| 1. |
- Malmberg, Maja, et al.
(författare)
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Genetic characterization of a novel adenovirus detected in captive bottlenose dolphin (Tursiops truncates) suffering from self-limiting gastroenteritis
- 2016
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Adenoviruses have a wide host range and are common pathogens in vertebrates. In cetaceans, adenoviruses have only rarely been detected and correlated with disease. A novel adenovirus was recently detected in captive bottlenose dolphin (Tursiops truncates) suffering from self-limiting gastroenteritis. The initial analysis of partial pol and hexon gene sequences indicated that this was a hitherto unknown adenovirus with less than 80% sequence identity to previously published sequences. The aim of this study was to further genetically characterize this novel adenovirus using a high-throughput sequencing approach for whole-genome sequencing. Fecal samples from affected bottlenose dolphins were collected as previously described. Samples were homogenized and centrifuged through filters with 0.22 μm pores. To remove non-viral DNA the filtrate was treated with DNase and RNase prior to DNA extraction. Nextera XT sequencing libraries were sequenced at the MiSeq platform. Sequence reads were assembled using the MIRA assembler. The longest contigs were used to identify the most similar reference genome using BLASTn. To generate a draft consensus sequence, matching contigs were aligned against the reference genome using CodonCode Aligner software. The complete genome sequence was verified using PCR and Sanger sequencing. The analysis of phylogenetic relationships was conducted in MEGA 5 [2]. Gene prediction and annotation were used using PROKKA, MAKER and GeneMark.hmm with heuristic models. High-throughput sequencing allowed the recovery of the complete sequence of Bottlenose dolphin Adenovirus-1 (BdAdV-1). The sequence is 34 040bp and has an ITR of about 220bp. A total of 26 coding sequences were identified out of which 3 were assigned as hypothetical and 23 were functionally annotated. The homology analysis indicates that the most similar genome is the Bottlenose dolphin Adenovirus 2 (KR024710) (71% identity), followed by the California sea lion adenovirus 1 (KJ563221), and then Bovine adenovirus type 2 (AF252854). We here describe the complete sequence of a recently identified adenovirus associated with gastroenteritis in dolphins. This virus is clearly different from previously published adenoviruses, demonstrating less than 72% sequence identity. A more in-depth analysis of the obtained sequence data and predicted proteins should allow predictions to be made regarding e.g. tropism. The study also demonstrate the usefulness of high-throughput sequencing to obtain full-length genomes of genetically divergent viruses.
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| 2. |
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| 3. |
- Hayer, Juliette, et al.
(författare)
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Four novel picornaviruses detected in Magellanic Penguins (Spheniscus magellanicus) in Chile
- 2021
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Ingår i: Virology. - : Elsevier BV. - 0042-6822 .- 1178-122X. ; 560, s. 116-123
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Tidskriftsartikel (refereegranskat)abstract
- Members of the Picornaviridae family comprise a significant burden on the poultry industry, causing diseases such as gastroenteritis and hepatitis. However, with the advent of metagenomics, a number of picornaviruses have now been revealed in apparently healthy wild birds. In this study, we identified four novel viruses belonging to the family Picornaviridae in healthy Magellanic penguins, a near threatened species. All samples were subsequently screened by RT-PCR for these new viruses, and approximately 20% of the penguins were infected with at least one of these viruses. The viruses were distantly related to members of the genera Hepatovirus, Tremovirus, Gruhelivirus and Crahelvirus. Further, they had more than 60% amino acid divergence from other picornaviruses, and therefore likely constitute novel genera. Our results demonstrate the vast undersampling of wild birds for viruses, and we expect the discovery of numerous avian viruses that are related to hepatoviruses and tremoviruses in the future.
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| 5. |
- Andersson, Mathias, et al.
