| 1. |
- Chang, Wei-Shan, et al.
(författare)
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Novel hepatitis D-like agents in vertebrates and invertebrates
- 2019
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Ingår i: Virus Evolution. - : OXFORD UNIV PRESS. - 2057-1577. ; 5:2
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Tidskriftsartikel (refereegranskat)abstract
- Hepatitis delta virus (HDV) is the smallest known RNA virus, encoding a single protein. Until recently, HDV had only been identified in humans, where it is strongly associated with co-infection with hepatitis B virus (HBV). However, the recent discovery of HDV-like viruses in metagenomic samples from birds and snakes suggests that this virus has a far longer evolutionary history. Herein, using additional meta-transcriptomic data, we show that highly divergent HDV-like viruses are also present in fish, amphibians, and invertebrates, with PCR and Sanger sequencing confirming the presence of the invertebrate HDV-like viruses. Notably, the novel viruses identified here share genomic features characteristic of HDV, such as a circular genome of only approximately 1.7 kb in length, and self-complementary, unbranched rod-like structures. Coiled-coil domains, leucine zippers, conserved residues with essential biological functions, and isoelectronic points similar to those in the human hepatitis delta virus antigens (HDAgs) were also identified in the putative non-human viruses. Importantly, none of these novel HDV-like viruses were associated with hepadnavirus infection, supporting the idea that the HDV-HBV association may be specific to humans. Collectively, these data not only broaden our understanding of the diversity and host range of HDV, but also shed light on its origin and evolutionary history.
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| 2. |
- Magnusson, Monika, 1965-, et al.
(författare)
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Digitalisering av krisövning : Erfarenheter från CriseIT-projekten
- 2021
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Genomförandet av övningar är en nyckel till stärkt förmåga att agera effektivt i kris. CriseIT-projekten har haft som mål att bidra till detta genom att skapa möjligheter för kommuner och andra aktörer med krisövningsbehov att öva enklare och oftare.Det finns en önskan om, och en medvetenhet om behoven av, att öva mer än vad som görs i nuläget i många organisationer. Digitala verktyg är ett sätt att göra det möjligt att öva oftare, med lägre resursåtgång och kortare tid för planering och genomförande. Corona-pandemin har ytterligare gjort det tydligt vilka möjligheter digitaliseringen innebär för att effektivisera processer som tidigare varit inramade av tids-och rumsbegränsningar –t.ex. övning.Denna rapport syftar till att på ett lättillgängligt sätt redogöra för och diskutera utmaningar och möjligheter med den digitala övningsprocessen, så som den kommit till uttryck i CriseIT-projekten, genom att beskriva metodiska arbetssätt för design, genomförande och utvärdering av digitala krisövningar samt några perspektiv på implementering av digital övningsmetodik i organisationer. Målgrupp för rapporten är den som arbetar med krisberedskap i offentlig eller privat verksamhet, och som önskar lära sig mer om möjligheten att digitalisera sin övningsprocess. Arbetsrapporten är del av resultatredovisning för CriseIT2.
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| 3. |
- Ortiz-Baez, Ayda Susana, et al.
(författare)
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Meta-transcriptomic identification of Trypanosoma spp. in native wildlife species from Australia
- 2020
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Ingår i: Parasites & Vectors. - : Springer Nature. - 1756-3305. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Wildlife species carry a remarkable diversity of trypanosomes. The detection of trypanosome infection in native Australian fauna is central to understanding their diversity and host-parasite associations. The implementation of total RNA sequencing (meta-transcriptomics) in trypanosome surveillance and diagnosis provides a powerful methodological approach to better understand the host species distribution of this important group of parasites.Methods: We implemented a meta-transcriptomic approach to detect trypanosomes in a variety of tissues (brain, liver, lung, skin, gonads) sampled from native Australian wildlife, comprising four marsupials (koala, Phascolarctos cinereus; southern brown bandicoot, Isoodon obesulus; swamp wallaby, Wallabia bicolor; bare-nosed wombat, Vombatus ursinus), one bird (regent honeyeater, Anthochaera phrygia) and one amphibian (eastern dwarf tree frog, Litoria fallax). Samples corresponded to both clinically healthy and diseased individuals. Sequencing reads were de novo assembled into contigs and annotated. The evolutionary relationships among the trypanosomatid sequences identified were determined through phylogenetic analysis of 18S rRNA sequences.Results: We detected trypanosome sequences in all six species of vertebrates sampled, with positive samples in multiple organs and tissues confirmed by PCR. Phylogenetic analysis indicated that the trypanosomes infecting marsupials were related to those previously detected in placental and marsupial mammals, while the trypanosome in the regent honeyeater grouped with avian trypanosomes. In contrast, we provide the first evidence for a trypanosome in the eastern dwarf tree frog that was phylogenetically distinct from those described in other amphibians.Conclusions: To our knowledge, this is the first meta-transcriptomic analysis of trypanosomes in native Australian wildlife, expanding the known genetic diversity of these important parasites. We demonstrated that RNA sequencing is sufficiently sensitive to detect low numbers of Trypanosoma transcripts and from diverse hosts and tissues types, thereby representing an effective means to detect trypanosomes that are divergent in genome sequence.
