1. Annual (2024) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota)Jens H. Kuhn, Scott Adkins, Sergey V. Alkhovsky, Wenxia An, Tatjana Avšič-Županc, María A. Ayllón, Katarina Bačnik, Justin Bahl, Anne Balkema-Buschmann, Matthew J. Ballinger, Ion Gutiérrez-Aguirre, Denis Kutnjak, Nataša Mehle, Anja Pecman, Maja Ravnikar, Ana Vučurović, 2025, izvirni znanstveni članek Povzetek: In April 2024, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was expanded by 1 new order, 1 new family, 6 new subfamilies, 34 new genera and 270 new species. One class, two orders and six species were renamed. Seven families and 12 genera were moved; ten species were renamed and moved; and nine species were abolished. This article presents the updated taxonomy of Negarnaviricota as currently accepted by the ICTV, providing an essential annual update on the classification of members of this phylum that deepen understandings of their evolution, and supports critical public health measures for virus identification and tracking.
Ključne besede: Aliusviridae, Arenaviridae, articulaviral, Articulavirales, Artoviridae, Aspiviridae, Bornaviridae, bunyaviral, Bunyavirales, Bunyaviricetes, bunyavirus, Crepuscuviridae, Discoviridae, Elliovirales, Filoviridae, Fimoviridae, Goujianvirales, Hantaviridae, Hareavirales, International Committee on Taxonomy of Viruses (ICTV), jingchuviral, Jingchuvirales, Konkoviridae, Lispiviridae, megaclassification, megataxonomy, mononegaviral, Mononegavirales, muviral, Muvirales, Mymonaviridae, Myriaviridae, naedreviral, Naedrevirales, Nairoviridae, Natareviridae, negarnaviricot, Negarnaviricota, Nyamiviridae, Orthomyxoviridae, Orthornavirae, Paramyxoviridae, Peribunyaviridae, Phasmaviridae, Phenuiviridae, Pneumoviridae, Rhabdoviridae, Riboviria, Sunviridae, Tenuivirus, Tosoviridae, Tospoviridae, Tulasviridae, virus classification, virus nomenclature, virus taxonomy, virology
Objavljeno v DiRROS: 24.06.2025; Ogledov: 134; Prenosov: 69
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2. One-step RT-droplet digital PCR : a breakthrough in the quantification of waterborne RNA virusesNejc Rački, Dany Morisset, Ion Gutiérrez-Aguirre, Maja Ravnikar, 2014, izvirni znanstveni članek Povzetek: Water contamination by viruses has an increasing worldwide impact on human health, and has led to requirements for accurate and quantitative molecular tools. Here, we report the first one-step reverse-transcription droplet digital PCR-based absolute quantification of a RNA virus (rotavirus) in different types of surface water samples. This quantification method proved to be more precise and more tolerant to inhibitory substances than the benchmarking reverse-transcription real-time PCR (RT-qPCR), and needs no standard curve. This new tool is fully amenable for the quantification of viruses in the particularly low concentrations usually found in water samples.
Ključne besede: waterborne virus, quantification, droplet digital PCR, real-time PCR, digital PCR
Objavljeno v DiRROS: 04.03.2025; Ogledov: 354; Prenosov: 200
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3. Detection of rare drug resistance mutations by digital PCR in a human influenza A virus model system and clinical samplesAlexandra S. Whale, Claire Bushell, Paul R. Grant, Simon Cowen, Ion Gutiérrez-Aguirre, Denise M. OʹSullivan, Jana Žel, Mojca Milavec, Carole A. Foy, Eleni Nastouli, Jeremy A. Garson, Jim F. Huggett, 2016, izvirni znanstveni članek Ključne besede: digital PCR, human influenza A viruses
Objavljeno v DiRROS: 26.02.2025; Ogledov: 293; Prenosov: 155
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4. Odkrivanje in z vodo povezana epidemiologija porajajočih se tobamovirusov, ki okužujejo kmetijske rastlineNataša Mehle, Denis Kutnjak, Ana Vučurović, Ion Gutiérrez-Aguirre, Katarina Bačnik, Luka Kranjc, Irena Bajde, Jakob Brodarič, Maja Ravnikar, Olivera Maksimović, Mark Paul Selda Rivarez, Tomaž Curk, Neža Pajek Arambašić, Rok Štravs, 2024, končno poročilo o rezultatih raziskav Ključne besede: diagnostika, rastlinski virusi, ToBRFV, ToMMV, tobamovirusi, epidemiologija, voda kot vir okužb, poročila
Objavljeno v DiRROS: 20.02.2025; Ogledov: 380; Prenosov: 103
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5. Odkrivanje in z vodo povezana epidemiologija porajajočih se tobamovirusov, ki okužujejo kmetijske rastline : aplikativni raziskovalni projekt L4-3179Nataša Mehle, Denis Kutnjak, Tomaž Curk, Neža Pajek Arambašić, Ion Gutiérrez-Aguirre, Rok Štravs, Katarina Bačnik, Luka Kranjc, Irena Bajde, Jakob Brodarič, Miha Kitek, Maja Ravnikar, Olivera Maksimović, Mark Paul Selda Rivarez, Ana Vučurović, 2024, končno poročilo o rezultatih raziskav Ključne besede: ToBRFV, ToMMV, tobamovirusi, epidemiologija, voda kot vir okužb, poročila
Objavljeno v DiRROS: 28.11.2024; Ogledov: 514; Prenosov: 602
