Puumala-viruksen molekyyligenetiikka ja evoluutio

Puumala virus (PUUV) is the causative agent of nephropathia epidemica (NE), a mild form of hemorrhagic fever with renal syndrome. Finland has the highest documented incidence of NE with around 1000 cases diagnosed annually. PUUV is also found in other Scandinavian countries, Central Europe and the European part of Russia. PUUV belongs to the genus Hantavirus in the family Bunyaviridae. Hantaviruses are rodent-borne viruses each carried by a specific host that is persistently and asymptomatically infected by the virus. PUUV is carried by the bank voles (Myodes glareolus, previously known as Clethrionomys glareolus). Hantaviruses have co-evolved with their carrier rodents for millions of years and these host animals are the evolutionary scene of hantaviruses. In this study, PUUV sequences were recovered from bank voles captured in Denmark and Russian Karelia to study the evolution of PUUV in Scandinavia. Phylogenetic analysis of these strains showed a geographical clustering of genetic variants following the presumable migration pattern of bank voles during the recolonization of Scandinavia after the last ice age approximately 10 000 years ago. The currently known PUUV genome sequences were subjected to in-depth phylogenetic analyses and the results showed that genetic drift seems to be the major mechanism of PUUV evolution. In general, PUUV seems to evolve quite slowly following a molecular clock. We also found evidence for recombination in the evolution of some genetic lineages of PUUV. Viral microevolution was studied in controlled virus transmission in colonized bank voles and changes in quasispecies dynamics were recorded as the virus was transmitted from one animal to another. We witnessed PUUV evolution in vivo, as one synonymous mutation became repeatedly fixed in the viral genome during the experiment. The detailed knowledge on the PUUV diversity was used to establish new sensitive and specific detection methods for this virus. Direct viral invasion of the hypophysis was demonstrated for the first time in a lethal case of NE. PUUV detection was done by immunohistochemistry, in situ hybridization and RT-nested-PCR of the autopsy tissue samples.Myyräkuumeeseen sairastuu vuosittain noin tuhat suomalaista. Myyräkuumeen eli epideemisen nefropatian aiheuttaa Puumala-virus, joka kuuluu hantavirusten ryhmään. Nämä virukset aiheuttavat ihmisillä munuaisoireisia verenvuotokuumeita. Hantavirukset ovat jyrsijöiden levittämiä ja Puumala-viruksen kantaja on metsämyyrä. Metsämyyriä ja myyräkuumetta esiintyy lähes koko Suomessa aivan pohjoisia alueita lukuunottamatta. Virus tarttuu ihmiseen hengitysteiden kautta metsämyyrän eritteistä. Tartunta voi olla oireeton, mutta kolmannekselle infektion saaneista kehittyy kliininen tauti, joka alkaa korkealla kuumeella, ja johon liittyy usein päänsärkyä, pahoinvointia sekä vatsa- ja selkäkipuja. Potilas paranee myyräkuumeesta lähes aina ilman pysyviä elinvaurioita. Tässä väitöskirjatyössä tutkittiin Puumala-viruksen muuntumista eli evoluutiota. Hantavirukset, mukaanlukien Puumala-virus, ovat kehittyneet yhdessä kantajajyrsijöidensä kanssa vuosimiljoonien ajan. Jyrsijöiden evoluutiohistorian todettiinkin heijastuvan Puumala-viruksen nykyisiin kantoihin. Tutkimuksessa havaittiin, että Puumala-virus muuntuu hitaasti lähinnä pistemutaatioiden kautta. Toisaalta huomattiin, että eri Puumala-viruskantojen geenit voivat myös muodostaa uusia kantoja rekombinaatio-mekanismin välityksellä. Tutkimus osoitti myös, että Puumala-virus voi muuntua nopeasti, mikäli viruksen elinympäristö muuttuu. Tässä väitöskirjatyössä kehitettiin myös menetelmiä, jolla voidaan tutkia viruksen esiintymistä kudoksissa ja kliinisissä näytteissä. Tutkimuksessa kuvattiin yksi myyräkuumeen aiheuttama kuolemantapaus, jossa Puumala-virusta löydettiin munuaisten ja pernan lisäksi aivolisäkkeestä. Lisäksi kuvattiin kaksi tapausta, joissa myyräkuumeeseen liittyi aivolisäkkeen verenvuoto, joka johti hormonikorvaushoitoa vaativaan aivolisäkkeen etulohkon vajaatoimintaan. Puumala-virus-infektiot ovat Suomessa yleisiä (keskimääräinen seroprevalenssi 5%), ja lisätutkimuksia tarvitaan, jotta voidaan selvittää, kuinka yleisiä myyräkuumeen aiheuttamat aivolisäkkeen vauriot ovat

