Here you will find descriptions of our projects for which the main funding comes from Jane and Aatos Erkko foundation, Academy of Finland, Helsinki University Hospital funds and Sigrid Juselius foundation.
Mosquito-borne viruses (MBVs) include globally important pathogens, such as dengue, West Nile and Zika. MBV’s are rapidly evolving RNA viruses, which have complex life cycles that include mosquito vectors and vertebrate hosts.
In Finland the known endemic human pathogenic MBVs include Sindbis virus (genus Alphavirus, family Togaviridae) and orthobunyaviruses Inkoo and Chatanga (family Bunyaviridae, genus Orthobunyavirus). Additionally we have discovered flaviviruses (genus Flavivirus) from the Finnish mosquitoes that apparently are not pathogens.
The MBV repertoire is more diverse in Southern Europe and tropical Africa. As the globalisation, climate change and human activities affect to vector and pathogen distributions, MBVs are topical research targets.
Currently we are studying MBVs from mosquitoes and patient samples collected in Finland, Italy and Kenya and developing laboratory diagnostics to detect them.
Ticks carry and transmit several important human pathogens. Tick-borne encephalitis virus (TBEV, family Flaviviridae, genus Flavivirus) is mainly transmitted by Ixodes ricinus and Ixodes persulcatus ticks, and is endemic in Finland and elsewhere in Europe. Human patients diagnosed as clinically ill represent “the tip of the iceberg” in these infections suggesting that host factors play a major role in the outcome of the infection. Our research focus is on the molecular interactions TBEV and the neuropathogenesis of clinical relevance in human host, as well as on host and viral determinants that contribute to disease severity in neuropathogenic infections caused by TBEV.
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, and Kibera slum in Nairobi. We anticipate soon expanding to other parts of Kenya.
The project is funded by the Academy of Finland, it includes PIs and collaborators at the University of Nairobi and Maasai Mara University, as well as graduate students and post-doctoral researchers based in Kenya and Finland. The arbovirus work is funded by Jane and Aatos Erkko Foundation.
Our group has long traditions in developing virus diagnostics. We specialize in both serological and molecular methods and have successfully delivered tests for both diagnostic companies, hospital laboratories and private sector. We have special expertise in ELISA tests and both conventional and real time- PCR but we are also developing completely new technologies especially suitable for non-invasive patient samples and rapid tests used also for field diagnostics.
For serological diagnostics we develop and produce recombinant antigens for multiple pathogens, IFA-slides based on infected cells, and jointly with prof Klaus Hedman's group, new Rapid FRET Serodiagnostics, comprising a new concept for measuring antibodies.
We have experience setting up PCR based assays for pathogen detection. Most of the assays in diagnostic use are designed on the real time- PCR platform for ease of use and rapid detection. We help diagnose both human and animal pathogens diverging from conventional zoonotic viruses to newly discovered bacterial pathogens. Our molecular detection methods include real-time PCR assays for hemorrhagic fever viruses, such as Ebola and Crimean-Congo hemorrhagic fever viruses. Other emerging viruses that we have targeted include Zika and Dengue viruses, hantaviruses, poxviruses, and arenaviruses. These are now in use in HUSLAB diagnostic laboratory and in the national biohazard preparedness program. We also have expertise in parvovirus diagnostics and a wide variety of bacterial pathogens of animals.
For novel metagenomics approaches to diagnose either known and previously unknown pathogens from a variety of samples, see below for "virome and microbiome".
Flaviviruses include globally important mosquito-borne dengue and zika (ZIKV) viruses, and tick-borne encephalitis virus (TBEV) endemic in Europe. Clinically ill patients represent a minority of these infections suggesting significant role for host factors in the outcome of the infection. We aim to discover host and viral determinants that contribute to disease severity especially in neuropathogenic TBEV and ZIKV, which are currently not well understood.
The flaviviral NS1 protein has been associated with contradictory roles in the pathogenesis. Our current research suggests changes in ZIKV NS1 protein to be associated with fetal infection, as well as that ZIKV and TBEV disturb neural cell transport and differentiation. The results from host genomic studies and in vitro culture models will shed light to the molecular interactions and neuropathogenesis of ZIKV and TBEV that will aid in development of therapy and control measures.
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 collaborate closely with researchers from LUKE and have used national field monitoring of rodents to elucidate the spatiotemporal distribution and prevalence dynamics of zoonotic viruses. We also conduct wild rodent laboratory infection experiments (BSL-3) to further study e.g. reservoir host competence and transmission mechanisms.
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 starting 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.
The projects on veterinary microbiology are supervised by Docent Tarja Sironen.
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 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 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 (Lazypipe) for this.
Apart from our own research our group also provide services for viral meta-genomic sequencing as well as 16S amplicon based meta-genomic sequencing. Our highly experienced team of experts performs strict quality to ensure precise and accurate results. The workflow for viral and microbial metagenome starts with sample preparation followed by library preparation, then sequencing and finally bioinformatics analysis.
Sequencing and bioinformatics analysis service can be ordered and prices can be agreed by contacting : Tarja Sironen (firstname.lastname@example.org)
Since the beginning of the SARS-CoV2 pandemic, we have taken part in various efforts in COVID-19 research, such as
-characterizing the genetic variation and molecular epidemiology of SARS-CoV 2 by sequencing of strains from Finnish patients
- setting up large scale seroassays based on immunofluorescence and enzymeimmunoassays with recombinant SARS-CoV nucleopcapsid and spike proteins, and microneutralization
- screening of drug libraries for inhibitors of SARS-CoV2 in cell culture models in BSL-3
- studying virus-host cell interactions
- cloning of human anti-SARS-CoV antibodies
We are conducting many collaborative efforts with other researchers where e.g. serology, infection work with live virus or virus detection is needed.
Some recent publications can be found here: https://pmlegacy.ncbi.nlm.nih.gov/pubmed/?term=vapalahti+sars+covid