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1.  Unique human immune signature of Ebola virus disease in Guinea 
Ruibal, Paula | Oestereich, Lisa | Lüdtke, Anja | Becker-Ziaja, Beate | Wozniak, David M. | Kerber, Romy | Korva, Miša | Cabeza-Cabrerizo, Mar | Bore, Joseph A. | Koundouno, Fara Raymond | Duraffour, Sophie | Weller, Romy | Thorenz, Anja | Cimini, Eleonora | Viola, Domenico | Agrati, Chiara | Repits, Johanna | Afrough, Babak | Cowley, Lauren A | Ngabo, Didier | Hinzmann, Julia | Mertens, Marc | Vitoriano, Inês | Logue, Christopher H. | Boettcher, Jan Peter | Pallasch, Elisa | Sachse, Andreas | Bah, Amadou | Nitzsche, Katja | Kuisma, Eeva | Michel, Janine | Holm, Tobias | Zekeng, Elsa-Gayle | García-Dorival, Isabel | Wölfel, Roman | Stoecker, Kilian | Fleischmann, Erna | Strecker, Thomas | Di Caro, Antonino | Avšič-Županc, Tatjana | Kurth, Andreas | Meschi, Silvia | Mély, Stephane | Newman, Edmund | Bocquin, Anne | Kis, Zoltan | Kelterbaum, Anne | Molkenthin, Peter | Carletti, Fabrizio | Portmann, Jasmine | Wolff, Svenja | Castilletti, Concetta | Schudt, Gordian | Fizet, Alexandra | Ottowell, Lisa J. | Herker, Eva | Jacobs, Thomas | Kretschmer, Birte | Severi, Ettore | Ouedraogo, Nobila | Lago, Mar | Negredo, Anabel | Franco, Leticia | Anda, Pedro | Schmiedel, Stefan | Kreuels, Benno | Wichmann, Dominic | Addo, Marylyn M. | Lohse, Ansgar W. | De Clerck, Hilde | Nanclares, Carolina | Jonckheere, Sylvie | Van Herp, Michel | Sprecher, Armand | Xiaojiang, Gao | Carrington, Mary | Miranda, Osvaldo | Castro, Carlos M. | Gabriel, Martin | Drury, Patrick | Formenty, Pierre | Diallo, Boubacar | Koivogui, Lamine | Magassouba, N’Faly | Carroll, Miles W. | Günther, Stephan | Muñoz-Fontela, César
Nature  2016;533(7601):100-104.
Despite the magnitude of the Ebola virus disease (EVD) outbreak in West Africa, there is still a fundamental lack of knowledge about the pathophysiology of EVD1. In particular, very little is known about human immune responses to Ebola virus (EBOV)2,3. Here, we have for the first time evaluated the physiology of the human T cell immune response in EVD patients at the time of admission at the Ebola Treatment Center (ETC) in Guinea, and longitudinally until discharge or death. Through the use of multiparametric flow cytometry established by the European Mobile Laboratory in the field, we have identified an immune signature that is unique in EVD fatalities. Fatal EVD was characterized by high percentage of CD4 and CD8 T cells expressing the inhibitory molecules cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) and programmed cell death-1 (PD-1), which was correlated with elevated inflammatory markers and high virus load. Conversely, surviving individuals showed significantly lower expression of CTLA-4 and PD-1 as well as lower inflammation despite comparable overall T cell activation. Concommittant with virus clearance, survivors mounted a robust EBOV-specific T cell response. Our findings suggest that dysregulation of the T cell response is a key component of EVD pathophysiology.
doi:10.1038/nature17949
PMCID: PMC4876960  PMID: 27147028
2.  Evaluation of RealStar Reverse Transcription–Polymerase Chain Reaction Kits for Filovirus Detection in the Laboratory and Field 
The Journal of Infectious Diseases  2016;214(Suppl 3):S243-S249.
Background. Diagnosis of Ebola virus (EBOV) disease (EVD) requires laboratory testing.
Methods. The RealStar Filovirus Screen reverse transcription–polymerase chain reaction (RT-PCR) kit and the derived RealStar Zaire Ebolavirus RT-PCR kit were validated using in vitro transcripts, supernatant of infected cell cultures, and clinical specimens from patients with EVD.