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| 4. |
- Pettersson, John H-O, 1981-, et al.
(författare)
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Meta-Transcriptomic Comparison of the RNA Viromes of the Mosquito Vectors Culex pipiens and Culex torrentium in Northern Europe
- 2019
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Ingår i: Viruses. - : MDPI. - 1999-4915. ; 11:11
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Tidskriftsartikel (refereegranskat)abstract
- Mosquitoes harbor an extensive diversity of 'insect-specific' RNA viruses in addition to those important to human and animal health. However, because most studies of the mosquito virome have been conducted at lower latitudes, little is known about the diversity and evolutionary history of RNA viruses sampled from mosquitoes in northerly regions. Here, we compared the RNA virome of two common northern mosquito species, Culex pipiens and Culex torrentium, collected in south-central Sweden. Following bulk RNA-sequencing (meta-transcriptomics) of 12 libraries, comprising 120 specimens of Cx. pipiens and 150 specimens of Cx. torrentium, we identified 40 viruses (representing 14 virus families) of which 28 were novel based on phylogenetic analysis of the RNA-dependent RNA polymerase (RdRp) protein. Hence, we documented similar levels of virome diversity as in mosquitoes sampled from the more biodiverse lower latitudes. Many viruses were also related to those sampled on other continents, indicative of a widespread global movement and/or long host-virus co-evolution. Although the two mosquito species investigated have overlapping geographical distributions and share many viruses, several viruses were only found at a specific location at this scale of sampling, such that local habitat and geography may play an important role in shaping viral diversity in Culex mosquitoes.
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| 5. |
- Porter, Ashleigh F., et al.
(författare)
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Novel hepaci- and pegi-like viruses in native Australian wildlife and non-human primates
- 2020
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Ingår i: Virus Evolution. - : OXFORD UNIV PRESS. - 2057-1577. ; 6:2
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Tidskriftsartikel (refereegranskat)abstract
- The Flaviviridae family of positive-sense RNA viruses contains important pathogens of humans and other animals, including Zika virus, dengue virus, and hepatitis C virus. The Flaviviridae are currently divided into four genera-Hepacivirus, Pegivirus, Pestivirus, and Flavivirus-each with a diverse host range. Members of the genus Hepacivirus are associated with an array of animal species, including humans, non-human primates, other mammalian species, as well as birds and fish, while the closely related pegiviruses have been identified in a variety of mammalian taxa, also including humans. Using a combination of total RNA and whole-genome sequencing we identified four novel hepaci-like viruses and one novel variant of a known hepacivirus in five species of Australian wildlife. The hosts infected comprised native Australian marsupials and birds, as well as a native gecko (Gehyra lauta). From these data we identified a distinct marsupial clade of hepaci-like viruses that also included an engorged Ixodes holocyclus tick collected while feeding on Australian long-nosed bandicoots (Perameles nasuta). Distinct lineages of hepaci-like viruses associated with geckos and birds were also identified. By mining the SRA database we similarly identified three new hepaci-like viruses from avian and primate hosts, as well as two novel pegi-like viruses associated with primates. The phylogenetic history of the hepaci-and pegi-like viruses as a whole, combined with co-phylogenetic analysis, provided support for virus-host co-divergence over the course of vertebrate evolution, although with frequent cross-species virus transmission. Overall, our work highlights the diversity of the Hepacivirus and Pegivirus genera as well as the uncertain phylogenetic distinction between.
