The human organism is colonized by a large number of different viruses. However, very little data are available on the role of viral communities in immunosuppressed patients who undergo transplantation of solid organs or hematopoietic stem cells. In this project, we will characterize the virome of these patients who are at high risk of reactivation of many latent infections and at risk of newly acquired viral infections. The project will focus on anelloviruses and their possible role in the prediction of transplant rejection and graft versus host disease. An understanding the variability and interaction of the anelloviruses with the human immune system can help reveal their role in the immune response after transplantation. The principal investigator Ruth Tachezy and her team have experience in the characterization of clinical samples by next-generation sequencing and virome analysis.

Oncogenic viruses are responsible for about 10% of malignancies worldwide. Progression of these tumours often results in patient death. The development of virus-induced tumours is usually accompanied by stimulation of anti-virus/anti-tumour immunity, but progression of tumours can finally be enabled by immune escape mechanisms. In this study, we will analyse the immune characteristics of human papillomavirus-induced tumours to reveal new therapeutic targets and biomarkers specific for different carcinogenesis pathways (integrated DNA-E6/E7 expression versus episomal DNA-E2/E4/E5 expression). Identification of potential mechanisms of resistance to treatment and predictive biomarkers can contribute to enhancing therapy efficacy. Principal investigator Ruth Tachezy is an expert in the analysis of tumours associated with human papillomaviruses including the detection of viral DNA integration and gene expression.

A rapid spread of multidrug-resistant bacteria leads to difficult-to-treat infections and higher mortality. Thus, to monitor the emergence of new epidemic lineages of nosocomial pathogens and or novel determinants of antimicrobial resistance in healthcare settings is of key importance. Besides bacterial pathogens, viral nosocomial and viral congenital, such as cytomegalovirus or adenovirus, will be studied along with the SARS-CoV-2 surveillance. An understanding of the factors driving the emergence of antimicrobial resistance in these nosocomial pathogens, the dynamics of patient colonization and subsequent infection will permit healthcare professionals to tackle nosocomial pathogens. Comparative studies on the genomic and phenotypic level currently circulating epidemic and non-epidemic lineages enable us to identify markers associated with spread in healthcare environment and/or poor outcome of patients. Principal investigator Pavel Dřevínek is an expert in antimicrobial resistance with a focus on healthcare-associated pathogens and chronic respiratory infections in patients with cystic fibrosis.

The aetiology of many human diseases is multifaceted, with a contribution from microbial exposures, in interaction with other exposome components. The virome comprises not only human and vertebrate viruses, but also a huge mass of bacteriophages whose direct or indirect interactions with the human host are now becoming explored. The project will help elucidate the structure and interactions of the human virome observed longitudinally in the course of several disease states, with special emphasis on diseases of childhood. The virome will be assessed in the context of other exposomic features, and its perturbations will be examined for causality or effects on the disease course. Principal investigator Pavel Dřevínek is an expert in virome, bacteriome and parasitome studies of primarily non-infectious human diseases.

Treatment of chronic hepatitis B with nucleot(s)ide analogues inhibits the formation of new infectious viral particles but does not eliminate stable covalently closed circular DNA (cccDNA) in hepatocytes. Pegylated interferon α (IFN-α) treatment can be considered as an alternative therapy. However, IFN-α monotherapy leads to functional cure in less than 8% of chronically infected people. We will investigate the HBV escape mechanism on the level of microenvironment of HBV-infected hepatocytes, the interplay between promyelocytic leukaemia protein nuclear bodies and HBV in the nucleus, and interactions of HBV core protein with proteins of the host. We propose to study mechanisms of HBV escape from intrinsic and innate immunity for discovery of new anti-viral therapeutic targets. Principal investigator Klára Grantz Šašková focuses on the characterization of viral and cellular protein interaction on structural, biochemical and functional level, with the goal to select new target candidates for therapeutic interventions.

Infections by DNA viruses replicating in nucleus induce enormous changes in the nuclear structures; however, there are many gaps in the understating of virus interactions with the nuclear components. We propose that SMC5/6 complex and PML associated proteins either directly or indirectly modify viral chromatin and thus affect viral genome transcription and/or replication. The interaction of these proteins with virus minichromosomes and their functional significance will be studied on the human BK and murine polyomaviruses. The search for novel cellular partners of the multifunctional viral regulatory protein – LT antigen will be another part of the research. Our study will bring new insights into the comprehension of the nuclear phase of DNA viruses. Principal investigator Sandra Huerfano is an expert in polyomavirus biology with strong background in techniques of molecular biology..

