| 1. |
- Akaberi, Dario, 1989-
(författare)
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Identification of protease inhibitors against Flaviviruses and Coronaviruses
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Vector-borne flaviviruses and coronaviruses of zoonotic origins are important human pathogens and represent a serious threat to public health worldwide. Flaviviruses can be found on all continents, apart from Antarctica, where they are transmitted by arthropod vectors causing millions of infections every year. While most of the infections are mild or asymptomatic, flaviviruses like dengue and yellow fever viruses can cause potentially lethal hemorrhagic fever and shock syndrome. Neurotropic flaviviruses like West Nile, Japanese encephalitis, and Tick-borne encephalitis (TBEV) can cause meningoencephalitis with long-term symptoms. Coronaviruses, and in particular betacoronaviruses of zoonotic origin like SARS (2003) and MERS (2012), have been periodically emerging since the early 2000s causing outbreaks of severe respiratory syndrome. The latest example is SARS-CoV-2 that after causing a cluster of infection in the Chinese city of Wuhan, spread all over the world causing at present over 6.9 million deaths. Although vaccines are essential in preventing infections or severe disease and hospitalization in the case of SARS-CoV-2, antivirals represent an extremely valuable tool for treatment and prevention of current and future flavivirus and coronavirus infections. In the work presented in this thesis we have used a combination of in silico and in vitro techniques to identify and test the activity of potential inhibitors of viral proteases. In our first study (paper 1) we unexpectedly identified an HIV protease inhibitor with in vitro activity against ZIKV NS2B-NS3 protease. The inhibitor was identified by virtual screening of a library of known protease inhibitors, evaluated by molecular dynamics simulation and finally tested against recombinant ZIKV protease using a FRET-based enzymatic assay. The same combination of molecular docking and molecular dynamics simulations were also used to correctly predict the activity of a known pan-Flavivirus protease inhibitor against TBEV protease (paper 2). As a result, we were the first to report peptide-based compounds with in vitro activity against TBEV. After the outbreak of the COVID-19 we switched our attention to SARS-CoV-2. We first tested the inhibitory effect of the broad-spectrum antiviral nitric oxide (NO) and found that the NO-releasing compound SNAP had a dose dependent inhibitory effect on SARS-CoV-2 replication in cell-based assays (paper 3). We speculated that SNAP could inhibit SARS-COV-2 protease by trans-nitration of the catalytic Cys145 of SARS-CoV-2 main protease and found that SNAP had a dose dependent inhibitory effect on recombinant SARS-CoV-2 Mpro protease activity in an in vitro enzymatic assay. In our last study (paper 4) we identified a new class of potent SARS-CoV-2 protease inhibitors through the affinity screening of DNA-encoded-chemical libraries containing 4.2 billion compounds. The identified compounds inhibited recombinant SARS-CoV-2 protease with IC50 as low as 25 nM and had a dose dependent antiviral effect in the low micromolar range in infected Calu-3 and Caco-2 cell lines.
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| 3. |
- Dey, Tushar, 1986-, et al.
(författare)
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Antibiotic Residues and Antimicrobial Resistant bacteria in the Poultry Value Chain of Two Indian States
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The poultry industry's rapid expansion has made it a significant global meat source, especially in India, which ranks as the eighth largest broiler meat producer. However, severe concerns have arisen over the increasing antibiotic resistance in low and middle-income countries, including India. This study systematically investigated the prevalence of Non-Typhoidal Salmonella (NTS) and Escherichia coli (E. coli) strains, along with their antimicrobial resistance (AMR) profiles, in poultry samples from Assam and Karnataka states in India. We found high prevalence of NTS (26%) and E. coli (53%) in various poultry samples, with substantial regional variations. Assam and Karnataka contribute differently to the overall NTS prevalence, with Karnataka bearing the highest burden (39% versus 14%). The presence of NTS and E. coli in treated water intended for watering poultry raises concerns about the effectiveness of water disinfection methods. Serovar analysis highlights the dominance of Typhimurium, Kentucky, Infantis and other serovars, some exhibiting multidrug resistance (MDR), including resistance to fluoroquinolones. The emergence of antibiotic-resistant strains, including carbapenem-resistant E. coli, presents a potential decline in treatment options. The study highlights the presence of MDR among NTS and stresses the importance of monitoring resistance profiles to devise effective antimicrobial strategies. The study underscores the necessity of collaborative efforts to combat AMR and ensure food safety, health, and wellbeing on a global scale.
