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1. A graph neural network-based model with Out-of-Distribution Robustness for enhancing Antiretroviral Therapy Outcome Prediction for HIV-1

Author

Di Teodoro, Giulia, Siciliano, Federico, Guarrasi, Valerio, Vandamme, Anne-Mieke, Ghisetti, Valeria, Sönnerborg, Anders, Zazzi, Maurizio, Silvestri, Fabrizio, and Palagi, Laura

Subjects
Quantitative Biology - Quantitative Methods, Computer Science - Machine Learning, 68, I.2.6
Abstract

Predicting the outcome of antiretroviral therapies for HIV-1 is a pressing clinical challenge, especially when the treatment regimen includes drugs for which limited effectiveness data is available. This scarcity of data can arise either due to the introduction of a new drug to the market or due to limited use in clinical settings. To tackle this issue, we introduce a novel joint fusion model, which combines features from a Fully Connected (FC) Neural Network and a Graph Neural Network (GNN). The FC network employs tabular data with a feature vector made up of viral mutations identified in the most recent genotypic resistance test, along with the drugs used in therapy. Conversely, the GNN leverages knowledge derived from Stanford drug-resistance mutation tables, which serve as benchmark references for deducing in-vivo treatment efficacy based on the viral genetic sequence, to build informative graphs. We evaluated these models' robustness against Out-of-Distribution drugs in the test set, with a specific focus on the GNN's role in handling such scenarios. Our comprehensive analysis demonstrates that the proposed model consistently outperforms the FC model, especially when considering Out-of-Distribution drugs. These results underscore the advantage of integrating Stanford scores in the model, thereby enhancing its generalizability and robustness, but also extending its utility in real-world applications with limited data availability. This research highlights the potential of our approach to inform antiretroviral therapy outcome prediction and contribute to more informed clinical decisions., Comment: 32 pages, 2 figures

Published
2023

2. Recommendations on data sharing in HIV drug resistance research.

Author

Avila-Rios, Santiago, Ayitewala, Alisen, Bosch, Ronald, Calvez, Vincent, Ceccherini-Silberstein, Francesca, Charpentier, Charlotte, Descamps, Diane, Eshleman, Susan, Fokam, Joseph, Frenkel, Lisa, Gupta, Ravindra, Ioannidis, John, Kaleebu, Pontiano, Kantor, Rami, Kassaye, Seble, Kosakovsky Pond, Sergei, Kouamou, Vinie, Kouyos, Roger, Kuritzkes, Daniel, Lessells, Richard, Marcelin, Anne-Genevieve, Mbuagbaw, Lawrence, Inzaule, Seth, Siedner, Mark, Minalga, Brian, Ndembi, Nicaise, Neher, Richard, Paredes, Roger, Pillay, Deenan, Raizes, Elliot, Rhee, Soo-Yon, Ruxrungtham, Kiat, Sabeti, Pardis, Schapiro, Jonathan, Sirivichayakul, Sunee, Steegen, Kim, Sugiura, Wataru, van Zyl, Gert, Vandamme, Anne-Mieke, Wensing, Annemarie, Wertheim, Joel, Gunthard, Huldrych, Jordan, Michael, Shafer, Robert, Little, Susan, and Richman, Douglas

Abstract

• Human immunodeficiency virus (HIV) drug resistance has implications for antiretroviral treatment strategies and for containing the HIV pandemic because the development of HIV drug resistance leads to the requirement for antiretroviral drugs that may be less effective, less well-tolerated, and more expensive than those used in first-line regimens.  • HIV drug resistance studies are designed to determine which HIV mutations are selected by antiretroviral drugs and, in turn, how these mutations affect antiretroviral drug susceptibility and response to future antiretroviral treatment regimens.  • Such studies collectively form a vital knowledge base essential for monitoring global HIV drug resistance trends, interpreting HIV genotypic tests, and updating HIV treatment guidelines.  • Although HIV drug resistance data are collected in many studies, such data are often not publicly shared, prompting the need to recommend best practices to encourage and standardize HIV drug resistance data sharing.  • In contrast to other viruses, sharing HIV sequences from phylogenetic studies of transmission dynamics requires additional precautions as HIV transmission is criminalized in many countries and regions.  • Our recommendations are designed to ensure that the data that contribute to HIV drug resistance knowledge will be available without undue hardship to those publishing HIV drug resistance studies and without risk to people living with HIV.

Published
2023

3. Four principles to establish a universal virus taxonomy

Author

Simmonds, Peter, Adriaenssens, Evelien M, Zerbini, F Murilo, Abrescia, Nicola GA, Aiewsakun, Pakorn, Alfenas-Zerbini, Poliane, Bao, Yiming, Barylski, Jakub, Drosten, Christian, Duffy, Siobain, Duprex, W Paul, Dutilh, Bas E, Elena, Santiago F, García, Maria Laura, Junglen, Sandra, Katzourakis, Aris, Koonin, Eugene V, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Lefkowitz, Elliot J, Łobocka, Małgorzata, Lood, Cédric, Mahony, Jennifer, Meier-Kolthoff, Jan P, Mushegian, Arcady R, Oksanen, Hanna M, Poranen, Minna M, Reyes-Muñoz, Alejandro, Robertson, David L, Roux, Simon, Rubino, Luisa, Sabanadzovic, Sead, Siddell, Stuart, Skern, Tim, Smith, Donald B, Sullivan, Matthew B, Suzuki, Nobuhiro, Turner, Dann, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, and Vasilakis, Nikos

Subjects
Infectious Diseases, Infection, Humans, Bacteriophages, Metagenomics, Phylogeny, Viruses, Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences, Developmental Biology
Abstract

A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., "arboviruses"), infecting a certain type of host (e.g., "mycoviruses," "bacteriophages") or displaying specific pathogenicity (e.g., "human immunodeficiency viruses"), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes apparent.

Published
2023

4. High viral suppression and detection of dolutegravir-resistance associated mutations in treatment-experienced Tanzanian adults living with HIV-1 in Dar es Salaam

Author

Bwire, George M., Aiko, Beatrice Godwin, Mosha, Idda H., Kilapilo, Mary S., Mangara, Alli, Kazonda, Patrick, Swai, Janeth P., Swalehe, Omary, Jordan, Michael R., Vercauteren, Jurgen, Sando, David, Temba, David, Shao, Amani, Mauka, Wilhellmuss, Decouttere, Catherine, Vandaele, Nico, Sangeda, Raphael Z., Killewo, Japhet, and Vandamme, Anne-Mieke

Published
2023
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5. Correction to: Changes to virus taxonomy and the ICTV Statutes ratifed by the International Committee on Taxonomy of Viruses (2023)

Author

Zerbini, Francisco Murilo, Siddell, Stuart G., Lefkowitz, Elliot J., Mushegian, Arcady R., Adriaenssens, Evelien M., Alfenas‑Zerbini, Poliane, Dempsey, Donald M., Dutilh, Bas E., García, María Laura, Hendrickson, R. Curtis, Junglen, Sandra, Krupovic, Mart, Kuhn, Jens H., Lambert, Amy J., Łobocka, Małgorzata, Oksanen, Hanna M., Robertson, David L., Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Smith, Donald B., Suzuki, Nobuhiro, Van Doorslaer, Koenraad, Vandamme, Anne‑Mieke, and Varsani, Arvind

Published
2023
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6. Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2023)

Author

Zerbini, Francisco Murilo, Siddell, Stuart G., Lefkowitz, Elliot J., Mushegian, Arcady R., Adriaenssens, Evelien M., Alfenas‑Zerbini, Poliane, Dempsey, Donald M., Dutilh, Bas E., García, María Laura, Hendrickson, R. Curtis, Junglen, Sandra, Krupovic, Mart, Kuhn, Jens H., Lambert, Amy J., Łobocka, Małgorzata, Oksanen, Hanna M., Robertson, David L., Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Smith, Donald B., Suzuki, Nobuhiro, Van Doorslaer, Koenraad, Vandamme, Anne‑Mieke, and Varsani, Arvind

Published
2023
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7. Recent changes to virus taxonomy ratified by the International Committee on Taxonomy of Viruses (2022)

