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1. Perceptions About Technologies That Help Community-Dwelling Older Adults Remain at Home: Qualitative Study

Author

Verloo, Henk, Kampel, Thomas, Vidal, Nicole, and Pereira, Filipa

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Public aspects of medicine, RA1-1270
Abstract

BackgroundThe population of Europe is aging rapidly. Most community-dwelling older adults (CDOAs) want to remain in their homes, particularly those experiencing functional decline. Politicians and academics repeatedly praise technological instruments for being the preferred solution for helping older adults with deteriorating health to remain at home. ObjectiveThis study aimed to understand the perceptions of CDOAs and their informal caregivers (ICs) and professional caregivers (PCs) about technologies that can help keep older adults at home. MethodsThis qualitative study used personal interviews, focus groups, and photo-elicitation interviews to better understand the perceptions of a convenience sample of 68 CDOAs, 21 ICs, and 32 PCs. ResultsA fraction of CDOAs did not perceive technological instruments to be a very useful means of helping them remain at home. However, the ICs and PCs were more positive. The CDOAs preferred and were more willing to adopt technologies related to their mobility and safety and those that would help slow down their cognitive decline. The ICs preferred technological aids that assist in the activities of daily living as well as safety-related technologies for detecting falls and helping to locate disoriented older adults. The PCs preferred integrated communication and information systems to improve collaboration between all stakeholders, housing equipped with technologies to manage complex care, high-performance ancillary equipment to transfer people with reduced mobility, and surveillance systems to ensure safety at home. ConclusionsAlthough our study reports that CDOAs have limited interest in innovative technologies to help them remain at home, their technological skills will undoubtedly improve in the future, as will those of ICs and PCs. Technological tools will play an increasingly important role in home health care.

Published
2020
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2. Use of strips of rapid diagnostic tests as a source of ribonucleic acid for genomic surveillance of viruses: an example of SARS-CoV-2

Author

Keita, Alpha Kabiné, Mbaye, Aminata, Soumah, Abdoul Karim, Kadio, Kadio Jean Jacques Olivier, Diallo, Haby, Gnimadi, Thibaut Armel Chérif, Koivogui, Joel Balla, Povogui, Moriba Kowa, Monemou, Jean Louis, Traore, Baba, Vidal, Nicole, Guichet, Emilande, Ayouba, Ahidjo, Delaporte, Eric, Peeters, Martine, Toure, Abdoulaye, and Keita, Alpha Kabinet

Published
2024
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4. Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa.

Author

Faria, Nuno R, Vidal, Nicole, Lourenco, José, Raghwani, Jayna, Sigaloff, Kim CE, Tatem, Andy J, van de Vijver, David AM, Pineda-Peña, Andrea-Clemencia, Rose, Rebecca, Wallis, Carole L, Ahuka-Mundeke, Steve, Muyembe-Tamfum, Jean-Jacques, Muwonga, Jérémie, Suchard, Marc A, Rinke de Wit, Tobias F, Hamers, Raph L, Ndembi, Nicaise, Baele, Guy, Peeters, Martine, Pybus, Oliver G, Lemey, Philippe, and Dellicour, Simon

Subjects
Humans, HIV-1, HIV Infections, Africa, Central, Africa, Eastern, Africa, Central, Eastern, Virology, Microbiology, Immunology, Medical Microbiology
Abstract

Since the ignition of the HIV-1 group M pandemic in the beginning of the 20th century, group M lineages have spread heterogeneously throughout the world. Subtype C spread rapidly through sub-Saharan Africa and is currently the dominant HIV lineage worldwide. Yet the epidemiological and evolutionary circumstances that contributed to its epidemiological expansion remain poorly understood. Here, we analyse 346 novel pol sequences from the DRC to compare the evolutionary dynamics of the main HIV-1 lineages, subtypes A1, C and D. Our results place the origins of subtype C in the 1950s in Mbuji-Mayi, the mining city of southern DRC, while subtypes A1 and D emerged in the capital city of Kinshasa, and subtypes H and J in the less accessible port city of Matadi. Following a 15-year period of local transmission in southern DRC, we find that subtype C spread at least three-fold faster than other subtypes circulating in Central and East Africa. In conclusion, our results shed light on the origins of HIV-1 main lineages and suggest that socio-historical rather than evolutionary factors may have determined the epidemiological fate of subtype C in sub-Saharan Africa.

Published
2019

6. Resurgence of Ebola virus in 2021 in Guinea suggests a new paradigm for outbreaks

Author

Keita, Alpha Kabinet, Koundouno, Fara R., Faye, Martin, Düx, Ariane, Hinzmann, Julia, Diallo, Haby, Ayouba, Ahidjo, Le Marcis, Frederic, Soropogui, Barre, Ifono, Kekoura, Diagne, Moussa M., Sow, Mamadou S., Bore, Joseph A., Calvignac-Spencer, Sebastien, Vidal, Nicole, Camara, Jacob, and Keita, Mamadou B.

Subjects
Ebola virus infections -- Distribution -- Forecasts and trends, Market trend/market analysis, Company distribution practices, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Seven years after the declaration of the first epidemic of Ebola virus disease in Guinea, the country faced a new outbreak--between 14 February and 19 June 2021--near the epicentre of the previous epidemic.sup.1,2. Here we use next-generation sequencing to generate complete or near-complete genomes of Zaire ebolavirus from samples obtained from 12 different patients. These genomes form a well-supported phylogenetic cluster with genomes from the previous outbreak, which indicates that the new outbreak was not the result of a new spillover event from an animal reservoir. The 2021 lineage shows considerably lower divergence than would be expected during sustained human-to-human transmission, which suggests a persistent infection with reduced replication or a period of latency. The resurgence of Zaire ebolavirus from humans five years after the end of the previous outbreak of Ebola virus disease reinforces the need for long-term medical and social care for patients who survive the disease, to reduce the risk of re-emergence and to prevent further stigmatization. The viral lineage responsible for the February 2021 outbreak of Ebola virus disease in Guinea is nested within a clade that predominantly consists of genomes sampled during the 2013-2016 epidemic, suggesting that the virus might have re-emerged after a long period of latency within a previously infected individual., Author(s): Alpha Kabinet Keita [sup.1] [sup.2] , Fara R. Koundouno [sup.3] [sup.4] , Martin Faye [sup.5] , Ariane Düx [sup.6] , Julia Hinzmann [sup.4] [sup.7] [sup.8] , Haby Diallo [sup.1] [...]

Published
2021
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8. 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

9. Survey of Ebola Viruses in Frugivorous and Insectivorous Bats in Guinea, Cameroon, and the Democratic Republic of the Congo, 2015-2017

Author

De Nys, Helene M., Kingebeni, Placide Mbala, Keita, Alpha K., Butel, Christelle, Thaurignac, Guillaume, Villabona-Arenas, Christian-Julian, Lemarcis, Thomas, Geraerts, Mare, Vidal, Nicole, Esteban, Amandine, Bourgarel, Mathieu, Roger, Francois, Leendertz, Fabian, Diallo, Ramadan, Ndimbo-Kumugo, Simon-Pierre, Nsio-Mbeta, Justus, Tagg, Nikki, Koivogui, Lamine, Toure, Abdoulaye, Delaporte, Eric, Ahuka-Mundeke, Steve, Tamfum, Jean-Jacques Muyembe, Mpoudi-Ngole, Eitel, Ayouba, Ahidjo, and Peeters, Martine

Subjects
Ebola hemorrhagic fever -- Risk factors, Bats (Animals) -- Research, Health
Abstract

Since the first outbreak of Ebola virus disease (EVD) in 1976 in the northern part of the Democratic Republic of the Congo (DRC), 26 recognized outbreaks have occurred in humans [...]

Published
2018
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13. High level of treatment failure and drug resistance to first-line antiretroviral therapies among HIV-infected children receiving decentralized care in Senegal

Author

Cissé, Abdoul-Magib, Laborde-Balen, Gabrièle, Kébé-Fall, Khady, Dramé, Aboubacry, Diop, Halimatou, Diop, Karim, FatouNiasse-Traoré, Coulibaly, Mohamed, Have, Ndeye-Ngone, Vidal, Nicole, Thiam, Safiatou, Wade, Abdoulaye S., Peeters, Martine, Taverne, Bernard, Msellati, Philippe, and Touré-Kane, Coumba

Published
2019
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15. Relational Dynamics of Treatment Behavior Among Individuals with Tuberculosis in High-Income Countries: A Scoping Review

Author

Arakelyan,Stella, Karat,Aaron S, Jones,Annie SK, Vidal,Nicole, Stagg,Helen R, Darvell,Marcia, Horne,Robert, Lipman,Marc CI, and Kielmann,Karina

