is today a well-recognized health threat. Studying these infectious agents has proven to be challenging due to the difficulty in accessing samples from wild animals. In the present study, we took advantage of a recent survey on the viral carriage of wild animals from Gabon, Central Africa, to screen animal samples for the presence of the zoonotic protozoan Toxoplasma gondii. This ubiquitous and highly prevalent parasite can theoretically infect all warm-blooded vertebrates, including humans. This parasite is the etiological agent of toxoplasmosis, a disease causing a substantial public health burden worldwide through different clinical manifestations and varying degrees of severity. A novel genotype was identified in a wild antelope from the Gabonese forest, and was found to be highly divergent from previously described T. gondii populations worldwide, including those from the domestic environment in Gabon. This discovery suggests the existence of a wild T. gondii population in Africa. It has been shown that wild strains of T. gondii are of significant epidemiological relevance, as they have been associated with more severe forms of toxoplasmosis in different regions of the world. The implications of wild T. gondii strains in the incidence of severe toxoplasmosis in Africa remain unclear and merit further investigation. [ABSTRACT FROM AUTHOR]

Published
2025
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21. 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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22. 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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24. Correction: Correction: A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa.

Author

Grard, Gilda, Fair, Joseph N, Lee, Deanna, Slikas, Elizabeth, Steffen, Imke, Muyembe, Jean-Jacques, Sittler, Taylor, Veeraraghavan, Narayanan, Ruby, J Graham, Wang, Chunlin, Makuwa, Maria, Mulembakani, Prime, Tesh, Robert B, Mazet, Jonna, Rimoin, Anne W, Taylor, Travis, Schneider, Bradley S, Simmons, Graham, Delwart, Eric, Wolfe, Nathan D, Chiu, Charles Y, and Leroy, Eric M

Subjects
Virology, Microbiology, Immunology, Medical Microbiology
Abstract

[This corrects the article DOI: 10.1371/journal.ppat.1002924.].

Published
2017

25. Possibility and Challenges of Conversion of Current Virus Species Names to Linnaean Binomials.

Author

Postler, Thomas S, Clawson, Anna N, Amarasinghe, Gaya K, Basler, Christopher F, Bavari, Sbina, Benko, Mária, Blasdell, Kim R, Briese, Thomas, Buchmeier, Michael J, Bukreyev, Alexander, Calisher, Charles H, Chandran, Kartik, Charrel, Rémi, Clegg, Christopher S, Collins, Peter L, Juan Carlos, De La Torre, Derisi, Joseph L, Dietzgen, Ralf G, Dolnik, Olga, Dürrwald, Ralf, Dye, John M, Easton, Andrew J, Emonet, Sébastian, Formenty, Pierre, Fouchier, Ron AM, Ghedin, Elodie, Gonzalez, Jean-Paul, Harrach, Balázs, Hewson, Roger, Horie, Masayuki, Jiang, Dàohóng, Kobinger, Gary, Kondo, Hideki, Kropinski, Andrew M, Krupovic, Mart, Kurath, Gael, Lamb, Robert A, Leroy, Eric M, Lukashevich, Igor S, Maisner, Andrea, Mushegian, Arcady R, Netesov, Sergey V, Nowotny, Norbert, Patterson, Jean L, Payne, Susan L, PaWeska, Janusz T, Peters, Clarence J, Radoshitzky, Sheli R, Rima, Bertus K, Romanowski, Victor, Rubbenstroth, Dennis, Sabanadzovic, Sead, Sanfaçon, Hélène, Salvato, Maria S, Schwemmle, Martin, Smither, Sophie J, Stenglein, Mark D, Stone, David M, Takada, Ayato, Tesh, Robert B, Tomonaga, Keizo, Tordo, Noël, Towner, Jonathan S, Vasilakis, Nikos, Volchkov, Viktor E, Wahl-Jensen, Victoria, Walker, Peter J, Wang, Lin-Fa, Varsani, Arvind, Whitfield, Anna E, Zerbini, F Murilo, and Kuhn, Jens H