Results. The Filovirus Screen kit detected EBOV, Sudan virus, Taï Forest virus, Bundibugyo virus, Reston virus, and Marburg virus and differentiated between the genera Ebolavirus and Marburgvirus. The amount of filovirus RNA that could be detected with a probability of 95% ranged from 11 to 67 RNA copies/reaction on a LightCycler 480 II. The Zaire Ebolavirus kit is based on the Filovirus Screen kit but was optimized for detection of EBOV. It has an improved signal-to-noise ratio at low EBOV RNA concentrations and is somewhat more sensitive than the Filovirus kit. Both kits show significantly lower analytical sensitivity on a SmartCycler II. Clinical evaluation revealed that the SmartCycler II, compared with other real-time PCR platforms, decreases the clinical sensitivity of the Filovirus Screen kit to diagnose EVD at an early stage.
Conclusions. The Filovirus Screen kit detects all human-pathogenic filoviruses with good analytical sensitivity if performed on an appropriate real-time PCR platform. High analytical sensitivity is important for early diagnosis of EVD.
doi:10.1093/infdis/jiw246
PMCID: PMC5050472  PMID: 27549586
Filovirus; Ebola virus disease; commercial RT-PCR kit; molecular diagnostics; sensitivity
3.  Analysis of Diagnostic Findings From the European Mobile Laboratory in Guéckédou, Guinea, March 2014 Through March 2015 
Kerber, Romy | Krumkamp, Ralf | Diallo, Boubacar | Jaeger, Anna | Rudolf, Martin | Lanini, Simone | Bore, Joseph Akoi | Koundouno, Fara Raymond | Becker-Ziaja, Beate | Fleischmann, Erna | Stoecker, Kilian | Meschi, Silvia | Mély, Stéphane | Newman, Edmund N. C. | Carletti, Fabrizio | Portmann, Jasmine | Korva, Misa | Wolff, Svenja | Molkenthin, Peter | Kis, Zoltan | Kelterbaum, Anne | Bocquin, Anne | Strecker, Thomas | Fizet, Alexandra | Castilletti, Concetta | Schudt, Gordian | Ottowell, Lisa | Kurth, Andreas | Atkinson, Barry | Badusche, Marlis | Cannas, Angela | Pallasch, Elisa | Bosworth, Andrew | Yue, Constanze | Pályi, Bernadett | Ellerbrok, Heinz | Kohl, Claudia | Oestereich, Lisa | Logue, Christopher H. | Lüdtke, Anja | Richter, Martin | Ngabo, Didier | Borremans, Benny | Becker, Dirk | Gryseels, Sophie | Abdellati, Saïd | Vermoesen, Tine | Kuisma, Eeva | Kraus, Annette | Liedigk, Britta | Maes, Piet | Thom, Ruth | Duraffour, Sophie | Diederich, Sandra | Hinzmann, Julia | Afrough, Babak | Repits, Johanna | Mertens, Marc | Vitoriano, Inês | Bah, Amadou | Sachse, Andreas | Boettcher, Jan Peter | Wurr, Stephanie | Bockholt, Sabrina | Nitsche, Andreas | Županc, Tatjana Avšič | Strasser, Marc | Ippolito, Giuseppe | Becker, Stephan | Raoul, Herve | Carroll, Miles W. | De Clerck, Hilde | Van Herp, Michel | Sprecher, Armand | Koivogui, Lamine | Magassouba, N'Faly | Keïta, Sakoba | Drury, Patrick | Gurry, Cèline | Formenty, Pierre | May, Jürgen | Gabriel, Martin | Wölfel, Roman | Günther, Stephan | Di Caro, Antonino
The Journal of Infectious Diseases  2016;214(Suppl 3):S250-S257.
Background. A unit of the European Mobile Laboratory (EMLab) consortium was deployed to the Ebola virus disease (EVD) treatment unit in Guéckédou, Guinea, from March 2014 through March 2015.
Methods. The unit diagnosed EVD and malaria, using the RealStar Filovirus Screen reverse transcription–polymerase chain reaction (RT-PCR) kit and a malaria rapid diagnostic test, respectively.
Results. The cleaned EMLab database comprised 4719 samples from 2741 cases of suspected EVD from Guinea. EVD was diagnosed in 1231 of 2178 hospitalized patients (57%) and in 281 of 563 who died in the community (50%). Children aged <15 years had the highest proportion of Ebola virus–malaria parasite coinfections. The case-fatality ratio was high in patients aged <5 years (80%) and those aged >74 years (90%) and low in patients aged 10–19 years (40%). On admission, RT-PCR analysis of blood specimens from patients who died in the hospital yielded a lower median cycle threshold (Ct) than analysis of blood specimens from survivors (18.1 vs 23.2). Individuals who died in the community had a median Ct of 21.5 for throat swabs. Multivariate logistic regression on 1047 data sets revealed that low Ct values, ages of <5 and ≥45 years, and, among children aged 5–14 years, malaria parasite coinfection were independent determinants of a poor EVD outcome.