From Microbial Genomics to Metagenomics

Non peer reviewe

Editorial : From genomics to antibiotic resistance in emerging pathogens

Non peer reviewe

Hantavirus maintenance and transmission in reservoir host populations

Hantaviruses are primarily hosted by mammalian species of the orders Rodentia, Eulipotyphla and Chiroptera. Spillover to humans is common, and understanding hantavirus maintenance and transmission in reservoir host populations is important for efforts to curtail human disease. Recent field research challenges traditional phases of virus shedding kinetics derived from laboratory rodent infection experiments. Organ infection sites in non-rodent hosts suggest similar transmission routes to rodents, but require direct assessment. Further advances have also been made in understanding virus persistence (and fadeouts) in fluctuating host populations, as well as occupational, recreational and environmental risk factors associated with spillover to humans. However, despite relevance for both intra-species and inter-species transmission, our understanding of the longevity of hantaviruses in natural environments remains limited.Peer reviewe

Pan and Core Genome Analysis of 183 Mycobacterium tuberculosis Strains Revealed a High Inter-Species Diversity among the Human Adapted Strains

Tuberculosis (TB) is an airborne communicable disease with high morbidity and mortality rates, especially in developing countries. The causal agents of TB belong to the complex Mycobacterium tuberculosis (MTBc), which is composed of different human and animal TB associated species. Some animal associated species have zoonotic potential and add to the burden of TB management. The BCG (“Bacillus Calmette-Guérin”) vaccine is widely used for the prevention against TB, but its use is limited in immunocompromised patients and animals due to the adverse effects and disseminated life-threatening complications. In this study, we aimed to carry out a comparative genome analysis between the human adapted species including BCG vaccine strains to identify and pinpoint the conserved genes related to the virulence across all the species, which could add a new value for vaccine development. For this purpose, the sequences of 183 Mycobacterium tuberculosis (MTB) strains were retrieved from the freely available WGS dataset at NCBI. The species included: 168 sensu stricto MTB species with other human MTB complex associated strains: M. tuberculosis var. africanum (3), M. tuberculosis var. bovis (2 draft genomes) and 10 BCG species, which enabled the analysis of core genome which contains the conserved genes and some virulence factor determinants. Further, a phylogenetic tree was constructed including the genomes of human (183); animals MTB adapted strains (6) and the environmental Mycobacterium strain “M. canettii”. Our results showed that the core genome consists of 1166 conserved genes among these species, which represents a small portion of the pangenome (7036 genes). The remaining genes in the pangenome (5870) are accessory genes, adding a high inter-species diversity. Further, the core genome includes several virulence-associated genes and this could explain the rare infectiousness potential of some attenuated vaccine strains in some patients. This study reveals that low number of conserved genes in human adapted MTBc species and high inter-species diversity of the pan-genome could be considered for vaccine candidate development

Pan and Core Genome Analysis of 183 Mycobacterium tuberculosis Strains Revealed a High Inter-Species Diversity among the Human Adapted Strains

Tuberculosis (TB) is an airborne communicable disease with high morbidity and mortality rates, especially in developing countries. The causal agents of TB belong to the complex Mycobacterium tuberculosis (MTBc), which is composed of different human and animal TB associated species. Some animal associated species have zoonotic potential and add to the burden of TB management. The BCG (“Bacillus Calmette-Guérin”) vaccine is widely used for the prevention against TB, but its use is limited in immunocompromised patients and animals due to the adverse effects and disseminated life-threatening complications. In this study, we aimed to carry out a comparative genome analysis between the human adapted species including BCG vaccine strains to identify and pinpoint the conserved genes related to the virulence across all the species, which could add a new value for vaccine development. For this purpose, the sequences of 183 Mycobacterium tuberculosis (MTB) strains were retrieved from the freely available WGS dataset at NCBI. The species included: 168 sensu stricto MTB species with other human MTB complex associated strains: M. tuberculosis var. africanum (3), M. tuberculosis var. bovis (2 draft genomes) and 10 BCG species, which enabled the analysis of core genome which contains the conserved genes and some virulence factor determinants. Further, a phylogenetic tree was constructed including the genomes of human (183); animals MTB adapted strains (6) and the environmental Mycobacterium strain “M. canettii”. Our results showed that the core genome consists of 1166 conserved genes among these species, which represents a small portion of the pangenome (7036 genes). The remaining genes in the pangenome (5870) are accessory genes, adding a high inter-species diversity. Further, the core genome includes several virulence-associated genes and this could explain the rare infectiousness potential of some attenuated vaccine strains in some patients. This study reveals that low number of conserved genes in human adapted MTBc species and high inter-species diversity of the pan-genome could be considered for vaccine candidate development

