Recent events have thrown the spotlight on infectious disease outbreak response. We developed a data-driven method, EpiGro, which can be applied to cumulative case reports to estimate the order of magnitude of the duration, peak and ultimate size of an ongoing outbreak. It is based on a surprisingly simple mathematical property of many epidemiological data sets, does not require knowledge or estimation of disease transmission parameters, is robust to noise and to small data sets, and runs quickly due to its mathematical simplicity. Using data from historic and ongoing epidemics, we present the model. We also provide modeling considerations that justify this approach and discuss its limitations. In the absence of other information or in conjunction with other models, EpiGro may be useful to public health responders. (C) 2016 The Authors. Published by Elsevier B.V.

Introduction Chikungunya virus (CHIKV) is an alphavirus in the family Togaviridae. Since 2005 the virus has caused a major epidemic of disease in humans, ranging from Central Africa, South-East Asia, Caribbean and more recently the Americas. The virus is spread by mosquitoes, most notably Aedes aegypti and Ae. albopictus. CHIKV causes an acute disease in humans, which is characterised by a rapid onset of high fever, rash, myalgia and arthralgia. The symptoms typically resolve within a week. Remarkably, up to a third of patients who recover from acute chikungunya develop chronic arthritis/arthralgia, which may last for months or years and has a large negative impact on the quality of life. The mechanism by which this occurs is not yet fully understood. CHIKV can infect human monocytes, and macrophages positive for CHIKV antigen have been observed in joint tissue from patients recovered from acute CHIKV infection but with chronic arthritis. Furthermore, it has been demonstrated that macrophages can be infected with CHIKV in vitro by a mechanism involving apoptotic debris from CHIKV-infected cells. Hypothesis and aims Infection of monocytes and macrophages with CHIKV contributes to clinical disease and virus persistence in vivo. The aim of this project was to investigate the mechanism by which alphaviruses infect macrophages in vitro, and to generate a CHIKV which is unable to replicate in monocytes and macrophages in vitro, and to study its pathogenicity in vivo. Materials and methods HeLa cells were infected with Semliki Forest virus (SFV), an alphavirus closely related to CHIKV, or SFV replicon particles (SFV VRP). Following cell death, whole cell supernatant or clarified cell supernatant from SFV- and SFV VRP-infected cells was passaged onto human monocyte-derived macrophages (MDMs). These cells were observed microscopically for expression of the fluorescent marker encoded by the SFV. Virus and VRP-infected apoptotic debris were inspected for the presence of alphavirus replication complexes by electron microscopy. Subsequently, a recognition element (RE) for a haematopoietic-specific miRNA (miR-142-3P) was incorporated into the genome of SFV (proof-of-concept) and CHIKV to investigate if blocking virus replication in cells of the mononuclear phagocyte system altered virus kinetics in vitro. The replication of the modified viruses was investigated in macrophage/monocyte cell lines Thp-1 and IC-21, and in HEK 293 cells modified to express miR-142-3P under the control of an inducible tetracycline promoter. Modified viruses were tested in animal models of disease (mouse for SFV and non-human primate for CHIKV) to investigate the pathogenicity of these viruses in vivo. Results The presence of apoptotic debris from SFV-infected cells was required to infect MDMs with SFV. The presence or absence of infectious virus particles in the apoptotic debris did not affect the infection rate. Intact alphavirus replication complexes were found within the apoptotic debris. MiR-142-3P RE was successfully incorporated into the genome of both SFV and CHIKV. RE-virus replication in all cells expressing miR-142-3P was reduced by 90-99% when compared to control viruses. RE-virus replication was not affected in cells which did not express miR- 142-3P. In interferon-α/β receptor knockout mice, RE-SFV generated viraemia comparable to the control virus, but could not infect efficiently the population of macrophages resident in the marginal zone of the spleen. RE-CHIKV was found to be genetically stable in vitro following multiple passages on BHK-21 cells in the absence of a selective pressure from miR-142-3P. RE-CHIKV was inoculated into two cynomolgus macaques. The data from this experiment are not yet available. Conclusion SFV was shown to infect MDM via apoptotic debris containing intact alphavirus replication complexes, which were the most likely infectious agent. SFV and CHIKV unable to replicate in haematopoietic cells in vitro were successfully engineered. The pathogenicity of modified SFV and CHIKV was investigated in vivo.