Author

Walker, Peter J., Siddell, Stuart G., Lefkowitz, Elliot J., Mushegian, Arcady R., Adriaenssens, Evelien M., Alfenas-Zerbini, Poliane, Dempsey, Donald M., Dutilh, Bas E., García, María Laura, Curtis Hendrickson, R., Junglen, Sandra, Krupovic, Mart, Kuhn, Jens H., Lambert, Amy J., Łobocka, Małgorzata, Oksanen, Hanna M., Orton, Richard J., Robertson, David L., Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Smith, Donald B., Suzuki, Nobuhiro, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, and Zerbini, Francisco Murilo

Published
2022
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8. Recommendations on data sharing in HIV drug resistance research

Author

Inzaule, Seth C., Siedner, Mark J., Little, Susan J., Avila-Rios, Santiago, Ayitewala, Alisen, Bosch, Ronald J., Calvez, Vincent, Ceccherini-Silberstein, Francesca, Charpentier, Charlotte, Descamps, Diane, Eshleman, Susan H., Fokam, Joseph, Frenkel, Lisa M., Gupta, Ravindra K., Ioannidis, John P.A., Kaleebu, Pontiano, Kantor, Rami, Kassaye, Seble G., Kosakovsky Pond, Sergei L., Kouamou, Vinie, Kouyos, Roger D., Kuritzkes, Daniel R., Lessells, Richard, Marcelin, Anne-Genevieve, Mbuagbaw, Lawrence, Minalga, Brian, Ndembi, Nicaise, Neher, Richard A., Paredes, Roger, Pillay, Deenan, Raizes, Elliot G., Rhee, Soo-Yon, Richman, Douglas D., Ruxrungtham, Kiat, Sabeti, Pardis C., Schapiro, Jonathan M., Sirivichayakul, Sunee, Steegen, Kim, Sugiura, Wataru, van Zyl, Gert U., Vandamme, Anne-Mieke, Wensing, Annemarie M.J., Wertheim, Joel O., Gunthard, Huldrych F., Jordan, Michael R., and Shafer, Robert W.

Subjects
United States. Centers for Disease Control and Prevention, United States. National Institutes of Health, Merck & Company Inc., Gilead Sciences Inc., Biological products industry, HIV (Viruses) -- Drug therapy, Rilpivirine, Drug resistance -- Drug therapy, Pharmaceutical industry, Biological sciences, World Health Organization
Abstract

Author(s): Seth C. Inzaule 1, Mark J. Siedner 2, Susan J. Little 3, Santiago Avila-Rios 4, Alisen Ayitewala 5, Ronald J. Bosch 6, Vincent Calvez 7, Francesca Ceccherini-Silberstein 8, Charlotte [...]

Published
2023
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9. Tracing the Impact of Public Health Interventions on HIV-1 Transmission in Portugal Using Molecular Epidemiology.

Author

du Plessis, Louis, Pineda-Peña, Andrea, Kühnert, Denise, Lemey, Philippe, Vandamme, Anne-Mieke, Gomes, Perpétua, Camacho, Ricardo, Pybus, Oliver, Abecasis, Ana, Faria, Nuno, and Vasylyeva, Tetyana

Subjects
HIV, Portugal, epidemiology, harm reduction, phylodynamics, reproductive number, transmission groups, Bayes Theorem, HIV Infections, HIV-1, Humans, Molecular Epidemiology, Phylogeny, Portugal, Public Health, pol Gene Products, Human Immunodeficiency Virus
Abstract

BACKGROUND: Estimation of temporal changes in human immunodeficiency virus (HIV) transmission patterns can help to elucidate the impact of preventive strategies and public health policies. METHODS: Portuguese HIV-1 subtype B and G pol genetic sequences were appended to global reference data sets to identify country-specific transmission clades. Bayesian birth-death models were used to estimate subtype-specific effective reproductive numbers (Re). Discrete trait analysis (DTA) was used to quantify mixing among transmission groups. RESULTS: We identified 5 subtype B Portuguese clades (26-79 sequences) and a large monophyletic subtype G Portuguese clade (236 sequences). We estimated that major shifts in HIV-1 transmission occurred around 1999 (95% Bayesian credible interval [BCI], 1998-2000) and 2000 (95% BCI, 1998-2001) for subtypes B and G, respectively. For subtype B, Re dropped from 1.91 (95% BCI, 1.73-2.09) to 0.62 (95% BCI,.52-.72). For subtype G, Re decreased from 1.49 (95% BCI, 1.39-1.59) to 0.72 (95% BCI, .63-.8). The DTA suggests that people who inject drugs (PWID) and heterosexuals were the source of most (>80%) virus lineage transitions for subtypes G and B, respectively. CONCLUSIONS: The estimated declines in Re coincide with the introduction of highly active antiretroviral therapy and the scale-up of harm reduction for PWID. Inferred transmission events across transmission groups emphasize the importance of prevention efforts for bridging populations.

Published
2019

10. Full-genome next-generation sequencing of hepatitis C virus to assess the accuracy of genotyping by the commercial assay LiPA and the prevalence of resistance-associated substitutions in a Belgian cohort

Author

Christensen, Kasper T., Pierard, Florian, Beuselinck, Kurt, Bonsall, David, Bowden, Rory, Lagrou, Katrien, Nevens, Frederik, Schrooten, Yoeri, Simmonds, Peter, Vandamme, Anne-Mieke, Van Wijngaerden, Eric, Dierckx, Tim, Cuypers, Lize, and Van Laethem, Kristel

Published
2022
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11. Differentiating between viruses and virus species by writing their names correctly

Author

Zerbini, Francisco Murilo, Siddell, Stuart G., Mushegian, Arcady R., Walker, Peter J., Lefkowitz, Elliot J., Adriaenssens, Evelien M., Alfenas-Zerbini, Poliane, Dutilh, Bas E., García, María Laura, Junglen, Sandra, Krupovic, Mart, Kuhn, Jens H., Lambert, Amy J., Łobocka, Małgorzata, Oksanen, Hanna M., Robertson, David L., Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Suzuki, Nobuhiro, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, and Varsani, Arvind

Published
2022
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14. Ethical considerations in global HIV phylogenetic research

Author

Coltart, Cordelia EM, Hoppe, Anne, Parker, Michael, Dawson, Liza, Amon, Joseph J, Simwinga, Musonda, Geller, Gail, Henderson, Gail, Laeyendecker, Oliver, Tucker, Joseph D, Eba, Patrick, Novitsky, Vladimir, Vandamme, Anne-Mieke, Seeley, Janet, Dallabetta, Gina, Harling, Guy, Grabowski, M Kate, Godfrey-Faussett, Peter, Fraser, Christophe, Cohen, Myron S, Pillay, Deenan, Group, Ethics in HIV Phylogenetics Working, Baggaley, Rachel, Bernard, Edwin J, Burns, David, Coltart, Cordelia C, Dedes, Nikos, Delpech, Valerie, Eba, Patrick M, German, Danielle, Grabowksi, M Kate, Hall, Irene, Kozlakidis, Zisis, Mwanza, Felix, Reis, Andreas, Simwanga, Musonda, Wertheim, Joel O, and Zimmerman, Rick

Subjects
Biomedical and Clinical Sciences, Public Health, Health Sciences, HIV/AIDS, Infectious Diseases, Genetics, 8.3 Policy, ethics, and research governance, Health and social care services research, 8.1 Organisation and delivery of services, Infection, Good Health and Well Being, Biomedical Research, Guidelines as Topic, HIV, HIV Infections, Human Rights, Humans, Phylogeny, Research Design, Risk Assessment, Ethics in HIV Phylogenetics Working Group, Medical and Health Sciences, Biomedical and clinical sciences, Health sciences
Abstract

Phylogenetic analysis of pathogens is an increasingly powerful way to reduce the spread of epidemics, including HIV. As a result, phylogenetic approaches are becoming embedded in public health and research programmes, as well as outbreak responses, presenting unique ethical, legal, and social issues that are not adequately addressed by existing bioethics literature. We formed a multidisciplinary working group to explore the ethical issues arising from the design of, conduct in, and use of results from HIV phylogenetic studies, and to propose recommendations to minimise the associated risks to both individuals and groups. We identified eight key ethical domains, within which we highlighted factors that make HIV phylogenetic research unique. In this Review, we endeavoured to provide a framework to assist researchers, public health practitioners, and funding institutions to ensure that HIV phylogenetic studies are designed, done, and disseminated in an ethical manner. Our conclusions also have broader relevance for pathogen phylogenetics.