Evaluation of Real-Time RT-PCR for Diagnostic Use in Detection of Puumala Virus

Puumala virus (PUUV) is the most common cause of hantavirus infection in Europe, with thousands of cases occurring particularly in Northern, Central and Eastern Europe and Russia. It causes a mild form of hemorrhagic fever with renal syndrome also known as nephropathia epidemica (NE) with clinical picture ranging from mild to severe. Currently, the laboratory diagnosis of NE is mainly based on serology. Here, we evaluated a real-time one-step qRT-PCR (PUUV-qRT-PCR) for detection of PUUV with 238 consecutive diagnostic serum samples from patients with suspected PUUV infection. The PUUV-qRT-PCR was both specific and sensitive for PUUV RNA. The analytical sensitivity (limit of detection) was estimated to be four copies of PUUV per reaction. Altogether 28 out of 30 (93%) PUUV IgM positive samples were positive also for PUUV RNA. No false positives were detected and the specificity was thus 100%. Interestingly, one sample was found positive in PUUV-qRT-PCR prior to subsequent IgM and IgG seroconversion. PUUV-qRT-PCR could be used for diagnostics in the early phase of NE infection and might be helpful especially in the rare severe cases when the patient’s condition may deteriorate rapidly

Evaluation of Real-Time RT-PCR for Diagnostic Use in Detection of Puumala Virus

Puumala virus (PUUV) is the most common cause of hantavirus infection in Europe, with thousands of cases occurring particularly in Northern, Central and Eastern Europe and Russia. It causes a mild form of hemorrhagic fever with renal syndrome also known as nephropathia epidemica (NE) with clinical picture ranging from mild to severe. Currently, the laboratory diagnosis of NE is mainly based on serology. Here, we evaluated a real-time one-step qRT-PCR (PUUV-qRT-PCR) for detection of PUUV with 238 consecutive diagnostic serum samples from patients with suspected PUUV infection. The PUUV-qRT-PCR was both specific and sensitive for PUUV RNA. The analytical sensitivity (limit of detection) was estimated to be four copies of PUUV per reaction. Altogether 28 out of 30 (93%) PUUV IgM positive samples were positive also for PUUV RNA. No false positives were detected and the specificity was thus 100%. Interestingly, one sample was found positive in PUUV-qRT-PCR prior to subsequent IgM and IgG seroconversion. PUUV-qRT-PCR could be used for diagnostics in the early phase of NE infection and might be helpful especially in the rare severe cases when the patient’s condition may deteriorate rapidly

Ecology of Neglected Rodent-Borne American Orthohantaviruses

The number of documented American orthohantaviruses has increased significantly over recent decades, but most fundamental research has remained focused on just two of them: Andes virus (ANDV) and Sin Nombre virus (SNV). The majority of American orthohantaviruses are known to cause disease in humans, and most of these pathogenic strains were not described prior to human cases, indicating the importance of understanding all members of the virus clade. In this review, we summarize information on the ecology of under-studied rodent-borne American orthohantaviruses to form general conclusions and highlight important gaps in knowledge. Information regarding the presence and genetic diversity of many orthohantaviruses throughout the distributional range of their hosts is minimal and would significantly benefit from virus isolations to indicate a reservoir role. Additionally, few studies have investigated the mechanisms underlying transmission routes and factors affecting the environmental persistence of orthohantaviruses, limiting our understanding of factors driving prevalence fluctuations. As landscapes continue to change, host ranges and human exposure to orthohantaviruses likely will as well. Research on the ecology of neglected orthohantaviruses is necessary for understanding both current and future threats to human health.Peer reviewe