Interaction of filovirus proteins with RIG-I signaling pathways

Filovirus family consist of highly pathogenic negative-strand RNA viruses that are characterized by their filamentous virion structure. The main focus in previous research has been on ebolaviruses and marburgviruses due to the large epidemics caused by them. Host innate immune system and interferon responses play a vital role in restriction of viral infections. One of the reasons for the high lethality of filovirus infections is their ability to effectively suppress host antiviral responses by different viral proteins and mechanisms. The aims of this project was to systematically analyze innate immune antagonistic functions of filovirus proteins and identify filovirus encoded proteins that specifically inhibit interferon (IFN) gene expression in model cell systems. The study showed that filoviruses interfere with host innate immune responses by inhibiting retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) RIG-I and melanoma differentiation-associated protein 5 (MDA5). Several filovirus VP24 proteins inhibit the expression of type I and III IFN genes. In Study I we produced recombinant proteins for Ebola virus and compared the adjuvant effect of AS03 and FCA in immunizing rabbits and guinea pigs to find that both systems are comparable in antibody response. Study II showed a new function for EBOV VP24 as it inhibits type III IFN-λ1 gene expression. In Study III we expanded these findings to cover nine filoviruses and compared their inhibition of IFN-ß and IFN- λ1 promoter activation and localization in the nucleus. Differences considering VP24 localization and inhibition of interferon gene expression were found between filovirus VP24 proteins. In summary, these results add to the knowledge on basic filovirus biology and open a door for future drug development as VP24 plays a significant role in filovirus life cycle and could be utilized as a target protein for further innovations.-- Filovirukset ovat negatiivi-juosteisia RNA viruksia, joiden viruspartikkelit ovat rakenteeltaan filamenttisia. Aiempi tutkimus on keskittynyt pääasiassa ebolaviruksiin ja marburgviruksiin, sillä nämä viruslajit ovat aiheuttaneet ajoittain laajojakin epidemioita paikallisesti. Luontainen immuniteettivaste ja interferonivaste ovat keskeisessä roolissa virusinfektion torjunnassa. Filovirusten vaarallisuus pohjautuukin näiden reaktioiden vaimentamiseen. Väitöskirjan tavoite on systemaattisesti tarkastella filovirusten proteiinien aiheuttamia spesifisiä vaikutuksia interferonin geeniekspression vaimentamissa. Tutkimus osoitti filovirusten heikentävän luontaista immuniteettivastetta vähentämällä RIG-I:n kaltaisten reseptorien aktivoitumista johtaen heikentyneeseen interferonivasteeseen. Monet filoviruksen VP24 proteiinit vaikuttivat tyypin I ja III interferoni-geeniekspressioon. Ensimmäisessä osatyössä tuotimme Ebolaviruksen proteiineja ja vertailimme kahden eri adjuvanttimenetelmän (AS03 ja FCA) eroja immunisoiduissa kaneissa ja marsuissa. Molemmat menetelmät tuottivat tehokkaasti vasta-aineita. Toisessa osatyössä havaitsimme uuden mekanismin EBOV VP24 proteiinille, sillä VP24 esti tyypin III IFN-λ1 geeniekspressiota. Kolmannessa osatyössä laajensimme tutkimusasetelmaamme kaikkiin saatavilla oleviin filovirus VP24 proteineihin ja tutkimme näiden vaikutusta IFN-ß ja IFN-λ1 vasteeseen. Lisäksi selvitimme VP24 proteiinien tumalokalisaation ja interferoni geeniekspressioiden erot filovirus VP24 proteiinien välillä. Väitöskirjan havaitsemat uudet ilmiöt tuovat filovirusten elämänkaareen ja molekyylibiologiaan uutta tutkimustietoa. Nämä mekanismit tarjoavat paremman mahdollisuuden tulevaisuuden lääkekehityksen kannalta, sillä VP24 on mahdollinen spesifi kohde tulevaisuuden lääkeinnovaatioissa

Ebola virus replication leading to viral load as a predictor of disease severity and transmission

