Our group at the intersection of Microbial Genomics and One Health focuses on understanding pathogen diversity, transmission, and emergence across humans, animals, and the environment. We combine next-generation sequencing, metagenomics, and advanced bioinformatics to unravel microbial and viral landscapes, supporting rapid diagnostics, surveillance, and predictive modeling.
PREPARE-TID targets three categories of infectious agents: a neglected ongoing epidemic, an emerging epidemic, and an infection under active elimination efforts. Factors such as increased global travel, climate change, and environmental shifts have accelerated the spread of zoonotic diseases, highlighting the urgent need for rapid, coordinated international responses. The COVID-19 pandemic has underscored that rapid diagnostics are essential for effective epidemic control. PREPARE-TID aims to develop advanced in vitro diagnostic tools to enhance preparedness for both existing and potential emerging infectious agents.
The consortium is a multidisciplinary collaboration of 16 European and 4 international research organizations and SMEs, bringing together biomedical researchers, epidemiologists, clinicians, veterinarians, and software engineers. Together, they are designing a comprehensive diagnostic pipeline that includes:
These innovations will provide rapid, scalable, and accessible diagnostic solutions for international health threats, enabling early detection of pathogens with pandemic potential. The consortium’s goal is to deliver easily deployable, mass-producible diagnostics that can be used in epidemic and pandemic scenarios worldwide.
Funding: European Union
Our group develops cutting-edge bioinformatics pipelines to detect and characterize pathogens from complex biological samples.
We use Lazypipe for high-throughput Illumina sequencing analysis and LazypipeNP for Oxford Nanopore data. HaVoC supports viral genome assembly and variant calling, while ClusTRace enables rapid phylogenetic clustering and outbreak tracing. These tools integrate metagenomics, phylogenomics, and epidemiological data to provide comprehensive pathogen surveillance.
Our pipelines are designed for One Health applications, spanning human, animal, and environmental samples. The platform supports rapid, accurate, and field-deployable pathogen identification.
The project investigates how viral genetic variations influence transmissibility, virulence, and host immune responses.
By combining clinical, epidemiological, and experimental data, the study explores genotype-to-phenotype linkages and the adaptive changes the virus undergoes under different selection pressures, including cell type, tissue, and host-specific environments. Particular focus is given to under-studied genomic regions such as Nsp1, where recurrent deletions may modulate interferon responses and viral persistence. The project employs next-generation sequencing to monitor intra-host viral diversity, assess evolutionary trade-offs, and identify pathogenetic determinants. Experimental work, including cell culture models, complements natural population studies to elucidate mechanisms of viral adaptation.
Findings are expected to improve understanding of SARS-CoV-2 evolution, host-pathogen interactions, and the molecular basis of disease severity, informing strategies for mitigation and therapeutic interventions.
As a Visiting Associate Professor at the Medical University of Gdańsk, I lead research on the virome of urban rats with Prof. M. Grzybek to uncover viral diversity and its public health implications.
Urban rats, including Norway rats (Rattus norvegicus) and roof rats (Rattus rattus), thrive in cities and interact closely with humans and domestic animals, making them potential reservoirs for zoonotic viruses. This project combines serology, molecular diagnostics, and viral metagenomics to identify known and novel pathogens. Samples are collected from multiple Polish cities, including feces, urine, spleen, and lungs, and analyzed for viral prevalence, genetic diversity, and phylogenetic relationships. Advanced bioinformatics tools such as Lazypipe, HaVoC, and ClusTRace are used for quality control, assembly, annotation, and evolutionary analysis.
The study also investigates intrinsic and extrinsic factors influencing the rat virome across urban environments. Insights from this research inform One Health strategies by mapping zoonotic risk and understanding pathogen ecology. It represents the first comprehensive, multisite virome study of urban rats in Poland, with implications for epidemic preparedness. Data generated contributes to global knowledge on virus evolution and emergence in urban wildlife.
Overall, the project bridges virology, ecology, and public health to enhance our understanding of zoonotic disease dynamics.
In collaboration with the Small Animal Hospital, University of Helsinki, and the Pathology Department, Faculty of Veterinary Medicine (Dr. Pernilla Syrjä), the group studies viral infections in Finnish dogs.
