During tick-borne encephalitis virus (TBEV) infection, the virus also induces the production of pro-inflammatory cytokines and chemokines, triggering an immune response. The immune response aims to control viral replication and clear the infection. However, in some cases, an excessive or dysregulated immune response can contribute to the pathogenesis of TBE. It can lead to inflammation and tissue damage within the central nervous system, where the virus primarily targets, resulting in encephalitis.

TBEV can cross the blood-brain barrier and directly infect neurons, causing neuronal injury and dysfunction. The virus induces neuronal apoptosis and disrupts neuronal signalling pathways, contributing to the neurological symptoms observed in TBE. The severity of neurological manifestations can vary, ranging from mild meningitis to severe encephalitis, with potential long-term neurological sequelae. In addition to the direct effects on neuronal cells, TBEV can also induce endothelial cell dysfunction, leading to vascular leakage and disruption of the blood-brain barrier. This allows immune cells and inflammatory mediators to enter the central nervous system, exacerbating the inflammatory response and contributing to the pathogenesis of TBE.

However, detailed mechanisms at the molecular level are still missing. We are therefore trying to address these issues to elucidate differences in viral infection patterns and host cell responses. Understanding these molecular mechanisms is vital for the development of effective diagnostic tools, treatments, and preventive strategies against TBEV and other flaviviruses.

The development and testing of new antivirals and vaccines for flaviviruses, including TBEV, are crucial for controlling the spread of these viral infections and preventing associated diseases.

Antiviral drug development for flaviviruses focuses on targeting specific steps of the viral replication cycle. One promising approach is the inhibition of viral enzymes involved in viral RNA replication. For example, the viral RNA-dependent RNA polymerase (NS5) is a prime target for drug development. Inhibitors that target viral replication, such as nucleoside analogues and non-nucleoside inhibitors, have shown effectiveness against flaviviruses in preclinical and early clinical studies. In our lab, we have made an important contribution to this field, having tested thousands of these compounds mainly against TBEV. And more importantly, we have identified several highly potent compounds in vitro and in vivo. Explanation of molecular mechanisms of viral resistance to nucleoside analogues, including identification of resistance-conferring mutations is also a part of our antiviral research.

Another potential antiviral strategy involves targeting viral entry and fusion. Flavivirus envelope proteins play a crucial role in mediating viral attachment and entry into host cells. Research efforts aim to develop entry inhibitors that block the interaction between viral envelope proteins and cellular receptors and/or inhibitors that destroy viral lipid bilayers. Small molecules, peptides, and neutralizing antibodies are being explored as potential entry inhibitors.

We have screened a library of perylene derivatives, porphyrins and other membrane-targeting agents and described peculiarities in the antiviral activities of these highly interesting compounds, which also block virus replication at the entry stage.

In addition, our studies focus on plant alkaloids that block the process of acidification of endosomes, which is used by many viruses to efficiently initiate viral infection, or on organic ligands that interact with secondary structures (guanine quadruplexes) in viral genomic RNA.

Vaccine development is a crucial approach to preventing flavivirus infections. Vaccines against yellow fever, Japanese encephalitis, and tick-borne encephalitis have already been developed and are in use. These vaccines induce the production of neutralizing antibodies that can effectively prevent viral infection. Together with our collaborators from academia and industry, we are developing and testing different platforms for different viruses. One of our projects is the production of a TBEV vaccine for veterinary medicine.

The development and characterization of therapeutic antibodies have revolutionized the field of medicine by offering targeted and effective treatments for a wide range of diseases. Antibodies are proteins produced by the immune system in response to foreign substances, such as viruses, bacteria, and cancer cells. Therapeutic antibodies are designed to mimic or enhance the natural immune response, providing a powerful tool for combating various diseases.

Our projects focus on the development and characterisation of human antibodies against flaviviruses, but we have also described effective neutralizing antibodies against SARS-CoV-2. We have characterised very promising antibodies against TBEV that are now entering phase I clinical trials. We also plan to turn our attention to a special variant of antibodies from llamas - nanobodies, which have many advantages and potential uses.

Flaviviruses interact with host cells in a complex manner, employing various strategies to establish infection and evade the host immune response. These interactions play a crucial role in the pathogenesis of flavivirus infections. 

Upon infection, flaviviruses enter host cells through receptor-mediated endocytosis. The specific receptors utilized by different flaviviruses vary, but they often involve interactions with cell surface molecules or receptors expressed on immune cells. The binding of the viral envelope proteins to these receptors facilitates viral entry and initiates the infection process.

Once inside the host cell, flaviviruses modulate various cellular processes to support viral replication. They induce extensive rearrangements of host cell membranes, creating specialized compartments called replication complexes. These complexes provide a favourable environment for viral RNA replication, shielding the viral genome from detection by the host immune system.

We are interested in factors from both sides - how viral components (viral proteins, RNA) can influence interactions with the host cell, but also how different cell types or cell populations expressing different markers influence susceptibility to infection, its kinetics and severity at cellular and complex levels.

Seroprevalence studies and accurate diagnostic methods play a vital role in understanding the epidemiology of flavivirus infections and facilitating their diagnosis. Seroprevalence refers to the proportion of individuals within a population who have antibodies against a specific virus. On the other hand, diagnostic tests are essential for detecting and confirming flavivirus infections in suspected cases. 

Seroprevalence studies provide valuable insights into the prevalence and distribution of flavivirus infections within a population. These studies involve analyzing blood samples to determine the presence of specific antibodies against flaviviruses. Serological tests, such as enzyme-linked immunosorbent assays (ELISAs) or virus neutralization assays, are commonly used to detect and measure flavivirus-specific antibodies in serum samples. Seroprevalence data helps in assessing the burden of past and current infections, identifying high-risk regions, and understanding the dynamics of transmission.

In recent years, we have carried out a comprehensive sero-epidemiology study of TBEV in small ruminants in the Czech Republic. We have also mapped the introduction of the Usutu virus into the Czech Republic in mosquitoes and blackbirds.

Diagnostic methods for flavivirus infections are crucial for accurate and timely diagnosis allowing appropriate patient management and disease surveillance. Different diagnostic techniques are available depending on the stage of infection and the target analytes.

We are looking for novel biomarkers for flavivirus infections (mainly TBEV) that could be used for early diagnosis and help to understand the severity of the disease. At the same time, we are conducting studies on the genetic background of patients with TBE and trying to find the genetic predisposition for severe TBE.