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| 4. |
- Eriksson, Per
(författare)
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Avian Influenza Virus : Deciphering receptor interactions and their role in interspecies transmission
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Influenza A virus (IAV) annually infects approximately 5–15 % of the human population, causing ~500,000 deaths globally. Novel IAVs have emerged and spread pandemically in the human population, but have over time established endemic circulation with reduced pathogenicity causing seasonal influenza. The natural reservoir of IAVs is wild waterfowl. The past pandemics have been associated with host switch and have partly or entirely originated from birds, or adapted via passage through pigs (postulated IAV mixing vessel). Understanding IAV interspecies transmission mechanisms is essential for pandemic preparedness. Enzootic circulation of avian IAV (AIV) is concentrated to a few waterfowl species, while other bird species seldom are infected. A species barrier preventing IAV interspecies transmission has been suggested. To investigate IAV host range and mixing vessels, histochemistry studies were conducted with tissues from avian species, pigs, and humans. Virus adaptation to new hosts was studied by challenging tufted ducks and chickens with mallard-derived AIVs, together with AIV receptor tropism and glycoproteomic analysis of receptor distribution. Finally, receptor and tissue tropism in ducks was studied systematically for AIV (H1–16). More abundant AIV attachment to human than pig tissues was observed, questioning the pig mixing vessel theory. Attachment patterns of AIVs to bird tissues was generally broad with abundant attachment to trachea. However, among ducks, pronounced attachment was observed to colon of Anas spp., suggesting that intestinal infection might be restricted to Anas spp., whereas other species may be susceptible to respiratory infection. Tufted ducks and chickens could not be infected by intraesophageal inoculation further supporting this hypothesis. Glycan array analysis revealed 3’SLN, 3’STF, and their fucosylated and sulfated analogues as main AIV receptors. Moreover, AIV Neu5Acα2,6 recognition was widespread. Avian respiratory and intestinal tracts glycoproteomic analysis revealed that avian and mammalian receptor structures are much more similar than earlier thought. Furthermore, observed AIV subtype titer variation in challenged tufted ducks and chickens did not correlate with virus receptor tropism. In summary, this thesis suggests that IAV receptor recognition, in particular α2,3 vs. α2,6 sialylated receptor structures, is less important for the IAV interspecies barrier than previously thought.
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| 6. |
- Hesson, Jenny C., 1980-
(författare)
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Clearing up Culex Confusion : A Basis for Virus Vector Discrimination in Europe
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Mosquito species of the Culex genus are the enzootic vectors for several bird-associated viruses that cause disease in humans. In Europe, these viruses include Sindbis (SINV), West Nile and Usutu viruses. The morphologically similar females of Cx. torrentium and Cx. pipiens are potential vectors of these viruses, but difficulties in correctly identifying the mosquito species have caused confusion regarding their respective distribution, abundance, ecology, and consequently their importance as vectors. Species-specific knowledge from correctly identified field material is however of crucial importance since previous research shows that the relatively unknown Cx. torrentium is a far more efficient SINV vector than the widely recognized Cx. pipiens. The latter is involved in the transmission of several other viruses, but its potential importance for SINV transmission is debated.In this thesis I describe the development of a molecular method for species identification, based on reliably identified males of Cx. torrentium and Cx. pipiens. This identification method was then used in consecutive studies on the distribution and relative abundance of the two species in Sweden and 12 other European countries, SINV field infection rates in mosquitoes identified to species level, and evaluation of potential trap bias associated with common sampling techniques.The results showed that Cx. torrentium is a far more common species in Europe than previously assumed. In Sweden and Finland, it is the dominant species, accounting for 89% of the sampled Culex population. In central Europe, it is equally common to Cx. pipiens, while Cx. pipiens dominates south of the Alps Mountain range. Larvae of both species are often found together in both artificial containers (e.g. car tires) and natural sites. Also, a trapping bias against Cx. torrentium was revealed for CDC-traps. For the first time, SINV was isolated from species-identified Cx. torrentium and Cx. pipiens mosquitoes caught in the field, with Cx. torrentium being superior in infection rates (36/1,000 vs. 8.2/1,000). Future studies on SINV, as well as other mosquito-borne bird viruses in Europe, can hopefully gain from the baseline information provided here, and from principles of vector discrimination discussed in the thesis.