Viral infections are constantly increasing and impose a large threat to the public health. Alphaviruses are responsible for several animal and human diseases and have a large medical importance with few treatments available today. Alphaviruses are small, spherical single stranded RNA viruses, and are most often transmitted by mosquito vectors. Alphaviruses contains a domain of nonstructural proteins that compose the replication machinery. The domain is crucial for viral replication to occur and is therefore an interesting target for antiviral therapy. With the focus on Chikungunya and Semliki Forest Virus this work investigates the events in the cells on molecular level during infections. To do this a panel of Camelid derived single domain antibodies are developed to target the nonstructural proteins of Chikungunya and Semliki Forest Virus. Binding of the produced nanobodies to the viral proteins was investigated by biochemical methods including immunoprecipitations, western blot, and ELISA. Cell lines that express nsP-specific nanobodies in the cytosol were employed for infection- and plaque assays with Semliki Forest Virus in order to determine the antiviral potential of the new nanobodies. Three of the nanobodies proved to bind two different nonstructural proteins of the viruses, providing opportunities for further investigations and a possible use of these nanobodies to identify viral vulnerabilities that could be exploited for antiviral intervention.

abstract: Antibodies are naturally occurring proteins that protect a host during infection through direct neutralization and/or recruitment of the innate immune system. Unfortunately, in some infections, antibodies present unique hurdles that must be overcome for a safer and more efficacious antibody-based therapeutic (e.g., antibody dependent viral enhancement (ADE) and inflammatory pathology). This dissertation describes the utilization of plant expression systems to produce N-glycan specific antibody-based therapeutics for Dengue Virus (DENV) and Chikungunya Virus (CHIKV). The Fc region of an antibody interacts with Fcγ Receptors (FcγRs) on immune cells and components of the innate immune system. Each class of immune cells has a distinct action of neutralization (e.g., antibody dependent cell-mediated cytotoxicity (ADCC) and antibody dependent cell-mediated phagocytosis (ADCP)). Therefore, structural alteration of the Fc region results in novel immune pathways of protection. One approach is to modulate the N-glycosylation in the Fc region of the antibody. Of scientific significance, is the plant’s capacity to express human antibodies with homogenous plant and humanized N-glycosylation (WT and GnGn, respectively). This allows to study how specific glycovariants interact with other components of the immune system to clear an infection, producing a tailor-made antibody for distinct diseases. In the first section, plant-produced glycovariants were explored for reduced interactions with specific FcγRs for the overall reduction in ADE for DENV infections. The results demonstrate a reduction in ADE of our plant-produced monoclonal antibodies in in vitro experiments, which led to a greater survival in vivo of immunodeficient mice challenged with lethal doses of DENV and a sub-lethal dose of DENV in ADE conditions. In the second section, plant-produced glycovariants were explored for increased interaction with specific FcγRs to improve ADCC in the treatment of the highly inflammatory CHIKV. The results demonstrate an increase ADCC activity in in vitro experiments and a reduction in CHIKV-associated inflammation in in vivo mouse models. Overall, the significance of this dissertation is that it can provide a treatment for DENV and CHIKV; but equally importantly, give insight to the role of N-glycosylation in antibody effector functions, which has a broader implication for therapeutic development for other viral infections. / Dissertation/Thesis / Doctoral Dissertation Molecular and Cellular Biology 2019