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6. Cold plasma within a stable supercavitation bubble - a breakthrough technology for efficient inactivation of viruses in waterArijana Filipić, David Dobnik, Ion Gutiérrez-Aguirre, Maja Ravnikar, Tamara Košir, Špela Baebler, Alja Štern, Bojana Žegura, Martin Petkovšek, Matevž Dular, Miran Mozetič, Rok Zaplotnik, Gregor Primc, 2023, izvirni znanstveni članek Povzetek: Water scarcity, one of the most pressing challenges we face today, has developed for many reasons, including the increasing number of waterborne pollutants that affect the safety of the water environment. Waterborne human, animal and plant viruses represent huge health, environmental, and financial burden and thus it is important to efficiently inactivate them. Therefore, the main objective of this study was to construct a unique device combining plasma with supercavitation and to evaluate its efficiency for water decontamination with the emphasis on inactivation of viruses. High inactivation (>5 log10 PFU/mL) of bacteriophage MS2, a human enteric virus surrogate, was achieved after treatment of 0.43 L of recirculating water for up to 4 min. The key factors in the inactivation were short-lived reactive plasma species that damaged viral RNA. Water treated with plasma for a short time required for successful virus inactivation did not cause cytotoxic effects in the in vitro HepG2 cell model system or adverse effects on potato plant physiology. Therefore, the combined plasma-supercavitation device represents an environmentally-friendly technology that could provide contamination-free and safe water.
Ključne besede: cold plasma, hydrodynamic cavitation, supercavitation, virus inactivation, water decontamination, toxicity assays
Objavljeno v DiRROS: 28.11.2024; Ogledov: 443; Prenosov: 621
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7. Discovery of novel and known viruses associated with toxigenic and non-toxigenic bloom forming diatoms from the Northern Adriatic SeaTimotej Turk Dermastia, Denis Kutnjak, Ion Gutiérrez-Aguirre, Corina P. D. Brussaard, Katarina Bačnik, 2024, izvirni znanstveni članek Povzetek: Algal blooms impact trophic interactions, community structure and element fluxes. Despite playing an important role in the demise of phytoplankton blooms, only few viruses infecting diatoms have been cultured. Pseudo-nitzschia is a widespread diatom genus that commonly blooms in coastal waters and contains toxin-producing species. This study describes the characterization of a novel virus infecting the toxigenic species Pseudo-nitzschia galaxiae isolated from the northern Adriatic Sea. The ssRNA virus PnGalRNAV has 29.5 nm ± 1.2 nm icosahedral virions and a genome size of 8.8 kb. It belongs to the picorna-like Marnaviridae family and shows high specificity for P. galaxiae infecting two genetically and morphologically distinct strains. We found two genetically distinct types of this virus and screening of the global virome database revealed matching sequences from the Mediterranean region and China, suggesting its global distribution. Another virus of similar shape and size infecting Pseudo-nitzschia calliantha was found, but its genome could not be determined. In addition, we have obtained and characterized a new virus that infects Chaetoceros tenuissimus. The replicase protein of this virus is very similar to the previously described ChTenDNAV type-II virus, but it has a unique genome and infection pattern. Our study is an important contribution to the collective diatom virus culture collection and will allow further investigation into how these viruses control diatom bloom termination, carbon export and toxin release in the case of Pseudo-nitzschia.
Ključne besede: algal blooms, diatoms, virus, PnGalRNAV, genome, Adriatic Sea, marine virology, phytoplankton ecology, marine biology
Objavljeno v DiRROS: 23.10.2024; Ogledov: 500; Prenosov: 1044
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8. Recommendations for testing water samples, in particular for tomato brown rugose fruit virusKatarina Bačnik, Ion Gutiérrez-Aguirre, Maja Ravnikar, Nataša Mehle, 2020, elaborat, predštudija, študija Povzetek: Water can be an important source of plant pathogenic viruses. Usually they are present in low concentrations, but environmental waters still represent a potential pathway for virus transmission. Already over 30 years ago, plant viruses have been shown to be present in environmental waters in considerable amounts (Koenig, 1986). Since then, many questions concerning the origin, survival, and spread of plant viruses by water have been raised, especially in the light of increased irrigation and use of hydroponic systems in agriculture (Mehle and Ravnikar 2012). The majority of the plant pathogenic viruses recovered from environmental waters so far are very stable. They can infect plants via the roots without the aid of a vector and often have a wide host range (Mehle and Ravnikar 2012). The release of such viruses from plants can lead to their diffusion in streams, rivers and lakes, thereby ensuring the long-distance spread of viruses that would otherwise remain restricted to limited areas (Mehle et al., 2014; Mehle and Ravnikar, 2012).