Published
2018

15. Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable

Author

Mavian, Carla, Pond, Sergei Kosakovsky, Marini, Simone, Magalis, Brittany Rife, Vandamme, Anne-Mieke, Dellicour, Simon, Scarpino, Samuel V., Houldcroft, Charlotte, Villabona-Arenas, Julian, Paisie, Taylor K., Trovão, Nídia S., Boucher, Christina, Zhang, Yun, Scheuermann, Richard H., Gascuel, Olivier, Lam, Tommy Tsan-Yuk, Suchard, Marc A., Abecasis, Ana, Wilkinson, Eduan, de Oliveira, Tulio, Bento, Ana I., Schmidt, Heiko A., Martin, Darren, Hadfield, James, Faria, Nuno, Grubaugh, Nathan D., Neher, Richard A., Baele, Guy, Lemey, Philippe, Stadler, Tanja, Albert, Jan, Crandall, Keith A., Leitner, Thomas, Stamatakis, Alexandros, Prosperi, Mattia, and Salemi, Marco

Published
2020

16. Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021)

Author

Walker, Peter J., Siddell, Stuart G., Lefkowitz, Elliot J., Mushegian, Arcady R., Adriaenssens, Evelien M., Alfenas-Zerbini, Poliane, Davison, Andrew J., Dempsey, Donald M., Dutilh, Bas E., García, María Laura, Harrach, Balázs, Harrison, Robert L., Hendrickson, R. Curtis, Junglen, Sandra, Knowles, Nick J., Krupovic, Mart, Kuhn, Jens H., Lambert, Amy J., Łobocka, Małgorzata, Nibert, Max L., Oksanen, Hanna M., Orton, Richard J., Robertson, David L., Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Smith, Donald B., Suzuki, Nobuhiro, Van Dooerslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, and Zerbini, Francisco Murilo

Published
2021
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17. Global and regional epidemiology of HIV-1 recombinants in 1990–2015: a systematic review and global survey

Author

Abimiku, Alash'le G, Agwale, Simon, Archibald, Chris, Avidor, Boaz, Barbás, María Gabriela, Barre-Sinoussi, Francoise, Barugahare, Banson, Belabbes, El Hadj, Bertagnolio, Silvia, Birx, Deborah, Bobkov, Aleksei F, Brandful, James, Bredell, Helba, Brennan, Catherine A, Brooks, James, Bruckova, Marie, Buonaguro, Luigi, Buonaguro, Franco, Buttò, Stefano, Buvé, Anne, Campbell, Mary, Carr, Jean, Carrera, Alex, Carrillo, Manuel Gómez, Celum, Connie, Chaplin, Beth, Charles, Macarthur, Chatzidimitriou, Dimitrios, Chen, Zhiwei, Chijiwa, Katsumi, Cooper, David, Cunningham, Philip, Dagnra, Anoumou, de Gascun, Cillian F, Del Amo, Julia, Delgado, Elena, Dietrich, Ursula, Dwyer, Dominic, Ellenberger, Dennis, Ensoli, Barbara, Essex, Max, Gao, Feng, Fleury, Hervé, Fonjungo, Peter N, Foulongne, Vincent, Gadkari, Deepak A, García, Federico, Garsia, Roger, Gershy-Damet, Guy Michel, Glynn, Judith R, Goodall, Ruth, Grossman, Zehava, Lindenmeyer-Guimarães, Monick, Hahn, Beatrice, Hamers, Raph L, Hamouda, Osamah, Handema, Ray, He, Xiang, Herbeck, Joshua, Ho, David D, Holguin, Africa, Hosseinipour, Mina, Hunt, Gillian, Ito, Masahiko, Bel Hadj Kacem, Mohamed Ali, Kahle, Erin, Kaleebu, Pontiano, Kalish, Marcia, Kamarulzaman, Adeeba, Kang, Chun, Kanki, Phyllis, Karamov, Edward, Karasi, Jean-Claude, Kayitenkore, Kayitesi, Kelleher, Tony, Kitayaporn, Dwip, Kostrikis, Leondios G, Kucherer, Claudia, Lara, Claudia, Leitner, Thomas, Liitsola, Kirsi, Lingappa, Jai, Linka, Marek, Lorenzana de Rivera, Ivette, Lukashov, Vladimir, Maayan, Shlomo, Mayr, Luzia, McCutchan, Francine, Meda, Nicolas, Menu, Elisabeth, Mhalu, Fred, Mloka, Doreen, Mokili, John L, Montes, Brigitte, Mor, Orna, Morgado, Mariza, Mosha, Fausta, Moussi, Awatef, Mullins, James, Najera, Rafael, Nasr, Mejda, Ndembi, Nicaise, Neilson, Joel R, Nerurkar, Vivek R, Neuhann, Florian, Nolte, Claudine, Novitsky, Vlad, Nyambi, Philippe, Ofner, Marianna, Paladin, Fem J, Papa, Anna, Pape, Jean, Parkin, Neil, Parry, Chris, Peeters, Martine, Pelletier, Alexandra, Pérez-Álvarez, Lucía, Pillay, Deenan, Pinto, Angie, Quang, Trinh Duy, Rademeyer, Cecilia, Raikanikoda, Filimone, Rayfield, Mark A, Reynes, Jean-Marc, Rinke de Wit, Tobias, Robbins, Kenneth E, Rolland, Morgane, Rousseau, Christine, Salazar-Gonzales, Jesus, Salem, Hanan, Salminen, Mika, Salomon, Horacio, Sandstrom, Paul, Santiago, Mario L, Sarr, Abdoulaye D, Schroeder, Bryan, Segondy, Michel, Selhorst, Philippe, Sempala, Sylvester, Servais, Jean, Shaik, Ansari, Shao, Yiming, Slim, Amine, Soares, Marcelo A, Songok, Elijah, Stewart, Debbie, Stokes, Julie, Subbarao, Shambavi, Sutthent, Ruengpung, Takehisa, Jun, Tanuri, Amilcar, Tee, Kok Keng, Thapa, Kiran, Thomson, Michael, Tran, Tyna, Urassa, Willy, Ushijima, Hiroshi, van de Perre, Philippe, van der Groen, Guido, van Laethem, Kristel, van Oosterhout, Joep, van Sighem, Ard, van Wijngaerden, Eric, Vandamme, Anne-Mieke, Vercauteren, Jurgen, Vidal, Nicole, Wallace, Lesley, Williamson, Carolyn, Wolday, Dawit, Xu, Jianqing, Yang, Chunfu, Zhang, Linqi, Zhang, Rong, Hemelaar, Joris, Elangovan, Ramyiadarsini, Yun, Jason, Dickson-Tetteh, Leslie, Kirtley, Shona, Gouws-Williams, Eleanor, and Ghys, Peter D

Published
2020
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18. Transferable data exclusivity vouchers are not the solution to the antimicrobial drug development crisis: a commentary on the proposed EU pharma regulation

Author

Berner-Rodoreda, Astrid, primary, Cobelens, Frank, additional, Vandamme, Anne-Mieke, additional, Froeschl, Günter, additional, Skordis, Jolene, additional, Renganathan, Elil, additional, t’Hoen, Ellen, additional, Raviglione, Mario, additional, Jahn, Albrecht, additional, and Bärnighausen, Till, additional

Published
2024
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20. Phylogenetic Analysis of Hepatitis C Virus Infections in a Large Belgian Cohort Using Next-Generation Sequencing of Full-Length Genomes

Author

Christensen, Kasper T., primary, Pierard, Florian, additional, Bonsall, David, additional, Bowden, Rory, additional, Barnes, Eleanor, additional, Florence, Eric, additional, Ansari, M. Azim, additional, Nguyen, Dung, additional, de Cesare, Mariateresa, additional, Nevens, Frederik, additional, Robaeys, Geert, additional, Schrooten, Yoeri, additional, Busschots, Dana, additional, Simmonds, Peter, additional, Vandamme, Anne-Mieke, additional, Van Wijngaerden, Eric, additional, Dierckx, Tim, additional, Cuypers, Lize, additional, and Van Laethem, Kristel, additional

Published
2023
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24. Assessing transmissibility of HIV-1 drug resistance mutations from treated and from drug-naive individuals

