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Klimawandel, Änderungen der Landnutzung und Habitatzerstörung sowie die Globalisierung tragen zu einer zunehmenden Ausbreitung von bekannten und noch unbekannten Viren bei, die eine Gefahr für Mensch und Tier darstellen können. Um potenziell gefährliche Viren frühzeitig zu entdecken, kann das in dieser Arbeit vorgestellte Protokoll für einen pan-viralen DNA-Microarray-gestützten (PVM) Virusnachweis verwendet werden, der optional mit einer Hochdurchsatzsequenzierung gekoppelt werden kann.
Für die Etablierung des PVM-Protokolls wurde die Leistungsfähigkeit von drei Probenbearbeitungs- und Datenauswertungsmethoden beim Nachweis von zwei Modellviren, einem DNA-Virus und einem RNA-Virus, verglichen. Für die Kopplung mit dem PVM wurden verschiedene Systeme für die Hochdurchsatzsequenzierung verwendet.
Das Ziel der Arbeit war die Etablierung eines optimierten PVM-Protokolls für einen robusten, breiten Virusnachweis, welcher einzeln oder in Kombination mit einer Hochdurchsatzsequenzierung als Teil einer mehrstufigen Analysepipeline verwendet werden kann.
Beim Nachweis beider Modellviren wies die Library-basierte Probenbearbeitungs- und Datenauswertungsmethode Limma die höchste Sensitivität auf. In der darauf folgenden Validierung konnten alle Viren, unabhängig von ihrer Genomorganisation und Komplexität der Probenmaterialien, korrekt identifiziert werden. In zwei publizierten Studien konnte der Nachweis der zum Zeitpunkt der Untersuchung noch unbekannten BBLV und SqAdV-1 gezeigt werden. Durch die Rückgewinnung von Virus-spezifischen Nukleinsäuren vom PVM und der anschließenden Sequenzierung
mittels Hochdurchsatzsequenzierung konnte das SqAdV-1 im Rahmen einer mehrstufigen Analysepipeline vollständig identifiziert, annotiert und taxonomisch eingeordnet werden. Durch die Kombination von PVM und Hochdurchsatzsequenzierung wurden für sechs Viren eine Virus-spezifische Anreicherung und ein damit verbundener Gewinn an Sequenzinformation erreicht. Die Library-basierte Probenbearbeitung mit Limma erlaubte einen robusten und sensitiven Virusnachweis; deshalb wurden beide Methoden für das PVM-Protokoll ausgewählt. Die Fähigkeit des hier etablierten PVM-Protokolls, Viren unabhängig von der Genomorganisation und in komplexen Probenmaterialien zu identifizieren, zeigt dessen Gleichwertigkeit mit bereits etablierten PVM-Systemen. Die Verwendung des PVM-Protokolls in einer mehrstufigen Analysepipeline erlaubt auch die Identifikation von bisher unbekannten Viren. Der durch die Kombination mit einer Hochdurchsatzsequenzierung erreichte Gewinn an Sequenzinformation ermöglicht eine Identifizierung und detailliertere Charakterisierung von Viren.
Der PVM stellt einzeln und in Verbindung mit einem Hochdurchsatzsequenzierungs- System ein wertvolles Werkzeug für die Virusdiagnostik dar, dessen Anwendung den Zeitaufwand für die Virusidentifizierung deutlich reduzieren kann.
The order of bats (Chiroptera) account for ~20% of all mammalian species and attracted immense global attention due to their identification as important viral reservoir. Bats can harbour a plethora of high-impact zoonotic viruses, such as filoviruses, lyssaviruses, and coronaviruses without displaying clinical signs of disease themselves. Given this striking diversity of the bat virome, their ability of self-powered flight, and global distribution, understanding chiropteran immunity is essential to facilitate assessment of future spillover events and risks.
However, scarcity of bat-specific or cross-reactive tools and standardized model systems impede progress until today. Furthermore, the richness of species led to generation of isolated datasets, hampering data interpretation and identification of general immune mechanisms, applicable for various chiropteran suborders/families. The key to unlocking bat immunity are coordinated research approaches that comprehensively define immunity in several species. In this work, an in-depth study of innate and adaptive immune mechanisms in the fructivorous Egyptian Rousette bat (Rousettus aegyptiacus, ERB) is presented.