Le virus chikungunya (CHIKV), transmis par les moustiques Aedes aegypti et Aedes albopictus, constitue un problème majeur de santé publique. Depuis 2004, des épidémies de CHIKV ont été rapportées en Afrique, en Asie, dans les îles de l'Océan Indien, et en Europe. Seule l'Amérique semblait épargnée malgré la présence de fortes densités de moustiques vecteurs et de multiples importations du virus dans le continent par des voyageurs de retour de pays où le virus circulait. Nous avons abordé dans cette thèse le risque d'émergence du CHIKV en Amérique à partir d'une évaluation de la compétence vectorielle de 35 populations d'Ae. aegypti et Ae. albopictus locaux avec différentes souches de CHIKV. Ces populations sont compétentes vis-à-vis du CHIKV avec un rôle des glandes salivaires comme "filtre" de la transmission. De plus, le génotypage des Ae. albopictus d'Amérique par microsatellites a permis d'identifier un cluster génétique de populations se caractérisant par une faible transmission des souches de CHIKV de génotype Est-Centre-Sud-africain. En octobre 2013, des souches asiatiques de CHIKV ont été signalées dans la Caraïbe. Nous avons alors évalué la réceptivité de 11 populations d'Ae. aegypti et Ae. albopictus d'Amérique vis-à-vis de CHIKV de génotype asiatique et avons mis en évidence que les deux espèces étaient compétents pour assurer la diffusion du virus sur le continent. On note aussi qu'Ae. albopictus peut faciliter la propagation du CHIKV vers l'Europe. Néanmoins, la compétence vectorielle d'Ae. albopictus de France vis-à-vis de CHIKV asiatique est affectée négativement par des températures plus basses que celles habituellement observées dans les pays tropicaux. / Chikungunya virus (CHIKV), transmitted mainly by the mosquitoes Aedes aegypti and Aedes albopictus, is a major public health problem. Since 2004, CHIKV epidemics have been reported in Africa, Asia, the Indian Ocean Islands, and Europe. Only the Americas seemed spared despite high densities of mosquitoes and multiple introductions of the virus to the continent by travelers returning from countries where CHIKV was circulating. We have assessed the risk of CHIKV emergence in the Americas by evaluating the vector competence of 35 local populations of Ae. aegypti and Ae. albopictus infected with different strains of CHIKV. These populations were shown to be susceptible to CHIKV infection, highlighting the predominant role of salivary glands as a "filter" of transmission. Genotyping of Ae. albopictus from the Americas using microsatellites allowed the identification of a genetic cluster of populations characterized by a low transmission of CHIKV strains of the East-Central-South-African genotype. In October 2013, Asian strains of CHIKV began circulating in the Caribbean. Thus, we evaluated the susceptibility of 11 populations of Ae. aegypti and Ae. albopictus to the Asian CHIKV genotype and showed that the two species were sufficiently competent to ensure dissemination of the virus throughout the continent. Furthermore, we showed that Ae. albopictus was likely to facilitate the spread of CHIKV to Europe. However, the vector competence of French Ae. albopictus to the Asian CHIKV genotype was negatively affected by temperatures lower than those usually found in tropical countries.

Background Arboviral diseases are one of the most common causes of acute febrile illness (AFI) and a significant health problem in South America. In Peru, laboratory etiologic identification of these infections occurs in less than 50% of cases, leading to underdiagnoses of important emerging arboviruses. Aim To assess the prevalence of the Dengue (DENV), Oropouche (OROV), Chikungunya (CHIKV), Mayaro (MAYV) and Zika (ZIKV) viruses in patients with acute febrile illness from Puerto Maldonado (Peru). Methodology Serum samples were obtained from patients with AFI during January 2016 to March 2016. A total of 139 specimens were analyzed for the presence of DENV, OROV, CHIKV, MAYV, and ZIKV using polymerase chain reaction (PCR). Results CHIKV in 9.4% and OROV in 8.6% were the most prevalent arboviruses, followed by DENV and ZIKV, with a prevalence of 6.5% and 5%, respectively. Among all patients, the most common symptoms accompanying fever were headaches 79.9%, muscle pain 65.5% and joint pain 63.3%. Conclusions During this short 3-month period, 4 arboviruses were detected by PCR, CHIKV and OROV being the most common arboviruses in Puerto Maldonado (Peru). Thus, it is crucial to include OROV detection in the national health surveillance. Furthermore, the etiologic clinical diagnosis of arboviral infections is not possible due to the low specificity of symptoms; therefore an increase of cases confirmed by molecular diagnostic methods will enhance arboviral surveillance in Peru.