Author

Winand, Raf, Theys, Kristof, Eusébio, Mónica, Aerts, Jan, Camacho, Ricardo J, Gomes, Perpetua, Suchard, Marc A, Vandamme, Anne-Mieke, and Abecasis, Ana B

Subjects
Infectious Diseases, Antimicrobial Resistance, HIV/AIDS, Clinical Research, 5.1 Pharmaceuticals, Evaluation of treatments and therapeutic interventions, Development of treatments and therapeutic interventions, 6.1 Pharmaceuticals, Infection, Adult, Disease Transmission, Infectious, Drug Resistance, Viral, Epidemiological Monitoring, Female, Genotyping Techniques, HIV Infections, HIV-1, Human Immunodeficiency Virus Proteins, Humans, Incidence, Male, Middle Aged, Mutation, Missense, Portugal, Prevalence, Retrospective Studies, antiretroviral therapy, HIV drug resistance, mutation, protease inhibitors, reverse transcriptase inhibitors, transmission, Portuguese HIV-1 Resistance Study Group, Biological Sciences, Medical and Health Sciences, Psychology and Cognitive Sciences, Virology
Abstract

ObjectivesSurveillance drug resistance mutations (SDRMs) in drug-naive patients are typically used to survey HIV-1-transmitted drug resistance (TDR). We test here how SDRMs in patients failing treatment, the original source of TDR, contribute to assessing TDR, transmissibility and transmission source of SDRMs.DesignThis is a retrospective observational study analyzing a Portuguese cohort of HIV-1-infected patients.MethodsThe prevalence of SDRMs to protease inhibitors, nucleoside reverse transcriptase inhibitors (NRTIs) and nonnucleoside reverse transcriptase inhibitors (NNRTIs) in drug-naive and treatment-failing patients was measured for 3554 HIV-1 subtype B patients. Transmission ratio (prevalence in drug-naive/prevalence in treatment-failing patients), average viral load and robust linear regression with outlier detection (prevalence in drug-naive versus in treatment-failing patients) were analyzed and used to interpret transmissibility.ResultsPrevalence of SDRMs in drug-naive and treatment-failing patients were linearly correlated, but some SDRMs were classified as outliers - above (PRO: D30N, N88D/S, L90 M, RT: G190A/S/E) or below (RT: M184I/V) expectations. The normalized regression slope was 0.073 for protease inhibitors, 0.084 for NRTIs and 0.116 for NNRTIs. Differences between SDRMs transmission ratios were not associated with differences in viral loads.ConclusionThe significant linear correlation between prevalence of SDRMs in drug-naive and in treatment-failing patients indicates that the prevalence in treatment-failing patients can be useful to predict levels of TDR. The slope is a cohort-dependent estimate of rate of TDR per drug class and outlier detection reveals comparative persistence of SDRMs. Outlier SDRMs with higher transmissibility are more persistent and more likely to have been acquired from drug-naive patients. Those with lower transmissibility have faster reversion dynamics after transmission and are associated with acquisition from treatment-failing patients.

Published
2015

25. Disentangling the impact of within-host evolution and transmission dynamics on the tempo of HIV-1 evolution

Author

Vrancken, Bram, Baele, Guy, Vandamme, Anne-Mieke, van Laethem, Kristel, Suchard, Marc A, and Lemey, Philippe

Subjects
HIV/AIDS, Prevention, Aetiology, 2.2 Factors relating to the physical environment, Infection, Good Health and Well Being, Amino Acid Substitution, Evolution, Molecular, Female, Genetic Drift, Genetic Variation, HIV Infections, HIV-1, Humans, Male, Mutation Rate, Selection, Genetic, Sequence Analysis, DNA, Sexual Behavior, env Gene Products, Human Immunodeficiency Virus, evolutionary rate, genetic diversity, HIV, risk group, transmission bottleneck, Biological Sciences, Medical and Health Sciences, Psychology and Cognitive Sciences, Virology
Abstract

ObjectiveTo determine how HIV-1 risk groups impact transmitted diversity and the tempo of viral evolution at a population scale.MethodsWe investigated a set of previously described transmission chains (n = 70) using a population genetic approach, and tested whether the expected differences in proportions of multivariant transmissions are reflected by varying proportions of transmitted diversity between men having sex with men (MSM) and heterosexual (HET) subpopulations - the largest contributors to HIV spread. To assess evolutionary rate differences among the different risk groups, we compiled risk group datasets for subtypes A1, B and CRF01_AE, and directly compared the absolute substitution rate and its synonymous and non-synonymous components.ResultsThere was sufficient demographic signal to inform the transmission model in Bayesian evolutionary analysis by sampling trees using env data to compare the transmission bottleneck size between the MSM and HET risk groups. We found no indications for a different proportion of transmitted genetic diversity at the population level between these groups. In the direct rate comparisons between the risk groups, however, we consistently recovered a higher evolutionary rate in the male-dominated risk group compared to the HET datasets.ConclusionWe find that the risk group composition affects the viral evolutionary rate and therefore potentially also the adaptation rate. In particular, risk group-specific sex ratios, and the variation in within-host evolutionary rates between men and women, impose evolutionary rate differences at the epidemic level, but we cannot exclude a role of varying transmission rates.

Published
2015

26. Correction: Geographic and Temporal Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted HIV-1 Drug Resistance: An Individual-Patient- and Sequence-Level Meta-Analysis

Author

Rhee, Soo-Yon, Blanco, Jose Luis, Jordan, Michael R, Taylor, Jonathan, Lemey, Philippe, Varghese, Vici, Hamers, Raph L, Bertagnolio, Silvia, de Wit, Tobias F Rinke, Aghokeng, Avelin F, Albert, Jan, Avi, Radko, Avila-Rios, Santiago, Bessong, Pascal O, Brooks, James I, Boucher, Charles AB, Brumme, Zabrina L, Busch, Michael P, Bussmann, Hermann, Chaix, Marie-Laure, Chin, Bum Sik, D'Aquin, Toni T, De Gascun, Cillian F, Derache, Anne, Descamps, Diane, Deshpande, Alaka K, Djoko, Cyrille F, Eshleman, Susan H, Fleury, Herve, Frange, Pierre, Fujisaki, Seiichiro, Harrigan, P Richard, Hattori, Junko, Holguin, Africa, Hunt, Gillian M, Ichimura, Hiroshi, Kaleebu, Pontiano, Katzenstein, David, Kiertiburanakul, Sasisopin, Kim, Jerome H, Kim, Sung Soon, Li, Yanpeng, Lutsar, Irja, Morris, Lynn, Ndembi, Nicaise, Kee, Peng NG, Paranjape, Ramesh S, Peeters, Martine, Poljak, Mario, Price, Matt A, Ragonnet-Cronin, Manon L, Reyes-Terán, Gustavo, Rolland, Morgane, Sirivichayakul, Sunee, Smith, Davey M, Soares, Marcelo A, Soriano, Vincent V, Ssemwanga, Deogratius, Stanojevic, Maja, Stefani, Mariane A, Sugiura, Wataru, Sungkanuparph, Somnuek, Tanuri, Amilcar, Tee, Kok Keng, Truong, Hong-Ha M, van de Vijver, David AMC, Vidal, Nicole, Yang, Chunfu, Yang, Rongge, Yebra, Gonzalo, Ioannidis, John PA, Vandamme, Anne-Mieke, and Shafer, Robert W

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Good Health and Well Being, Medical and Health Sciences, General & Internal Medicine, Biomedical and clinical sciences, Health sciences
Published
2015

29. Global and regional molecular epidemiology of HIV-1, 1990–2015: a systematic review, global survey, and trend analysis