Conclusions. Virus load, age, and malaria parasite coinfection play a role in the outcome of EVD.
doi:10.1093/infdis/jiw269
PMCID: PMC5050480  PMID: 27638946
Filovirus; Ebola virus disease; malaria; Guinea; epidemic; mobile laboratory
4.  Chimeric Mice with Competent Hematopoietic Immunity Reproduce Key Features of Severe Lassa Fever 
PLoS Pathogens  2016;12(5):e1005656.
Lassa fever (LASF) is a highly severe viral syndrome endemic to West African countries. Despite the annual high morbidity and mortality caused by LASF, very little is known about the pathophysiology of the disease. Basic research on LASF has been precluded due to the lack of relevant small animal models that reproduce the human disease. Immunocompetent laboratory mice are resistant to infection with Lassa virus (LASV) and, to date, only immunodeficient mice, or mice expressing human HLA, have shown some degree of susceptibility to experimental infection. Here, transplantation of wild-type bone marrow cells into irradiated type I interferon receptor knockout mice (IFNAR-/-) was used to generate chimeric mice that reproduced important features of severe LASF in humans. This included high lethality, liver damage, vascular leakage and systemic virus dissemination. In addition, this model indicated that T cell-mediated immunopathology was an important component of LASF pathogenesis that was directly correlated with vascular leakage. Our strategy allows easy generation of a suitable small animal model to test new vaccines and antivirals and to dissect the basic components of LASF pathophysiology.
Author Summary
Lassa fever is an arenaviral hemorrhagic fever that causes high morbidity and mortality in West Africa. Unfortunately, the lack of immunocompetent small animal models of disease has precluded understanding of the basic pathophysiology mechanisms of Lassa fever. Here we show how transplantation of a wild-type hematopoietic system into type I interferon deficient recipient mice results in a lethal mouse model of disease. Importantly, experimental infection of these chimeric mice reproduced key features of Lassa fever in humans and underscored the important role of T cells on Lassa fever-associated immunopathology.
doi:10.1371/journal.ppat.1005656
PMCID: PMC4871546  PMID: 27191716
5.  Correction: Experimental Treatment with Favipiravir for Ebola Virus Disease (the JIKI Trial): A Historically Controlled, Single-Arm Proof-of-Concept Trial in Guinea 
Sissoko, Daouda | Laouenan, Cedric | Folkesson, Elin | M’Lebing, Abdoul-Bing | Beavogui, Abdoul-Habib | Baize, Sylvain | Camara, Alseny-Modet | Maes, Piet | Shepherd, Susan | Danel, Christine | Carazo, Sara | Conde, Mamoudou N. | Gala, Jean-Luc | Colin, Géraldine | Savini, Hélène | Bore, Joseph Akoi | Le Marcis, Frederic | Koundouno, Fara Raymond | Petitjean, Frédéric | Lamah, Marie-Claire | Diederich, Sandra | Tounkara, Alexis | Poelart, Geertrui | Berbain, Emmanuel | Dindart, Jean-Michel | Duraffour, Sophie | Lefevre, Annabelle | Leno, Tamba | Peyrouset, Olivier | Irenge, Léonid | Bangoura, N’Famara | Palich, Romain | Hinzmann, Julia | Kraus, Annette | Barry, Thierno Sadou | Berette, Sakoba | Bongono, André | Camara, Mohamed Seto | Munoz, Valérie Chanfreau | Doumbouya, Lanciné | Harouna, Souley | Kighoma, Patient Mumbere | Koundouno, Fara Roger | Lolamou, Réné | Loua, Cécé Moriba | Massala, Vincent | Moumouni, Kinda | Provost, Célia | Samake, Nenefing | Sekou, Conde | Soumah, Abdoulaye | Arnould, Isabelle | Komano, Michel Saa | Gustin, Lina | Berutto, Carlotta | Camara, Diarra | Camara, Fodé Saydou | Colpaert, Joliene | Delamou, Léontine | Jansson, Lena | Kourouma, Etienne | Loua, Maurice | Malme, Kristian | Manfrin, Emma | Maomou, André | Milinouno, Adele | Ombelet, Sien | Sidiboun, Aboubacar Youla | Verreckt, Isabelle | Yombouno, Pauline | Bocquin, Anne | Carbonnelle, Caroline | Carmoi, Thierry | Frange, Pierre | Mely, Stéphane | Nguyen, Vinh-Kim | Pannetier, Delphine | Taburet, Anne-Marie | Treluyer, Jean-Marc | Kolie, Jacques | Moh, Raoul | Gonzalez, Minerva Cervantes | Kuisma, Eeva | Liedigk, Britta | Ngabo, Didier | Rudolf, Martin | Thom, Ruth | Kerber, Romy | Gabriel, Martin | Di Caro, Antonino | Wölfel, Roman | Badir, Jamal | Bentahir, Mostafa | Deccache, Yann | Dumont, Catherine | Durant, Jean-François | El Bakkouri, Karim | Uwamahoro, Marie Gasasira | Smits, Benjamin | Toufik, Nora | Van Cauwenberghe, Stéphane | Ezzedine, Khaled | D’Ortenzio, Eric | Pizarro, Louis | Etienne, Aurélie | Guedj, Jérémie | Fizet, Alexandra | de Sainte Fare, Eric Barte | Murgue, Bernadette | Tran-Minh, Tuan | Rapp, Christophe | Piguet, Pascal | Poncin, Marc | Draguez, Bertrand | Duverger, Thierry Allaford | Barbe, Solenne | Baret, Guillaume | Defourny, Isabelle | Carroll, Miles | Raoul, Hervé | Augier, Augustin | Eholie, Serge P. | Yazdanpanah, Yazdan | Levy-Marchal, Claire | Antierrens, Annick | Van Herp, Michel | Günther, Stephan | de Lamballerie, Xavier | Keïta, Sakoba | Mentre, France | Anglaret, Xavier | Malvy, Denis
PLoS Medicine  2016;13(4):e1002009.
doi:10.1371/journal.pmed.1002009
PMCID: PMC4821578  PMID: 27046271
6.  Experimental Treatment with Favipiravir for Ebola Virus Disease (the JIKI Trial): A Historically Controlled, Single-Arm Proof-of-Concept Trial in Guinea 
Sissoko, Daouda | Laouenan, Cedric | Folkesson, Elin | M’Lebing, Abdoul-Bing | Beavogui, Abdoul-Habib | Baize, Sylvain | Camara, Alseny-Modet | Maes, Piet | Shepherd, Susan | Danel, Christine | Carazo, Sara | Conde, Mamoudou N. | Gala, Jean-Luc | Colin, Géraldine | Savini, Hélène | Bore, Joseph Akoi | Le Marcis, Frederic | Koundouno, Fara Raymond | Petitjean, Frédéric | Lamah, Marie-Claire | Diederich, Sandra | Tounkara, Alexis | Poelart, Geertrui | Berbain, Emmanuel | Dindart, Jean-Michel | Duraffour, Sophie | Lefevre, Annabelle | Leno, Tamba | Peyrouset, Olivier | Irenge, Léonid | Bangoura, N’Famara | Palich, Romain | Hinzmann, Julia | Kraus, Annette | Barry, Thierno Sadou | Berette, Sakoba | Bongono, André | Camara, Mohamed Seto | Chanfreau Munoz, Valérie | Doumbouya, Lanciné | Souley Harouna,  | Kighoma, Patient Mumbere | Koundouno, Fara Roger | Réné Lolamou,  | Loua, Cécé Moriba | Massala, Vincent | Moumouni, Kinda | Provost, Célia | Samake, Nenefing | Sekou, Conde | Soumah, Abdoulaye | Arnould, Isabelle | Komano, Michel Saa | Gustin, Lina | Berutto, Carlotta | Camara, Diarra | Camara, Fodé Saydou | Colpaert, Joliene | Delamou, Léontine | Jansson, Lena | Kourouma, Etienne | Loua, Maurice | Malme, Kristian | Manfrin, Emma | Maomou, André | Milinouno, Adele | Ombelet, Sien | Sidiboun, Aboubacar Youla | Verreckt, Isabelle | Yombouno, Pauline | Bocquin, Anne | Carbonnelle, Caroline | Carmoi, Thierry | Frange, Pierre | Mely, Stéphane | Nguyen, Vinh-Kim | Pannetier, Delphine | Taburet, Anne-Marie | Treluyer, Jean-Marc | Kolie, Jacques | Moh, Raoul | Gonzalez, Minerva Cervantes | Kuisma, Eeva | Liedigk, Britta | Ngabo, Didier | Rudolf, Martin | Thom, Ruth | Kerber, Romy | Gabriel, Martin | Di Caro, Antonino | Wölfel, Roman | Badir, Jamal | Bentahir, Mostafa | Deccache, Yann | Dumont, Catherine | Durant, Jean-François | El Bakkouri, Karim | Gasasira Uwamahoro, Marie | Smits, Benjamin | Toufik, Nora | Van Cauwenberghe, Stéphane | Ezzedine, Khaled | Dortenzio, Eric | Pizarro, Louis | Etienne, Aurélie | Guedj, Jérémie | Fizet, Alexandra | Barte de Sainte Fare, Eric | Murgue, Bernadette | Tran-Minh, Tuan | Rapp, Christophe | Piguet, Pascal | Poncin, Marc | Draguez, Bertrand | Allaford Duverger, Thierry | Barbe, Solenne | Baret, Guillaume | Defourny, Isabelle | Carroll, Miles | Raoul, Hervé | Augier, Augustin | Eholie, Serge P. | Yazdanpanah, Yazdan | Levy-Marchal, Claire | Antierrens, Annick | Van Herp, Michel | Günther, Stephan | de Lamballerie, Xavier | Keïta, Sakoba | Mentre, France | Anglaret, Xavier | Malvy, Denis
PLoS Medicine  2016;13(3):e1001967.