Subjects
Classification, Terminology as Topic, Viruses, Arenaviridae, binomials, ICTV, International Committee on Taxonomy of Viruses, Mononegavirales, virus nomenclature, virus taxonomy, Evolutionary Biology, Genetics
Abstract

Botanical, mycological, zoological, and prokaryotic species names follow the Linnaean format, consisting of an italicized Latinized binomen with a capitalized genus name and a lower case species epithet (e.g., Homo sapiens). Virus species names, however, do not follow a uniform format, and, even when binomial, are not Linnaean in style. In this thought exercise, we attempted to convert all currently official names of species included in the virus family Arenaviridae and the virus order Mononegavirales to Linnaean binomials, and to identify and address associated challenges and concerns. Surprisingly, this endeavor was not as complicated or time-consuming as even the authors of this article expected when conceiving the experiment. [Arenaviridae; binomials; ICTV; International Committee on Taxonomy of Viruses; Mononegavirales; virus nomenclature; virus taxonomy.].

Published
2017

27. Serological evidence of natural exposure to rabies in rural populations in Gabon.

Author

Kombila, Linda Bohou, N'dilimabaka, Nadine, Lannoy, Julien, Elguero, Eric, Leroy, Eric M., Dacheux, Laurent, and Becquart, Pierre

Subjects
ZOONOSES, DISEASE vectors, NEGLECTED diseases, VACCINATION status, RABIES
Abstract

Rabies is one of the oldest known zoonotic diseases, with dogs being the main reservoir for 99% of the cases of human rabies. However, wild animals may also be rabies vectors. In most cases, contact with a rabid animal results in rabies without pre- or post-exposure prophylaxis, and the disease is nearly always fatal. Nevertheless, a few studies have documented cases of rabies-specific antibodies detection in people with no history of vaccination, suggesting that individuals can be in contact with the virus without developing fatal rabies. To further investigate this possibility of non-lethal human rabies exposure, we carried out a retrospective serological analysis, using both immunoassays (ELISA) and seroneutralization assays (RFFIT), on 430 sera collected between 2005 and 2008 from rural unvaccinated Gabonese populations in the Estuaire and Ogooué-Ivindo provinces. Eleven (11) samples (2.5%) were positive for rabies-specific antibodies using both techniques: 1 in Estuaire and 10 in Ogooué-Ivindo. One of three positive people from the Ogooué-Ivindo province, resampled in early 2023, was still positive for rabies-specific antibodies, suggesting that some degree of immunity can be maintained over many years. Our results also show a marginally significant higher prevalence among hunters. This study demonstrates that rabies circulates actively in Gabon and some unvaccinated individuals living in rural environments can be exposed to the virus and survive, with the development of a significant and specific humoral response that can persist for more than 15 years. This passive seroprevalence survey underlines the need to establish a national surveillance system of rabies in both humans and animals in urban and rural areas, and to enhance access to pre- and post-exposure prophylaxis. Author summary: Rabies is one of the oldest neglected tropical diseases transmitted to humans, generally by dogs, but wild animals can also act as vectors of the disease. In most cases, a risk-contact with an infected animal without proper prophylaxis results in rabies, and the disease is nearly always fatal. Nevertheless, a few studies have documented the detection of rabies-specific antibodies in people having no history of vaccination, suggesting that exposition to the virus is possible without developing fatal rabies. To further investigate this possibility, we carried out a retrospective serological analysis on 430 sera collected between 2005 and 2008 from rural Gabonese populations. We detected 11 positive samples (2.5%). Three of these positive people was resampled in early 2023 and one was still found positive for rabies-specific antibodies, suggesting that immunity can persist over many years. This study demonstrates that rabies is actively circulating in Gabon and that some unvaccinated individuals living in rural environments can be exposed to the virus and survive. Survival despite exposure to rabies could be associated to the development of a significant and specific humoral response that persists for more than 15 years. [ABSTRACT FROM AUTHOR]

Published
2024
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32. Toxoplasma gondii from Gabonese forest, Central Africa: first report of an African wild population