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| 6. |
- Alfsnes, Kristian, et al.
(författare)
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Retrospective meta-transcriptomic identification of severe dengue in a traveller returning from Africa to Sweden, 1990
- 2021
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Ingår i: One Health. - : Elsevier. - 2352-7714. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Pathogens associated with haemorrhagic fever commonly have zoonotic origins. The first documented imported case of likely viral severe haemorrhagic fever in Sweden occurred in 1990. Despite extensive study, no aetiological agent was identified. Following retrospective investigation with total RNA-sequencing of samples collected between 7 and 36 days from onset of symptoms we identified dengue virus 3 (DENV-3) and a human pegivirus (HPgV). We conclude that the patient likely suffered from haemorrhagic symptoms due to an atypical severe and undiagnosed dengue infection.
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| 7. |
- Alfsnes, Kristian, et al.
(författare)
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Tracing and tracking the emergence, epidemiology and dispersal of dengue virus to Africa during the 20th century
- 2021
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Ingår i: One Health. - : Elsevier. - 2352-7714. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- The four mosquito-borne dengue virus serotypes (DENV1-DENV4) cause a high burden of disease throughout the tropical and sub-tropical regions of the world. Nevertheless, their precise epidemiological history in Africa, including when and where they originated and were distributed during the 20th century, remains unclear stressing the need for One Health focused research. Accordingly, we conducted a time-scaled molecular epide-miological reconstruction using publicly available and newly sequenced dengue virus genomes of African origin representing all four serotypes to deduce the most likely temporal and spatial transmission routes of each DENV serotype from their ancestral regions to, within and from Africa. Our analyses suggest that during the 20th century, serotypes DENV1-DENV3 were introduced to Africa from South East Asia on multiple occasions. The earliest evidence recorded indicates introduction of DENV2 during the early-1940s and of DENV1 during the mid-1940s to Western Africa from South East Asia. The analysis also implies an early introduction of DENV4 during the mid-1940s to Western Africa, alongside DENV1, probably originating in South East Asia. Establishment of DENV3 in Africa appears to have occurred later in the 1960s, apparently originating from South East Asia. However, with the re-establishment of DENV in the Americas, following the cessation of the PAHO mosquito control programme during the mid-20th century, evidence of introductions of DENV1 and DENV2 from the Americas to Western Africa was also observed. The data also identify intra-regional circulation of DENV, but also inter-regional dispersal of all four serotypes within Africa, which has led to a high degree of geographical overlap among serotypes. It is also noteworthy that DENV from both Eastern and Western Africa, have been introduced into Central Africa but there is no support for the converse relationship. For serotypes DENV1-DENV3, we observed probable exports from within established African DENV clusters (>= 2 sequences) primarily to Eastern and Southern Asia. Collectively, our findings support the view that all DENV serotypes, apart from DENV4, have been introduced on multiple occasions to Africa, primarily originating from South East Asia, and subsequently to neighbouring regions within Africa.
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| 8. |
- Asghar, Naveed, et al.
(författare)
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Deep sequencing analysis of tick-borne encephalitis virus from questing ticks at natural foci reveals similarities between quasispecies pools of the virus
- 2017
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Ingår i: Journal of General Virology. - : The Microbiology Society. - 0022-1317 .- 1465-2099. ; 98:3, s. 413-421
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Tidskriftsartikel (refereegranskat)abstract
- Every year, tick-borne encephalitis virus (TBEV) causes severe central nervous system infection in 10 000 to 15 000 people in Europe and Asia. TBEV is maintained in the environment by an enzootic cycle that requires a tick vector and a vertebrate host, and the adaptation of TBEV to vertebrate and invertebrate environments is essential for TBEV persistence in nature. This adaptation is facilitated by the error-prone nature of the virus's RNA-dependent RNA polymerase, which generates genetically distinct virus variants called quasispecies. TBEV shows a focal geographical distribution pattern where each focus represents a TBEV hotspot. Here, we sequenced and characterized two TBEV genomes, JP-296 and JP-554, from questing Ixodes ricinus ticks at a TBEV focus in central Sweden. Phylogenetic analysis showed geographical clustering among the newly sequenced strains and three previously sequenced Scandinavian strains, Toro-2003, Saringe-2009 and Mandal-2009, which originated from the same ancestor. Among these five Scandinavian TBEV strains, only Mandal-2009 showed a large deletion within the 3' non-coding region (NCR), similar to the highly virulent TBEV strain Hypr. Deep sequencing of JP-296, JP-554 and Mandal-2009 revealed significantly high quasispecies diversity for JP-296 and JP-554, with intact 3' NCRs, compared to the low diversity in Mandal-2009, with a truncated 3' NCR. Single-nucleotide polymorphism analysis showed that 40% of the single-nucleotide polymorphisms were common between quasispecies populations of JP-296 and JP-554, indicating a putative mechanism for how TBEV persists and is maintained within its natural foci.
