1. Metadata from: First report of watermelon crinkle leaf-associated virus 1 (WCLAV-1) and WCLAV-2 in watermelon in SloveniaAna Vučurović, Irena Bajde, Jakob Brodarič, Anja Pecman, Zala Kogej Zwitter, Veronika Bukvič, Nejc Jakoš, Denis Kutnjak, Mojca Rot, Nataša Mehle, 2025, complete scientific database of research data Keywords: WCLaV-1, WCLaV-2, watermelon, viruses, diagnostics
Published in DiRROS: 02.04.2026; Views: 175; Downloads: 139
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2. Supplementary material: microbiome analysis of groundwaters in the Slovenian Dinaric Karst, a recognized biodiversity hotspot : version v1Katarina Bačnik, Cene Gostinčar, Rok Kostanjšek, Janez Mulec, Monika Novak Babič, Ion Gutiérrez-Aguirre, Nina Gunde-Cimerman, Martina Turk, Denis Kutnjak, 2026, complete scientific database of research data Keywords: Karst cave waters, high-throughput sequencing, viruses, archaea, bacteria, fungi, protozoa
Published in DiRROS: 24.03.2026; Views: 154; Downloads: 172
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3. Microbiome analysis of groundwaters in the Slovenian Dinaric Karst, a recognized biodiversity hotspotKatarina Bačnik, Denis Kutnjak, Cene Gostinčar, Rok Kostanjšek, Janez Mulec, Monika Novak Babič, Ion Gutiérrez-Aguirre, Nina Gunde-Cimerman, Martina Turk, 2026, original scientific article Abstract: Groundwater is the most important source of drinking water supply, irrigation, and industrial use, as well as a habitat for a diverse range of (micro)organisms. Some of the first studies of underground environments were carried out in the Dinaric Karst region of Slovenia, which harbors one of the highest subterranean biodiversities in the world. Despite their ecological importance, groundwater microbial communities remain underexplored. In this study, we conducted a comprehensive microbiome analysis of karst groundwater, investigating the abundance and diversity of viruses, archaea, bacteria, fungi, and protozoa. We detected a high diversity of both prokaryote- and eukaryote-infecting viruses, indicating the connection of subterranean environments with surface waters. In the archaeal community, seven different phyla were identified, dominated by members of "Candidatus Woesearchaeota" and Nitrososphaerota (syn. Thermoproteota). In the bacterial community of majority of the samples, the Pseudomonadota was the most abundant phylum, followed by Bacteroidota, Actinomycetota, and Verrucomicrobiota. Fungal abundance and diversity differed greatly between cave water samples, with the Ascomycota families Cladosporiaceae, Didymellaceae, Aspergillaceae and saprotrophic Basidiomycota detected in all samples. Besides fungi, microscopic eukaryotic diversity consisted of ciliates, copepods and golden-brown algae present in all samples. Differences in microbial communities between the sampling sites highlight the need for tailored site-specific groundwater conservation and monitoring strategies. Moreover, the identification of microbes associated with anthropogenic activities underscores their potential as source-specific indicators of groundwater pollution. As the first holistic overview of microbial diversity of subterranean water, the study establishes a valuable baseline for future research and conservation of these unique karst ecosystems.