Author

Galal, Lokman, primary, Fritz, Matthieu, additional, Becquart, Pierre, additional, Passebosc-Faure, Karine, additional, Plault, Nicolas, additional, Boundenga, Larson, additional, Mombo, Illich Manfred, additional, Kombila, Linda Bohou, additional, Mebaley, Telstar Ndong, additional, Lenguiyah, Leadisaelle Hosanna, additional, Ngoubangoye, Barthelemy, additional, N'Dilimabaka, Nadine, additional, Leroy, Eric M., additional, Maganga, Gael Darren, additional, and Mercier, Aurelien, additional

Published
2024
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33. Evidence for circulation of Rift Valley fever virus in wildlife and domestic animals in a forest environment in Gabon, Central Africa

Author

Becquart, Pierre, primary, Bohou Kombila, Linda, additional, Mebaley, Telstar Ndong, additional, Paupy, Christophe, additional, Garcia, Déborah, additional, Nesi, Nicolas, additional, Olive, Marie-Marie, additional, Vanhomwegen, Jessica, additional, Boundenga, Larson, additional, Mombo, Illich Manfred, additional, Piro-Mégy, Camille, additional, Fritz, Matthieu, additional, Lenguiya, Léadisaelle Hosanna, additional, Ar Gouilh, Meriadeg, additional, Leroy, Eric M., additional, N’Dilimabaka, Nadine, additional, Cêtre-Sossah, Catherine, additional, and Maganga, Gael Darren, additional

Published
2024
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34. Early Circulation of SARS-CoV-2, Congo, 2020

Author

Bonguili, Novy Charel Bobouaka, Fritz, Matthieu, Lenguiya, Leadisaelle Hosanna, Mayengue, Pembe Issamou, Koukouikila-Koussounda, Felix, Dossou-Yovo, Louis Regis, Badzi, Cynthia Nkoua, Leroy, Eric M., and Niama, Fabien R.

Subjects
Diagnosis, Distribution, Company distribution practices, Epidemics -- Statistics -- Risk factors -- Distribution -- Congo (Brazzaville), COVID-19 -- Statistics -- Risk factors -- Distribution -- Diagnosis -- 2020 AD
Abstract

After coronavirus disease (COVID-19) was reported in China in December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rapidly spread around the world; most countries officially reported their first cases [...]

Published
2022
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36. 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author