RNA adenosine deaminase ADAR1 is responsible for most of the A-to-I RNA editing events in human cells. ADAR1 is inducible by virus infection; however, its function is poorly understood and, depending on the virus, can be manifested both as antiviral and/or proviral. We will study functional interactions of ADAR1 with RNA viruses using HCV, TOSV and SARS-CoV-2 models. We will employ our newly developed methods of translatome and A-to-I editome analyses to map and evaluate A-to-I edited sites in the viral and cellular RNAs and to decipher a role, which ADAR1 plays in synthesis of viral and host proteins in the course of viral infection. Principal investigator Martin Pospíšek’s expertise includes analysis of transcriptome, translatome and RNA editome, generation and characterization of ADAR1 knock-out cell lines and analysis of translation initiation in viruses.

Poxviruses are important human and animal pathogens and variola virus is ranked among the highest risk bioterrorism and biological warfare agents. Despite the poxviruses were in the forefront of the biological and medical research for many years, our understanding of their biology is incomplete, and only one antiviral drug has been approved for the treatment of smallpox. We discovered that postreplicative poxviral mRNAs are not capped at their 5′ ends. We will study synthesis and translation of these unusual poxviral mRNAs with the aim to answer the long-lasting question how poxviruses can overcome the host cell antiviral mechanisms and usurp the host protein synthesis apparatus for the production of viral proteins. Principal investigator Martin Pospíšek’s expertise includes a broad range of techniques for analysis of viral and cellular transcriptomes, translatomes and proteomes. His team discovered 5′ uncapped mRNAs in poxviruses.

Although phleboviruses have a significant impact on human and animal health and cause serious economic problems, information about their biology and transmission is mostly missing. Predicted or confirmed vectors of most phleboviruses are bloodsucking sand flies (Diptera: Psychodidae). Thanks to a unique collection of sand fly colonies, we will study: i) the susceptibility of various sand fly species to phleboviruses, ii) the various routes of their transmission, iii) the development of different phlebovirus mutants in sand flies and iv) the virus interactions with another important sand fly-borne pathogens, particularly Leishmania. The obtained results would help to predict establishment of new disease foci, as well as to monitor and possibly control the phlebovirus transmission. Principle investigator Petr Volf is the leading expert in biology of phlebotomine sand flies and sand fly-borne pathogens, particularly Leishmania and phleboviruses.

The increasing incidence of antibiotic resistance represents a major clinical challenge and public health concern worldwide. Therefore, the understanding of evolution of resistant bacteria on molecular level is desperately needed. Whole-genome sequencing of bacterial genomes can provide a deep insight into the evolution, routes of the spread, identification of reservoirs, and high-risk population groups. The data can be used to propose a strategy for alternative combating antibiotic resistance. Describing common mobile genetic elements spreading the antibiotic resistance genes and studying their complex structure, plasticity, and plasmid-gene-host interactions will also help us to set up preventive measures for the spread of antibiotic resistance. Principal investigator Jaroslav Hrabák works in molecular epidemiology of multidrug-resistant Gram-negative bacteria since 2005. He is also a member of several international boards focused on antibiotic resistance (e.g., ECDC).

Novel techniques used in microbiological diagnostics, especially mass spectrometry-based and molecular genetic methods revolutionized diagnostics of infectious diseases in the last two decades. Further development of functional assays and proteomic analysis of bacteria, especially their antibiotic resistance, can significantly help in diagnostics of life-threatening diseases to improve patient’s outcome. The use of mass spectrometry in microbiological diagnostics is usually limited to taxonomical identification of microbes and detection of resistance mechanisms. The technology, however, can be used for deep analysis, including precise detection of resistance mechanisms and host/pathogen interaction. During the project, new methods for LC/MS and MALDI-TOF MS will be developed. The methods will further decrease turnaround time required for diagnostics and will positively influence patients’ outcome especially in life-threatening infections. Principal investigator Jaroslav Hrabák is focused on development of rapid methods for microbiological diagnostics, especially using mass spectrometry. He is also an inventor of several patents in the topic.

Proteins are produced by ribosome-catalyzed translation of mRNAs in all domains of life. Translation is also critical in the context of human host-pathogen interaction where the ribosome, as the central molecular machine for genetic information expression, is the subject to numerous regulatory and quality control events and pathological interventions. The strategies adopted by viruses to reprogram translation and co-translational quality control machinery to promote infection are poorly understood. Thus, there is an urgent need for further research in this area to develop effective strategies for combating viral infections. To address this knowledge gap, I propose a research aimed at elucidating the mechanistic details of viral reprogramming of translation and translational control processes using state-of-the-art biochemical and structural techniques. By elucidating the mechanistic details behind viral manipulation of these processes at a molecular level, we can lay the foundation for developing effective strategies against viral infections. Theprincipal investigator Zdeněk Těšina and his team deals with mapping high-fitness-maintaining mutational trajectories of SARS-CoV-2 virus for future variants prediction.