Subjects
Patient Preference and Adherence
Abstract

Stella Arakelyan,1 Aaron S Karat,1,2 Annie SK Jones,3 Nicole Vidal,1 Helen R Stagg,4 Marcia Darvell,5 Robert Horne,3 Marc CI Lipman,5,6,* Karina Kielmann1,* 1Institute for Global Health and Development, Queen Margaret University, Edinburgh, UK; 2TB Centre, London School of Hygiene & Tropical Medicine, London, UK; 3Centre for Behavioural Medicine, Research Department of Practice and Policy, UCL School of Pharmacy, London, UK; 4Usher Institute, University of Edinburgh, Edinburgh, UK; 5UCL Respiratory, Division of Medicine, University College London, London, UK; 6Royal Free London NHS Foundation Trust, London, UK*These authors contributed equally to this workCorrespondence: Karina KielmannQueen Margaret University, Queen Margaret University Way, Edinburgh, EH216UU, UKTel +44 131 474 0000Email KKielmann@qmu.ac.ukAbstract: Although tuberculosis (TB) incidence has significantly declined in high-income, low-incidence (HILI) countries, challenges remain in managing TB in vulnerable populations who may struggle to stay on anti-TB treatment (ATT). Factors associated with non-adherence to ATT are well documented; however, adherence is often narrowly conceived as a fixed binary variable that places emphasis on individual agency and the act of taking medicines, rather than on the demands of being on treatment more broadly. Further, the mechanisms through which documented factors act upon the experience of being on treatment are poorly understood. Adopting a relational approach that emphasizes the embeddedness of individuals within dynamic social, structural, and health systems contexts, this scoping review aims to synthesize qualitative evidence on experiences of being on ATT and mechanisms through which socio-ecological factors influence adherence in HILI countries. Six electronic databases were searched for peer-reviewed literature published in English between January 1990 and May 2020. Additional studies were obtained by searching references of included studies. Narrative synthesis was used to analyze qualitative data extracted from included studies. Of 28 included studies, the majority (86%) reported on health systems factors, followed by personal characteristics (82%), structural influences (61%), social factors (57%), and treatment-related factors (50%). Included studies highlighted three points that underpin a relational approach to ATT behavior: 1) individual motivation and capacity to take ATT is dynamic and intertwined with, rather than separate from, social, health systems, and structural factors; 2) individuals’ pre-existing experiences of health-seeking influence their views on treatment and their ability to commit to long-term regular medicine-taking; and 3) social, cultural, and political contexts play an important role in mediating how specific factors work to support or hinder ATT adherence behavior in different settings. Based on our analysis, we suggest that person-centered clinical management of tuberculosis should 1) acknowledge the ways in which ATT both disrupts and is managed within the everyday lives of individuals with TB; 2) appreciate that individuals’ circumstances and the support and resources they can access may change over the course of treatment; and 3) display sensitivity towards context-specific social and cultural norms affecting individual and collective experiences of being on ATT.Keywords: tuberculosis, adherence, qualitative research, patient-centered care, socio-ecological, low incidence

Published
2021

17. Investigating the Circulation of Ebola Viruses in Bats during the Ebola Virus Disease Outbreaks in the Equateur and North Kivu Provinces of the Democratic Republic of Congo from 2018

Author

Lacroix, Audrey, Mbala Kingebeni, Placide, Ndimbo Kumugo, Simon Pierre, Lempu, Guy, Butel, Christelle, Serrano, Laetitia, Vidal, Nicole, Thaurignac, Guillaume, Esteban, Amandine, Mukadi Bamuleka, Daniel, Likofata, Jacques, Delaporte, Eric, Muyembe Tamfum, Jean-Jacques, Ayouba, Ahidjo, Peeters, Martine, Ahuka Mundeke, Steve, Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Institut National de Recherche Biomédicale [Kinshasa] (INRB), Cliniques Universitaires de Kinshasa [Congo], Laboratoire Provincial de Mbandaka, Salvy-Córdoba, Nathalie, and Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI)

Subjects
Ebola virus, the Democratic Republic of the Congo, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.BA.MVSA] Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, bats, Medicine, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Article
Abstract

International audience; With 12 of the 31 outbreaks, the Democratic Republic of Congo (DRC) is highly affected by Ebolavirus disease (EVD). To better understand the role of bats in the ecology of Ebola viruses, we conducted surveys in bats during two recent EVD outbreaks and in two areas with previous outbreaks. Dried blood spots were tested for antibodies to ebolaviruses and oral and rectal swabs were screened for the presence of filovirus using a broadly reactive semi-nested RT-PCR. Between 2018 and 2020, 892 (88.6%) frugivorous and 115 (11.4%) insectivorous bats were collected. Overall, 11/925 (1.2%) to 100/925 (10.8%) bats showed antibodies to at least one Ebolavirus antigen depending on the positivity criteria. Antibodies were detected in fruit bats from the four sites and from species previously documented to harbor Ebola antibodies or RNA. We tested for the first time a large number of bats during ongoing EVD outbreaks in DRC, but no viral RNA was detected in the 676 sampled bats. Our study illustrates the difficulty to document the role of bats as a source of Ebolaviruses as they might clear quickly the virus. Given the increasing frequency of EVD outbreaks, more studies on the animal reservoir are urgently needed.

Published
2021

18. High prevalence of HIV-1 drug resistance among patients on first-line antiretroviral treatment in Lomé, Togo

Author

Dagnra, Anoumou Y., Vidal, Nicole, Mensah, Akovi, Patassi, Akouda, Aho, Komi, Salou, Mounerou, Monleau, Marjorie, Prince?David, Mireille, Singo, Assétina, Pitche, Palokinam, Delaporte, Eric, and Peeters, Martine

Subjects
Antiviral agents -- Dosage and administration -- Patient outcomes, Drug resistance -- Risk factors, HIV infection -- Drug therapy, Health
Abstract

Background: With widespread use of antiretroviral (ARV) drugs in Africa, one of the major potential challenges is the risk of emergence of ARV drug‐resistant HIV strains. Our objective is to evaluate the virological failure and genotypic drug‐resistance mutations in patients receiving first‐line highly active antiretroviral therapy (HAART) in routine clinics that use the World Health Organization public health approach to monitor antiretroviral treatment (ART) in Togo. Methods: Patients on HAART for one year (10‐14 months) were enrolled between April and October 2008 at three sites in Lomé, the capital city of Togo. Plasma viral load was measured with the NucliSENS EasyQ HIV‐1 assay (Biomérieux, Lyon, France) and/or a Generic viral load assay (Biocentric, Bandol, France). Genotypic drug‐resistance testing was performed with an inhouse assay on plasma samples from patients with viral loads of more than 1000 copies/ml. CD4 cell counts and demographic data were also obtained from medical records. Results: A total of 188 patients receiving first‐line antiretroviral treatment were enrolled, and 58 (30.8%) of them experienced virologic failure. Drug‐resistance mutations were present in 46 patients, corresponding to 24.5% of all patients enrolled in the study. All 46 patients were resistant to non‐nucleoside reverse‐transcriptase inhibitors (NNRTIs): of these, 12 were resistant only to NNRTIs, 25 to NNRTIs and lamivudine/emtricitabine, and eight to all three drugs of their ARV regimes. Importantly, eight patients were already predicted to be resistant to etravirine, the new NNRTI, and three patients harboured the K65R mutation, inducing major resistance to tenofovir. Conclusions: In Togo, efforts to provide access to ARV therapy for infected persons have increased since 2003, and scaling up of ART started in 2007. The high number of resistant strains observed in Togo shows clearly that the emergence of HIV drug resistance is of increasing concern in countries where ART is now widely used, and can compromise the long‐term success of first‐ and second‐line ART., Background Implementation of antiretroviral therapy (ART) is recognized as a public health priority in resource‐limited countries. In order to allow a rapid roll out of ART, countries use the World [...]

Published
2011
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19. Multiplex detection and dynamics of IgG antibodies to SARS-CoV2 and the highly pathogenic human coronaviruses SARS-CoV and MERS-CoV

Author

Ayouba, Ahidjo, Thaurignac, Guillaume, Morquin, David, Tuaillon, Edouard, Raulino, Raisa, Nkuba, Antoine, Lacroix, Audrey, Vidal, Nicole, Foulongne, Vincent, Le Moing, Vincent, Reynes, Jacques, Delaporte, Eric, Peeters, Martine, Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Pathogénèse et contrôle des infections chroniques (PCCI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre Hospitalier Universitaire de Montpellier (CHU Montpellier ), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), ANR-20-COVI-0048,TargEnt-Covid-19,Découverte et développement de nouveaux antiviraux pour le contrôle et le traitement de l'infection par le SARS-CoV-2 (COVID-19)(2020), and CCSD, Accord Elsevier

Subjects
[SDV] Life Sciences [q-bio], SARS, Infectious Diseases, Serology, Virology, [SDV]Life Sciences [q-bio], SARS-CoV2, Luminex, COVID-19
Abstract

Background: Knowledge of the COVID-19 epidemic extent and the level of herd immunity is urgently needed to help manage this pandemic. Methods: We used a panel of 167 samples (77 pre-epidemic and 90 COVID-19 seroconverters) and SARS-CoV1, SARS-CoV2 and MERS-CoV Spike and/or Nucleopcapsid (NC) proteins to develop a high throughput multiplex screening assay to detect IgG antibodies in human plasma. Assay performances were determined by ROC curves analysis. A subset of the COVID-19+ samples (n= 36) were also tested by a commercial NC-based ELISA test and the results compared with those of the novel assay. Results: On samples collected >= 14 days after symptoms onset, the accuracy of the assay is 100 % (95 % CI: 100-100) for the Spike antigen and 99.9 % (95 % CI:99.7-100) for NC. By logistic regression, we estimated that 50 % of the patients have seroconverted at 5.7 +/- 1.6; 5.7 +/- 1.8 and 7.9 +/- 1.0 days after symptoms onset against Spike, NC or both antigens, respectively and all have seroconverted two weeks after symptoms onset. IgG titration in a subset of samples showed that early phase samples present lower IgG titers than those from later phase. IgG to SARS-CoV2 NC cross-reacted at 100 % with SARS-CoV1 NC. Twenty-nine of the 36 (80.5 %) samples tested were positive by the commercial ELISA while 31/36 (86.1 %) were positive by the novel assay. Conclusions: Our assay is highly sensitive and specific for the detection of IgG antibodies to SARS-CoV2 proteins, suitable for high throughput epidemiological surveys. The novel assay is more sensitive than a commercial ELISA.