Le virus Ebola (EBOV) est l'agent étiologique de la maladie à virus Ebola (MVE), une maladie à progression fulgurante qui peut atteindre des taux de mortalité allant jusqu'à 90%. Malgré le fait que ce virus ait été découvert en 1976, ce n'est pas avant 2014 que le public fut exposé à ses effets dévastateurs, alors que l'épidémie de 2014-2016 qui a frappé l'Afrique de l'Ouest ne soit déclarée une urgence de santé publique à portée internationale, et où plus de 28 000 individus seront touchés principalement en Guinée, au Sierra Leone, et au Libéria, mais également aux États-Unis et en Europe. Une des raisons principales qui fait en sorte que notre compréhension du virus n'évolue pas aussi rapidement que pour d'autres agents pathogènes est qu'EBOV doit être manipulé dans le plus haut niveau de sécurité biologique, c'est-à-dire un laboratoire de niveau de confinement 4. Ce type de laboratoire est rare, et le fait de devoir contenir le virus à l'intérieur de celui-ci complexifie le nombre d'expériences pouvant y être effectué. De plus, aucune intervention prophylactique ou thérapeutique n'a été disponible pendant plus de 40 ans. La majorité des travaux effectués ont donc continuellement cherché à pallier à ce manque. Ainsi, un important travail a été effectué afin de comprendre la nature des réponses immunitaires suite à l'infection, puisque cette dernière peut mieux diriger le développement de mesures efficaces. Cependant, peu d'études se sont penchées sur la caractérisation des propriétés virales basiques, tels que les déterminants viraux associés avec la pathogénèse et la transmission du virus. Dans cette thèse, le rôle spécifique de la charge virale, résultant de la réplication du virus Ebola, est évalué dans un contexte de sévérité de la maladie et de transmission. Dans un premier temps, un état général des connaissances quant à EBOV et son cycle de vie est présenté, ainsi que de la manière dont le virus se comporte chez l'humain et dans les modèles animaux. Dans le premier chapitre de cette thèse, l'association entre la charge virale et l'issue suite à la maladie est décrite dans un contexte d'une épidémie naturelle chez l'humain. Dans un contexte de diagnostic, la virémie de patients qui se sont présentés à un centre de traitement Ebola a été évaluée, mais de plus amples analyses ont révélées que ceux qui se présentaient avec une virémie moindre étaient plus susceptible de se rétablir, une mesure indirecte de la sévérité de la maladie. Dans le second chapitre, un nouveau modèle de transmission chez le furet est décrit, où la transmission résultant d'un contact direct ou indirect a été évaluée simultanément. Alors que les mâles en contact direct avec un furet infecté ont développé et succombé à la MVE dans un laps de temps correspondant à une infection par leur compagnon de cage en phase terminale, aucune femelle n'a développer la MVE ou possédait une charge virale détectable. Cependant, tous les animaux contacts directs et indirects ont expérimenté une séroconversion à EBOV, suggérant que dans ce modèle une transmission par contact indirect est fréquente, mais résulte en une maladie clinique moins sévère. Finalement, dans le dernier chapitre de cette thèse, le rôle de la charge virale et de la voie d'infection est évalué dans un modèle de primates non-humains. Dans une série d'expériences indépendantes, une infection intraoesophagienne ou par exposition du visage des animaux à des aérosols n'a pas résulté en une infection clinique ou une virémie. Cependant, les animaux en contact direct avec ceux infecté par aérosol ont tous développé des anticorps spécifiques contre EBOV. Des expériences additionnelles utilisant un modèle d'infection intramusculaire ou intratrachéale suggèrent que la charge virale détermine la transmission d'EBOV dans un contexte d'infection intramusculaire, puisque le seul animal ayant transmis avec succès EBOV à son compagnon de cage était celui démontrant les plus hauts niveaux de virémie et sécrétion virale. Cette transmission est facilitée dans un modèle d'infection intratrachéale, puisqu'elle a été observée de manière consistante entre les animaux infectés et contacts. En effet, la charge virale mesurée dans les sécrétions mucosales des animaux infectés était plus élevée que celle de l'animal ayant transmis EBOV lors de l'infection intramusculaire, suggérant que dans ce modèle d'infection, la charge virale sécrétée est associée avec la transmission d'EBOV.Ebola virus (EBOV) is the etiological agent responsible for Ebola virus disease (EVD), a rapidly progressing infection which has historically reached case fatality rates of up to 90%. Although the virus was first identified in 1976, it was not until 2014 that the general public was exposed to its devastating impacts, as the 2014-2016 West African Ebola outbreak was declared a public health emergency of international concern and affected over 28,000 individuals, mostly in Guinea, Sierra Leone, and Liberia, but also in the United States and Europe. One of the main reasons that hinders our ability to characterize this disease extensively and rapidly is that handling this virus requires the highest level of biosafety containment available, namely biosafety level 4. These facilities are scarce world-wide, and the need to maintain high confinement usually limits the size and volume of the experiments that can be safely performed within. Given that for over 40 years, no medical countermeasures were available, a large proportion of available biosafety level 4 (BSL-4) resources was dedicated to solving this pressing issue. As such, a large amount of important work has focused on understanding the immune responses to infection, as they can better direct the development of efficacious countermeasures. Conversely, little has been done to characterize basic viral properties, such as viral determinants associated with pathogenicity and transmission of this virus. In this thesis, the role of viral loads specifically, as a result of virus replication, is evaluated with regards to pathogenicity and transmission. In the first section of this document, the current state of knowledge related to EBOV and its life cycle is presented, as well as what is currently known about how the virus behaves in both humans and animal models. In the first chapter of this thesis, the association between viral load and outcome is described from a human outbreak perspective. In the context of diagnostics, viremia of individuals who presented at an Ebola management center was assessed, but a follow-up analysis revealed that individuals who presented for care with a lower viremia better associated with recovery -- an indirect measure of disease severity. In the second chapter, a novel ferret model for transmission is described, where transmission resulting from direct and indirect contact could be evaluated simultaneously. While male direct contact animals developed and succumbed to clinical EVD in a timeframe consistent with infection by their terminally-ill challenged cagemate, no female contact animals became viremic or symptomatic. Interestingly, all direct and indirect contact animals seroconverted against EBOV, suggesting that in this model indirect transmission is frequent but results in a less-severe disease. Finally, in the final chapter of this thesis, the role of viral loads, as well as route of infection, was evaluated thoroughly in non-human primates. In a series of independent experiments, intraesophageal and facial aerosol exposure did not result in clinical EVD or viremia, but interestingly, all contact animals from the latter challenge seroconverted. Additional intramuscular or intratracheal challenge studies suggest that viral loads determine transmission of EBOV in an intramuscular challenge, as only the animal exhibiting the highest viral load was able o transmit EBOV to its contact cagemate. This transmission was found to be facilitated when using an intratracheal route of infection, as transmission was observed consistently from an infected to a naïve cagemate. Interestingly, viral loads as a result of shedding were found to be higher than those of the transmitting animal from the intramuscular challenge, suggesting that in this model, viral load as a result from shedding associate with transmission