Detailed stability analyses identified EEF1A1 as superior reference gene to ACTB, and GAPDH, which rendered unstable upon temperature increase or presence of type-I-IFN. Since the body core temperatures of pteropid bats reach from 35°C to 41°C and it has been postulated that bats display constitutive expression of IFNs, a suitable reference gene has to be stable under these physiologically relevant conditions. To study cellular innate immunity in detail, cell lines from the nasal epithelium, the olfactory compartment and the cerebrum were generated. To include immune responses of epithelia cells, essential for immunity at sites of primary viral infection, primary epithelia cells from the nasal epithelium, trachea, lung and small intestine were generated. Cellular identities were determined by comprehensive analyses of transcripts and proteins expressed by each cell line. The capacity of each cell line to produce type-I- and III-IFNs was assessed at 37°C and 40°C upon stimulation with viral mimetics. This revealed cell type-dependent differences is the capability to express IFNs upon stimulation. Furthermore, the constitutive expression of type-I- and III-IFNs was significantly elevated in higher temperatures and quantified at mRNA copy levels. To characterize ERB innate immunity upon infection with high-impact zoonotic viruses, cells from the nasal epithelium, the olfactory system, and the brain were infected with several lyssaviruses. This revealed striking differences in susceptibility: cells from the nasal epithelium rendered least whereas cells from the olfactory epithelium rendered most susceptible to viral infection and replication. Additionally, due to a lack of IFN expression in infected cells, it could be shown that LBV possibly possesses advanced strategies to ensure successful replication in ERB cells. Since the current SARS-CoV-2 pandemic put bats even further in the focus of zoonotic research, primary epithelial cells and animals were infected with this virus to monitor ERB-specific immune transcripts in cells and tissues. These studies revealed a notably early IFNG expression in the respiratory tract of infected individuals.
To understand immunomaturation in bats, the immune cell landscape in periphery and various tissue in adult and juvenile ERB was analyzed by flow cytometry and scRNA-seq, revealing intriguing, age-dependent variations in the abundance of granulocytes and lymphocytes. Flow cytometry revealed a significantly higher number of granulocytes in adults, as well as higher numbers of B cells in juveniles. scRNA-seq allowed detailed identification of different leukocyte subsets, uncovering the presence of highly-abundant NKT-like cells and a unique PLAC8 expressing B cell population. A functional characterization of phagocytic cells and lymphocytes derived from adult and juvenile ERB revealed no significant differences in cellular functionality.
In conclusion, the presented work demonstrated suitability of all established ERB cell lines to study bat immunity in vitro, which led to striking findings regarding IFN expression at steady state, or upon stimulation or viral infection. In addition, established qRT-PCR protocols allowed definition of constitutive and temperature-dependent elevation of IFN expression magnitudes, as well as insights into expression of immune-related transcripts in SARS-CoV-2 infected ERB. Finally, based on optimized scRNA-seq technologies and flow cytometry, frequencies and absolute cell counts could be determined in ERB of different ages, revealing e.g. age-dependent variations in leukocyte profile compositions.
Midges are small mosquitoes that can transmit pathogens to susceptible hosts through their blood-sucking act. They are known as biological vectors that can transmit the bluetongue virus (BTV) and the Schmallenberg virus (SBV) to ruminants, among others. Various vector control measures can be used to curtail the spread of the virus during an epidemic. However, for effective vector measures, it is essential to have profound knowledge of the role of biting midges as vectors, as well as their biology and phenology. For several years, midges were not in the focus of research and there are still considerable gaps in knowledge. Therefore, the present work examines various aspects of biting midges of the genus Culicoides, whose function as vectors of the Schmallenberg virus was already proven at the beginning of the project.