Background
Ebola virus disease (EVD) is a highly lethal condition for which no specific treatment has proven efficacy. In September 2014, while the Ebola outbreak was at its peak, the World Health Organization released a short list of drugs suitable for EVD research. Favipiravir, an antiviral developed for the treatment of severe influenza, was one of these. In late 2014, the conditions for starting a randomized Ebola trial were not fulfilled for two reasons. One was the perception that, given the high number of patients presenting simultaneously and the very high mortality rate of the disease, it was ethically unacceptable to allocate patients from within the same family or village to receive or not receive an experimental drug, using a randomization process impossible to understand by very sick patients. The other was that, in the context of rumors and distrust of Ebola treatment centers, using a randomized design at the outset might lead even more patients to refuse to seek care.
Therefore, we chose to conduct a multicenter non-randomized trial, in which all patients would receive favipiravir along with standardized care. The objectives of the trial were to test the feasibility and acceptability of an emergency trial in the context of a large Ebola outbreak, and to collect data on the safety and effectiveness of favipiravir in reducing mortality and viral load in patients with EVD. The trial was not aimed at directly informing future guidelines on Ebola treatment but at quickly gathering standardized preliminary data to optimize the design of future studies.
Methods and Findings
Inclusion criteria were positive Ebola virus reverse transcription PCR (RT-PCR) test, age ≥ 1 y, weight ≥ 10 kg, ability to take oral drugs, and informed consent. All participants received oral favipiravir (day 0: 6,000 mg; day 1 to day 9: 2,400 mg/d). Semi-quantitative Ebola virus RT-PCR (results expressed in “cycle threshold” [Ct]) and biochemistry tests were performed at day 0, day 2, day 4, end of symptoms, day 14, and day 30. Frozen samples were shipped to a reference biosafety level 4 laboratory for RNA viral load measurement using a quantitative reference technique (genome copies/milliliter). Outcomes were mortality, viral load evolution, and adverse events. The analysis was stratified by age and Ct value. A “target value” of mortality was defined a priori for each stratum, to guide the interpretation of interim and final analysis.
Between 17 December 2014 and 8 April 2015, 126 patients were included, of whom 111 were analyzed (adults and adolescents, ≥13 y, n = 99; young children, ≤6 y, n = 12). Here we present the results obtained in the 99 adults and adolescents. Of these, 55 had a baseline Ct value ≥ 20 (Group A Ct ≥ 20), and 44 had a baseline Ct value < 20 (Group A Ct < 20). Ct values and RNA viral loads were well correlated, with Ct = 20 corresponding to RNA viral load = 7.7 log10 genome copies/ml. Mortality was 20% (95% CI 11.6%–32.4%) in Group A Ct ≥ 20 and 91% (95% CI 78.8%–91.1%) in Group A Ct < 20. Both mortality 95% CIs included the predefined target value (30% and 85%, respectively). Baseline serum creatinine was ≥110 μmol/l in 48% of patients in Group A Ct ≥ 20 (≥300 μmol/l in 14%) and in 90% of patients in Group A Ct < 20 (≥300 μmol/l in 44%). In Group A Ct ≥ 20, 17% of patients with baseline creatinine ≥110 μmol/l died, versus 97% in Group A Ct < 20. In patients who survived, the mean decrease in viral load was 0.33 log10 copies/ml per day of follow-up. RNA viral load values and mortality were not significantly different between adults starting favipiravir within <72 h of symptoms compared to others. Favipiravir was well tolerated.
