We are interested in understanding the molecular principles of the functions of viruses and how viruses interact with their host cells. In addition, we investigate how sequence or structural similarity reflects the common evolution of viruses which are infecting different cellular domains of life. Results will be also exploited to establish genome-based classification criteria that will serve as the basis for virus taxonomy.
We study the extent of viral genetic diversity and various aspects of virus biology including virus-host interactions, molecular mechanisms of virus entry and virion assembly with a special focus on archaeal viruses and specific model systems or groups of double-stranded DNA bacteriophages including Antactic sea ice and Finnish fresh water phages.
Archaeal viruses form a special group of viruses of which we know very much less than about bacterial and eukaryotic viruses. Many archaeal viruses present their own unique virus families. Most of the characterized archaeal viruses infect extremophilic hosts e.g. from high salinity or temperature. We have a large number of culturable archaeal viruses isolated from high-salt environmental samples (e.g. 2012, 2015, 2019) and we are investigating their functions and relationships. See also the Horizon Europe ARCTECH project.
Selected references:
Kuiper BP, Schöntag AMC, Oksanen HM, Daum B, Quax TEF. 2024. Archaeal virus entry and egress. Microlife. 5:uqad048.
Laanto E, Oksanen HM. 2023. Three phages from a boreal lake during ice cover infecting Xylophilus, Caulobacter, and Polaromonas species. Viruses. 15(2):307.
Schwarzer S, Hackl T, Oksanen HM, Quax TEF. 2023. Archaeal host cell recognition and viral binding of HFTV1 to its Haloferax host. mBio. 14:e0183322.
Demina TA, Luhtanen AM, Roux S, Oksanen HM. 2022. Virus-host interactions and genetic diversity of Antarctic sea ice bacteriophages. mBio. 13:e0065122.
Liu Y, Demina TA, Roux S, Aiewsakun P, Kazlauskas D, Simmonds P, Prangishvili D, Oksanen HM, Krupovic M. 2021. Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes. PLoS Biol. 19:e3001442.
The International Committee on Taxonomy of Viruses (ICTV) oversees the official classification of viruses and nomenclature of taxa (Virus Taxonomy). The recent and rapid development in discovery of new viruses and the accumulation of metagenomic sequence data has led to a change in virus taxonomy. This has resulted in modernization of the rank structure of virus taxonomy, which has been reported in Nature Microbiology (2020). New levels of the virus taxonomy will also stimulate further research on virus origins and evolution.
It is our responsibility to coordinate the families Corticoviridae, Pleolipoviridae, and the order Halopanivirales including the families Spherolipoviridae, Simuloviridae, and Matsushitaviridae as the Study Group Chairs in the Bacterial and Archaeal Viruses Subcommittees. We have also contributed into the description of the families of Tectiviridae, Finnlakeviridae, and Halspiviridae. Our work on archaeal tailed double-stranded DNA viruses originating from highly saline environments led to the understanding of their relationships and position in the virus taxonomy (the class Caudoviricetes).
Selected references:
Simmonds et al., 2023. Four principles to establish a universal virus taxonomy. PLoS Biol. 21:e3001922.
Liu Y, Du S, Chen X, Dyall-Smith M, Jalasvuori M, Oksanen HM, ICTV Report Consortium. 2023. ICTV Virus Taxonomy Profile: Simuloviridae 2023. J Gen Virol. 104(4).
Demina TA, Dyall-Smith M, Jalasvuori M, Du S, Oksanen HM. 2023. ICTV Virus Taxonomy Profile: Sphaerolipoviridae 2023. J Gen Virol. 104(3).
Large biocomplexes such as viruses, virus-like particles, exosomes, vesicles or large protein complexes cannot be purified by conventional protein purification methods. We are developing new strategies for purifying large complexes in connection with the Biocomplex core facility that we co-host. Main technologies are ultracentrifugation, asymmetrical flow field-flow fractionation and monolithic chromatography. We also coordinate the national Structural Biology Finland Research Infrastructure and the ESFRI Instruct-ERIC Centre Finland.
Selected references:
Schönn MA, Eskelin K, Bamford DH, Poranen MM, Unoson C, Oksanen HM. 2022. Inline-tandem purification of viruses from cell lysate by agarose-based chromatography. J Chromatogr B Analyt Technol Biomed Life Sci. 1192:123140.
Eskelin K, Oksanen HM. 2022. Archaeal viruses: Production of virus particles and vesicle-like viruses and purification using asymmetrical flow field-flow fractionation. Methods Mol Biol. 2022;2522:449-465.