The aim of the first part of this work was to determine the percentage of infected midges in various German areas in order to determine the influence of Culicoides midges within the virus epidemic. For this purpose, samples, collected during 2011 and 2012 as part of monitoring projects, were analysed. Additionally, in early 2013, various farms in southern and eastern regions of Germany, where SBV was considered to be largely absent, were equipped with UV traps. The small number of virus-positive samples did not allow a more precise assessment of the viral spread in culicoid midges. Instead, it revealed the importance to conduct targeted samplings of its vectors during an acute outbreak. Additionally, the presented results and statements made by several animal owners, gave reason to believe, that SBV must have affected the southern and eastern parts of Germany earlier than actually assumed. This would consequently have led to an increased immunity in host animals, which provides a reasonable explanation for the low positive values and is in agrement with the statements made by various farmers.
The second part of this work identifies the conditions and surrounding factors under which acute SBV diseases emerged in ruminants in the cold winter months of 2012/2013. After the diagnosis of several acute SBV infections of sheep in a sheep pen in Mecklenburg-Western Pomerania, culicoid midge activity could be proven. This demonstrates that, suitable conditions for its vectors given, an infection of SBV can also take place during wintertime. A more detailed analysis of the surrounding conditions revealed, that the outdoor temperatures during infection were consistently at values of at least 5-9 ° C for several consecutive days, which enabled the flight and blood-sucking activity of the midges within
the shelter.
Midge activity during wintertime represents a crucial component in understanding how the virus can outlast the cold season. A constant midge presence could lead to a low but permanent infection rate throughout the cold months, enabling a recurrence of the pathogen the following year. Instead, a longer vector-free timeperiod would point to other mechanisms that allow the virus to re-occur in Germany on a yearly basis. Thus, the acute cases of SBV infections in sheep rose the question of critical threshold temperatures, representing the beginning of midge activity. The investigation of several stables sheltering cattle, horse or sheep addressed potential differences between indoor and outdoor activity and whether the type of host animal has an influence on the beginning of the flight. In the third part of this work, a long vector-free period and several differences in the onset of midge activity between different types of host animals could be detected. It could also be illustrated that the progression of the flight began differently depending on the present type of host animal/type of stable. For all cattle stables and the sheep barn the first midge activity was measured indoors, whereas for horses, culicoid midges were found to become active either at the same time or almost simultaneously inside and outside the animal shelters. This suggests that the horse stables do not represent good breeding sites for midges, which might be attributed to husbandry practices. In addition, it was possible to determine specific threshold temperatures for the different types of host animals and for various midge species. Altogether, the late beginning of flight, measured at the beginning of March, was surprising. This raises more questions of alternative mechanisms enabling the virus to outlast the winter months. The documentation of species-specific threshold temperatures can be a useful tool f.i. within automated large stables to keep indoor temperatures under the threshold value in order to postpone the onset of culicoid activity of various vector species. This may help to prevent virus transmissions during winter or to evoke a delay in spring, making it more difficult for the virus to overwinter.
To be able to start instant defense measures during an ongoing virus epidemic, which is transmitted by Culicoides midges, reducing the ground-living midge larvae offers a promising option during the warm season. For targeted vector control measures, it is important to know the breeding sites of culicoid midge species. Therefore, four agriculturally used biotopes were sampled and compared to four biotopes of a forest-dominated area. The results clearly show that meadows per se are not suitable breeding habitats for Culicoides
spp. Only the influence of livestock animals induces their potential as developmental sites. The various biotopes of the forest-dominated region were less subject to anthropogenic influences. Although fewer individual midges were found here, it displayed a higher biodiversity than the agricultural habitats. These results demonstrate once more the potential of forests in regards to the preservation of biodiversity. In Particular, the alder on fen site revealed most midge species and also the highest number of collected specimens among the studied biotopes. That illustrates the high impact of this specific humid type of habitat in respect to species diversity and the need of its perpetuation.
As part of this work, new breeding sites for a variety of culicoid species were identified and assigned to the usually rather short profiles of known Culicoides species. For one part, previous observations of chosen substrates could be consolidated. Furthermore, new breeding substrates were identified. Additionally, information of abiotic factors such as ph-value, soil moisture or organic compound of all sampled breeding substrates obtained from a soil analysis, extended the knowledge about the species-specific choice of breeding habitats and their characteristical traits. The additional knowledge about potential breeding substrates and their soil factors might be useful for future epidemiological modelling approaches. It can also raise the effectiveness and accuracy of targeted vector control measurements during an epidemic outbreak. Therefore, it may indirectly contribute to the preservation of endangered rare species. However, there is still an enormous need for more research before this goal can be fully achieved.