Conclusions
In the context of an outbreak at its peak, with crowded care centers, randomizing patients to receive either standard care or standard care plus an experimental drug was not felt to be appropriate. We did a non-randomized trial. This trial reaches nuanced conclusions. On the one hand, we do not conclude on the efficacy of the drug, and our conclusions on tolerance, although encouraging, are not as firm as they could have been if we had used randomization. On the other hand, we learned about how to quickly set up and run an Ebola trial, in close relationship with the community and non-governmental organizations; we integrated research into care so that it improved care; and we generated knowledge on EVD that is useful to further research. Our data illustrate the frequency of renal dysfunction and the powerful prognostic value of low Ct values. They suggest that drug trials in EVD should systematically stratify analyses by baseline Ct value, as a surrogate of viral load. They also suggest that favipiravir monotherapy merits further study in patients with medium to high viremia, but not in those with very high viremia.
Trial registration
ClinicalTrials.gov NCT02329054
In the context the recent Ebola outbreak, Xavier Anglaret and colleagues test an experimental treatment, favipiravir, for Ebola virus disease in a multicenter non-randomized trial.
Editors' Summary
Background
In 2014 and 2015, an Ebola virus outbreak larger than any known before occurred in West Africa. Ebola virus disease (EVD) is highly contagious, and many infected people die. Central to the emergency response to the recent outbreak were local Ebola treatment centers where patients were diagnosed, were isolated, and received supportive care. With thousands of patients dying and many health workers contracting the disease, fear was ubiquitous and distrust abundant. While conducting research in this environment was extremely challenging, the urgent need for treatments and the opportunity to conduct studies that could bring such treatments closer to reality was also recognized. In September 2014, WHO released a short list of existing drugs that were candidates for clinical trials among patients infected in the outbreak. Favipiravir, an antiviral drug developed in Japan for patients with severe influenza, was on the list.
Why Was This Study Done?
Because of the urgent need to find drugs that could reduce deaths caused by Ebola, the researchers decided to conduct a clinical trial using favipiravir in patients with EVD in Guinea. In view of the circumstances, they decided against a randomized controlled trial and instead designed a study where all participants would receive the same treatment. In randomized controlled trials only some participants receive the treatment in addition to standard care, while others serve as a control group and receive standard care only, or standard care plus a placebo. Such studies allow stronger conclusions to be drawn about whether a treatment is safe and whether it works or not. The researchers had two main reasons for this decision. First, patients from the same family or village often sought EVD treatment at the same time, and the researchers felt that it was ethically unacceptable to randomize such groups, with only some of them receiving the experimental drug. Second, the strict isolation procedures imposed to interrupt virus transmission had intensified fear in affected communities and fueled rumors of illicit drug experimentation and organ theft at the treatment centers. In this context, the researchers worried that a randomized study might increase distrust among the community and the reluctance of patients to seek care.
Rather than seeking definitive answers about the safety and efficacy of favipiravir in patients with EVD, the objectives of the study as it was designed were to test the feasibility and acceptability of an emergency trial in the context of a large Ebola outbreak and to learn lessons from the experience. In addition, the researchers planned to collect data on the safety and effectiveness of favipiravir in reducing mortality and viral load in patients with EVD in the hope that their preliminary findings could improve the design of subsequent trials and the chance to provide conclusive answers.
What Did the Researchers Do and Find?
After 13 weeks of preparation, the trial took place from December 2014 to April 2015 at four separate Ebola treatment centers, three in rural areas and one in an urban setting. In addition to standard care (which included rehydration, antimalarial and antibacterial therapies, and medication to reduce fever, pain, and nausea), all participants were given favipiravir by mouth for ten days, at doses substantially higher than those recommended for patients with influenza. Outcomes measured were mortality, viral load changes over time (based on blood samples), and adverse events.
EVD was confirmed with an assay that used patient blood and provided an estimate of the viral load, that is, of how much virus the blood contained. Because viral load was known to influence the course of EVD, the researchers analyzed the participants in two groups, namely, those with a viral load estimate above a certain threshold and those with viral load estimate below the threshold. They also used existing data from Guinean patients diagnosed with Ebola earlier in the outbreak who had received only standard care and calculated an expected mortality rate for patients above and below the viral load threshold.
