Molecular and clinical virology

Aim and focus

This research program addresses the biology of viral pathogens and virus-host interactions, to enhance our understanding of their molecular biology and pathogenesis and the host’s response to infection. We aim to develop strategies to identify, prevent, or treat infection, in particular the use of vaccines and antiviral drugs. Different viral pathogens are studied, selected for their clinical relevance, their recent (re)emergence, or their suitability as a research model. The replication and evolution of RNA viruses is a major research theme. The molecular biology of this important group of pathogens is studied on the level of (i) the genome and its replicative enzymes, (ii) virus-host interactions, including innate immune responses and viral replication organelles, (iii) viral pathogenesis, (iv) virus evolution and adaptation. The program further includes studies on persistent DNA virus infections, which are addressed in both clinical and experimental settings, as well as from an evolutionary perspective. We aim to identify triggers and markers of viral reactivation and unravel pathogenesis in the immunocompromised host (including pregnancy), enabling early detection and prevention of symptomatic disease.

Position in international context

Research program 40601 strongly benefits from the synergy between virus bioinformatics, molecular and clinical virology, and our team has become leading in Europe in several fields. In particular, basic research on (re)emerging RNA viruses, including Zika virus, the SARS- and MERS-coronaviruses, and chikungunya virus, has contributed to this success, in terms of both output and external funding, in particular from the Netherlands Organization for Scientific Research (NWO) and the European Union. The program contributes to a variety of EU-funded projects on RNA virus replication and drug or vaccine discovery (SysVirDrug, VacTrain, ZAPI, ANTIVIRALS, ZIKAlliance) and virus diversity and collection (EVAg). The rational design of antiviral strategies is the overarching objective. The facilities and experience to work safely with highly pathogenic viruses (at Biosafety Level-3; mandatory for the MERS/SARS, Zika and chikungunya viruses) were instrumental in establishing productive collaborations with numerous leading investigators and institutes around the world. In 2017, LUMC became a full partner of the Netherlands Center for One Health (NCOH) that aims to integrate research in the human and veterinary medical fields to tackle cross-border problems, like emerging zoonotic agents and vector-borne pathogens. Together with the LUMC Departments of Parasitology and Infectious Diseases, the Experimental Bacteriology and Molecular Virology groups of our Department participate in the NCOH program on emerging infectious diseases (EID). The DNA virus group is recognized for its pivotal role in the EPI-HPV-UV-CA EU consortium of European and Australian centers that study the epidemiological relationship between papillomavirus infection and skin cancer. Since our discovery of a previously unknown and clinically relevant human polyomavirus (TSPyV) in 2010, the DNA virus team has been acting in the frontline of biomedical polyomavirus research, supported by the Dutch Kidney Foundation and others. The cytomegalovirus (CMV) group coordinates a high-impact clinical trial in the congenital CMV field, and trained a cohort of young vaccinologists supported by the Marie Skłodowska-Curie VacTrain network.