(författare)
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Management Measures to Reduce Continuous Underwater Noise from Shipping
- 2023
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Rapport (refereegranskat)abstract
- Underwater radiated noise (URN) from commercial ships is a significant source of elevated noise levels in the oceans and can have a negative impact on marine wildlife. Noise from commercial shipping places additional stress on the oceans, but is one of the least studied environmental pollutants, and there is an urgent need to reduce the aggregate stress levels. Until recently, reduction of underwater noise has not been prioritised by ship designers, shipowners, or crews. Even within the field of marine management, noise has received limited interest. However, the International Maritime organization (IMO) has adopted global guidelines on URN reduction, which are currently being updated. Within the EU, the Marine Strategy Framework Directive (MSFD 2008/56/EC) Descriptor 11 criteria 11.2, now provides a framework for marine administrators to manage noise by establishing threshold values. Marine management focuses on the total noise load on the marine environment. Management entails several considerations before recommendations can be made. As a first step, interdisciplinary teams need to assess the aggregated noise levels and determine acceptable thresholds based on the local ecosystem, then assess which existing mandates and management tools can be used, and finally assess how effective these mandates have been in improving the environment. These activities must also be managed in a way that is acceptable to various relevant stakeholders, who would need to follow the decisions. The URN from a ship can be affected by the vessel’s design, either during its construction or during upgrades, and balances a trade-off against fuel efficiency. However, the URN can also depend on how the ship is operated. Regulating ship speed is one potential management tool, and its effectiveness needs to be assessed. Other management measures include how shipping lanes are drawn, areas to avoid, financial support, information, etc. This report focuses on possible policy measures that the Swedish authorities could adopt to lower URN by regulating the speed of ships. The report presents an interdisciplinary analysis, using a case study of an area in the southern Kattegat that covered several maritime zones, different national jurisdictions, intensive traffic, and high natural values. An important part of the work was to assess whether existing source models for ship noise could be used for the type of ships that are common in waters around Sweden. In this study, the JOMOPANS-ECHO (J-E) model was used.The J-E model was validated by comparing measurement data from a hydrophone station at Vinga on the Swedish coast that collected data from ships (254 passages) that used the port of Gothenburg. The analysis showed some deviation between the J-E model and measurement data, which could be due to differences in the length and speed of ships in waters around Sweden compared to the ships used in the development of the J-E model. However, this was likely to have negligible impact on the outcome of the case study.Analyses of ship traffic in 2021 showed that 4,511 unique vessels visited the study area at least once. Most ships followed the main routes, but no part of the study area was completely free from ship traffic. About 68% of the ships visited the study area for 1-4 days, while about 32% visited the area more regularly. The most common ship types were General Cargo Ships, Dry Bulk Ships, and Tankers. The ships that on average travelled at highest speeds were RoPax Ships, RoRo Ships, Vehicle Carriers, and Container Ships. The ships were registered in 64 countries. About two percent of the ships were registered in Sweden and about four percent in Denmark.Legal analysis showed that Sweden has the right and the responsibility to take measures to reduce underwater noise from ships to the extent that the noise can be deemed to pollute the marine environment. However, this mainly applies to Sweden’s territorial seas, which cover roughly half the area being studied for this report. In the portion that constitutes Danish territorial sea, Denmark has comparable opportunities for managing URN. In areas that are Swedish or Danish exclusive economic zones (EEZs), the ability to introduce mandatory speed limits is significantly limited. There, the most realistic option would be to request the IMO to establish speed limits, or alternatively to issue a recommendation to navigate at lower speeds, although such guidance could not be enforced on ships that do not voluntarily reduce their speed.It was estimated that lowering the ships' speeds to a hypothetical limit of 11 kn would reduce the average URN levels by 4.4 ± 2 dB, as registered by local receivers in the study area. This speed limit would affect approximately 44% of the ships in the area. A maximum speed of 13 kn would instead reduce the level by 1.9 ± 0.5 dB and would affect 11% of the ships on average. The reduction in noise levels may temporarily be much higher in the immediate vicinity of individual fast ships, and there might be a high degree of variation between different ships.The study and report make it clear that it is a complex task to assess the feasibility and benefit of introducing a specific marine management tool, in this case an enforceable local speed limit. But it is also clear that there are reliable methods to make the preliminary assessments, and that it requires interdisciplinary analyses and competence.
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| 8. |
- Granberg, Fredrik, et al.