Kuhn, Jens H., Adkins, Scott, Alioto, Daniela, Alkhovsky, Sergey V., Amarasinghe, Gaya K., Anthony, Simon J., Avšič-Županc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, Anne, Ballinger, Matthew J., Bartonička, Tomáš, Basler, Christopher, Bavari, Sina, Beer, Martin, Bente, Dennis A., Bergeron, Éric, Bird, Brian H., Blair, Carol, Blasdell, Kim R., Bradfute, Steven B., Breyta, Rachel, Briese, Thomas, Brown, Paul A., Buchholz, Ursula J., Buchmeier, Michael J., Bukreyev, Alexander, Burt, Felicity, Buzkan, Nihal, Calisher, Charles H., Cao, Mengji, Casas, Inmaculada, Chamberlain, John, Chandran, Kartik, Charrel, Rémi N., Chen, Biao, Chiumenti, Michela, Choi, Il-Ryong, Clegg, J. Christopher S., Crozier, Ian, da Graça, John V., Dal Bó, Elena, Dávila, Alberto M. R., de la Torre, Juan Carlos, de Lamballerie, Xavier, de Swart, Rik L., Di Bello, Patrick L., Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G., Digiaro, Michele, Dolja, Valerian V., Dolnik, Olga, Drebot, Michael A., Drexler, Jan Felix, Dürrwald, Ralf, Dufkova, Lucie, Dundon, William G., Duprex, W. Paul, Dye, John M., Easton, Andrew J., Ebihara, Hideki, Elbeaino, Toufic, Ergünay, Koray, Fernandes, Jorlan, Fooks, Anthony R., Formenty, Pierre B. H., Forth, Leonie F., Fouchier, Ron A. M., Freitas-Astúa, Juliana, Gago-Zachert, Selma, Gāo, George Fú, García, María Laura, García-Sastre, Adolfo, Garrison, Aura R., Gbakima, Aiah, Goldstein, Tracey, Gonzalez, Jean-Paul J., Griffiths, Anthony, Groschup, Martin H., Günther, Stephan, Guterres, Alexandro, Hall, Roy A., Hammond, John, Hassan, Mohamed, Hepojoki, Jussi, Hepojoki, Satu, Hetzel, Udo, Hewson, Roger, Hoffmann, Bernd, Hongo, Seiji, Höper, Dirk, Horie, Masayuki, Hughes, Holly R., Hyndman, Timothy H., Jambai, Amara, Jardim, Rodrigo, Jiāng, Dàohóng, Jin, Qi, Jonson, Gilda B., Junglen, Sandra, Karadağ, Serpil, Keller, Karen E., Klempa, Boris, Klingström, Jonas, Kobinger, Gary, Kondō, Hideki, Koonin, Eugene V., Krupovic, Mart, Kurath, Gael, Kuzmin, Ivan V., Laenen, Lies, Lamb, Robert A., Lambert, Amy J., Langevin, Stanley L., Lee, Benhur, Lemos, Elba R. S., Leroy, Eric M., Li, Dexin, Lǐ, Jiànróng, Liang, Mifang, Liú, Wénwén, Liú, Yàn, Lukashevich, Igor S., Maes, Piet, Marciel de Souza, William, Marklewitz, Marco, Marshall, Sergio H., Martelli, Giovanni P., Martin, Robert R., Marzano, Shin-Yi L., Massart, Sébastien, McCauley, John W., Mielke-Ehret, Nicole, Minafra, Angelantonio, Minutolo, Maria, Mirazimi, Ali, Mühlbach, Hans-Peter, Mühlberger, Elke, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, Beatriz, Navarro, José A., Netesov, Sergey V., Neumann, Gabriele, Nowotny, Norbert, Nunes, Márcio R. T., Nylund, Are, Økland, Arnfinn L., Oliveira, Renata C., Palacios, Gustavo, Pallas, Vicente, Pályi, Bernadett, Papa, Anna, Parrish, Colin R., Pauvolid-Corrêa, Alex, Pawęska, Janusz T., Payne, Susan, Pérez, Daniel R., Pfaff, Florian, Radoshitzky, Sheli R., Rahman, Aziz-ul, Ramos-González, Pedro L., Resende, Renato O., Reyes, Carina A., Rima, Bertus K., Romanowski, Víctor, Robles Luna, Gabriel, Rota, Paul, Rubbenstroth, Dennis, Runstadler, Jonathan A., Ruzek, Daniel, Sabanadzovic, Sead, Salát, Jiří, Sall, Amadou Alpha, Salvato, Maria S., Sarpkaya, Kamil, Sasaya, Takahide, Schwemmle, Martin, Shabbir, Muhammad Z., Shí, Xiǎohóng, Shí, Zhènglì, Shirako, Yukio, Simmonds, Peter, Širmarová, Jana, Sironi, Manuela, Smither, Sophie, Smura, Teemu, Song, Jin-Won, Spann, Kirsten M., Spengler, Jessica R., Stenglein, Mark D., Stone, David M., Straková, Petra, Takada, Ayato, Tesh, Robert B., Thornburg, Natalie J., Tomonaga, Keizō, Tordo, Noël, Towner, Jonathan S., Turina, Massimo, Tzanetakis, Ioannis, Ulrich, Rainer G., Vaira, Anna Maria, van den Hoogen, Bernadette, Varsani, Arvind, Vasilakis, Nikos, Verbeek, Martin, Wahl, Victoria, Walker, Peter J., Wang, Hui, Wang, Jianwei, Wang, Xifeng, Wang, Lin-Fa, Wèi, Tàiyún, Wells, Heather, Whitfield, Anna E., Williams, John V., Wolf, Yuri I., Wú, Zhìqiáng, Yang, Xin, Yáng, Xīnglóu, Yu, Xuejie, Yutin, Natalya, Zerbini, F. Murilo, Zhang, Tong, Zhang, Yong-Zhen, Zhou, Guohui, and Zhou, Xueping