Published
2020

20. Wide Diversity of Coronaviruses in Frugivorous and Insectivorous Bat Species: A Pilot Study in Guinea, West Africa

Author

Lacroix, Audrey, Vidal, Nicole, Keita, Alpha Kabinet, Thaurignac, G., Esteban, Amandine, De nys, Hélène, Diallo, R., Toure, A., Goumou, S., Soumah, A. K., Povogui, M., Koivogui, J., Monemou, J. L., Raulino, R., Nkuba, A., Foulongne, V., Delaporte, E., Ayouba, Ahidjo, Peeters, Martine, Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Centre de Recherche et de Formation en Infectiologie de Guinée [Conakry, Guinée] (CERFIG), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Ministère de L'Elevage et des Productions Animales [Conakry, Guinée], Institut National de Santé Publique [Conakry, Guinée] (INSP), Ministère de la Santé [Conakry, Guinea], Cliniques Universitaires de Kinshasa [Congo], Pathogénèse et contrôle des infections chroniques (PCCI), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), This work was supported in part by grants from Institut National de la Sante et de la Recherche Medicale (INSERM)/the Ebola Task Force/REACTing, EBO-SURSY project funded by the European Union, Institut de Recherche pour le Developpement (IRD) and Agence Nationale de Recherches sur le SIDA (Grant Number ANRS-COVID10). A.K.K. was supported by fellowships from IRD and the University of Montpellier (MUSE, ANR-16-IDEX-0006). Raisa Raulino was supported by a PhD grant from INSERM and University of Montpellier and Antoine Nkuba was supported by a doctoral fellowship from the French foreign office., ANR-16-IDEX-0006,MUSE,MUSE(2016), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre Hospitalier Universitaire de Montpellier (CHU Montpellier ), LESUR, Hélène, and Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)

Subjects
Male, viruses, [SDV]Life Sciences [q-bio], Pneumonia, Viral, lcsh:QR1-502, coronavirus, virus diversity, Pilot Projects, bat, Genome, Viral, lcsh:Microbiology, Article, Betacoronavirus, Chiroptera, Zoonoses, Animals, Humans, Pandemics, Phylogeny, ComputingMilieux_MISCELLANEOUS, SARS-CoV-2, COVID-19, virus diseases, Biodiversity, [SDV] Life Sciences [q-bio], Africa, Female, Guinea, Coronavirus Infections
Abstract

Zoonoses can constitute a threat for public health that can have a global importance, as seen with the current COVID-19 pandemic of severe acute respiratory syndrome coronavirus (SARS-CoV2). Bats have been recognized as an important reservoir of zoonotic coronaviruses (CoVs). In West Africa, where there is a high diversity of bat species, little is known on the circulation of CoVs in these hosts, especially at the interface with human populations. In this study, in Guinea, we tested a total of 319 bats belonging to 14 genera and six families of insectivorous and frugivorous bats across the country, for the presence of coronaviruses. We found CoVs in 35 (11%) of the tested bats&mdash, in three insectivorous bat species and five fruit bat species that were mostly captured close to human habitat. Positivity rates varied from 5.7% to 100%, depending on bat species. A wide diversity of alpha and beta coronaviruses was found across the country, including three sequences belonging to SarbeCoVs and MerbeCoVs subgenera known to harbor highly pathogenic human coronaviruses. Our findings suggest that CoVs are widely spread in West Africa and their circulation should be assessed to evaluate the risk of exposure of potential zoonotic CoVs to humans.

Published
2020

22. Additional file 1 of Moderate rate of transmitted resistance mutations to antiretrovirals and genetic diversity in newly HIV-1 patients diagnosed in Benin

Author

Tchiakpe, Edmond, Keke, Rene K., Vidal, Nicole, Ahoussinou, Clément, Sekpe, Olga, Hermione G. Dagba, Gbaguidi, Eric, Tonoukouen, Conrad, Afangnihoun, Aldric, Bachabi, Moussa, Gangbo, Flore A., Halimatou Diop-Ndiaye, and Coumba Toure-Kane

Abstract

Additional file 1: Figure S1. Phylogenetic analysis of transmission chains. Maximum likelihood tree with 1000 bootstrap resamplings for 30 sample sequences (in red). Bootstrap values are indicated on the branches and clusters are numbered. Table S1. Branch lengths for each cluster or sequences pair indicated in the tree of Figure S1.

Published
2020
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24. A 40-Month Follow-Up of Ebola Virus Disease Survivors in Guinea (PostEbogui) Reveals Long-Term Detection of Ebola Viral Ribonucleic Acid in Semen and Breast Milk

Author

Keita, Alpha Kabinet, Vidal, Nicole, Toure, Abdoulaye, Diallo, Mamadou Saliou Kalifa, Magassouba, N’fally, Baize, Sylvain, Mateo, Mathieu, Raoul, Herve, Mely, Stephane, Subtil, Fabien, Kpamou, Cécé, Koivogui, Lamine, Traore, Falaye, Sow, Mamadou Saliou, Ayouba, Ahidjo, Etard, Jean Francois, Delaporte, Eric, Peeters, Martine, Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Institut de Recherche pour le Développement (IRD [France-Sud]), Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abdel Nasser de Conakry, Institut National de Santé Publique [Conakry, Guinée] (INSP), Ministère de la Santé [Conakry, Guinea], Biologie des Infections Virales Émergentes - Biology of Emerging Viral Infections (UBIVE), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Laboratoire P4 Jean Mérieux-Inserm [Lyon] (Unité de service 3), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Européen de Recherche en Virologie et Immunologie [Lyon] (Tour Inserm CERVI), Hospices Civils de Lyon (HCL), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Hôpital National Donka, This work was funded in part by grants from the Institut National de la Santé et de la Recherche Médicale/Ebola Task Force, REACTing (REsearch and ACTion targeting emerging infectious diseases) and the Institut de Recherche pour le Développement and Montpellier Université d’Excellence (EBOHEALTH, I-Site MUSE, ANR-16-IDEX-0006). A. K. K. was supported by a postdoctoral fellowship from Montpellier Université d’Excellence (I-Site MUSE, ANR-16-IDEX-0006)., We thank the PostEbogui team for their daily work, all of the survivors, the Guinean survivors’ associations for their help in identifying and tracing survivors, the laboratory staff of Institut National de Santé Publique and Centre de Recherche et de Formation en Infectiologie (CERFIG) (Moriba Povogui, Jean-louis Monemou, Joel Ballè Koivogui, Abdoul Karim Soumah, Amara Bamba, and Saran Doumbouya), the laboratory facility from Macenta (Guillain Mikaty), and European West African Mobile Laboratory (Brunel Joanna, Belarbi Essia, Martinez Prudencio, Pannetier Delphine, Picard Caroline, Escudero Beatriz, Mengardi Chloe, Nguyen Xuan-Nhi, Tracqui Elodie, Hamied Lola, Olausson Mikaela, Verner-Carlsson Jenny, Godard Sabine, Moroso Marie, Thomas Damien, Ottmann Michele, Bernard Sandra, Yonga Wansi Gide Martial, Sylla Yahaya, Bocquin Anne, Sautter Carmen-Alexandra, Rittaud Adeline, Carbonnelle Caroline, Mundweiler Stephanie, Calland Noemie, Chevillard Eve, and Juven Fabienne)., PostEbogui Study Group, Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), ANR-16-IDEX-0006,MUSE,MUSE(2016), Recherches Translationnelles sur le VIH et les maladies infectieuses (TransVIHMI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 1 (UM1)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Universtié Yaoundé 1 [Cameroun]-Université de Montpellier (UM), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Donka National Hospital

Subjects
Editor's Choice, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Ebola, Major Article, breast milk, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Guinea, semen, body fluids
Abstract