Keywords: Karst cave water, high-throughput sequencing, viruses, archaea, bacteria, fungi, protozoa
Published in DiRROS: 02.03.2026; Views: 256; Downloads: 147
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4. Syndromic molecular testing in mechanically ventilated patients with severe pneumonia : a supportive diagnostic approachTina Uršič, Kaja Erzar, Katja Seme, Matjaž Jereb, Franc Strle, Miroslav Petrovec, 2026, original scientific article Abstract: Rapid identification of pathogens is critical in severe pneumonia patients for timely therapy in mechanically ventilated intensive care unit patients. Conventional diagnostics are time-consuming. The Allplex Respiratory Panels 1-4 detect 16 viruses and seven bacteria and provide faster results; however, because this molecular assay does not yield viable organisms, antimicrobial susceptibility testing cannot be performed. We compared conventional diagnostics with commercial panels to evaluate diagnostic performance and clinical utility. In this prospective study, a total of 30 bronchoalveolar lavage fluids and 80 tracheal aspirates were obtained from 110 unique ICU patients with severe pneumonia (January 2014 and April 2016). Conventional diagnostics were performed during illness, whereas testing of these specimens by commercial panels was performed retrospectively. Pathogen detection rates and co-detections were analyzed by pneumonia type (community-acquired, hospital-acquired, and ventilator-associated). Conventional diagnostics detected pathogens in 87 of 110 patients (79.1%) versus 70 of 110 (63.6%) detected by the commercial approach (P = 0.016). Detection of viruses was most frequent, predominantly influenza A and human rhinoviruses; common bacterial detections included Haemophilus influenzae, Legionella pneumophila, and Streptococcus pneumoniae. Co-detections occurred in 12.7% patients by the commercial approach and in 21.8% by the conventional approach, including virus-bacterium co-detections in 10.9% and 14.5% of cases, respectively. The commercial approach missed eight bacterial and four fungal detections identified by conventional methods. Conventional diagnostics showed higher yield in hospital-acquired pneumonia (82.5% vs 50.0%; P = 0.004), whereas both approaches were comparable in community-acquired cases (75% vs 73.4%). Conventional diagnostics (including culture-based methods) provide broader detection and offer the ability for phenotypic antimicrobial susceptibility testing to be performed, whereas commercial panels offer speed; together, they may optimize pathogen detection and therapy in critically ill patients.IMPORTANCESevere pneumonia in critically ill patients remains a major clinical challenge due to its diverse etiology, rapid progression, and the need for timely, targeted therapy. This study demonstrates that conventional diagnostic approaches-combining culture and molecular tests-identify the etiology more effectively than a commercial multiplex PCR-based syndromic panel in ICU patients. While the molecular approach offers faster results, it lacks the breadth of bacterial and fungal targets and does not provide the opportunity for antimicrobial susceptibility testing. Importantly, viral pathogens-particularly influenza A and rhinoviruses-were frequently detected, underscoring their role in severe pneumonia and the relevance of viral-bacterial co-infections. This work highlights that syndromic molecular diagnostics may be valuable for rapid screening or in community-acquired pneumonia but are insufficient for hospital- or ventilator-associated pneumonia. Our findings support a complementary diagnostic strategy to optimize pneumonia management in ICU settings, improve antimicrobial stewardship, and ultimately impact clinical outcomes for patients with life-threatening respiratory infections.
Keywords: bacteria, fungi, intensive care unit, molecular methods, severe pneumonia, viruses
Published in DiRROS: 08.01.2026; Views: 321; Downloads: 207
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5. Paediatric invasive group A streptococcal infections and associations with viral infections in 15 European countries after lifting non-pharmaceutical interventions against SARS-CoV-2 : an interrupted time-series analysisLéa Lenglart, Izel Özmen, David Aguilera-Alonso, Daniel Blazquez-Gamero, Navin P. Boeddha, Emilie Pauline Buddingh, Danilo Buonsenso, Tina Plankar Srovin, Katarina Vincek, 2025, original scientific article Abstract: Background: After lifting non-pharmaceutical interventions (NPIs) against the transmission of SARS-CoV-2, various countries experienced an increase in invasive Group A Streptococcal (iGAS) infections. We aimed to characterise the paediatric outbreak across Europe and to analyse the influence of viral infections. Methods: We conducted an interrupted time-series analysis based on data from 15 European countries from the PEGASUS consortium. We assessed the evolution of the number of iGAS cases aged 1 month to 18 years between 01/01/2018 and 03/31/2024, comparing the post-NPIs period (01-04-2022 until 31-03-2024) to the baseline period (01-01-2018 until 31-03-2020). Further analyses were performed by country, clinical phenotype, age and severity, including sensitivity analyses. We then explored whether certain iGAS phenotypes correlated with trends in RSV, influenza and VZV across countries over time using Google Trends data. Findings: We included 2091 iGAS cases over the study period; 79 children (3.6%) died and 580 (27.7%) required PICU admission. We estimated an overall increase of +229.8% (95% CI (141.9-341.6)) among iGAS cases from October 2022 to March 2024, compared to the baseline period. The observed increases varied across clinical phenotypes, ranging from +62.7% (95% CI (8.3-157.9)) for osteo-articular infections to +238.7% (95% CI 75.8-464.8) for pneumonia. We observed a strong correlation between the incidence of iGAS pneumonia and RSV (Rho: 0.57, 95% CI [0.11-0.79]) and influenza (Rho 0.69, 95% CI 0.35-0.87); and between skin and soft tissue infections and VZV (Rho: 0.73, 95% CI [0.42-0.89]). Interpretation: The patterns observed across Europe during this outbreak demonstrate an association between respiratory viruses as well as VZV, and iGAS.