Published
2020
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40. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples

Author

Naccache, Samia N, Federman, Scot, Veeraraghavan, Narayanan, Zaharia, Matei, Lee, Deanna, Samayoa, Erik, Bouquet, Jerome, Greninger, Alexander L, Luk, Ka-Cheung, Enge, Barryett, Wadford, Debra A, Messenger, Sharon L, Genrich, Gillian L, Pellegrino, Kristen, Grard, Gilda, Leroy, Eric, Schneider, Bradley S, Fair, Joseph N, Martínez, Miguel A, Isa, Pavel, Crump, John A, DeRisi, Joseph L, Sittler, Taylor, Hackett, John, Miller, Steve, and Chiu, Charles Y

Subjects
Microbiology, Biological Sciences, Bioinformatics and Computational Biology, Bioengineering, Prevention, Vaccine Related, Human Genome, Biodefense, Infectious Diseases, Genetics, Detection, screening and diagnosis, 4.1 Discovery and preclinical testing of markers and technologies, Infection, Good Health and Well Being, Computational Biology, Databases, Nucleic Acid, High-Throughput Nucleotide Sequencing, Humans, Metagenomics, ROC Curve, Reproducibility of Results, Software, Medical and Health Sciences, Bioinformatics
Abstract

Unbiased next-generation sequencing (NGS) approaches enable comprehensive pathogen detection in the clinical microbiology laboratory and have numerous applications for public health surveillance, outbreak investigation, and the diagnosis of infectious diseases. However, practical deployment of the technology is hindered by the bioinformatics challenge of analyzing results accurately and in a clinically relevant timeframe. Here we describe SURPI ("sequence-based ultrarapid pathogen identification"), a computational pipeline for pathogen identification from complex metagenomic NGS data generated from clinical samples, and demonstrate use of the pipeline in the analysis of 237 clinical samples comprising more than 1.1 billion sequences. Deployable on both cloud-based and standalone servers, SURPI leverages two state-of-the-art aligners for accelerated analyses, SNAP and RAPSearch, which are as accurate as existing bioinformatics tools but orders of magnitude faster in performance. In fast mode, SURPI detects viruses and bacteria by scanning data sets of 7-500 million reads in 11 min to 5 h, while in comprehensive mode, all known microorganisms are identified, followed by de novo assembly and protein homology searches for divergent viruses in 50 min to 16 h. SURPI has also directly contributed to real-time microbial diagnosis in acutely ill patients, underscoring its potential key role in the development of unbiased NGS-based clinical assays in infectious diseases that demand rapid turnaround times.

Published
2014

41. Prevalence and Genetic Diversity of Bat Hepatitis B Viruses in Bat Species Living in Gabon.

Author

Koumba Mavoungou, Danielle S., Bohou Kombila, Linda, Longo Pendy, Neil M., Koumba Moukouama, Schedy E., Lekana-Douki, Sonia Etenna, Maganga, Gaël D., Leroy, Eric M., Aghokeng, Avelin F., and N'dilimabaka, Nadine

Subjects
HEPATITIS viruses, GENETIC variation, SPECIES diversity, GENE targeting, BATS
Abstract

Hepatitis B virus (HBV) infection leads to around 800,000 deaths yearly and is considered to be a major public health problem worldwide. However, HBV origins remain poorly understood. Here, we looked for bat HBV (BtHBV) in different bat species in Gabon to investigate the role of these animals as carriers of ancestral hepadnaviruses because these viruses are much more diverse in bats than in other host species. DNA was extracted from 859 bat livers belonging to 11 species collected in caves and villages in the southeast of Gabon and analyzed using PCRs targeting the surface gene. Positive samples were sequenced using the Sanger method. BtHBV DNA was detected in 64 (7.4%) individuals belonging to eight species mainly collected in caves. Thirty-six (36) sequences among the 37 obtained after sequencing were phylogenetically close to the RBHBV strain recently isolated in Gabonese bats, while the remaining sequence was close to a rodent HBV strain isolated in America. The generalized linear mixed model showed that the variable species best explained the occurrence of BtHBV infection in bats. The discovery of a BtHBV strain homologous to a rodent strain in bats raises the possibility that these animals may be carriers of ancestral hepadnaviruses. [ABSTRACT FROM AUTHOR]