(författare)
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Complete Genome Sequence of an African Swine Fever Virus Isolate from Sardinia, Italy
- 2016
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Ingår i: Microbiology Resource Announcements. - 2576-098X. ; 4
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Tidskriftsartikel (refereegranskat)abstract
- Previous genetic characterization of African swine fever virus isolates from the Italian island of Sardinia, where the virus has been present since 1978, has largely been limited to a few selected genomic regions. Here, we report the complete genome sequence of the isolate 47/Ss/08 collected during an outbreak in 2008.
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| 9. |
- Grandi, Giulio, et al.
(författare)
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Morphological and molecular identification of ixodid tick species (Acari: Ixodidae) infesting cattle in Uganda
- 2020
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Ingår i: Parasitology Research. - : Springer Science and Business Media LLC. - 0932-0113 .- 1432-1955. ; 119, s. 2411-2420
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Tidskriftsartikel (refereegranskat)abstract
- In Uganda, the role of ticks in zoonotic disease transmission is not well described, partly, due to limited available information on tick diversity. This study aimed to identify the tick species that infest cattle. Between September and November 2017, ticks (n = 4362) were collected from 5 districts across Uganda (Kasese, Hoima, Gulu, Soroti, and Moroto) and identified morphologically at Uganda Virus Research Institute. Morphological and genetic validation was performed in Germany on representative identified specimens and on all unidentified ticks. Ticks were belonging to 15 species: 8Rhipicephalusspecies (Rhipicephalus appendiculatus,Rhipicephalus evertsi evertsi,Rhipicephalus microplus,Rhipicephalus decoloratus,Rhipicephalus afranicus,Rhipicephalus pulchellus,Rhipicephalus simus, andRhipicephalus sanguineustropical lineage); 5Amblyommaspecies (Amblyomma lepidum,Amblyomma variegatum,Amblyomma cohaerens,Amblyomma gemma, andAmblyomma paulopunctatum); and 2Hyalommaspecies (Hyalomma rufipesandHyalomma truncatum). The most common species wereR. appendiculatus(51.8%),A. lepidum(21.0%),A. variegatum(14.3%),R. evertsi evertsi(8.2%), andR. decoloratus(2.4%). R. afranicusis a new species recently described in South Africa and we report its presence in Uganda for the first time. The sequences ofR. afranicuswere 2.4% divergent from those obtained in Southern Africa. We confirm the presence of the invasiveR. microplusin two districts (Soroti and Gulu). Species diversity was highest in Moroto district (p = 0.004) and geographical predominance by specific ticks was observed (p = 0.001). The study expands the knowledge on tick fauna in Uganda and demonstrates that multiple tick species with potential to transmit several tick-borne diseases including zoonotic pathogens are infesting cattle.
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| 10. |
- Hayer, Juliette, et al.
(författare)
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Identification and molecular characterization of highly divergent RNA viruses in cattle, Uganda
- 2022
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Ingår i: Virus Research. - : Elsevier BV. - 0168-1702 .- 1872-7492. ; 313
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Tidskriftsartikel (refereegranskat)abstract
- The risk for the emergence of novel viral zoonotic diseases in animals and humans in Uganda is high given its geographical location with high biodiversity. We aimed to identify and characterize viruses in 175 blood samples from cattle selected in Uganda using molecular approaches. We identified 8 viral species belonging to 4 families (Flaviviridae, Peribunyaviridae, Reoviridae and Rhabdoviridae) and 6 genera (Hepacivirus, Pestivirus, Orthobunya-virus, Coltivirus, Dinovernavirus and Ephemerovirus). Four viruses were highly divergent and tetantively named Zikole virus (Family: Flaviviridae), Zeboroti virus (Family: Reoviridae), Zebtine virus (Family: Rhabdoviridae) and Kokolu virus (Family: Rhabdoviridae). In addition, Bovine Hepacivirus, Obodhiang virus, Aedes pseudoscutellaris reovirus and Schmallenberg virus were identified for the first time in Ugandan cattle. We report 8 viral species belonging to 4 viral families including divergent ones in the blood of cattle in Uganda. Hence, cattle may be reservoir hosts for likely emergence of novel viruses with pathogenic potential to cause zoonotic diseases in different species with serious public health implications.
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