Background With the increasing frequency and impact of Ebola virus disease (EVD) outbreaks illustrated by recent epidemics, a good understanding of the extent of viral persistance or ribonucleic acid (RNA) detection in body fluids from survivors is urgently needed. Methods Ebola viral RNA shedding was studied with molecular assays in semen (n = 1368), urine (n = 1875), cervicovaginal fluid (n = 549), saliva (n = 900), breast milk (n = 168), and feces (n = 558) from EVD survivors in Guinea (PostEbogui cohort, n = 802) at a regular base period until 40 months after inclusion. Results Twenty-seven of 277 (9.8%) male survivors tested positive for Ebola RNA in at least 1 semen sample. The probability of remaining positive for Ebola RNA in semen was estimated at 93.02% and 60.12% after 3 and 6 months. Viral RNA in semen was more frequent in patients with eye pain (P = .036), joint pain (P = .047), and higher antibody levels to Ebola virus antigens (nucleoprotein [P = .001], glycoprotein [P = .05], and viral protein-40 [P = .05]). Ebola RNA was only rarely detected in the following body fluids from EVD survivors: saliva (1 of 454), urine (2 of 593), breast milk (2 of 168), cervicovaginal secretions (0 of 273), and feces (0 of 330). Ribonucleic acid was detected in breast milk 1 month after delivery but 500 days after discharge of Ebola treatment unit (ETU) in 1 woman who became pregnant 7 months after discharge from the ETU. Conclusions The frequency and potential long-term presence of viral RNA in semen confirmed that systematic prevention measures in male survivors are required. Our observation in breast milk suggests that our knowledge on viral reservoir in immune-privileged sites and its impact are still incomplete., On 5,400 body fluid samples from Ebola Virus Disease (EVD) survivors, during 40 months follow-up in Guinea, RNA was observed in semen and breast milk for up to 500 days, illustrating the complexity of the viral reservoir and management of survivors.

Published
2019

25. Distribution of HIV-1 variants in the Democratic Republic of Congo suggests increase of subtype C in Kinshasa between 1997 and 2002

Author

Vidal, Nicole, Mulanga, Claire, Bazepeo, Samuel Edidi, Mwamba, Jeanne Kasali, Tshimpaka, Jean-Willy, Kashi, Mulowayi, Mama, Nicasia, Laurent, Christian, Lepira, Francois, Delaporte, Eric, and Peeters, Martine

Subjects
Congo (Kinshasa) -- Health policy, Congo (Kinshasa) -- Political aspects, AIDS research -- Political aspects, HIV infection -- Care and treatment, HIV infection -- Research, AIDS (Disease) -- Research, AIDS (Disease) -- Political aspects, Health
Abstract

A study that was carried out to see the distribution of HIV-1 variants over a 5-year period against the background of political instability and civil war in the Democratic Republic of Congo (DRC) is described. It was found that genetic characterization of HIV-positive samples from scentinel surveys can provide significant additional information on new trends in the HIV epidemic.

Published
2005

26. High genetic diversity of HIV-1 strains in Chad, West Central Africa

Author

Vidal, Nicole, Koyalta, Donato, Richard, Vincent, Lechiche, Catherine, Ndinaromtan, Thomas, Djimasngar, Abakar, Delaporte, Eric, and Peeters, Martine

Subjects
Chad -- Health aspects, Biological diversity -- Research, HIV infection -- Research, HIV infection -- Care and treatment, Health
Published
2003

28. IMPACT study on intervening with a manualised package to achieve treatment adherence in people with tuberculosis: protocol paper for a mixed-methods study, including a pilot randomised controlled trial

Author

Stagg, Helen R, primary, Abubakar, Ibrahim, additional, Campbell, Colin NJ, additional, Copas, Andrew, additional, Darvell, Marcia, additional, Horne, Robert, additional, Kielmann, Karina, additional, Kunst, Heinke, additional, Mandelbaum, Mike, additional, Pickett, Elisha, additional, Story, Alistair, additional, Vidal, Nicole, additional, Wurie, Fatima B, additional, and Lipman, Marc, additional

Published
2019
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30. High rates of virological failure and drug resistance in perinatally HIV-1-infected children and adolescents receiving lifelong antiretroviral therapy in routine clinics in Togo

Author

Salou, Mounerou, Dagnra, Anoumou Y., Butel, Christelle, Vidal, Nicole, Serrano, Laetitia, Takassi, Elom, Konou, Abla A., Houndenou, Spero, Dapam, Nina, Singo-Tokofai, Assetina, Pitche, Palokinam, Atakouma, Yao, Prince-David, Mireille, Delaporte, Eric, and Peeters, Martine

Subjects
Highly active antiretroviral therapy -- Health aspects, HIV infections -- Drug therapy -- Research, Protease inhibitors -- Comparative analysis, Drug resistance -- Care and treatment -- Research, Health
Abstract

Introduction: Antiretroviral treatment (ART) has been scaled up over the last decade but compared to adults, children living with HIV are less likely to receive ART. Moreover, children and adolescents are more vulnerable than adults to virological failure (VF) and emergence of drug resistance. In this study we determined virological outcome in perinatally HIV-1-infected children and adolescents receiving ART in Togo. Methods: HIV viral load (VL) testing was consecutively proposed to all children and adolescents who were on ART for at least 12 months when attending HIV healthcare services for their routine follow-up visit (June to September 2014). Plasma HIV-1 VL was measured using the m2000 RealTime HIV-1 assay (Abbott Molecular, Des Plaines, IL, USA). Genotypic drug resistance was done for all samples with VL >1000 copies/ml. Results and discussion: Among 283 perinatally HIV-1-infected children and adolescents included, 167 (59%) were adolescents and 116 (41%) were children. The median duration on ART was 48 months (interquartile range: 28 to 68 months). For 228 (80.6%), the current ART combination consisted of two nucleoside reverse transcriptase inhibitors (NRTIs) (zidovudine and lamivudine) and one non-nucleoside reverse transcriptase inhibitor (NNRTI) (nevirapine or efavirenz). Only 28 (9.9%) were on a protease inhibitor (PI)-based regimen. VL was below the detection limit (i.e. 40 copies/ml) for 102 (36%), between 40 and 1000 copies/ml for 35 (12.4%) and above 1000 copies/ml for 146 (51.6%). Genotypic drug-resistance testing was successful for 125/146 (85.6%); 110/125 (88.0%) were resistant to both NRTIs and NNRTIs, 1/125 (0.8%) to NRTIs only, 4/125 (3.2%) to NNRTIs only and three harboured viruses resistant to reverse transcriptase and PIs. Overall, 86% (108/125) of children and adolescents experiencing VF and successfully genotyped, corresponding thus to at least 38% of the study population, had either no effective ART or had only a single effective drug in their current ART regimen. Conclusions: Our study provided important information on virological outcome on lifelong ART in perinatally HIV- 1infected children and adolescents who were still on ART and continued to attend antiretroviral (ARV) clinics for follow-up visits. Actual conditions for scaling up and monitoring lifelong ART in children in resource-limited countries can have dramatic long-term outcomes and illustrate that paediatric ART receives inadequate attention. Keywords: HIV; virological failure; drug resistance; children; antiretroviral treatment; Togo; Africa., Introduction Of the more than three million children infected with HIV, 90% live in sub-Saharan Africa [1]. Over the last decade major advances have been made in almost every area [...]

Published
2016
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31. Apport des nouvelles technologies pour le contrôle des maladies infectieuses émergentes en Guinée et République démocratique du Congo : l'exemple de la réponse à l'épidémie d'Ebola

Author

Ayouba, Ahidjo, Mbala-Kingebeni, P., Keita, A.K., Vidal, Nicole, Lacroix, A., Touré, A., Muyembe-Tamfum, J.J., Delaporte, E., Peeters, Martine, Ahuka-Mundeke, S., Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Raoult, D. (ed.), and Parola, P. (ed.)

Subjects
DIAGNOSTIC, TECHNOLOGIE, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, GUINEE, INNOVATION, INFECTION, EPIDEMIE, VIROLOGIE
Abstract

Les maladies infectieuses émergentes sont récurrentes et représentent un enjeu de sécurité sanitaire planétaire. Le continent africain est particulièrement exposé aux risques infectieux épidémiques à cause du nombre d'agents infectieux qui y circulent, en particulier dans la faune, mais aussi de par des facteurs sociaux et environnementaux qui favorisent leur diffusion épidémique. Les épidémies à virus Ebola en Afrique de l'Ouest en 2014 et celles en République démocratique du Congo (RDC) ayant débuté en 2018 ont été l'occasion de mettre au point et de déployer de nouvelles techniques diagnostiques pour des laboratoires en Guinée et en RDC. Ces outils ont permis d'identifier rapidement l'agent infectieux, de retracer en temps réel les chaînes de contamination pour intervenir efficacement et développer un outil sérologique fiable permettant un diagnostic différentiel. Aujourd'hui, des structures équipées et fonctionnelles existent en Guinée et en RDC pour répondre aux risques d'émergence épidémique, pilotées par des chercheurs guinéens et congolais formés à des niveaux de compétence élevés et bénéficiant d'expérience et de connaissance de terrain unique.