Stochastic programming and agent-based simulation approaches for epidemics control and logistics planning

This dissertation addresses the resource allocation challenges of fighting against infectious disease outbreaks. The goal of this dissertation is to formulate multi-stage stochastic programming and agent-based models to address the limitations of former literature in optimizing resource allocation for preventing and controlling epidemics and pandemics. In the first study, a multi-stage stochastic programming compartmental model is presented to integrate the uncertain disease progression and the logistics of resource allocation to control a highly contagious infectious disease. The proposed multi-stage stochastic program, which involves various disease growth scenarios, optimizes the distribution of treatment centers and resources while minimizing the total expected number of new infections and funerals due to an epidemic. Two new equity metrics are defined and formulated, namely infection and capacity equity, to explicitly consider equity for allocating treatment funds and facilities for fair resource allocation in epidemics control. The multi-stage value of the stochastic solution (VSS), demonstrating the superiority of the proposed stochastic programming model over its deterministic counterpart, is studied. The first model is applied to the Ebola Virus Disease (EVD) case in West Africa, including Guinea, Sierra Leone, and Liberia. In the following study, the previous model is extended to a mean-risk multi-stage vaccine allocation model to capture the influence of the outbreak scenarios with low probability but high impact. The Conditional Value at Risk (CVaR) measure used in the model enables a trade-off between the weighted expected loss due to the outbreak and expected risks associated with experiencing disastrous epidemic scenarios. A method is developed to estimate the migration rate between each infected region when limited migration data is available. The second study is applied to the case of EVD in the Democratic Republic of the Congo. In the third study, a new risk-averse multi-stage stochastic epidemics-ventilator-logistics compartmental stochastic programming model is developed to address the resource allocation challenges of mitigating COVID-19. This epidemiological logistics model involves the uncertainty of untested asymptomatic infections and incorporates short-term human migration. Disease transmission is also forecasted through deriving a new formulation of transmission rates that evolve over space and time with respect to various non-pharmaceutical interventions, such as wearing masks, social distancing, and lockdown. In the fourth study, a simulation-optimization approach is introduced to address the vaccination facility location and allocation challenges of the COVID-19 vaccines. A detailed agent-based simulation model of the COVID-19 is extended and integrated with a new vaccination center and vaccine-allocation optimization model. The proposed agent-based simulation-optimization framework simulates the disease transmission first and then minimizes the total number of infections over all the considered regions by choosing the optimal vaccine center locations and vaccine allocation to those centers. Specifically, the simulation provides the number of susceptible and infected individuals in each geographical region for the current time period as an input into the optimization model. The optimization model then minimizes the total number of estimated infections and provides the new vaccine center locations and vaccine allocation decisions for the following time period. Decisions are made on where to open vaccination centers and how many people should be vaccinated at each future stage in each region of the considered geographical location. Then these optimal decision values are imported back into the simulation model to simulate the number of susceptible and infected individuals for the subsequent periods. The agent-based simulation-optimization framework is applied to controlling COVID-19 in the states of New Jersey. The results provide insights into the optimal vaccine center location and vaccine allocation problem under varying budgets and vaccine types while foreseeing potential epidemic growth scenarios over time and spatial locations