The researchers were able to enroll 126 participants in the trial. Of these, 111 were included in the final analysis. Of 99 adult and adolescent participants 13 years and older, 55 were in the lower viral load group and 44 in the higher viral load group. Mortality was 20% in the former and 91% in the latter. Neither mortality rate was significantly different from that of earlier patients who had received only standard care. The researchers also found that favipiravir was well tolerated. None of the patients stopped the course of treatment, vomiting following drug intake was rare, and no severe adverse events were attributed to the drug. The researchers did not see a difference in mortality between patients who reported onset of symptoms less than three days before the start of treatment and those whose symptoms had started more than three days the start of treatment.
What Do these Findings Mean?
The report shows that it is possible to conduct an emergency trial during an outbreak in a low-resource setting. In fact, at the time of its acceptance, this paper reported on an Ebola treatment trial larger than any other yet published. The experience described should be useful for similar undertakings in the future. The following conditions contributed to the success of the trial: close collaboration between researchers, local health officials, and affected communities on one hand, and flexibility in design, conduct, and analysis based on close monitoring and interim assessments on the other. Besides using interim results to influence the conduct and analysis of their own trial, the researchers also shared these results with the scientific community in real time, and this feedback influenced other research during the outbreak.
The trial could not answer definitively whether favipiravir treatment was safe or reduced mortality in patients with EVD. The results suggest that the drug is unlikely to be beneficial for patients with very high viral loads, at least when given by itself. They also suggest that favipiravir is safe in patients with lower viral loads, and that in such patients additional efficacy studies are warranted. Intermediate analysis of various measurements in trial participants showed that the estimate of viral load from the field EVD diagnosis test is a good proxy for the actual viral load (determined after the samples were shipped to and analyzed in a reference laboratory in France) and suitable as a surrogate marker. The results also confirm that viral load is a strong predictor of mortality.
Additional Information
This list of resources contains links that can be accessed when viewing the PDF on a device or via the online version of the article at http://dx.doi.org/10.1371/journal.pmed.1001967.
The World Health Organization has pages on Ebola virus disease, trials of Ebola treatments and vaccines, and the current update of the list of suitable drugs for testing or use in patients infected with Ebola (originally compiled in September 2014)
US Centers for Disease Control and Prevention has information on the Ebola outbreak in West Africa
The European Centre for Disease Prevention and Control also has information on the Ebola outbreak in West Africa
doi:10.1371/journal.pmed.1001967
PMCID: PMC4773183  PMID: 26930627
7.  A Basic Cluster in the N Terminus of Yellow Fever Virus NS2A Contributes to Infectious Particle Production 
Journal of Virology  2015;89(9):4951-4965.
ABSTRACT
The flavivirus NS2A protein is involved in the assembly of infectious particles. To further understand its role in this process, a charged-to-alanine scanning analysis was performed on NS2A encoded by an infectious cDNA clone of yellow fever virus (YFV). Fifteen mutants containing single, double, or triple charged-to-alanine changes were tested. Five of them did not produce infectious particles, whereas efficient RNA replication was detectable for two of the five NS2A mutants (R22A-K23A-R24A and R99A-E100A-R101A mutants). Prolonged cultivation of transfected cells resulted in the recovery of pseudorevertants. Besides suppressor mutants in NS2A, a compensating second-site mutation in NS3 (D343G) arose for the NS2A R22A-K23A-R24A mutant. We found this NS3 mutation previously to be suppressive for the NS2Aα cleavage site Q189S mutant, also deficient in virion assembly. In this study, the subsequently suggested interaction between NS2A and NS3 was proven by coimmunoprecipitation analyses. Using selectively permeabilized cells, we could demonstrate that the regions encompassing R22A-K23A-R24A and Q189S in NS2A are localized to the cytoplasm, where NS3 is also known to reside. However, the defect in particle production observed for the NS2A R22A-K23A-R24A and Q189S mutants was not due to a defect in physical interaction between NS2A and NS3, as the NS2A mutations did not interrupt NS3 interaction. In fact, a region just upstream of R22-K23-R24 was mapped to be critical for NS2A-NS3 interaction. Taken together, these data support a complex interplay between YFV NS2A and NS3 in virion assembly and identify a basic cluster in the NS2A N terminus to be critical in this process.