Author

Abimiku, Alash'le G, Agwale, Simon, Archibald, Chris, Avidor, Boaz, Barbás, María Gabriela, Barre-Sinoussi, Francoise, Barugahare, Banson, Belabbes, El Hadj, Bertagnolio, Silvia, Birx, Deborah, Bobkov, Aleksei F, Brandful, James, Bredell, Helba, Brennan, Catherine A, Brooks, James, Bruckova, Marie, Buonaguro, Luigi, Buonaguro, Franco, Buttò, Stefano, Buve, Anne, Campbell, Mary, Carr, Jean, Carrera, Alex, Carrillo, Manuel Gómez, Celum, Connie, Chaplin, Beth, Charles, Macarthur, Chatzidimitriou, Dimitrios, Chen, Zhiwei, Chijiwa, Katsumi, Cooper, David, Cunningham, Philip, Dagnra, Anoumou, de Gascun, Cillian F, Del Amo, Julia, Delgado, Elena, Dietrich, Ursula, Dwyer, Dominic, Ellenberger, Dennis, Ensoli, Barbara, Essex, Max, Gao, Feng, Fleury, Herve, Fonjungo, Peter N, Foulongne, Vincent, Gadkari, Deepak A, García, Federico, Garsia, Roger, Gershy-Damet, Guy Michel, Glynn, Judith R, Goodall, Ruth, Grossman, Zehava, Lindenmeyer-Guimarães, Monick, Hahn, Beatrice, Hamers, Raph L, Hamouda, Osamah, Handema, Ray, He, Xiang, Herbeck, Joshua, Ho, David D, Holguin, Africa, Hosseinipour, Mina, Hunt, Gillian, Ito, Masahiko, Bel Hadj Kacem, Mohamed Ali, Kahle, Erin, Kaleebu, Pontiano Kaleebu, Kalish, Marcia, Kamarulzaman, Adeeba, Kang, Chun, Kanki, Phyllis, Karamov, Edward, Karasi, Jean-Claude, Kayitenkore, Kayitesi, Kelleher, Tony, Kitayaporn, Dwip, Kostrikis, Leondios G, Kucherer, Claudia, Lara, Claudia, Leitner, Thomas, Liitsola, Kirsi, Lingappa, Jai, Linka, Marek, Lorenzana de Rivera, Ivette, Lukashov, Vladimir, Maayan, Shlomo, Mayr, Luzia, McCutchan, Francine, Meda, Nicolas, Menu, Elisabeth, Mhalu, Fred, Mloka, Doreen, Mokili, John L, Montes, Brigitte, Mor, Orna, Morgado, Mariza, Mosha, Fausta, Moussi, Awatef, Mullins, James, Najera, Rafael, Nasr, Mejda, Ndembi, Nicaise, Neilson, Joel R, Nerurkar, Vivek R, Neuhann, Florian, Nolte, Claudine, Novitsky, Vlad, Nyambi, Philippe, Ofner, Marianna, Paladin, Fem J, Papa, Anna, Pape, Jean, Parkin, Neil, Parry, Chris, Peeters, Martine, Pelletier, Alexandra, Pérez-Álvarez, Lucía, Pillay, Deenan, Pinto, Angie, Quang, Trinh Duy, Rademeyer, Cecilia, Raikanikoda, Filimone, Rayfield, Mark A, Reynes, Jean-Marc, Rinke de Wit, Tobias, Robbins, Kenneth E, Rolland, Morgane, Rousseau, Christine, Salazar-Gonzales, Jesus, Salem, Hanan, Salminen, Mika, Salomon, Horacio, Sandstrom, Paul, Santiago, Mario L, Sarr, Abdoulaye D, Schroeder, Bryan, Segondy, Michel, Selhorst, Philippe, Sempala, Sylvester, Servais, Jean, Shaik, Ansari, Shao, Yiming, Slim, Amine, Soares, Marcelo A, Songok, Elijah, Stewart, Debbie, Stokes, Julie, Subbarao, Shambavi, Sutthent, Ruengpung, Takehisa, Jun, Tanuri, Amilcar, Tee, Kok Keng, Thapa, Kiran, Thomson, Michael, Tran, Tyna, Urassa, Willy, Ushijima, Hiroshi, van de Perre, Philippe, van der Groen, Guido, van Laethem, Kristel, van Oosterhout, Joep, van Sighem, Ard, van Wijngaerden, Eric, Vandamme, Anne-Mieke, Vercauteren, Jurgen, Vidal, Nicole, Wallace, Lesley, Williamson, Carolyn, Wolday, Dawit, Xu, Jianqing, Yang, Chunfu, Zhang, Linqi, Zhang, Rong, Hemelaar, Joris, Elangovan, Ramyiadarsini, Yun, Jason, Dickson-Tetteh, Leslie, Fleminger, Isabella, Kirtley, Shona, Williams, Brian, Gouws-Williams, Eleanor, and Ghys, Peter D

Published
2019
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30. The genealogical population dynamics of HIV-1 in a large transmission chain: bridging within and among host evolutionary rates.

Author

Vrancken, Bram, Rambaut, Andrew, Suchard, Marc A, Drummond, Alexei, Baele, Guy, Derdelinckx, Inge, Van Wijngaerden, Eric, Vandamme, Anne-Mieke, Van Laethem, Kristel, and Lemey, Philippe

Subjects
Humans, HIV-1, HIV Infections, Evolution, Molecular, Host-Pathogen Interactions, Evolution, Molecular, Mathematical Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Abstract

Transmission lies at the interface of human immunodeficiency virus type 1 (HIV-1) evolution within and among hosts and separates distinct selective pressures that impose differences in both the mode of diversification and the tempo of evolution. In the absence of comprehensive direct comparative analyses of the evolutionary processes at different biological scales, our understanding of how fast within-host HIV-1 evolutionary rates translate to lower rates at the between host level remains incomplete. Here, we address this by analyzing pol and env data from a large HIV-1 subtype C transmission chain for which both the timing and the direction is known for most transmission events. To this purpose, we develop a new transmission model in a Bayesian genealogical inference framework and demonstrate how to constrain the viral evolutionary history to be compatible with the transmission history while simultaneously inferring the within-host evolutionary and population dynamics. We show that accommodating a transmission bottleneck affords the best fit our data, but the sparse within-host HIV-1 sampling prevents accurate quantification of the concomitant loss in genetic diversity. We draw inference under the transmission model to estimate HIV-1 evolutionary rates among epidemiologically-related patients and demonstrate that they lie in between fast intra-host rates and lower rates among epidemiologically unrelated individuals infected with HIV subtype C. Using a new molecular clock approach, we quantify and find support for a lower evolutionary rate along branches that accommodate a transmission event or branches that represent the entire backbone of transmitted lineages in our transmission history. Finally, we recover the rate differences at the different biological scales for both synonymous and non-synonymous substitution rates, which is only compatible with the 'store and retrieve' hypothesis positing that viruses stored early in latently infected cells preferentially transmit or establish new infections upon reactivation.

Published
2014

31. Ethical considerations in global HIV phylogenetic research

Author

Amon, Joseph J., Baggaley, Rachel, Bernard, Edwin J., Burns, David, Cohen, Myron S., Coltart, Cordelia C., Dallabetta, Gina, Dawson, Liza, Dedes, Nikos, Delpech, Valerie, Eba, Patrick M., Fraser, Christophe, Geller, Gail, German, Danielle, Godfrey-Faussett, Peter, Grabowksi, M. Kate, Hall, Irene, Harling, Guy, Henderson, Gail, Hoppe, Anne, Kozlakidis, Zisis, Laeyendecker, Oliver, Mwanza, Felix, Novitsky, Vladimir, Parker, Michael, Pillay, Deenan, Reis, Andreas, Seeley, Janet, Simwanga, Musonda, Tucker, Joseph D., Vandamme, Anne-Mieke, Wertheim, Joel O., Zimmerman, Rick, Coltart, Cordelia E M, Amon, Joseph J, Simwinga, Musonda, Tucker, Joseph D, Eba, Patrick, Grabowski, M Kate, and Cohen, Myron S

Published
2018
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32. More than one crisis: COVID-19 response actors navigating multi-dimensional crises in Flanders, Belgium

Author

Kattumana, Tarun, primary, Heyerdahl, Leonardo W., additional, Nguyen, ToTran, additional, Dielen, Stef, additional, Peeters Grietens, Koen, additional, Vandamme, Anne-Mieke, additional, Giles-Vernick, Tamara, additional, Larson, Heidi J., additional, Vandaele, Nico, additional, Vandermeulen, Corinne, additional, Gryseels, Charlotte, additional, and Van Riet, Carla, additional

Published
2023
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33. High seroprevalence of Leishmania infantum is linked to immune activation in people with HIV: a two-stage cross-sectional study in Bahia, Brazil