Published
2019

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

Author

Hemelaar, Joris, Elangovan, Ramyiadarsini, Yun, Jason, Dickson-Tetteh, Leslie, Fleminger, Isabella, Kirtley, Shona, Williams, Brian, Gouws-Williams, Eleanor, Ghys, Peter D, 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, John Radcliffe Hospital [Oxford University Hospital], Centre for Statistics in Medicine, University of Oxford [Oxford], Stellenbosch University, UNAIDS [Genève, Suisse] (ONUSIDA), Institut Pasteur [Paris], Noguchi Memorial Institute for Medical Research [Accra, Ghana] (NMIMR), University of Ghana, Institute of Tropical Medicine [Antwerp] (ITM), State Key Laboratory of Silkworm Genome Biology, Southwest University, Commissariat à l'énergie atomique et aux énergies alternatives - Laboratoire d'Electronique et de Technologie de l'Information (CEA-LETI), Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Georg-Speyer-Haus, The University of Sydney, National AIDS Centre, Istituto Superiore di Sanita [Rome], Harvard School of Public Health, Digital Enterprise Research Institute (DERI-NUIG), National University of Ireland [Galway] (NUI Galway), Microbiologie cellulaire et moléculaire et pathogénicité (MCMP), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Virologie, Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Pathogénèse et contrôle des infections chroniques (PCCI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre Hospitalier Universitaire de Montpellier (CHU Montpellier ), Departments of Medicine and Microbiology, University of Alabama at Birmingham [ Birmingham] (UAB), Robert Koch Institute [Berlin] (RKI), Beihang University (BUAA), Statens Serum Institut [Copenhagen], Immuno-Rhumatologie Moléculaire, Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), SANTE/SIDA [Bobo-Dioulasso, Burkina Faso], Institut de Recherche en Sciences de la Santé (IRSS) / Centre Muraz, Department of Microbiology, University of Washington School of Medicine, Department of Microbiology, Medical School, University of Thessaly [Volos] (UTH), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Africa Centre for Health and Population Studies, University of KwaZulu-Natal (UKZN)-Medical Research Council of South Africa, Lab-STICC_UBO_CID_IHSEV, Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS), State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Laboratory of Virology, CHU Rouen, Normandie Université (NU)-Normandie Université (NU), Universidade Federal do Rio de Janeiro (UFRJ), Departements of Medicine and Microbiology, University of Alabama [Tuscaloosa] (UA), Stichting HIV Monitoring [Amsterdam], Universiteit van Amsterdam (UvA), Département Génétique Internal Médecine, Hôpital Universitaire Leuven, Department of Chemical and Biomolecular Engineering [Baltimore], Johns Hopkins University (JHU), Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, China Academy of Chinese Medical Sciences, Chatzidimitriou, Dimitrios [0000-0001-9656-5898], University of Oxford, Institut Pasteur [Paris] (IP), Istituto Superiore di Sanità (ISS), Microbiologie Fondamentale et Pathogénicité (MFP), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), University of KwaZulu-Natal [Durban, Afrique du Sud] (UKZN)-Medical Research Council of South Africa, Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS), UNAIDS, Noguchi Memorial Institute for Medical Research, University of Ghana, Laboratoire d'Electronique et des Technologies de l'Information (CEA-LETI), Université Grenoble Alpes (UGA)-Direction de Recherche Technologique (CEA) (DRT (CEA)), Beihang University, Recherches Translationnelles sur le VIH et les maladies infectieuses (TransVIHMI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 1 (UM1)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Universtié Yaoundé 1 [Cameroun]-Université de Montpellier (UM), Universidade Federal do Rio de Janeiro [Rio de Janeiro] (UFRJ), Nuffield Department of Women's and Reproductive Health (NDWRH), University of Oxford- John Radcliffe Hospital [Oxford University Hospital], South African Centre for Epidemiological Modelling and Analysis, JH is supported by the Oxford University Clinical Academic Graduate School (Oxford, UK) and Linacre College, Oxford University (Oxford, UK)., WHO–UNAIDS Network for HIV Isolation Characterisation : Alash'le G Abimiku, Simon Agwale, Chris Archibald, Boaz Avidor, María Gabriela Barbás, Francoise Barre-Sinoussi, Banson Barugahare, El Hadj Belabbes, Silvia Bertagnolio, Deborah Birx, Aleksei F Bobkov, James Brandful, Helba Bredell, Catherine A Brennan, James Brooks, Marie Bruckova, Luigi Buonaguro, Franco Buonaguro, Stefano Buttò, Anne Buve, Mary Campbell, Jean Carr, Alex Carrera, Manuel Gómez Carrillo, Connie Celum, Beth Chaplin, Macarthur Charles, Dimitrios Chatzidimitriou, Zhiwei Chen, Katsumi Chijiwa, David Cooper, Philip Cunningham, Anoumou Dagnra, Cillian F de Gascun, Julia Del Amo, Elena Delgado, Ursula Dietrich, Dominic Dwyer, Dennis Ellenberger, Barbara Ensoli, Max Essex, Feng Gao, Herve Fleury, Peter N Fonjungo, Vincent Foulongne, Deepak A Gadkari, Federico García, Roger Garsia, Guy Michel Gershy-Damet, Judith R Glynn, Ruth Goodall, Zehava Grossman, Monick Lindenmeyer-Guimarães, Beatrice Hahn, Raph L Hamers, Osamah Hamouda, Ray Handema, Xiang He, Joshua Herbeck, David D Ho, Africa Holguin, Mina Hosseinipour, Gillian Hunt, Masahiko Ito, Mohamed Ali Bel Hadj Kacem, Erin Kahle, Pontiano Kaleebu Kaleebu, Marcia Kalish, Adeeba Kamarulzaman, Chun Kang, Phyllis Kanki, Edward Karamov, Jean-Claude Karasi, Kayitesi Kayitenkore, Tony Kelleher, Dwip Kitayaporn, Leondios G Kostrikis, Claudia Kucherer, Claudia Lara, Thomas Leitner, Kirsi Liitsola, Jai Lingappa, Marek Linka, Ivette Lorenzana de Rivera, Vladimir Lukashov, Shlomo Maayan, Luzia Mayr, Francine McCutchan, Nicolas Meda, Elisabeth Menu, Fred Mhalu, Doreen Mloka, John L Mokili, Brigitte Montes, Orna Mor, Mariza Morgado, Fausta Mosha, Awatef Moussi, James Mullins, Rafael Najera, Mejda Nasr, Nicaise Ndembi, Joel R Neilson, Vivek R Nerurkar, Florian Neuhann, Claudine Nolte, Vlad Novitsky, Philippe Nyambi, Marianna Ofner, Fem J Paladin, Anna Papa, Jean Pape, Neil Parkin, Chris Parry, Martine Peeters, Alexandra Pelletier, Lucía Pérez-Álvarez, Deenan Pillay, Angie Pinto, Trinh Duy Quang, Cecilia Rademeyer, Filimone Raikanikoda, Mark A Rayfield, Jean-Marc Reynes, Tobias Rinke de Wit, Kenneth E Robbins, Morgane Rolland, Christine Rousseau, Jesus Salazar-Gonzales, Hanan Salem, Mika Salminen, Horacio Salomon, Paul Sandstrom, Mario L Santiago, Abdoulaye D Sarr, Bryan Schroeder, Michel Segondy, Philippe Selhorst, Sylvester Sempala, Jean Servais, Ansari Shaik, Yiming Shao, Amine Slim, Marcelo A Soares, Elijah Songok, Debbie Stewart, Julie Stokes, Shambavi Subbarao, Ruengpung Sutthent, Jun Takehisa, Amilcar Tanuri, Kok Keng Tee, Kiran Thapa, Michael Thomson, Tyna Tran, Willy Urassa, Hiroshi Ushijima, Philippevan de Perre, Guidovan der Groen, Kristel van Laethem, Joep van Oosterhout, Ard van Sighem, Eric van Wijngaerden, Anne-Mieke Vandamme, Jurgen Vercauteren, Nicole Vidal, Lesley Wallace, Carolyn Williamson, Dawit Wolday, Jianqing Xu, Chunfu Yang, Linqi Zhang, and Rong Zhang

Subjects
0301 basic medicine, Serotype, Genotype, Genotyping Techniques, 030106 microbiology, DIVERSITY, MULTICENTER, VACCINE, HIV Infections, Genome, Viral, Biology, Global Health, Serogroup, SUBTYPES, 03 medical and health sciences, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Surveys and Questionnaires, INFECTION, Genetic variation, Global health, Humans, HIV vaccine, Serotyping, AIDS Vaccines, Science & Technology, Molecular epidemiology, Genetic Variation, Subtyping, 3. Good health, Trend analysis, 030104 developmental biology, Infectious Diseases, 13. Climate action, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, HIV-1, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Life Sciences & Biomedicine, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Demography
Abstract