Keywords: Streptococcus pyogenes, group A streptococcus, invasive streptococcal disease, outbreak, paediatrics, viral infections, viruses, influenza, flu, RSV, respiratory syncytial virus, VZV, varicella, immunity debt, non pharmaceutical interventions
Published in DiRROS: 12.12.2025; Views: 349; Downloads: 243
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6. Validation of molecular diagnostic methods for the detection and identification of tomato mottle mosaic virus (ToMMV-detect) : final reportNataša Mehle, Ana Vučurović, Sabine Grausgruber Groeger, Amandine Lê Van, Mylène Ruh, Heiko Ziebell, 2025, final research report Keywords: validation, plant viruses, tobamovirus, ToMMV
Published in DiRROS: 03.10.2025; Views: 578; Downloads: 255
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7. Vertical transmission of tomato virusesNataša Mehle, Adrian Fox, Antonio Tiberini, Heiko Ziebell, 2025, independent scientific component part or a chapter in a monograph Abstract: The vertical transmission of tomato viruses through seeds and pollen is a significant yet often overlooked pathway for the persistence and global spread of these pathogens. This review provides a comprehensive synthesis of current knowledge on the mechanisms, epidemiological implications, and management strategies of vertically transmitted tomato viruses. While recent advances in diagnostic techniques such as high-throughput sequencing (HTS), have improved virus detection, key research gaps remain in understanding the molecular and ecological dynamics of seed and pollen transmission. The interaction between vertical and horizontal transmission modes complicates virus epidemiology, necessitating an integrated management approach that includes rigorous seed health testing, genetic resistance breeding, and biosecurity measures. Emerging threats, such as resistance-breaking virus strains and the impact of climate change on vector distribution, underscore the need for enhanced surveillance and stronger international regulatory cooperation. This review highlights the need for interdisciplinary research and collaboration to develop sustainable virus mitigation strategies. Future research priorities include optimizing detection methods, exploring next-generation breeding technologies, and strengthening international biosecurity frameworks to safeguard global tomato production against the growing threat of vertically transmitted viruses.
Keywords: Solanum lycopersicum, tomato, vertical virus transmission, high economic impact, seed-transmitted viruses, plant diseases, virology, biology
Published in DiRROS: 26.09.2025; Views: 716; Downloads: 334
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8. Digital PCR genotyping of pepino mosaic virusAmadej Jelenčič, David Dobnik, Alexandra Bogožalec Košir, Nataša Mehle, 2025, independent scientific component part or a chapter in a monograph Abstract: Pepino mosaic virus (PepMV) is a plant pathogen causing significant economic losses in tomato production. Sensitive, reliable, and robust detection methods are crucial for containing the spread of PepMV and reducing its damaging effects. Digital PCR (dPCR) presents several advantages to conventional real-time quantitative PCR (qPCR), including absolute quantification ability, robust quantitative multiplexing capabilities, and straightforward result analysis. Furthermore, dPCR is especially suitable for analysis of complex samples due to its remarkable tolerance to PCR inhibitors, which makes it a promising method for plant virus genotyping. In this chapter, we present two protocols for PepMV genotyping and quantification using one-step reverse transcription digital PCR (RT-dPCR). The first protocol outlines four simplex assays, while the second describes two duplex assays for precise and comprehensive genotyping of PepMV variants.
Keywords: plant viruses, detection, quantification, Pepino mosaic virus, PepMV, digital PCR, dPCR, RT-dPCR, duplex
Published in DiRROS: 08.09.2025; Views: 692; Downloads: 101
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10. 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, original scientific article Abstract: 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.
Keywords: 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
Published in DiRROS: 24.06.2025; Views: 805; Downloads: 582
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