Author

de Moraes, Laise, primary, Santos, Luciane Amorim, additional, Arruda, Liã Bárbara, additional, Silva, Maria da Purificação Pereira da, additional, Silva, Márcio de Oliveira, additional, Silva, José Adriano Góes, additional, Ramos, André, additional, Santos, Marcos Bastos dos, additional, Torres, Felipe Guimarães, additional, Orge, Cibele, additional, Teixeira, Antonio Marcos dos Santos, additional, Vieira, Thiago Santos, additional, Ramírez, Laura, additional, Soto, Manuel, additional, Grassi, Maria Fernanda Rios, additional, Siqueira, Isadora Cristina de, additional, Costa, Dorcas Lamounier, additional, Costa, Carlos Henrique Nery, additional, Andrade, Bruno de Bezerril, additional, Akrami, Kevan, additional, de Oliveira, Camila Indiani, additional, Boaventura, Viviane Sampaio, additional, Barral-Netto, Manoel, additional, Barral, Aldina, additional, Vandamme, Anne-Mieke, additional, Van Weyenbergh, Johan, additional, and Khouri, Ricardo, additional

Published
2023
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39. Expert consensus statement on the science of HIV in the context of criminal law

Author

Barre-Sinoussi, Francoise, Karim, Salim S. Abdool, Albert, Jan, Bekker, Linda-Gail, Beyrer, Chris, Cahn, Pedro, Calmy, Alexandra, Grinsztejn, Beatriz, Grulich, Andrew, Kamarulzaman, Adeeba, Kumarasamy, Nagalingeswaran, Loutfy, Mona R., Filali, Kamal M. El, Mboup, Souleymane, Montaner, Julio S.G., Munderi, Paula, Pokrovsky, Vadim, Vandamme, Anne-Mieke, Young, Benjamin, and Godfrey-Fausset, Peter

Subjects
HIV infections -- Risk factors -- Control -- Laws, regulations and rules, Disease transmission -- Control, Human rights -- Social aspects, Criminal law, Government regulation, Health
Abstract

Introduction: Globally, prosecutions for non-disclosure, exposure or transmission of HIV frequently relate to sexual activity, biting, or spitting. This includes instances in which no harm was intended, HIV transmission did not occur, and HIV transmission was extremely unlikely or not possible. This suggests prosecutions are not always guided by the best available scientific and medical evidence. Discussion: Twenty scientists from regions across the world developed this Expert Consensus Statement to address the use of HIV science by the criminal justice system. A detailed analysis of the best available scientific and medical research data on HIV transmission, treatment effectiveness and forensic phylogenetic evidence was performed and described so it may be better understood in criminal law contexts. Description of the possibility of HIV transmission was limited to acts most often at issue in criminal cases. The possibility of HIV transmission during a single, specific act was positioned along a continuum of risk, noting that the possibility of HIV transmission varies according to a range of intersecting factors including viral load, condom use, and other risk reduction practices. Current evidence suggests the possibility of HIV transmission during a single episode of sex, biting or spitting ranges from no possibility to low possibility. Further research considered the positive health impact of modern antiretroviral therapies that have improved the life expectancy of most people living with HIV to a point similar to their HIV-negative counterparts, transforming HIV infection into a chronic, manageable health condition. Lastly, consideration of the use of scientific evidence in court found that phylogenetic analysis alone cannot prove beyond reasonable doubt that one person infected another although it can be used to exonerate a defendant. Conclusions: The application of up-to-date scientific evidence in criminal cases has the potential to limit unjust prosecutions and convictions. The authors recommend that caution be exercised when considering prosecution, and encourage governments and those working in legal and judicial systems to pay close attention to the significant advances in HIV science that have occurred over the last three decades to ensure current scientific knowledge informs application of the law in cases related to HIV. Keywords: human rights; law and policy; risk factors; policy; criminalization; criminal law; prosecution, 1 | INTRODUCTION At least 68 countries have laws that specifically criminalize HIV non-disclosure, exposure, or transmission. Thirty-three countries are known to have applied other criminal law provisions in similar [...]

Published
2018
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40. Analyses of Early ZIKV Genomes Are Consistent with Viral Spread from Northeast Brazil to the Americas

Author

de Moraes, Laise, primary, Portilho, Moyra M., additional, Vrancken, Bram, additional, Van den Broeck, Frederik, additional, Santos, Luciane Amorim, additional, Cucco, Marina, additional, Tauro, Laura B., additional, Kikuti, Mariana, additional, Silva, Monaise M. O., additional, Campos, Gúbio S., additional, Reis, Mitermayer G., additional, Barral, Aldina, additional, Barral-Netto, Manoel, additional, Boaventura, Viviane Sampaio, additional, Vandamme, Anne-Mieke, additional, Theys, Kristof, additional, Lemey, Philippe, additional, Ribeiro, Guilherme S., additional, and Khouri, Ricardo, additional

Published
2023
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41. Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV)

Author

Siddell, Stuart G., primary, Smith, Donald B., additional, Adriaenssens, Evelien, additional, Alfenas-Zerbini, Poliane, additional, Dutilh, Bas E., additional, Garcia, Maria Laura, additional, Junglen, Sandra, additional, Krupovic, Mart, additional, Kuhn, Jens H., additional, Lambert, Amy J., additional, Lefkowitz, Elliot J., additional, Łobocka, Małgorzata, additional, Mushegian, Arcady R., additional, Oksanen, Hanna M., additional, Robertson, David L., additional, Rubino, Luisa, additional, Sabanadzovic, Sead, additional, Simmonds, Peter, additional, Suzuki, Nobuhiro, additional, Van Doorslaer, Koenraad, additional, Vandamme, Anne-Mieke, additional, Varsani, Arvind, additional, and Zerbini, F. Murilo, additional

Published
2023
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42. Analyses of Early ZIKV Genomes are Consistent with Viral Spread from Northeast Brazil to The Americas

Author

De Moraes, Laise Eduarda Paixão, primary, Portilho, Moyra Machado, additional, Vrancken, Bram, additional, Van den Broeck, Frederik, additional, Santos, Luciane Amorim, additional, Cucco, Marina Silveira, additional, Tauro, Laura Beatriz, additional, Kikuti, Mariana, additional, Silva, Monaise Madalena Oliveira, additional, Campos, Gubio Soares, additional, Reis, Mitermayer Galvão, additional, Barral, Aldina Maria Prado, additional, Barral-Netto, Manoel, additional, Boaventura, Viviane Sampaio, additional, Vandamme, Anne-Mieke, additional, Theys, Kristof, additional, Lemey, Philippe, additional, Ribeiro, Guilherme de Sousa, additional, and Khouri, Ricardo, additional

Published
2023
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43. Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV)

Author

Sub Bioinformatics, Theoretical Biology and Bioinformatics, Siddell, Stuart G, Smith, Donald B, Adriaenssens, Evelien, Alfenas-Zerbini, Poliane, Dutilh, Bas E, Garcia, Maria Laura, Junglen, Sandra, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Lefkowitz, Elliot J, Łobocka, Małgorzata, Mushegian, Arcady R, Oksanen, Hanna M, Robertson, David L, Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Suzuki, Nobuhiro, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, Zerbini, F Murilo, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Siddell, Stuart G, Smith, Donald B, Adriaenssens, Evelien, Alfenas-Zerbini, Poliane, Dutilh, Bas E, Garcia, Maria Laura, Junglen, Sandra, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Lefkowitz, Elliot J, Łobocka, Małgorzata, Mushegian, Arcady R, Oksanen, Hanna M, Robertson, David L, Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Suzuki, Nobuhiro, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, and Zerbini, F Murilo