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| 9. |
- Ayhan, Nazli, et al.
(författare)
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Field surveys in Croatia and North Macedonia reveal two novel phleboviruses circulating in sandflies
- 2021
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Ingår i: Journal of General Virology. - : Microbiology Society. - 0022-1317 .- 1465-2099. ; 102:11
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Tidskriftsartikel (refereegranskat)abstract
- Sandfly-borne phleboviruses are distributed widely throughout the Mediterranean Basin, presenting a threat to public health in areas where they circulate. However, the true diversity and distribution of pathogenic and apathogenic sandfly-borne phleboviruses remains a key issue to be studied. In the Balkans, most published data rely on serology-based studies although virus isolation has occasionally been reported. Here, we report the discovery of two novel sandfly-borne phleboviruses, provisionally named Zaba virus (ZABAV) and Bregalaka virus (BREV), which were isolated in Croatia and North Macedonia, respectively. This constitutes the first isolation of phleboviruses in both countries. Genetic analysis based on complete coding sequences indicated that ZABAV and BREV are distinct from each other and belong to the genus Phlebovirus, family Phenuiviridae. Phylogenetic and amino acid modelling of viral polymerase shows that ZABAV and BREV are new members of the Salehabad phlebovirus species and the Adana phlebovirus species, respectively. Moreover, sequence-based vector identification suggests that ZABAV is mainly transmitted by Phlebotomus neglectus and BREV is mainly transmitted by Phlebotomus perfiliewi. BREV neutralizing antibodies were detected in 3.3% of human sera with rates up to 16.7% in certain districts, demonstrating that BREV frequently infects humans in North Macedonia. In vitro viral growth kinetics experiments demonstrated viral replication of both viruses in mammalian and mosquito cells. In vivo experimental studies in mice suggest that ZABAV and BREV exhibit characteristics making them possible human pathogens.
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| 10. |
- Bellström, Peter, 1971-, et al.
(författare)
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Canvas som plattform för digitala krisövningar : Några första resultat från en demonstrationsövning
- 2020
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Ingår i: Kursdesign i Canvas. - Karlstad : Karlstads universitet. - 9789178671540 - 9789178671588 ; , s. 11-42
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Övning ger färdighet och det gäller inte bara i traditionell undervisning utan också vid krisledning. Krisledning kännetecknas av att medlemmarna i en krisledningsgrupp ska ansvara för sina respektive verksamhetsområden och genom snabb interaktion och samordning över verksamhetsgränserna mildra effekterna av krisen för organisationen eller samhället som helhet. Det innebär att rollmedvetenhet och kommunikationsförmåga måste tränas för den enskilde så väl som för gruppen som helhet. På gruppnivå är också samverkan och koordinering internt och externt viktigt att öva. Tidigare studier visar att organisationer är intresserade av möjligheten att öva mer via digitala verktyg (Wik et al., 2017). Inom ramen för det till och med 2021 pågående Interregprojektet CriseIT 2 utvecklar vi ett koncept för övningsstöd baserat på lärplattformar. Kapitlet beskriver genom en fallstudie hur en seminarieövning kan genomföras med stöd av lärplattformen Canvas. Data till studien har samlats in genom observationer, enkäter, storgruppsdiskussion och deltagarnas indata till Canvas. Erfarenheter från fallstudien sammanfattas i möjligheter, problem och förbättringsbehov kopplade till Canvas och övningsdesignen, och rekommendationer ges både för krisövning och för undervisning baserad på problematisering och dilemmaövningar i klassrummet.
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