Published
2024
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45. Exposure to Ebola Virus and Risk for Infection with Malaria Parasites, Rural Gabon

Author

Abbate, Jessica L., Becquart, Pierre, Leroy, Eric, Ezenwa, Vanessa O., and Roche, Benjamin

Subjects
Risk factors, Health aspects, Ebola hemorrhagic fever -- Risk factors -- Health aspects, Ebola virus -- Health aspects, Plasmodium falciparum -- Health aspects, Virus diseases -- Risk factors -- Health aspects, Antibodies -- Health aspects, Malaria -- Risk factors -- Health aspects, Death, Intelligence gathering, Diseases
Abstract

Major outbreaks of infections with Ebola virus, such as the 2014-2016 West Africa epidemic and the ongoing 2018-2019 outbreak in eastern Democratic Republic of the Congo, pose several obvious and [...]

Published
2020
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48. Taxonomy of the order Mononegavirales: update 2019

Author

Amarasinghe, Gaya K., Ayllón, María A., Bào, Yīmíng, Basler, Christopher F., Bavari, Sina, Blasdell, Kim R., Briese, Thomas, Brown, Paul A., Bukreyev, Alexander, Balkema-Buschmann, Anne, Buchholz, Ursula J., Chabi-Jesus, Camila, Chandran, Kartik, Chiapponi, Chiara, Crozier, Ian, de Swart, Rik L., Dietzgen, Ralf G., Dolnik, Olga, Drexler, Jan F., Dürrwald, Ralf, Dundon, William G., Duprex, W. Paul, Dye, John M., Easton, Andrew J., Fooks, Anthony R., Formenty, Pierre B. H., Fouchier, Ron A. M., Freitas-Astúa, Juliana, Griffiths, Anthony, Hewson, Roger, Horie, Masayuki, Hyndman, Timothy H., Jiāng, Dàohóng, Kitajima, Elliott W., Kobinger, Gary P., Kondō, Hideki, Kurath, Gael, Kuzmin, Ivan V., Lamb, Robert A., Lavazza, Antonio, Lee, Benhur, Lelli, Davide, Leroy, Eric M., Lǐ, Jiànróng, Maes, Piet, Marzano, Shin-Yi L., Moreno, Ana, Mühlberger, Elke, Netesov, Sergey V., Nowotny, Norbert, Nylund, Are, Økland, Arnfinn L., Palacios, Gustavo, Pályi, Bernadett, Pawęska, Janusz T., Payne, Susan L., Prosperi, Alice, Ramos-González, Pedro Luis, Rima, Bertus K., Rota, Paul, Rubbenstroth, Dennis, Shī, Mǎng, Simmonds, Peter, Smither, Sophie J., Sozzi, Enrica, Spann, Kirsten, Stenglein, Mark D., Stone, David M., Takada, Ayato, Tesh, Robert B., Tomonaga, Keizō, Tordo, Noël, Towner, Jonathan S., van den Hoogen, Bernadette, Vasilakis, Nikos, Wahl, Victoria, Walker, Peter J., Wang, Lin-Fa, Whitfield, Anna E., Williams, John V., Zerbini, F. Murilo, Zhāng, Tāo, Zhang, Yong-Zhen, and Kuhn, Jens H.