Content / highlights / achievements

The 40601 research program is internationally recognized for its important contributions to in particular studies on the evolution, RNA synthesis, non-structural protein functions, and virus-host interactions of several groups of RNA viruses, including nidoviruses (corona- and arteriviruses), alphaviruses, flaviviruses and picornaviruses. This position was further enhanced by our response to the emergence of the zoonotic SARS- and MERS-coronaviruses (in 2003 and 2012, respectively), the Chikungunya virus (2006), and the Zika virus (2016), and by work on other important RNA viruses such as yellow fever virus and enteroviruses. The RNA virus studies include (i) innate immune responses, viral innate immune evasion and vaccine development, (ii) inhibitor screening and mechanism-of-action studies, and (iii) the (ultra)structure and function of viral replication organelles, the latter in close collaboration with the LUMC Electron Microscopy group (Department of Molecular Cell Biology). Furthermore, we pioneered the field of reverse genetics and vector development for several +RNA virus families. This knowledge is currently applied in vaccine-related research projects, for example by the structure-based inactivation of viral immune suppression functions to develop live vaccines with enhanced immunogenicity, and in the context of the development of vaccine vectors based on the yellow fever virus 17D vaccine strain (ZAPI project). Recently, using systems biology approaches, a range of host cell factors involved in nidovirus and chikungunya virus replication was identified and these are currently being followed up, to explore their role in more detail and to assess their potential as targets for antiviral therapy. State-of-the-art technologies, including (phospho)proteomics, CRISPR/Cas-based and haploid genetic screens, next-generation sequencing, and advanced EM methods are applied in research project. For example, with collaborators at the Netherlands Cancer Institute (NKI), a novel high-confidence haploid genetic screening approach is used to map and explore Zika virus-host interactions.
The virus bioinformatics group led the ground-breaking analysis of the SARS- and MERS-coronavirus proteomes, proposed innovative concepts regarding the control of replication fidelity in RNA viruses with large genomes, and developed and validated a quantitative approach to the genome-based classification of viruses. Our multidisciplinary approach to virology has also been the basis for the characterization of newly discovered or (re)emerging viruses (including new nidoviruses, chikungunya virus, and human polyomaviruses) and our leading position in research on the disease burden and prevention of congenital CMV infection. The Department coordinates a nation-wide clinical trial on early intervention as well as late consequences of this most prevalent congenital virus infection, and in conjunction with those trials the virological and immunological parameters of the outcome of this herpesvirus infection are being dissected. Human papillomavirus-related epidemiological evidence, obtained in close collaboration with the LUMC Dermatology department, served as a basis for skin cancer risk analyses by WHO’s International Agency for Research on Cancer. Our research on the BK polyomavirus (BKV) recently revealed a major role for donor BKV-seroimmunity in the risk of developing BKV infection in renal transplant recipients, a new dimension whose exploration may have important practical consequences.
The Department was among the first laboratories to introduce novel molecular techniques into the clinical diagnosis of microbial diseases, applied to a variety of viral infections in the immunocompromised host as well as to respiratory infections, including influenza. In line with this history of innovation, we are developing initiatives, also in a broader LUMC context, to benefit from the rapidly increasing possibilities of next-generation sequencing and its application to basic, applied, and clinical research questions. Currently, a cohort of pulmonary disease patients is analyzed to directly compare classical PCR-based diagnosis of respiratory viral infection with primary NGS-based diagnosis. This may lead to the introduction of radically different approaches in diagnostic virology.
Over the past decade, our work attracted substantial external funding from NWO (6 grants), the European Union (10 grants), the Dutch Cancer and Kidney foundations (2 grants), and various other funding agencies and industrial research partners, partially in the context of patent applications.

Future themes

• Molecular biology and evolution of (emerging) RNA viruses, including SARS- and MERS-coronavirus, Zika virus and chikungunya virus
• RNA virus-host interactions, including host factors supporting viral RNA synthesis and the (ultra)structure and function of replication organelles
• RNA viral immune evasion strategies and their underlying mechanisms, in particular the role of (de)ubiquitination
• Development of antiviral strategies, including vaccines and (broad-spectrum) RNA virus inhibitors targeting viral enzymes or host factors supporting virus replication
• Explore and implement next-generation sequencing in clinical virology, providing unbiased diagnostics and the opportunity to dissect the complete virome using advanced bioinformatics
• Reducing risk and impact of polyomavirus infections, for example BK virus, in immunocompromised hosts, and exploring polyomavirus screening and prevention strategies.
• Screening, antiviral therapy, and vaccination in relation to congenital cytomegalovirus infection, aiming to establish correlates of protection, specifically in newborns, to facilitate targeted neonatal screening and vaccine development

Cohesion within LUMC

Infectious diseases, academic drug discovery, genomics and proteomics, cell imaging and bioinformatics are major LUMC research themes, which is the basis for a range of internal collaborations. In addition to being embedded in the biomedical research profile Immunity, Infection & Tolerance, close collaborations exists with the Department of Molecular Cell Biology (in particular the electron microscopy unit), the Center for Proteomics and Metabolomics, the Department of Chemical Immunology, the Department of Medical Statistics and Bioinformatics and a large number of clinical departments, including Dermatology, Pediatrics, Nephrology, Pulmonology, and Immunology, thus connecting our program to multiple other research profile areas and TFAs within LUMC.