IoMT amid COVID-19 pandemic: Application, architecture, technology, and security

In many countries, the Internet of Medical Things (IoMT) has been deployed in tandem with other strategies to curb the spread of COVID-19, improve the safety of front-line personnel, increase efficacy by lessening the severity of the disease on human lives, and decrease mortality rates. Significant inroads have been achieved in terms of applications and technology, as well as security which have also been magnified through the rapid and widespread adoption of IoMT across the globe. A number of on-going researches show the adoption of secure IoMT applications is possible by incorporating security measures with the technology. Furthermore, the development of new IoMT technologies merge with Artificial Intelligence, Big Data and Blockchain offers more viable solutions. Hence, this paper highlights the IoMT architecture, applications, technologies, and security developments that have been made with respect to IoMT in combating COVID-19. Additionally, this paper provides useful insights into specific IoMT architecture models, emerging IoMT applications, IoMT security measurements, and technology direction that apply to many IoMT systems within the medical environment to combat COVID-19

Sero-prevalence of Ebola and Lassa virus in the Republic of Guinea, Macenta prefecture

Following the 2013-2016 West Africa Ebolavirus (EBOV) outbreak, a broad range of scientific research has been conducted to understand and prevent future epidemics. Our current study, supported by the United States Food and Drug Administration (FDA), uses sero-epidemiology to look at the foot-print incidence of EBOV and Lassa virus (LASV) in the prefecture of Macen-ta located in forested Guinea. Our study assesses seroprevalence of these zoonotic viruses in bushmeat hunters and their household members. These groups of people are at risk of exposure to multiple viral zoonotic infections via constant contact with wildlife, either by hunting, trapping or butchering. In order to investigate potential historical EBOV and/or Lassa virus LASV infections, serum samples were collected from villages that were affected or unaffected by the 2013-2016 EBOV outbreak in Guinea. We performed En-zyme-Linked Immunosorbent Assay (ELISA), western blot analysis and flow cytometry for the detection of EBOV glycoprotein (GP) and LASV nucleopro-tein (NP) antigens specific immunoglobulin G. A number of positive sam-ples were detected for both pathogens, suggesting that these two pathogens are circulating in Guinea and may cause mild or asymptomatic infection in a proportion of cases. Importantly, this study suggests EBOV may have been circulating in Guinea before the 2013-2016 outbreak

The Politics of Uncertainty

"Why is uncertainty so important to politics today? To explore the underlying reasons, issues and challenges, this book’s chapters address finance and banking, insurance, technology regulation and critical infrastructures, as well as climate change, infectious disease responses, natural disasters, migration, crime and security and spirituality and religion. The book argues that uncertainties must be understood as complex constructions of knowledge, materiality, experience, embodiment and practice. Examining in particular how uncertainties are experienced in contexts of marginalisation and precarity, this book shows how sustainability and development are not just technical issues, but depend on deeply political values and choices. What burgeoning uncertainties require lies less in escalating efforts at control, but more in a new – more collective, mutualistic and convivial – politics of responsibility and care. If hopes of much-needed progressive transformation are to be realised, then currently-blinkered understandings of uncertainty need to be met with renewed democratic struggle. Written in an accessible style and illustrated by multiple case studies from across the world, this book will appeal to a wide cross-disciplinary audience in fields ranging from economics to law to science studies to sociology to anthropology and geography, as well as professionals working in risk management, disaster risk reduction, emergencies and wider public policy fields.