Objavljeno v DiRROS: 03.09.2024; Ogledov: 529; Prenosov: 234
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9. The International cookbook for wastewater practitioners : testing wastewater for public health, SARS-CoV-2Bernd Manfred Gawlik, Sara Comero, Daniel A. Deere, Gertjan Medema, Ismahane Remonnay, Jean-François Loret, Ana Maria de Roda Husman, Stephanie Rinck-Pfeiffer, Shelesh Agrawal, Ion Gutiérrez-Aguirre, 2024, končno poročilo o rezultatih raziskav Povzetek: During the 2020-2023 COVID-19 Global Public Health Emergency of International Concern, rapid progress was made with the application of Wastewater-Based Surveillance (WBS) (also known as Wastewater-Based Epidemiology (WBE)) to provide population-scale evidence of SARS-CoV-2 shedding into wastewater. The information gained was used to help monitor, communicate, and manage the COVID-19 pandemic.
Rapid and significant innovations in the field of WBS were realised in parallel in multiple jurisdictions globally. Global collaboration resulted in step-change improvements in multiple aspects of WBS simultaneously, including: health sector leadership; integration with public health surveillance; social and ethical guidance; high-level tactical wastewater catchment sampling strategies; wastewater sampling techniques; transport and storage of samples; laboratory analysis; normalisation and standardisation; data analysis and interpretation; and communication of results.
Innovations in WBS relating to COVID-19 continue to take place, and the benefits of those improvements are now being applied to other targets, such as other pathogens and genes. There are many journal articles and other publications describing these innovations. However, valuable lessons from the COVID-19 pandemic for WBS have not been systematically documented into a practical and readily digestible format.
The purpose of this ‘Cookbook’ is to provide practical and proven ‘recipes’ for WBS for SARS-CoV-2 for two reasons: firstly to help those considering new or extended WBS programmes targeting SARS-CoV-2; and secondly to provide a valuable record of what has been learned from the 2020- 2023 period to help inform WBS programmes to respond to future pandemics and for surveillance of other targets.
The Cookbook is structured into eight parts: 1. Introduction; 2. High-level Overview; 3. Health Sector Perspectives; 4. Methods and Methodologies - From data to action; 5. Methods and Methodologies - Measurement and testing; 6. Methods and Methodologies - Sampling; 6. Methods and Methodologies - Transportation protocols; 8. Conclusions. Multiple authors have contributed to each part, primarily from the European Union, as well as others from the global community of practice.
The Cookbook has been drafted by a global team of authors, with one or more lead authors identified for each chapter and working with their co-authors. The chapters were then subjected to extensive peer review from the external review group. These authors and reviewers are acknowledged in the Cookbook.
Ključne besede: coronavirus disease, disease surveillance, innovation, public health, report, sampling, standardisation, testing, wastewater
Objavljeno v DiRROS: 02.09.2024; Ogledov: 598; Prenosov: 5081
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10. Cyanobacterial cyclic peptides can disrupt cytoskeleton organization in human astrocytes : a contribution to the understanding of the systemic toxicity of cyanotoxinsAnja Bubik, Robert Frangež, Monika C. Žužek, Ion Gutiérrez-Aguirre, Tamara Lah Turnšek, Bojan Sedmak, 2024, izvirni znanstveni članek Povzetek: The systemic toxicity of cyclic peptides produced by cyanobacteria (CCPs) is not yet completely understood. Apart from the most known damages to the liver and kidneys, symptoms of their neurotoxicity have also been reported. Hepatotoxic CCPs, like microcystins, as well as non-hepatotoxic anabaenopeptins and planktopeptins, all exhibit cytotoxic and cytostatic effects on mammalian cells. However, responses of different cell types to CCPs depend on their specific modes of interaction with cell membranes. This study demonstrates that non-hepatotoxic planktopeptin BL1125 and anabaenopeptins B and F, at concentrations up to 10 µM, affect normal and tumor human astrocytes (NHA and U87-GM) in vitro by their almost immediate insertion into the lipid monolayer. Like microcystin-LR (up to 1 µM), they inhibit Ser/Thr phosphatases and reorganize cytoskeletal elements, with modest effects on their gene expression. Based on the observed effects on intermediate filaments and intermediate filament linkage elements, their direct or indirect influence on tubulin cytoskeletons via post-translational modifications, we conclude that the basic mechanism of CCP toxicities is the induction of inter- and intracellular communication failure. The assessed inhibitory activity on Ser/Thr phosphatases is also crucial since the signal transduction cascades are modulated by phosphorylation/dephosphorylation processes.
Ključne besede: astrocytes, cyclic cyanobacterial peptides, cytoskeletal organization, Ser/Thr phosphatases, systemic toxicity, cyanobacteria
Objavljeno v DiRROS: 28.08.2024; Ogledov: 763; Prenosov: 537
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