BACKGROUND: Global genetic diversity of HIV-1 is a major challenge to the development of HIV vaccines. We aimed to estimate the regional and global distribution of HIV-1 subtypes and recombinants during 1990-2015. METHODS: We searched PubMed, EMBASE (Ovid), CINAHL (Ebscohost), and Global Health (Ovid) for HIV-1 subtyping studies published between Jan 1, 1990, and Dec 31, 2015. We collected additional unpublished HIV-1 subtyping data through a global survey. We included prevalence studies with HIV-1 subtyping data collected during 1990-2015. We grouped countries into 14 regions and analysed data for four time periods (1990-99, 2000-04, 2005-09, and 2010-15). The distribution of HIV-1 subtypes, circulating recombinant forms (CRFs), and unique recombinant forms (URFs) in individual countries was weighted according to the UNAIDS estimates of the number of people living with HIV (PLHIV) in each country to generate regional and global estimates of HIV-1 diversity in each time period. The primary outcome was the number of samples designated as HIV-1 subtypes A, B, C, D, F, G, H, J, K, CRFs, and URFs. The systematic review is registered with PROSPERO, number CRD42017067164. FINDINGS: This systematic review and global survey yielded 2203 datasets with 383 519 samples from 116 countries in 1990-2015. Globally, subtype C accounted for 46·6% (16 280 897/34 921 639 of PLHIV) of all HIV-1 infections in 2010-15. Subtype B was responsible for 12·1% (4 235 299/34 921 639) of infections, followed by subtype A (10·3%; 3 587 003/34 921 639), CRF02_AG (7·7%; 2 705 110/34 921 639), CRF01_AE (5·3%; 1 840 982/34 921 639), subtype G (4·6%; 1 591 276/34 921 639), and subtype D (2·7%; 926 255/34 921 639). Subtypes F, H, J, and K combined accounted for 0·9% (311 332/34 921 639) of infections. Other CRFs accounted for 3·7% (1 309 082/34 921 639), bringing the proportion of all CRFs to 16·7% (5 844 113/34 921 639). URFs constituted 6·1% (2 134 405/34 921 639), resulting in recombinants accounting for 22·8% (7 978 517/34 921 639) of all global HIV-1 infections. The distribution of HIV-1 subtypes and recombinants changed over time in countries, regions, and globally. At a global level during 2005-15, subtype B increased, subtypes A and D were stable, and subtypes C and G and CRF02_AG decreased. CRF01_AE, other CRFs, and URFs increased, leading to a consistent increase in the global proportion of recombinants over time. INTERPRETATION: Global and regional HIV diversity is complex and evolving, and is a major challenge to HIV vaccine development. Surveillance of the global molecular epidemiology of HIV-1 remains crucial for the design, testing, and implementation of HIV vaccines. FUNDING: None. ispartof: LANCET INFECTIOUS DISEASES vol:19 issue:2 pages:143-155 ispartof: location:United States status: published

Published
2018

33. Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa

Author

Faria, Nuno R., Vidal, Nicole, Lourenco, José, Raghwani, Jayna, Sigaloff, Kim C.E., Tatem, Andy J., Van De Vijver, David A.M., Pineda-Peña, Andrea Clemencia, Rose, Rebecca, Wallis, Carole L., Ahuka-Mundeke, Steve, Muyembe-Tamfum, Jean Jacques, Muwonga, Jérémie, Suchard, Marc A., De Wit, Tobias F.Rinke, Hamers, Raph L., Ndembi, Nicaise, Baele, Guy, Peeters, Martine, Pybus, Oliver G., Lemey, Philippe, Dellicour, Simon, Faria, Nuno R., Vidal, Nicole, Lourenco, José, Raghwani, Jayna, Sigaloff, Kim C.E., Tatem, Andy J., Van De Vijver, David A.M., Pineda-Peña, Andrea Clemencia, Rose, Rebecca, Wallis, Carole L., Ahuka-Mundeke, Steve, Muyembe-Tamfum, Jean Jacques, Muwonga, Jérémie, Suchard, Marc A., De Wit, Tobias F.Rinke, Hamers, Raph L., Ndembi, Nicaise, Baele, Guy, Peeters, Martine, Pybus, Oliver G., Lemey, Philippe, and Dellicour, Simon

Abstract

Since the ignition of the HIV-1 group M pandemic in the beginning of the 20th century, group M lineages have spread heterogeneously throughout the world. Subtype C spread rapidly through sub-Saharan Africa and is currently the dominant HIV lineage worldwide. Yet the epidemiological and evolutionary circumstances that contributed to its epidemiological expansion remain poorly understood. Here, we analyse 346 novel pol sequences from the DRC to compare the evolutionary dynamics of the main HIV-1 lineages, subtypes A1, C and D. Our results place the origins of subtype C in the 1950s in Mbuji-Mayi, the mining city of southern DRC, while subtypes A1 and D emerged in the capital city of Kinshasa, and subtypes H and J in the less accessible port city of Matadi. Following a 15-year period of local transmission in southern DRC, we find that subtype C spread at least three-fold faster than other subtypes circulating in Central and East Africa. In conclusion, our results shed light on the origins of HIV-1 main lineages and suggest that socio-historical rather than evolutionary factors may have determined the epidemiological fate of subtype C in sub-Saharan Africa.

Published
2019

34. Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa

Author

Faria, Nuno Rodrigues, Vidal, Nicole, Lourenco, José, Raghwani, Jayna, Sigaloff, Kim Catherina Eve, Tatem, Andrew J, van de Vijver, D.A.M., Pineda-Peña, Andrea Clemencia, Rose, Rebecca, Wallis, Carole Lorraine, Ahuka-Mundeke, Steve, Muyembe-Tamfum, Jean Jacques, Muwonga, Jérémie, Suchard, Marc M.A., Rinke de Wit, Tobias T.F., Hamers, Raph R.L., Ndembi, Nicaise, Baele, Guy, Peeters, Martine, Pybus, Oliver George, Lemey, Philippe, Dellicour, Simon, Faria, Nuno Rodrigues, Vidal, Nicole, Lourenco, José, Raghwani, Jayna, Sigaloff, Kim Catherina Eve, Tatem, Andrew J, van de Vijver, D.A.M., Pineda-Peña, Andrea Clemencia, Rose, Rebecca, Wallis, Carole Lorraine, Ahuka-Mundeke, Steve, Muyembe-Tamfum, Jean Jacques, Muwonga, Jérémie, Suchard, Marc M.A., Rinke de Wit, Tobias T.F., Hamers, Raph R.L., Ndembi, Nicaise, Baele, Guy, Peeters, Martine, Pybus, Oliver George, Lemey, Philippe, and Dellicour, Simon

Abstract

Since the ignition of the HIV-1 group M pandemic in the beginning of the 20th century, group M lineages have spread heterogeneously throughout the world. Subtype C spread rapidly through sub-Saharan Africa and is currently the dominant HIV lineage worldwide. Yet the epidemiological and evolutionary circumstances that contributed to its epidemiological expansion remain poorly understood. Here, we analyse 346 novel pol sequences from the DRC to compare the evolutionary dynamics of the main HIV-1 lineages, subtypes A1, C and D. Our results place the origins of subtype C in the 1950s in Mbuji-Mayi, the mining city of southern DRC, while subtypes A1 and D emerged in the capital city of Kinshasa, and subtypes H and J in the less accessible port city of Matadi. Following a 15-year period of local transmission in southern DRC, we find that subtype C spread at least three-fold faster than other subtypes circulating in Central and East Africa. In conclusion, our results shed light on the origins of HIV-1 main lineages and suggest that socio-historical rather than evolutionary factors may have determined the epidemiological fate of subtype C in sub-Saharan Africa., SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2019

36. New and old complex recombinant HIV-1 strains among patients with primary infection in 1996–2006 in France: The French ANRS CO06 primo cohort study

Author

Peeters Martine, Souala Faouzi, Deveau Christiane, Goujard Cécile, Vidal Nicole, Galimand Julie, Frange Pierre, Meyer Laurence, Rouzioux Christine, and Chaix Marie-Laure

Subjects
Immunologic diseases. Allergy, RC581-607
Abstract

Abstract Background Prevalence of HIV-1 non-B subtypes has increased overtime in patients diagnosed at the time of primary infection (PHI) in France. Our objective was to characterize in detail non-B strains which could not be genetically classified into the known subtypes/Circulating Recombinant Forms (CRFs). Methods Among 744 patients enrolled in the ANRS PRIMO Cohort since 1996, 176 (23.7%) were infected with HIV-1 non-B strains. The subtype/CRF could not be identified in RT for 15 (2%). The V3-V5 env region was sequenced and 3 strains (04FR-KZS, 06FR-CRN, 04FR-AUK) were full-length sequenced. Phylogenetic and bootscan analyses were used to characterize the mosaic structures. Results Among V3-V5 sequences, 6 were divergent A, 2 distantly related to E or D, 2 C, 1 B and 2 remained unclassified. 04FR-KZS, isolated in a Congolese woman infected in France, clustered with 2 previously described viruses from the Democratic Republic of Congo. They represent CRF27_cpx involving A/E/G/H/J/K/U subtypes. 06FR-CRN, isolated in a homosexual Caucasian patient, was a B/C/U recombinant involving a Brazilian C strain. 04FR-AUK, isolated in a Congolese patient infected in France, was a A/K/CRF09/U recombinant clustering from gag to vif with HIV-1 MAL. Others PHI were further observed in 2006–2007 with 1 KZS and 5 CRN-like viruses, suggesting their spread in France. Conclusion This study illustrates the increasing HIV-1 diversity in France associating new (06FR-CRN) and old (CRF27_cpx and "MAL-like" 04FR-AUK) strains, which are rare in their region of origin but may have a possible founder effect in France. Our results strengthen the French guidelines recommending viro-epidemiological surveillance of HIV-1 diversity.