Published
2023

44. Four principles to establish a universal virus taxonomy

Author

Theoretical Biology and Bioinformatics, Sub Bioinformatics, Simmonds, Peter, Adriaenssens, Evelien M, Zerbini, F Murilo, Abrescia, Nicola G A, Aiewsakun, Pakorn, Alfenas-Zerbini, Poliane, Bao, Yiming, Barylski, Jakub, Drosten, Christian, Duffy, Siobain, Duprex, W Paul, Dutilh, Bas E, Elena, Santiago F, García, Maria Laura, Junglen, Sandra, Katzourakis, Aris, Koonin, Eugene V, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Lefkowitz, Elliot J, Łobocka, Małgorzata, Lood, Cédric, Mahony, Jennifer, Meier-Kolthoff, Jan P, Mushegian, Arcady R, Oksanen, Hanna M, Poranen, Minna M, Reyes-Muñoz, Alejandro, Robertson, David L, Roux, Simon, Rubino, Luisa, Sabanadzovic, Sead, Siddell, Stuart, Skern, Tim, Smith, Donald B, Sullivan, Matthew B, Suzuki, Nobuhiro, Turner, Dann, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, Vasilakis, Nikos, Theoretical Biology and Bioinformatics, Sub Bioinformatics, Simmonds, Peter, Adriaenssens, Evelien M, Zerbini, F Murilo, Abrescia, Nicola G A, Aiewsakun, Pakorn, Alfenas-Zerbini, Poliane, Bao, Yiming, Barylski, Jakub, Drosten, Christian, Duffy, Siobain, Duprex, W Paul, Dutilh, Bas E, Elena, Santiago F, García, Maria Laura, Junglen, Sandra, Katzourakis, Aris, Koonin, Eugene V, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Lefkowitz, Elliot J, Łobocka, Małgorzata, Lood, Cédric, Mahony, Jennifer, Meier-Kolthoff, Jan P, Mushegian, Arcady R, Oksanen, Hanna M, Poranen, Minna M, Reyes-Muñoz, Alejandro, Robertson, David L, Roux, Simon, Rubino, Luisa, Sabanadzovic, Sead, Siddell, Stuart, Skern, Tim, Smith, Donald B, Sullivan, Matthew B, Suzuki, Nobuhiro, Turner, Dann, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, and Vasilakis, Nikos

Published
2023

45. Erratum: Correction to: Changes to virus taxonomy and the ICTV Statutes ratifed by the International Committee on Taxonomy of Viruses (2023) (Archives of virology (2023) 168 7 (175))

Author

Theoretical Biology and Bioinformatics, Sub Bioinformatics, Zerbini, Francisco Murilo, Siddell, Stuart G, Lefkowitz, Elliot J, Mushegian, Arcady R, Adriaenssens, Evelien M, Alfenas-Zerbini, Poliane, Dempsey, Donald M, Dutilh, Bas E, García, María Laura, Hendrickson, R Curtis, Junglen, Sandra, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Łobocka, Małgorzata, Oksanen, Hanna M, Robertson, David L, Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Smith, Donald B, Suzuki, Nobuhiro, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, Theoretical Biology and Bioinformatics, Sub Bioinformatics, Zerbini, Francisco Murilo, Siddell, Stuart G, Lefkowitz, Elliot J, Mushegian, Arcady R, Adriaenssens, Evelien M, Alfenas-Zerbini, Poliane, Dempsey, Donald M, Dutilh, Bas E, García, María Laura, Hendrickson, R Curtis, Junglen, Sandra, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Łobocka, Małgorzata, Oksanen, Hanna M, Robertson, David L, Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Smith, Donald B, Suzuki, Nobuhiro, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, and Varsani, Arvind

Published
2023

46. Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2023)

Author

Theoretical Biology and Bioinformatics, Sub Bioinformatics, Zerbini, Francisco Murilo, Siddell, Stuart G, Lefkowitz, Elliot J, Mushegian, Arcady R, Adriaenssens, Evelien M, Alfenas-Zerbini, Poliane, Dempsey, Donald M, Dutilh, Bas E, García, María Laura, Hendrickson, R Curtis, Junglen, Sandra, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Łobocka, Małgorzata, Oksanen, Hanna M, Robertson, David L, Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Smith, Donald B, Suzuki, Nobuhiro, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, Theoretical Biology and Bioinformatics, Sub Bioinformatics, Zerbini, Francisco Murilo, Siddell, Stuart G, Lefkowitz, Elliot J, Mushegian, Arcady R, Adriaenssens, Evelien M, Alfenas-Zerbini, Poliane, Dempsey, Donald M, Dutilh, Bas E, García, María Laura, Hendrickson, R Curtis, Junglen, Sandra, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Łobocka, Małgorzata, Oksanen, Hanna M, Robertson, David L, Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Smith, Donald B, Suzuki, Nobuhiro, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, and Varsani, Arvind

Published
2023

47. High seroprevalence of Leishmania infantum is linked to immune activation in people with HIV: a two-stage cross-sectional study in Bahia, Brazil

Author

Fundaçao Capes (Brasil), Ministério da Ciência e Tecnologia (Brasil), Fundação de Amparo à Pesquisa do Estado da Bahia, de Moraes, Laise, Santos, Luciane Amorim, Arruda, Liã Bárbara, Silva, Maria da Purificação Pereira da, Silva, Márcio de Oliveira, Silva, José Adriano Góes, Ramos, André, Santos, Marcos Bastos dos, Torres, Felipe Guimarães, Orge, Cibele, Teixeira, Antonio Marcos dos Santos, Vieira, Thiago Santos, Ramírez, Laura, Soto, Manuel, Grassi, Maria Fernanda Rios, Siqueira, Isadora Cristina de, Costa, Dorcas Lamounier, Costa, Carlos Henrique Nery, Andrade, Bruno de Bezerril, Akrami, Kevan, de Oliveira, Camila Indiani, Boaventura, Viviane Sampaio, Barral-Netto, Manoel, Barral, Aldina, Vandamme, Anne-Mieke, Van Weyenbergh, Johan, Khouri, Ricardo, Fundaçao Capes (Brasil), Ministério da Ciência e Tecnologia (Brasil), Fundação de Amparo à Pesquisa do Estado da Bahia, de Moraes, Laise, Santos, Luciane Amorim, Arruda, Liã Bárbara, Silva, Maria da Purificação Pereira da, Silva, Márcio de Oliveira, Silva, José Adriano Góes, Ramos, André, Santos, Marcos Bastos dos, Torres, Felipe Guimarães, Orge, Cibele, Teixeira, Antonio Marcos dos Santos, Vieira, Thiago Santos, Ramírez, Laura, Soto, Manuel, Grassi, Maria Fernanda Rios, Siqueira, Isadora Cristina de, Costa, Dorcas Lamounier, Costa, Carlos Henrique Nery, Andrade, Bruno de Bezerril, Akrami, Kevan, de Oliveira, Camila Indiani, Boaventura, Viviane Sampaio, Barral-Netto, Manoel, Barral, Aldina, Vandamme, Anne-Mieke, Van Weyenbergh, Johan, and Khouri, Ricardo

Abstract

Visceral leishmaniasis is an opportunistic disease in HIV-1 infected individuals, unrecognized as a determining factor for AIDS diagnosis. The growing geographical overlap of HIV-1 and Leishmania infections is an emerging challenge worldwide, as co-infection increases morbidity and mortality for both infections. Here, we determined the prevalence of people living with HIV (PWH) with a previous or ongoing infection by Leishmania infantum and investigated the virological and immunological factors associated with co-infection. We adopted a two-stage cross-sectional cohort (CSC) desig

Published
2023

48. Analyses of Early ZIKV Genomes Are Consistent with Viral Spread from Northeast Brazil to the Americas

Author

de Moraes, Laise, Portilho, Moyra Machado, Vrancken, Bram, Van den Broeck, Frederik, Santos, Luciane Amorim, Cucco, Marina, Tauro, Laura Beatriz, Kikuti, Mariana, Silva, Monaíse Madalena Oliveira, Campos, Gúbio Soares Soares G.S., Reis, Mitermayer M.G., Barral, Aldina, Barral-Netto, Manoel, Boaventura, Viviane Sampaio, Vandamme, Anne-Mieke, Theys, Kristof, Lemey, Philippe, Ribeiro, Guilherme G.S., Khouri, Ricardo, de Moraes, Laise, Portilho, Moyra Machado, Vrancken, Bram, Van den Broeck, Frederik, Santos, Luciane Amorim, Cucco, Marina, Tauro, Laura Beatriz, Kikuti, Mariana, Silva, Monaíse Madalena Oliveira, Campos, Gúbio Soares Soares G.S., Reis, Mitermayer M.G., Barral, Aldina, Barral-Netto, Manoel, Boaventura, Viviane Sampaio, Vandamme, Anne-Mieke, Theys, Kristof, Lemey, Philippe, Ribeiro, Guilherme G.S., and Khouri, Ricardo