Chikungunya virus (CHIKV) is classified as an alphavirus in the Togaviridae family. This virus is known to rely on Aedes arthropod vectors for its dissemination. Human infection is characterized by rash, high fever, and severe chronic polyarthritis that can last for years. Recently, efforts in developing animal models have been made in an attempt to better understand CHIKV pathogenesis. CHIKV infection starts with a 7 to 10 day long febrile acute phase, in which most of the symptoms occur (rash, fever, and incapacitating pain in joints and muscle). Once the immune system clears most of the viral infection, a chronic phase starts in as many as 70% of the infected patients. Long term virus-related polyarthralgia is the hallmark of the CHIKV chronic phase. It is believed that CHIKV-infected macrophages infiltrate the joints during the acute phase, and CHIKV infects joint tissue and persists in it. Research into the effects of CHIKV infection in human and murine macrophages revealed that CHIKV-infected human macrophages produce high amounts of virions as well as induce the production of pro-inflammatory cytokines and monocyte recruiting chemokines. This contrasts with murine macrophage infection where low quantities of the virus were detected as well as lower production of pro-inflammatory cytokines. This may contribute to the lack of polyarthritis in murine animal models. Current literature suggests that CHIKV’s viral proteins bind and interact with human host cell machinery promoting viral replication more efficiently in humans than in mice. CHIKV-related neuropathology is not the most common outcome of the disease. However, recent outbreaks suggest that this pathology is becoming more prevalent, affecting as many as 30% of confirmed patients. The role of adaptive and innate immunity in CHIKV disease amelioration has been extensively, yet separately, explored. A RAG2-/-γc-/- Balb/c mouse model was used to study the role of these immune pathways and their associated immune cells in CHIKV infection. The mice in this study developed local arthritis at the site of inoculation as well as showed signs of viral invasion in the brain. This study added to the hypothesis that both innate and adaptive immune responses are necessary to ameliorate the disease and that the lack of adequately matured lymphocytes and STAT6-activation deficient macrophages may result in more severe pathologies.

Mosquito-borne diseases remain a significant burden on global public health. Maintenance of mosquito-borne viruses in nature requires a biological transmission cycle that involves alternating virus replication in a susceptible vertebrate and mosquito host. Although infection of the vertebrate host is acute and often associated with disease, continual transmission of these viruses in nature depends on the establishment of a persistent, nonpathogenic infection in the mosquito vector. It is well known that invertebrates rely on small RNA pathways as an adaptive antiviral defense. The canonical antiviral response in these organisms involves dicer enzymes that cleave viral double-stranded RNA replicative intermediates (RIs) into small interfering RNAs (siRNAs; ~21-24 nucleotides). One strand of the siRNA duplex guides the targeting and destruction of complementary viral RNAs when loaded and retained in a multi-protein complex called the RNA-induced silencing complex. Here, we show that mosquito vectors mount a redundant double defense against virus infection mediated by two different small RNA pathways. Specifically, we demonstrate that in addition to a canonical antiviral response mediated by siRNAs, virus infection of the mosquito soma also triggers an antiviral immune pathway directed by ping-pong-dependent PIWI-interacting RNAs (piRNAs; ~24-30 nucleotides). The complexity of mosquito antiviral immunity has important implications for understanding how viruses both induce and modulate RNA-silencing responses in mosquito vectors. In mammals, viral RIs induce a range of relatively nonspecific antiviral responses. However, it remains unclear if viral RIs also trigger RNA silencing in mammals. Mosquito-borne viruses represent an ideal model for addressing this question as their transmission cycles involve alternating replication in mammalian and invertebrate hosts. Although we report identifying a subset of virus-derived small RNAs that appear to be products of RNA silencing in two mammalian cell lines infected with the mosquito-borne chikungunya virus (CHIKV), our studies suggest these small RNAs have little biological relevance in combating virus infections. Thus, while the accumulation of virus-derived siRNAs is essential to the survival of mosquitoes infected with CHIKV, they appear to have little functional significance in mammalian antiviral immunity. / Ph. D.