Published
2008
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37. Survey of ebola viruses in frugivorous and insectivorous bats in Guinea, Cameroon, and the Democratic Republic of the Congo, 2015–2017

Author

De Nys, Hélène, Mbala Kingebeni, Placide, Keita, Alpha K., Butel, Christelle, Thaurignac, Guillaume, Villabona-Arenas, Christian-Julian, Lemarcis, Thomas, Geraerts, Mare, Vidal, Nicole, Esteban, Amandine, Bourgarel, Mathieu, Roger, François, Leendertz, Fabian, Diallo, Ramadan, Ndimbo-Kumugo, Simon-Pierre, Nsio-Mbeta, Justus, Tagg, Nikki, Koivogui, Lamine, Toure, Abdoulaye, Delaporte, Eric, Ahuka-Mundeke, Steve, Muyembe Tamfum, Jean-Jacques, Mpoudi-Ngole, Eitel, Ayouba, Ahidjo, Peeters, Martine, De Nys, Hélène, Mbala Kingebeni, Placide, Keita, Alpha K., Butel, Christelle, Thaurignac, Guillaume, Villabona-Arenas, Christian-Julian, Lemarcis, Thomas, Geraerts, Mare, Vidal, Nicole, Esteban, Amandine, Bourgarel, Mathieu, Roger, François, Leendertz, Fabian, Diallo, Ramadan, Ndimbo-Kumugo, Simon-Pierre, Nsio-Mbeta, Justus, Tagg, Nikki, Koivogui, Lamine, Toure, Abdoulaye, Delaporte, Eric, Ahuka-Mundeke, Steve, Muyembe Tamfum, Jean-Jacques, Mpoudi-Ngole, Eitel, Ayouba, Ahidjo, and Peeters, Martine

Abstract

To clarify the role of bats in the ecology of Ebola viruses, we assessed the prevalence of Ebola virus antibodies in a large-scale sample of bats collected during 2015–2017 from countries in Africa that have had previous Ebola outbreaks (Guinea, the Democratic Republic of the Congo) or are at high risk for outbreaks (Cameroon). We analyzed 4,022 blood samples of bats from >12 frugivorous and 27 insectivorous species; 2–37 (0.05%–0.92%) bats were seropositive for Zaire and 0–30 (0%–0.75%) bats for Sudan Ebola viruses. We observed Ebola virus antibodies in 1 insectivorous bat genus and 6 frugivorous bat species. Certain bat species widespread across Africa had serologic evidence of Zaire and Sudan Ebola viruses. No viral RNA was detected in the subset of samples tested (n = 665). Ongoing surveillance of bats and other potential animal reservoirs are required to predict and prepare for future outbreaks.

Published
2018

38. The predominance of Human Immunodeficiency Virus type 1 (HIV-1) circulating recombinant form 02 (CRF02_AG) in West Central Africa may be related to its replicative fitness

Author

Butel Christelle, Vidal Nicole, Jennes Wim, Clybergh Claude, Vanham Guido, Gali Youssef, Njai Harr F, Mpoudi-Ngolle Eitel, Peeters Martine, and Ariën Kevin K

Subjects
Immunologic diseases. Allergy, RC581-607
Abstract

Abstract Background CRF02_AG is the predominant HIV strain circulating in West and West Central Africa. The aim of this study was to test whether this predominance is associated with a higher in vitro replicative fitness relative to parental subtype A and G viruses. Primary HIV-1 isolates (10 CRF02_AG, 5 subtype A and 5 subtype G) were obtained from a well-described Cameroonian cohort. Growth competition experiments were carried out at equal multiplicity of infection in activated T cells and monocyte-derived dendritic cells (MO-DC) in parallel. Results Dual infection/competition experiments in activated T cells clearly indicated that CRF02_AG isolates had a significant replication advantage over the subtype A and subtype G viruses. The higher fitness of CRF02_AG was evident for isolates from patients with CD4+ T cell counts >200 cells/μL (non-AIDS) or CD4+ T cell counts Conclusion We observed a higher ex vivo replicative fitness of CRF02_AG isolates compared to subtype A and G viruses from the same geographic region and showed that this was independent of the co-receptor tropism and irrespective of high or low CD4+ T cell count. This advantage in replicative fitness may contribute to the dominant spread of CRF02_AG over A and G subtypes in West and West Central Africa.

Published
2006
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39. Understanding fragility: implications for global health research and practice.

Author

Diaconu, Karin, Falconer, Jennifer, Vidal, Nicole, O'May, Fiona, Azasi, Esther, Elimian, Kelly, Bou-Orm, Ibrahim, Sarb, Cristina, Witter, Sophie, and Ager, Alastair

Subjects
WORLD health, MEDICAL care use, PUBLIC health, LITERARY sources, POPULATION health, HEALTH services accessibility, SYSTEMATIC reviews, MEDICAL care, MEDICAL care research, CONCEPTS, SOCIAL responsibility
Abstract

Advances in population health outcomes risk being slowed-and potentially reversed-by a range of threats increasingly presented as 'fragility'. Widely used and critiqued within the development arena, the concept is increasingly used in the field of global health, where its relationship to population health, health service delivery, access and utilization is poorly specified. We present the first scoping review seeking to clarify the meaning, definitions and applications of the term in the global health literature. Adopting the theoretical framework of concept analysis, 10 bibliographic and grey literature sources, and five key journals, were searched to retrieve documents relating to fragility and health. Reviewers screened titles and abstracts and retained documents applying the term fragility in relation to health systems, services, health outcomes and population or community health. Data were extracted according to the protocol; all documents underwent bibliometric analysis. Narrative synthesis was then used to identify defining attributes of the concept in the field of global health. A total of 377 documents met inclusion criteria. There has been an exponential increase in applications of the concept in published literature over the last 10 years. Formal definitions of the term continue to be focused on the characteristics of 'fragile and conflict-affected states'. However, synthesis indicates diverse use of the concept with respect to: level of application (e.g. from state to local community); emphasis on particular antecedent stressors (including factors beyond conflict and weak governance); and focus on health system or community resources (with an increasing tendency to focus on the interface between two). Amongst several themes identified, trust is noted as a key locus of fragility at this interface, with critical implications for health seeking, service utilization and health system and community resilience. [ABSTRACT FROM AUTHOR]

Published
2020
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40. "Treatment is of primary importance, and social assistance is secondary": A qualitative study on the organisation of tuberculosis (TB) care and patients' experience of starting and staying on TB treatment in Riga, Latvia

Author

Kielmann, Karina, primary, Vidal, Nicole, additional, Riekstina, Vija, additional, Krutikov, Maria, additional, van der Werf, Marieke J., additional, Biraua, Evita, additional, Duric, Predrag, additional, and Moore, David A. J., additional

Published
2018
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43. HIV-1 genetic diversity and primary drug resistance mutations before large-scale access to antiretroviral therapy, Republic of Congo

Author

Niama, Fabien Roch, primary, Vidal, Nicole, additional, Diop-Ndiaye, Halimatou, additional, Nguimbi, Etienne, additional, Ahombo, Gabriel, additional, Diakabana, Philippe, additional, Bayonne Kombo, Édith Sophie, additional, Mayengue, Pembe Issamou, additional, Kobawila, Simon-Charles, additional, Parra, Henri Joseph, additional, and Toure-Kane, Coumba, additional

Published
2017
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44. Geographic and Temporal Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted HIV-1 Drug Resistance

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 A B, 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, NG, Kee Peng, 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 A M C, Vidal, Nicole, Yang, Chunfu, Yang, Rongge, Yebra, Gonzalo, Ioannidis, John P A, Vandamme, Anne Mieke, Shafer, Robert W., Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), and TB, HIV and opportunistic diseases and pathogens (THOP)

Subjects
SDG 3 - Good Health and Well-being, virus diseases, Cell Biology, Biochemistry, Molecular Biology, Biotechnology
Abstract