Abstract

The Americas, particularly Brazil, were greatly impacted by the widespread Zika virus (ZIKV) outbreak in 2015 and 2016. Efforts were made to implement genomic surveillance of ZIKV as part of the public health responses. The accuracy of spatiotemporal reconstructions of the epidemic spread relies on the unbiased sampling of the transmission process. In the early stages of the outbreak, we recruited patients exhibiting clinical symptoms of arbovirus-like infection from Salvador and Campo Formoso, Bahia, in Northeast Brazil. Between May 2015 and June 2016, we identified 21 cases of acute ZIKV infection and subsequently recovered 14 near full-length sequences using the amplicon tiling multiplex approach with nanopore sequencing. We performed a time-calibrated discrete phylogeographic analysis to trace the spread and migration history of the ZIKV. Our phylogenetic analysis supports a consistent relationship between ZIKV migration from Northeast to Southeast Brazil and its subsequent dissemination beyond Brazil. Additionally, our analysis provides insights into the migration of ZIKV from Brazil to Haiti and the role Brazil played in the spread of ZIKV to other countries, such as Singapore, the USA, and the Dominican Republic. The data generated by this study enhances our understanding of ZIKV dynamics and supports the existing knowledge, which can aid in future surveillance efforts against the virus., SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2023

49. Application of Phylodynamic Tools to Inform the Public Health Response to COVID-19: Qualitative Analysis of Expert Opinions

Author

Rich, Shannan S.N., Richards, Veronica, Mavian, Carla, Magalis, Brittany Rife, Grubaugh, Nathan, Rasmussen, Sonja Ann, Dellicour, Simon, Vrancken, Bram, Carrington, Christine, Fisk-Hoffman, Rebecca, Danso-Odei, Demi, Chacreton, Daniel, Shapiro, Jerne, Seraphin, Marie Nancy, Hepp, Crystal, Black, Allison, Dennis, Ann, Trovão, Nídia Sequeira, Vandamme, Anne-Mieke, Rasmussen, Angela, Lauzardo, Michael, Dean, Natalie, Salemi, Marco, Prosperi, Mattia, Rich, Shannan S.N., Richards, Veronica, Mavian, Carla, Magalis, Brittany Rife, Grubaugh, Nathan, Rasmussen, Sonja Ann, Dellicour, Simon, Vrancken, Bram, Carrington, Christine, Fisk-Hoffman, Rebecca, Danso-Odei, Demi, Chacreton, Daniel, Shapiro, Jerne, Seraphin, Marie Nancy, Hepp, Crystal, Black, Allison, Dennis, Ann, Trovão, Nídia Sequeira, Vandamme, Anne-Mieke, Rasmussen, Angela, Lauzardo, Michael, Dean, Natalie, Salemi, Marco, and Prosperi, Mattia

Abstract

Background: In the wake of the SARS-CoV-2 pandemic, scientists have scrambled to collect and analyze SARS-CoV-2 genomic data to inform public health responses to COVID-19 in real time. Open source phylogenetic and data visualization platforms for monitoring SARS-CoV-2 genomic epidemiology have rapidly gained popularity for their ability to illuminate spatial-temporal transmission patterns worldwide. However, the utility of such tools to inform public health decision-making for COVID-19 in real time remains to be explored. Objective: The aim of this study is to convene experts in public health, infectious diseases, virology, and bioinformatics—many of whom were actively engaged in the COVID-19 response—to discuss and report on the application of phylodynamic tools to inform pandemic responses. Methods: In total, 4 focus groups (FGs) occurred between June 2020 and June 2021, covering both the pre- and postvariant strain emergence and vaccination eras of the ongoing COVID-19 crisis. Participants included national and international academic and government researchers, clinicians, public health practitioners, and other stakeholders recruited through purposive and convenience sampling by the study team. Open-ended questions were developed to prompt discussion. FGs I and II concentrated on phylodynamics for the public health practitioner, while FGs III and IV discussed the methodological nuances of phylodynamic inference. Two FGs per topic area to increase data saturation. An iterative, thematic qualitative framework was used for data analysis. Results: We invited 41 experts to the FGs, and 23 (56%) agreed to participate. Across all the FG sessions, 15 (65%) of the participants were female, 17 (74%) were White, and 5 (22%) were Black. Participants were described as molecular epidemiologists (MEs; n=9, 39%), clinician-researchers (n=3, 13%), infectious disease experts (IDs; n=4, 17%), and public health professionals at the local (PHs; n=4, 17%), state (n=2, 9%), and federal, SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2023

50. Women in the European Virus Bioinformatics Center

Author

Hufsky, Franziska, Abecasis, Ana, Agudelo-Romero, Patricia, Bletsa, Magda, Brown, Katherine, Claus, Claudia, Deinhardt-Emmer, Stefanie, Deng, Li, Friedel, Caroline C, Gismondi, María Inés, Kostaki, Evangelia Georgia, Kühnert, Denise, Kulkarni-Kale, Urmila, Metzner, Karin J, Meyer, Irmtraud M, Miozzi, Laura, Nishimura, Luca, Paraskevopoulou, Sofia, Pérez-Cataluña, Alba, Rahlff, Janina, Thomson, Emma, Tumescheit, Charlotte, van der Hoek, Lia, Van Espen, Lore, Vandamme, Anne-Mieke, Zaheri, Maryam, Zuckerman, Neta, Marz, Manja, Hufsky, Franziska [0000-0002-9489-3182], Abecasis, Ana [0000-0002-3903-5265], Agudelo-Romero, Patricia [0000-0002-3703-4111], Bletsa, Magda [0000-0003-3184-6618], Brown, Katherine [0000-0002-8400-6922], Claus, Claudia [0000-0003-4962-6568], Deinhardt-Emmer, Stefanie [0000-0003-4495-4052], Deng, Li [0000-0003-0225-0663], Friedel, Caroline C [0000-0003-3569-4877], Gismondi, María Inés [0000-0002-2566-1169], Kostaki, Evangelia Georgia [0000-0002-3346-0930], Kühnert, Denise [0000-0002-5657-018X], Kulkarni-Kale, Urmila [0000-0002-1168-2479], Metzner, Karin J [0000-0003-4862-1503], Meyer, Irmtraud M [0000-0002-4048-3479], Miozzi, Laura [0000-0003-0410-8230], Nishimura, Luca [0000-0003-2144-7867], Paraskevopoulou, Sofia [0000-0003-2608-2596], Pérez-Cataluña, Alba [0000-0002-4784-8346], Rahlff, Janina [0000-0002-2132-2709], Thomson, Emma [0000-0003-1482-0889], Tumescheit, Charlotte [0000-0002-7563-5575], van der Hoek, Lia [0000-0003-2803-642X], Van Espen, Lore [0000-0002-3870-4551], Vandamme, Anne-Mieke [0000-0002-6594-2766], Zaheri, Maryam [0000-0003-2777-835X], Zuckerman, Neta [0000-0001-6074-2100], Marz, Manja [0000-0003-4783-8823], Apollo - University of Cambridge Repository, Medical Microbiology and Infection Prevention, AII - Infectious diseases, University of Zurich, Hufsky, Franziska, and Marz, Manja

Subjects
10028 Institute of Medical Virology, virus evolution, virus discovery, Cancer Research, viral ecology, Virus Bioinformatics, Big Data, Networking, Virus Discovery, Virus Evolution, Viral Infection, Transcriptomics, Emerging Viruses, Epidemiology, Viral Ecology, networking, virus bioinformatics, Computational Biology, 610 Medicine & health, 2725 Infectious Diseases, Research Personnel, Europe, emerging viruses, transcriptomics, big data, Viruses, 2406 Virology, 570 Life sciences, biology, Humans, epidemiology, Female, viral infection
Abstract

Viruses are the cause of a considerable burden to human, animal and plant health, while on the other hand playing an important role in regulating entire ecosystems. The power of new sequencing technologies combined with new tools for processing "Big Data" offers unprecedented opportunities to answer fundamental questions in virology. Virologists have an urgent need for virus-specific bioinformatics tools. These developments have led to the formation of the European Virus Bioinformatics Center, a network of experts in virology and bioinformatics who are joining forces to enable extensive exchange and collaboration between these research areas. The EVBC strives to provide talented researchers with a supportive environment free of gender bias, but the gender gap in science, especially in math-intensive fields such as computer science, persists. To bring more talented women into research and keep them there, we need to highlight role models to spark their interest, and we need to ensure that female scientists are not kept at lower levels but are given the opportunity to lead the field. Here we showcase the work of the EVBC and highlight the achievements of some outstanding women experts in virology and viral bioinformatics. ispartof: VIRUSES-BASEL vol:14 issue:7 ispartof: location:Switzerland status: published

Published
2022

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