Chikungunya is a mosquito-transmitted disease caused by Chikungunya virus (CHIKV). Symptoms of Chikungunya include debilitating joint pain and swelling, fever and rash. CHIKV was first discovered in 1953 in Tanzania, and has since caused periodic outbreaks of disease. The virus reemerged recently in 2004 and has since spread around the world affecting more than 3 million people. The different strains of CHIKV have been grouped into three phylogenetic clades: West African, Asian and East/Central/South African (ECSA). There are no FDA approved medicines or vaccines used to treat or prevent CHIKV infection. The antiviral drug, T-705 (commercially known as Favipiravir), has recently been shown to have activity against CHIKV. T-705 has already been approved in Japan for the treatment of influenza and is currently going through clinical trials in the US. Since there may be phenotypic differences between the clades of CHIKV, it is important to first characterize distinctions between the strains and determine the susceptibility of these strains to treatment. To do this, we obtained two different CHIKV strains from each of the three phylogenetic groups. These CHIKV strains displayed differences in their ability to replicate in cell culture and exhibited only slight differences in susceptibility to T-705 treatment. However, more profound differences were observed in mouse models where differences in disease severity and response to T-705 treatment were observed.

Aedes albopictus et Aedes aegypti sont des moustiques vecteurs d’arbovirus tels que le virus de la dengue et le virus du chikungunya. En plus des virus transmis, les moustiques hébergent également des bactéries dont certaines affectent la biologie des hôtes. Par exemple, la bactérie Wolbachia infecte naturellement Aedes albopictus. Comme chez la plupart des insectes, cette bactérie est un parasite qui manipule la reproduction du moustique et peut également interagir avec certains pathogènes, modifiant ainsi la transmission du pathogène par le moustique hôte. Hors Wolbachia, peu d’études ont été consacrées à l’étude des populations bactériennes hébergées par les moustiques du genre Aedes et aux interactions entre ces populations bactériennes et les arbovirus transmis. Dans ce contexte, le travail de cette thèse a consisté à caractériser la diversité des communautés bactériennes des moustiques du genre Aedes et à explorer l’interférence possible entre le compartiment bactérien et le virus chikungunya. L’utilisation de techniques telles que les isolements bactériens, l’amplification par PCR, la DGGE et l’hybridation in situ ont permis de détecter et localiser certaines bactéries présentes chez des populations naturelles et de laboratoires d’Aedes. Ces populations appartiennent aux Alpha, Beta et Gammaprotéobactéries ainsi qu’aux Firmicutes. L’étude de la dynamique des communautés bactériennes symbiotiques et de l’infection par le virus chikungunya chez Aedes albopictus par PCR quantitative et puces taxonomiques a révélé l’existence d’interactions entre les différents partenaires de ce système vectoriel / Aedes albopictus and Aedes aegypti transmit a large number of arboviruses, including dengue and chikungunya. In addition to viruses, mosquitoes harbour other symbionts that are able to affect its biology. For instance, the bacterium Wolbachia infects naturally Aedes albopictus. As for many insects, this bacterium is an obligate parasite that manipulates the host reproduction and can also interact with pathogens, modifying the transmission of the pathogens by the mosquitoes. Except Wolbachia, little is known about the bacteria associated with Aedes mosquitoes. First, we detected and localized bacteria in field-caught and laboratory populations of Aedes, using culture and non-culture methods including PCR, DGGE and in situ hybridization. The bacterial populations belonged to Alpha, Beta and Gammaproteobacteria as well as to Firmicutes. Then, the effects of chikungunya infection on Wolbachia and total bacterial community were measured using quantitative PCR and taxonomic microarrays. Results showed interactions between the different partners in this vectorial system