The project, involving Dr. Sanna Viitanen, Henriikka Neittaanmäki, and Ilona Burck, focuses on canine respiratory disease, meningoencephalitis of unknown etiology, and includes postpartum dog samples from the Pathology Department. Using next-generation sequencing (NGS) and Nanopore metagenomics, the team identifies both known and novel viral agents.
The project provides insights into pathogen diversity, evolution, and the emergence of viral infections in companion animals.stance profiling.
In collaboration with the University of Nairobi, alongside researchers Dr. Kariuki Njaanake and Dr. Moses Masika, where I holds a visiting professorship, we investigate carcinogenesis associated with urogenital schistosomiasis.
Using multi-omics approaches, the team explores the molecular mechanisms and host–pathogen interactions driving cancer development in infected individuals. The study integrates clinical data with controlled animal experiments and pathological analyses to model disease progression and validate key molecular pathways. By combining genomics, transcriptomics, and proteomics, the project aims to identify biomarkers and potential therapeutic targets.
This work enhances understanding of the links between chronic parasitic infection and cancer risk, advancing both basic science and translational research in schistosomiasis-associated malignancies.
In collaboration with Metsähallitus and the University of Eastern Finland, our group investigates the microbiota and virome of the endangered Saimaa ringed seal.
We use metagenomic sequencing to explore microbial and viral diversity and understand how host ecology and environmental factors shape these communities. Comparative analyses with Baltic ringed seals reveal patterns of microbial adaptation and potential pathogen exposure. This research informs wildlife conservation and One Health strategies by identifying emerging viral threats in vulnerable populations. Advanced bioinformatics pipelines such as Lazypipe and ClusTRace enable precise characterization and phylogenetic analysis.
Our findings contribute to ecosystem health monitoring and the development of targeted conservation measures. Ultimately, the project bridges wildlife genomics and pathogen surveillance for long-term ecological and public health benefits.
The project investigates the differential virulence and host responses of the three main TBEV subtypes—European, Siberian, and Far Eastern—using multiple animal models. Laboratory mice and hamsters develop severe disease upon infection, whereas bank voles, natural reservoir hosts, remain asymptomatic, providing a unique opportunity to study tolerance mechanisms.
The study integrates virological, immunological, and pathological analyses, including viral kinetics, tissue tropism, histopathology, and immune profiling, to delineate host-pathogen interactions. High-throughput techniques such as RNA-seq, flow cytometry, and immunohistochemistry are employed to characterize molecular and cellular responses across species. Additionally, clinical samples from Finnish TBE patients are analyzed to correlate experimental findings with human disease outcomes. By combining comparative animal experiments with patient data, the project aims to identify immunological and molecular determinants of disease severity, uncover mechanisms of viral persistence, and inform vaccine and therapeutic development.
Overall, this research advances understanding of TBEV pathogenesis and host-specific responses in a One Health context.
We are also actively engaged in research on a variety of pathogenic bacteria and parasites. Our work leverages advanced genomics and bioinformatics tools to improve pathogen detection and characterization. We aim to enhance surveillance of emerging and re-emerging infectious agents in both human and animal populations. This research supports rapid outbreak response and informs public health interventions. Additionally, we focus on discovering novel pathogens and understanding their genetic diversity, evolution, and mechanisms of resistance. By integrating genomic data with epidemiological insights, we strive to develop more effective strategies for disease control and prevention.
The recently completed Erkko Foundation–funded project, focused on rapid detection and characterization of drug-resistant TB directly from clinical samples. The team, led by Tarja Sironen with collaborators Fathiah Zakham and Ravi Kant, developed a novel NGS-based pipeline using RNA probe–based target enrichment to identify resistance-conferring mutations across all relevant TB genes.
This approach bypasses lengthy culture methods and allows timely, accurate diagnosis of MDR, XDR, and potentially TDR TB cases. The project also included epidemiological investigations, contact tracing, and comparative genomics to better understand circulating strains in Finland and globally. Clinical validation was performed on patient samples in collaboration with Huslab, THL, and international partners.
Overall, the study advanced rapid, cost-effective TB diagnostics and laid the groundwork for broader applications in bacterial resistance profiling.