Untersuchung der zytotoxischen Aktivität unterschiedlich virulenter NDV-Stämme auf Krebszelllinien
(2009)
In dieser Arbeit wurde der Zusammenhang zwischen NDV-Stamm und onkolytischer Wirkung auf Tumorzellen untersucht. Die Analyse der onkolytischen Eigenschaft ausgewählter NDV zeigte, dass die Wirkung auf die Tumorzellen von der Art des NDV abhängt. Desweiteren erfolgte die Herstellung und Charakterisierung von rekombinanten Viren mit substituierten Oberflächenproteinen.
Rabies virus (RABV) is an ancient, highly neurotropic rhabdovirus that causes lethal encephalitis. Most RABV pathogenesis determinants have been identified with laboratory-adapted or attenuated RABVs, but details of natural RABV pathogenesis and attenuation mechanisms are still poorly understood. To provide a deeper insight in the cellular mechanism of pathogenies of field RABV, this work was performed to assess virus strain specific differences in intra-neuronal virus transport, to identify cell culture adaptive mutations in recombinant field viruses and to explore shRNA-expressing RABVs as research tools for targeted host manipulation in infected cells.
Comparison of chimeric RABVs with glycoprotein (G) ecto-domains of different lyssaviruses, together with field RABVs from dog and fox in dorsal root ganglion (DRG) neurons revealed no detectable differences in the axonal accumulation of the viruses. This indicates that previously described G-dependent transport of newly formed RABV in axons can occur both in laboratory-adapted and field RABV. Moreover, partial overlap of nucleoprotein (N) and G protein particles in field virus infected DRG axons supported the hypothesis of the “separate model” for anterograde RABV transport.
Serial passages of recombinant dog and fox field clones in different cell lines led to the identification of general (D266N) and cell line specific (K444N) adaptive mutations in the G ecto-domain of both viruses. In BHK cells, synergistic effects of D226N, K444N and A417T on field dog virus G protein surface localization led to the loss of endoplasmic reticulum (ER) retention of G and increased virus titers in the supernatant, indicating that limited virus release by ER retention is a major bottleneck in cell culture adaptation. In addition, selection of mutations within the C-terminus of the RABV phosphoprotein (P) (R293H and R293C in fox and dog viruses, respectively) led to the hypothesis of altered binding affinities to nucleoprotein and RNP complexes. Identification of the above mentioned amino acid substitutions together with alterations in a suboptimal transcription stop signal in the P/M gene border indicated that adaptation to cell culture replication occurs on both levels, RNA transcription/replication and virus release.
To evaluate the possibility of an expression of a functional microRNA-adapted short-hairpin RNAs (miR-shRNA) expressing RABV, recombinant RABVs encoding miR-shRNAs against cellular Dynein Light Chain 1 (DYNLL1) and Acidic Nuclear Phosphoprotein 32 family member B (ANP32B) were generated. In spite of cytoplasmic transcription of the respective mRNAs, downregulation of DYNLL1 and ANP32B mRNA and respective protein levels in infected cells revealed correct processing to functional shRNAs. Specific downregulation of the cellular genes at 2, 3 and 4 days post infection further demonstrated feasibility of the approach in standard cell lines. However, it remained open whether miR-shRNA expressing RABV can be used to study neuro-infection in vivo. Since first attempts in primary rat neuron cultures failed, it has to be clarified in further experiments whether this strategy can be used in mature, non-dividing neurons or whether breakdown of the nucleus in the course of cell division is a requirement for the processing of cytoplasmically expressed miR-RNA by nuclear RNases.
By providing novel insights in axonal RABV transport and cell culture adaptive mutations this work extends the current understanding of RABV pathogenesis in natural and non-natural cell environments. Moreover, it provides a basis for further pathogenicity studies in which the impact of cell culture adaptation through increased virus release on RABV virulence can be investigated. With successful expression of functional miR-shRNAs from RABV vectors, this work also provides a tool for RABV gene targeting in infected cell lines and thus may contribute to the further investigation of RABV-host-cell-interactions.