Development of diagnostics methods for new emerging viruses

The impact of new emerging viruses on human and animal health, as well as on the economy, has recently increased due to environmental and socio-economic changes such as global warming, land development, and ease of travel. These changes have led to the emergence or re-emergence of viruses that can cross the species barrier and infect humans. Thus, some zoonotic viruses such as the Crimean-Congo haemorrhagic fever virus (CCHFV) and Rift Valley fever virus (RVFV) have the potential to become major public health threats. Indeed, CCHFV and RVFV are considered by the World Health Organization to have epidemic potential and for which the necessary countermeasures do not currently exist. Thus, this thesis, as part of the work package “advanced diagnostics” within the EU-financed Marie Skłodowska-Curie Action (MSCA) training network ‘HONOURs’, aimed to develop new diagnostic tools, both for pathogen detection and serology studies, of emerging viruses in case of an outbreak or in cases of the discovery of new viruses that could emerge unexpectedly during the course of this project. In this last scenario, the technologies and resources would be adapted to the new isolates, as it happened at the end of 2019 with the discovery of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As a first approach for test development, CCHFV and RVFV, both belonging to the Bunyavirales order, were the initial focus of this work with the aim of addressing the gaps identified in their diagnosis. For this purpose, some of the most immunogenic viral antigens identified for each virus were expressed in different expression systems and were used to produce detection molecules: monoclonal antibodies by hybridoma technology and non-antibody molecules (Affimers) by phage display. These tools were further used to develop several serological assays detecting antibodies against CCHFV and RVFV or antigens of these viruses. For the differential diagnosis of CCHFV, RVFV and other related pathogens affecting ruminants, a multiplex assay for antibody detection was developed. Finally, the discovery of SARS-CoV-2 at the end of 2019 created a high demand for diagnostic tools. After identification and production of immunogenic targets of this virus, new serological diagnostic assays were developed. The new diagnostic tools described in this thesis could be used in surveillance programs and in epidemiological studies, to provide a better understanding of the immune response to these viruses and to help in preventing the spread of some of these viruses, such as CCHFV or RVFV, to countries that are currently free of these pathogens. Moreover, the knowledge acquired during the present work could be applied and adapted to future situations, in cases of infectious outbreaks in animals and humans that can emerge unexpectedly, or caused by a yet undiscovered pathogen, as it has been illustrated by the recent outbreak of SARS-CoV-2.