IMPORTANCE Despite an available vaccine, yellow fever remains endemic in tropical areas of South America and Africa. To control the disease, antiviral drugs are required, and an understanding of the determinants of virion assembly is central to their development. In this study, we identified a basic cluster of amino acids in the N terminus of YFV NS2A which inhibited virion assembly upon mutation. The defect was rescued by a spontaneously occurring mutation in NS3. Our study proves an interaction between NS2A and NS3, which, remarkably, was maintained for the NS2A mutant in the presence and absence of the NS3 mutation. This suggests a role for other viral and/or cellular proteins in virion assembly. Residues important for YFV virion production reported here only partially coincided with those reported for other flaviviruses, suggesting that the determinants for particle production are virus specific. Reconstruction of a YFV encoding tagged NS2A paves the way to identify further NS2A interaction partners.
doi:10.1128/JVI.03351-14
PMCID: PMC4403467  PMID: 25694595
8.  Cross-Species Analysis of the Replication Complex of Old World Arenaviruses Reveals Two Nucleoprotein Sites Involved in L Protein Function▿ 
Journal of Virology  2011;85(23):12518-12528.
Lassa virus (LASV) causing hemorrhagic Lassa fever in West Africa, Mopeia virus (MOPV) from East Africa, and lymphocytic choriomeningitis virus (LCMV) are the main representatives of the Old World arenaviruses. Little is known about how the components of the arenavirus replication machinery, i.e., the genome, nucleoprotein (NP), and L protein, interact. In addition, it is unknown whether these components can function across species boundaries. We established minireplicon systems for MOPV and LCMV in analogy to the existing LASV system and exchanged the components among the three systems. The functional and physical integrity of the resulting complexes was tested by reporter gene assay, Northern blotting, and coimmunoprecipitation studies. The minigenomes, NPs, and L proteins of LASV and MOPV could be exchanged without loss of function. LASV and MOPV L protein was also active in conjunction with LCMV NP, while the LCMV L protein required homologous NP for activity. Analysis of LASV/LCMV NP chimeras identified a single LCMV-specific NP residue (Ile-53) and the C terminus of NP (residues 340 to 558) as being essential for LCMV L protein function. The defect of LASV and MOPV NP in supporting transcriptional activity of LCMV L protein was not caused by a defect in physical NP-L protein interaction. In conclusion, components of the replication complex of Old World arenaviruses have the potential to functionally and physically interact across species boundaries. Residue 53 and the C-terminal domain of NP are important for function of L protein during genome replication and transcription.
doi:10.1128/JVI.05091-11
PMCID: PMC3209397  PMID: 21917982
9.  The N-Terminal Domain of the Arenavirus L Protein Is an RNA Endonuclease Essential in mRNA Transcription 
PLoS Pathogens  2010;6(9):e1001038.
Arenaviridae synthesize viral mRNAs using short capped primers presumably acquired from cellular transcripts by a ‘cap-snatching’ mechanism. Here, we report the crystal structure and functional characterization of the N-terminal 196 residues (NL1) of the L protein from the prototypic arenavirus: lymphocytic choriomeningitis virus. The NL1 domain is able to bind and cleave RNA. The 2.13 Å resolution crystal structure of NL1 reveals a type II endonuclease α/β architecture similar to the N-terminal end of the influenza virus PA protein. Superimposition of both structures, mutagenesis and reverse genetics studies reveal a unique spatial arrangement of key active site residues related to the PD…(D/E)XK type II endonuclease signature sequence. We show that this endonuclease domain is conserved and active across the virus families Arenaviridae, Bunyaviridae and Orthomyxoviridae and propose that the arenavirus NL1 domain is the Arenaviridae cap-snatching endonuclease.
Author Summary
The Arenaviridae virus family includes several life-threatening human pathogens that cause meningitis or hemorrhagic fever. These RNA viruses replicate and transcribe their genome using an RNA synthesis machinery for which no structural data currently exist. They synthesize viral mRNAs using short capped primers presumably acquired from cellular transcripts by a ‘cap-snatching’ mechanism thought to involve the large L protein, which carries RNA-dependent RNA polymerase signature sequences. Here, we report the crystal structure and functional characterization of an isolated N-terminal domain of the L protein (NL1) from the prototypic arenavirus: lymphocytic choriomeningitis virus. The NL1 domain is able to bind and cleave RNA. The 2.13 Å resolution crystal structure of NL1 reveals a type II endonuclease α/β architecture similar to the N-terminal end of the influenza virus PA protein. Superimposition of both structures and mutagenesis studies reveal a unique spatial arrangement of key active site residues related to the PD…(D/E)XK type II endonuclease signature sequence. Reverse genetic studies show that mutation of active site residues selectively abolish transcription, not replication. We show that this endonuclease domain is conserved and active across the virus families: Arenaviridae, Bunyaviridae and Orthomyxoviridae and propose that the arenavirus NL1 domain is the Arenaviridae cap-snatching endonuclease.
doi:10.1371/journal.ppat.1001038
PMCID: PMC2940758  PMID: 20862324

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