Published
2019
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49. Taxonomy of the order Mononegavirales: second update 2018

Author

Maes, Piet, Amarasinghe, Gaya K., Ayllón, María A., Basler, Christopher F., Bavari, Sina, Blasdell, Kim R., Briese, Thomas, Brown, Paul A., Bukreyev, Alexander, Balkema-Buschmann, Anne, Buchholz, Ursula J., Chandran, Kartik, Crozier, Ian, de Swart, Rik L., Dietzgen, Ralf G., Dolnik, Olga, Domier, Leslie L., Drexler, Jan F., Dürrwald, Ralf, Dundon, William G., Duprex, W. Paul, Dye, John M., Easton, Andrew J., Fooks, Anthony R., Formenty, Pierre B. H., Fouchier, Ron A. M., Freitas-Astúa, Juliana, Ghedin, Elodie, Griffiths, Anthony, Hewson, Roger, Horie, Masayuki, Hurwitz, Julia L., Hyndman, Timothy H., Jiāng, Dàohóng, Kobinger, Gary P., Kondō, Hideki, Kurath, Gael, Kuzmin, Ivan V., Lamb, Robert A., Lee, Benhur, Leroy, Eric M., Lǐ, Jiànróng, Marzano, Shin-Yi L., Mühlberger, Elke, Netesov, Sergey V., Nowotny, Norbert, Palacios, Gustavo, Pályi, Bernadett, Pawęska, Janusz T., Payne, Susan L., Rima, Bertus K., Rota, Paul, Rubbenstroth, Dennis, Simmonds, Peter, Smither, Sophie J., Song, Qisheng, Song, Timothy, Spann, Kirsten, Stenglein, Mark D., Stone, David M., Takada, Ayato, Tesh, Robert B., Tomonaga, Keizō, Tordo, Noël, Towner, Jonathan S., van den Hoogen, Bernadette, Vasilakis, Nikos, Wahl, Victoria, Walker, Peter J., Wang, David, Wang, Lin-Fa, Whitfield, Anna E., Williams, John V., Yè, Gōngyín, Zerbini, F. Murilo, Zhang, Yong-Zhen, and Kuhn, Jens H.

Published
2019
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50. A novel rhabdovirus associated with acute hemorrhagic fever in central Africa.

Author

Grard, Gilda, Fair, Joseph N, Lee, Deanna, Slikas, Elizabeth, Steffen, Imke, Muyembe, Jean-Jacques, Sittler, Taylor, Veeraraghavan, Narayanan, Ruby, J Graham, Wang, Chunlin, Makuwa, Maria, Mulembakani, Prime, Tesh, Robert B, Mazet, Jonna, Rimoin, Anne W, Taylor, Travis, Schneider, Bradley S, Simmons, Graham, Delwart, Eric, Wolfe, Nathan D, Chiu, Charles Y, and Leroy, Eric M

Subjects
Animals, Humans, Mice, Rhabdoviridae, Hemorrhagic Fevers, Viral, Rhabdoviridae Infections, Antibodies, Viral, Disease Outbreaks, Phylogeny, Genome, Viral, Molecular Sequence Data, Adolescent, Adult, Democratic Republic of the Congo, Female, Male, High-Throughput Nucleotide Sequencing, Hemorrhagic Fevers, Viral, Antibodies, Genome, Virology, Microbiology, Immunology, Medical Microbiology
Abstract

Deep sequencing was used to discover a novel rhabdovirus (Bas-Congo virus, or BASV) associated with a 2009 outbreak of 3 human cases of acute hemorrhagic fever in Mangala village, Democratic Republic of Congo (DRC), Africa. The cases, presenting over a 3-week period, were characterized by abrupt disease onset, high fever, mucosal hemorrhage, and, in two patients, death within 3 days. BASV was detected in an acute serum sample from the lone survivor at a concentration of 1.09 × 10(6) RNA copies/mL, and 98.2% of the genome was subsequently de novo assembled from ≈ 140 million sequence reads. Phylogenetic analysis revealed that BASV is highly divergent and shares less than 34% amino acid identity with any other rhabdovirus. High convalescent neutralizing antibody titers of >1:1000 were detected in the survivor and an asymptomatic nurse directly caring for him, both of whom were health care workers, suggesting the potential for human-to-human transmission of BASV. The natural animal reservoir host or arthropod vector and precise mode of transmission for the virus remain unclear. BASV is an emerging human pathogen associated with acute hemorrhagic fever in Africa.

Published
2012

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