Here you will find short descriptions of our projects
The ease of travel, global warming, and environmental changes have accelerated the spread of zoonotic infectious diseases. International collaboration is crucial for controlling disease epidemics, with rapid diagnostics being a key component, as demonstrated by the COVID pandemic. PREPARE-TID will focus on three types of infectious agents: a neglected ongoing epidemic, an emerging ongoing epidemic, and an ongoing elimination effort. The goal is to develop in vitro diagnostic tools for preparedness against potential new infectious agents.
PREPARE-TID is a multidisciplinary research consortium comprising 16 European and 4 international research organizations and SMEs. The team includes biomedical researchers, epidemiologists, clinicians, veterinarians, and software engineers working together to create a comprehensive diagnostic pipeline. This pipeline will feature mobile suitcase sequencing labs with straightforward bioinformatics, fieldable rapid nucleic acid extraction procedures, mobile smartphone-linked molecular point-of-care diagnostics, a multiplex PCR one-health surveillance platform, and a one-health digital platform.
These innovations will offer advanced diagnostic solutions for international health threats, enhancing the accessibility of novel diagnostics for detecting pathogens with pandemic potential. The consortium aims to deliver easily deployable and mass-producible point-of-care and mobile diagnostics for use in epidemics or pandemics.
Funded by EU
GLOBEID project is part of DEVELOP2, the Academy Programme for Development Research call (2023–2026). The project is led by Assoc. Prof. Tarja Sironen, and is jointly funded by the Academy of Finland and the Ministry for Foreign Affairs of Finland.
Emerging infectious diseases (EIDs) pose one of the most significant global threats to human and animal health, economy and safety, hindering global development. The rise of EIDs is driven by global processes such as increased human-wildlife interactions, urbanization, and changes in climate and land use. The impact of these challenges is not equal, and the burden of EIDs is highest in developing regions, including Africa. An effective response to these threats relies on early detection and rapid response at the outbreak sites. Unfortunately, many countries at the frontline of pandemic prevention lack the necessary resources. The overarching aim of GLOBEID is to understand, mitigate, and prevent potential EID threats in Kenya. This project stems from an already strong collaboration between the University of Helsinki (UH) and the University of Nairobi (UoN). In GLOBEID, we focus on detecting, identifying, and surveying viral zoonoses in Kenya, as well as studying the anthropogenic and environmental factors influencing the prevalence and spread of these diseases in a biodiversity hotspot, Taita–Taveta county, southeastern Kenya. We primarily focus on vector-borne pathogens, which are significantly affected by changing environmental conditions, and on bat- and rodent-borne pathogens, which are key reservoirs of zoonotic viruses. GLOBEID seeks to assess the impacts of climate and land use changes on wildlife, identify the drivers and hotspots of potential spillover events, and explore practical solutions for locals to prevent EIDs. Locally collected data on vectors, reservoirs, and humans combined with disease risk modelling, enable effective decision-making in the study regions and more broadly in Kenya and Africa. In GLOBEID, we aim to build capacities for early detection and rapid response to EID threats and predict areas where spillovers typically emerge. To enhance early detection of disease emergence, we aim to improve pathogen diagnostics and respond to outbreaks through training programs organized with the KAVI Institute of UoN. We actively engage stakeholders, from the general public to public health authorities, in communicating and disseminating research findings, thereby raising awareness about EIDs and mitigation measures. As we are living in an era of infectious disease outbreaks, the time to act is now.
Bats and rodents are the two most species-rich taxa of mammals, and are major reservoir hosts for zoonotic pathogens. Bats are considered unique in their ability to host zoonotic viruses with severe public health consequences. Meanwhile, the sheer abundance of rodent species worldwide (approximately twice as many as bats) and their close associations with humans, render rodent hosts a constant threat for zoonotic disease emergence.
We study bat-borne pathogens currently in Finland and Kenya, while rodent-borne pathogens are studied widely with our network of collaborators.
We have a number of projects on companion, production and wild animals. Our research includes pathogen discovery, development of diagnostics, and epidemiology. Recently we have studied e.g. Bartonella infections in dogs and moose, causes of diarrhea in production animals, mechanisms of tolerance in Aleutian disease, and a novel pathogen causing severe skin infections. We are also developing new vaccines for veterinary use. We are currently launching new projects using molecular epidemiology and statistics to do large scale research on the causes of morbidity and mortality in production animal populations both within Finland and with international collaborators.
Tuberculosis is a major public health problem around the globe with more than 10 million cases annually. Emergence of multidrug resistant tuberculosis worsens the treatment and control options continuously. Our goal is to develop a culture-independent next generation sequencing based assay for obtaining full diagnostic information, including prediction of resistance to all anti-mycobacterial drugs rapidly, accurately, and cheaply. This method should be able to identify resistance-conferring mutations or single nucleotide polymorphisms (SNPs) related to each anti-tuberculosis drug. The same methodology can be later used in other bacterial MDR infections, and is part of our efforts to use bacterial whole genome sequencing as a tool in characterization of bacterial infections.
Next-generation sequencing technologies have enabled us to investigate the gut microbiome and virome role in health and disease of different vertebrates. To explore and study the composition of microbiota and its effect on health and disease our group collaborates with Prof. Olli Vapalahti who has acquired Illumina’s state of the art MiSeq next generation sequencing platform.
Currently, our group is busy studying microbiome and virome of canine, bovine, mink, fox, chicken, vole and humans. To understand the biology and evolution of pathogens we are also sequencing and studying full genomes of various viral and bacterial pathogens. In projects with HUSLAB, we are developing applications to identify any viral sequences directly from human samples and have developed a laboratory and bioinformatic pipeline for this.
This multi-disciplinary and collaborative project embraces the principles of One Health to investigate emerging zoonotic viruses in Kenya. Using samples collected from febrile patients, arthropod vectors, rodents, bats and livestock, we are applying cutting-edge diagnostic tools to study the diversity and prevalence of viruses in selected ecosystems, and the possibility of cross-species virus transmission amongst host taxa. Most research so far has been conducted in the Taita Hills in south-east rural Kenya, supported by the University of Helsinki Taita Research Station.