PMID: 25849352 WOS:000354825700001 Regional and subtype-specific mutational patterns of HIV-1 transmitted drug resistance (TDR) are essential for informing first-line antiretroviral (ARV) therapy guidelines and designing diagnostic assays for use in regions where standard genotypic resistance testing is not affordable. We sought to understand the molecular epidemiology of TDR and to identify the HIV-1 drug-resistance mutations responsible for TDR in different regions and virus subtypes.We reviewed all GenBank submissions of HIV-1 reverse transcriptase sequences with or without protease and identified 287 studies published between March 1, 2000, and December 31, 2013, with more than 25 recently or chronically infected ARV-naïve individuals. These studies comprised 50,870 individuals from 111 countries. Each set of study sequences was analyzed for phylogenetic clustering and the presence of 93 surveillance drug-resistance mutations (SDRMs). The median overall TDR prevalence in sub-Saharan Africa (SSA), south/southeast Asia (SSEA), upper-income Asian countries, Latin America/Caribbean, Europe, and North America was 2.8%, 2.9%, 5.6%, 7.6%, 9.4%, and 11.5%, respectively. In SSA, there was a yearly 1.09-fold (95% CI: 1.05–1.14) increase in odds of TDR since national ARV scale-up attributable to an increase in non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance. The odds of NNRTI-associated TDR also increased in Latin America/Caribbean (odds ratio [OR] = 1.16; 95% CI: 1.06–1.25), North America (OR = 1.19; 95% CI: 1.12–1.26), Europe (OR = 1.07; 95% CI: 1.01–1.13), and upper-income Asian countries (OR = 1.33; 95% CI: 1.12–1.55). In SSEA, there was no significant change in the odds of TDR since national ARV scale-up (OR = 0.97; 95% CI: 0.92–1.02). An analysis limited to sequences with mixtures at less than 0.5% of their nucleotide positions—a proxy for recent infection—yielded trends comparable to those obtained using the complete dataset. Four NNRTI SDRMs—K101E, K103N, Y181C, and G190A—accounted for >80% of NNRTI-associated TDR in all regions and subtypes. Sixteen nucleoside reverse transcriptase inhibitor (NRTI) SDRMs accounted for >69% of NRTI-associated TDR in all regions and subtypes. In SSA and SSEA, 89% of NNRTI SDRMs were associated with high-level resistance to nevirapine or efavirenz, whereas only 27% of NRTI SDRMs were associated with high-level resistance to zidovudine, lamivudine, tenofovir, or abacavir. Of 763 viruses with TDR in SSA and SSEA, 725 (95%) were genetically dissimilar; 38 (5%) formed 19 sequence pairs. Inherent limitations of this study are that some cohorts may not represent the broader regional population and that studies were heterogeneous with respect to duration of infection prior to sampling.Most TDR strains in SSA and SSEA arose independently, suggesting that ARV regimens with a high genetic barrier to resistance combined with improved patient adherence may mitigate TDR increases by reducing the generation of new ARV-resistant strains. A small number of NNRTI-resistance mutations were responsible for most cases of high-level resistance, suggesting that inexpensive point-mutation assays to detect these mutations may be useful for pre-therapy screening in regions with high levels of TDR. In the context of a public health approach to ARV therapy, a reliable point-of-care genotypic resistance test could identify which patients should receive standard first-line therapy and which should receive a protease-inhibitor-containing regimen. publishersversion published

Published
2015

45. Virological outcome among HIV-1 infected patients on first-line antiretroviral treatment in semi-rural HIV clinics in Togo

Author

Konou, Abla A., primary, Salou, Mounerou, additional, Vidal, Nicole, additional, Kodah, Pascal, additional, Kombate, Damobé, additional, Kpanla, Pyabalo, additional, Nabroulaba, Tchabia, additional, Nyametso, Djifa, additional, Singo-Tokofaï, Assétina, additional, Pitche, Palokinam, additional, Delaporte, Eric, additional, Prince-David, Mireille, additional, Peeters, Martine, additional, and Dagnra, Anoumou Y., additional

Published
2015
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46. Software de generación de evaluaciones

Author

Bobadilla Vidal, Nicole, Madariaga López, Matías, Facultad de Ingeniería, and Escuela de Informática

Subjects
Tecnología Educativa, Chile, Desarrollo de Software
Abstract

Tesis (Ingeniero en Computación e Informática) El presente documento, entrega los resultados del desarrollo de un proyecto donde el producto final es una aplicación web que genere evaluaciones, está enfocada a ser una herramienta útil para los docentes, debido a que permite obtener una evaluación de calidad en un tiempo óptimo, dicho proyecto da vida a GESP. La aplicación web, generador de evaluaciones SIMCE y PSU, es una herramienta de creación que utiliza nuevas tecnologías, en comparación con los productos existentes, proporciona al usuario una serie de opciones, aparte de las ya existentes. Desde la creación de una evaluación, hasta la carga de material académico, pasando por un calendario de fechas, la estadística real del uso de dicho material, y la principal función que lo diferencia de las demás, la importación de preguntas mediante la carga de un archivo con formato previamente definido. El proyecto y el producto se realizaron en base a los conocimientos adquiridos por el equipo de trabajo durante sus años de estudios universitarios y se desarrolló en el contexto de su proyecto de título. Éste se inicia una vez que se define el problema y las necesidades que tiene el cliente, para luego pasar a la etapa de análisis de la solución donde se definen formalmente los requerimientos de la aplicación en conjunto y acuerdo con el cliente. Luego de esto se pasa a la etapa de diseño, de la aplicación y de las pruebas del software, y la definición de arquitectura. Es en base a éste diseño que se inicia la etapa de construcción que finaliza con las pruebas definidas y la aceptación y presentación del producto final. Finalizando el proceso de desarrollo del proyecto, se obtiene el producto definido, el cual es aceptado y validado por el cliente, en cuanto al equipo de proyecto, cumple con las metas propuestas, tanto de tiempo como de calidad, adquiriendo con esto habilidades para futuros proyectos del área de las tecnologías de la informática.

Published
2013

47. Funciñn de Dulac en la Familia Loud.

Author

Vidal, Nicole Carrasco

Abstract

En este trabajo consideramos la familia Loud. Estudiamos la función de Dulac en un caso particular de esta familia. Calculamos el primer tèrmino del desarrollo de Dulac de esta función y determinamos que este desarrollo no tiene tèrminos con logaritmos. [ABSTRACT FROM AUTHOR]

Published
2017
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48. Molecular epidemiology of Human Immunodeficiency Virus Type 1 in Guangdong Province of Southern China

Author

Chen, S., Cai, W. P., He, J. Y., Vidal, Nicole, Lai, C. H., Guo, W. Z., He, H. L., Chen, X. J., Fu, L. S., Peeters, Martine, Delaporte, Eric, Andrieu, J. M., and Lu, Louis

Subjects
virus diseases
Abstract

Background: Although the outbreak of human immunodeficiency virus type 1 (HIV-1) in Guangdong has been documented for more than a decade, the molecular characteristics of such a regional HIV-1 epidemic remained unknown. Methodology/Principal Findings: By sequencing of HIV-1 pol/env genes and phylogenetic analysis, we performed a molecular epidemiologic study in a representative subset (n = 200) of the 508 HIV-1-seropositive individuals followed up at the center for HIV/AIDS care and treatment of Guangzhou Hospital of Infectious Diseases. Of 157 samples (54.1% heterosexual acquired adults, 20.4% needle-sharing drug users, 5.7% receivers of blood transfusion, 1.3% men who have sex with men, and 18.5% remained unknown) with successful sequencing for both pol and env genes, 105 (66.9%) HIV-1 subtype CRF01_AE and 24 (15.3%) CRF07_BC, 9 (5.7%) B', 5 (3.2%) CRF08_BC, 5 (3.2%) B, 1 (0.6%) C, 3 (1.9%) CRF02_AG, and 5 (3.2%) inter-region recombinants were identified within pol/env sequences. Thirteen (8.3%) samples (3 naives, 6 and 5 received with antiretroviral treatment [ART] 1-21 weeks and >= 24 weeks respectively) showed mutations conferring resistance to nucleoside/nonnucleoside reverse transcriptase inhibitors or protease inhibitors. Among 63 ART-naive patients, 3 (4.8%) showed single or multiple drug resistant mutations. Phylogenetic analysis showed 8 small clusters (2-3 sequences/cluster) with only 17 (10.8%) sequences involved. Conclusion/Significance: This study confirms that sexual transmission with dominant CRF01_AE strain is a major risk for current HIV-1 outbreak in the Guangdong's general population. The transmission with drug-resistant variants is starting to emerge in this region.

Published
2012

49. High HIV type 1 group M pol diversity and low rate of antiretroviral resistance mutations among the uniformed services in Kinshasa, Democratic Republic of the Congo

Author

Djoko, C. F., Rimoin, A. W., Vidal, Nicole, Tamoufe, U., Wolfe, N. D., Butel, Christelle, LeBreton, M., Tshala, F. M., Kayembe, P. K., Muyembe, J. J., Edidi-Basepeo, S., Pike, B. L., Fair, J. N., Mbacham, W. F., Saylors, K. E., Mpoudi-Ngole, E., Delaporte, Eric, Grillo, M., and Peeters, Martine

Abstract

For the first time the genetic diversity among the uniformed personnel in Kinshasa, the capital city of the Democratic Republic of Congo (DRC), a country that has experienced military conflicts since 1998 and in which the global HIV-1/M pandemic started, has now been documented. A total of 94 HIV-1-positive samples, collected in 2007 in Kinshasa garrison settings from informed consenting volunteers, were genetically characterized in the pol region (protease and RT). An extensive diversity was observed, with 51% of the strains corresponding to six pure subtypes (A 23%, C 13.8%, D, G, H, J, and untypable), 15% corresponding to nine different CRFs (01, 02, 11, 13, 25, 26, 37, 43, and 45), and 34% being unique recombinants with one-third being complex mosaic viruses involving three or more different subtypes/CRFs. Only one strain harbored a single mutation, I54V, associated with drug resistance to protease inhibitors. Due to their high mobility and potential risk behavior, HIV infections in military personnel can lead to an even more complex epidemic in the DRC and to a possible increase of subtype C.

Published
2011

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

Published
2015
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