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| 7. |
- Hoffman, Tove
(författare)
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Dispersal of ticks and their microorganisms by African-Western Palaearctic migratory birds
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In Europe, tick-borne diseases are the most widespread and common vector-borne diseases and their geographical distribution is increasing. The dispersal of ticks depends on the movements of their vertebrate hosts. Avian hosts are more likely to be involved in long-distance range expansion of ticks due to their migration pattern. Billions of birds in the African-Palaearctic migration system migrate biannually between breeding grounds in the Palaearctic and wintering grounds in Africa and thereby create natural links between Africa, Europe, and Asia. In this thesis the dispersal of ticks and their microorganisms by northbound migratory birds utilizing flyways in the African-Western Palaearctic region has been investigated and the association between bird ecology and tick taxon addressed. The results suggest that long-distance migratory birds with wintering regions in Africa are involved in northward dispersal of the tick species Hyalomma rufipes, a known vector or Crimean-Congo hemorrhagic fever virus, and that birds with an open or wetland habitat have more H. rufipes in comparison to birds with a winter habitat comprising forest and shrubs. The results also suggest a role for birds in the ecology of Alkhurma hemorrhagic fever virus, a hemorrhagic flavivirus, and a potential mechanism for dispersal of the virus to new regions, including Europe and Asia Minor. The results did not provide evidence for immature ticks of the Hyalomma marginatum complex and birds having a major role in the ecology and northward dispersal of tick-borne Anaplasma phagocytophilum, a zoonotic bacterium causing febrile illness in humans and domestic animals. However, the results give support to the idea of a divergent enzootic cycle of A. phagocytophilum involving birds as hosts. Finally, the results of this thesis suggest that H. rufipes do not serve as vectors or contribute to the transmission of the tularemia-causing bacterium Francisella tularensis and that migratory birds do not contribute to northward dispersal of F. tularensis-infected ticks. However, the results suggest that migratory birds contribute to northward dispersal of H. rufipes carrying both Francisella and spotted fever group Rickettsia species, including Francisella-like endosymbionts and Rickettsia aeschlimannii. In conclusion, this thesis helps to clarify the knowledge about the dispersal of ticks and the microorganisms they carry by northbound migrating birds in the African-Western Palaearctic region. Furthermore, it highlights the need of establishing surveillance programs for monitoring the risk of introduction and establishment of important exotic tick species, such as H. rufipes, and tick-borne pathogens in the Western Palaearctic.
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| 9. |
- Järhult, Josef, et al.
(författare)
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Environmental levels of oseltamivir induce development of resistance mutation H274Y in influenza A/H1N1 virus in mallards – implications for the risk of an oseltamivir resistant influenza pandemic
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Resistance in influenza is a growing problem. Oseltamivir carboxylate (OC), the active substance of the most widely used antiviral drug oseltamivir (Tamiflu ®), is poorly degraded in sewage treatment plants and surface water. OC has been detected in aquatic environments where the natural influenza reservoir, dabbling ducks, can be exposed to it. To test if resistance can occur in this situation, we infected mallards with influenza A/H1N1 virus and exposed the birds to 0.08 μg /L, 1.00 μg/L and 80.00 μg/L of OC. The resistance mutation H274Y occurred at 1 μg/L and rapidly dominated the viral population at 80 μg/L. The environmental levels of OC are expected to reach this magnitude. IC50 for OC was increased from 1-4 nM to 400-700 nM in H274Y-positive isolates, confirming a resistant phenotype. As influenza viruses can cross the species barrier, resistance to oseltamivir can spread to human-adapted strains with pandemic potential disabling one of the cornerstones in pandemic preparedness planning.
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| 10. |
- Katsaros, Ioannis, et al.
(författare)
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Antiviral Properties of Oxidized Silicon Nitride Against SARS-CoV-2
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The spread of SARS-CoV-2 led to a global pandemic that caused several million deaths. The severity of this pandemic created challenges for scientists worldwide regarding the prevention of the spread of COVID-19, the disease the virus causes. While the use of personal protective equipment and social distancing limited the spread of the virus, high transmission rates were noted. A solution to the issue of viral spread can be partially given by the utilization of antiviral materials for long-term protection against pathogens on environmental surfaces. To this end, nitrides are materials of high interest due to their proven efficiency in inactivating bacteria and viruses. Silicon nitride (Si3N4) is a ceramic material that possesses an inactivation mechanism termed ‘catch and kill’. In this study we hypothesized that a surface-modified Si3N4 material whose hydrophilicity has been increased through a heat treatment could lead to high attachment and inactivation of SARS-CoV-2 virions. Si3N4 powders were oxidized, characterized and the inactivation of SARS-CoV-2 by them was tested. The results showed that oxidized Si3N4 was highly effective in binding and inactivating SARS-CoV-2 after as little as one minute of contact and can be used to inhibit the spread of COVID-19 under certain circumstances.
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