TY - JOUR AB - Remdesivir (RDV) is a broad-spectrum nucleotide analog prodrug approved for the treatment of COVID-19 in hospitalized and non-hospitalized patients with clinical benefit demonstrated in multiple Phase 3 trials. Here we present SARS-CoV-2 resistance analyses from the Phase 3 SIMPLE clinical studies evaluating RDV in hospitalized participants with severe or moderate COVID-19 disease. The severe and moderate studies enrolled participants with radiologic evidence of pneumonia and a room-air oxygen saturation of ≤94% or >94%, respectively. Virology sample collection was optional in the study protocols. Sequencing and related viral load data were obtained retrospectively from participants at a subset of study sites with local sequencing capabilities (10 of 183 sites) at timepoints with detectable viral load. Among participants with both baseline and post-baseline sequencing data treated with RDV, emergent Nsp12 substitutions were observed in 4 of 19 (21%) participants in the severe study and none of the 2 participants in the moderate study. The following 5 substitutions emerged: T76I, A526V, A554V, E665K, and C697F. The substitutions T76I, A526V, A554V, and C697F had an EC50 fold change of ≤1.5 relative to the wildtype reference using a SARS-CoV-2 subgenomic replicon system, indicating no significant change in the susceptibility to RDV. The phenotyping of E665K could not be determined due to a lack of replication. These data reveal no evidence of relevant resistance emergence and further confirm the established efficacy profile of RDV with a high resistance barrier in COVID-19 patients. AU - Hedskog, C.* AU - Spinner, C.D.* AU - Protzer, U. AU - Hoffmann, D.* AU - Ko, C. AU - Gottlieb, R.L.* AU - Askar, M.* AU - Roestenberg, M.* AU - de Vries, J.J.C.* AU - Carbo, E.C.* AU - Martin, R.* AU - Li, J.* AU - Han, D.* AU - Rodriguez, L.* AU - Parvangada, A.* AU - Perry, J.K.* AU - Ferrer, R.* AU - Anton, A.* AU - Andres, C.* AU - Casares, V.* AU - Günthard, H.F.* AU - Huber, M.* AU - McComsey, G.A.* AU - Sadri, N.* AU - Aberg, J.A.* AU - van Bakel, H.* AU - Porter, D.P.* C1 - 70550 C2 - 55668 TI - No remdesivir resistance observed in the phase 3 severe and moderate COVID-19 SIMPLE trials. JO - Viruses VL - 16 IS - 4 PY - 2024 SN - 1999-4915 ER - TY - JOUR AB - This study analyzes immune responses to SARS-CoV-2 vaccination and infection, including asymptomatic cases, focusing on infection risks during the Omicron wave, particularly among high-risk healthcare workers. In the KoCo-Impf study, we monitored 6088 vaccinated participants in Munich aged 18 and above. From 13 May to 31 July 2022, 2351 participants were follow-uped. Logistic regression models evaluated primary, secondary, and breakthrough infections (BTIs). Roche Elecsys® Anti-SARS-CoV-2 assays detected prior infections (via anti-Nucleocapsid antibodies) and assessed vaccination/infection impact (via anti-Spike antibodies) using dried blood spots. Our findings revealed an anti-Nucleocapsid seroprevalence of 44.1%. BTIs occurred in 38.8% of participants, with reinfections in 48.0%. Follow-up participation was inversely associated with current smoking and non-vaccination, while significantly increasing with age and receipt of three vaccine doses. Larger household sizes and younger age increased infection risks, whereas multiple vaccinations and older age reduced them. Household size and specific institutional subgroups were risk factors for BTIs. The anti-Nucleocapsid value prior to the second infection was significantly associated with reinfection risk. Institutional subgroups influenced all models, underscoring the importance of tailored outbreak responses. The KoCo-Impf study underscores the importance of vaccination, demographic factors, and institutional settings in understanding SARS-CoV-2 infection risks during the Omicron wave. AU - Janke, C.* AU - Rubio-Acero, R.* AU - Weigert, M.* AU - Reinkemeyer, C.* AU - Khazaei, Y.* AU - Kleinlein, L.* AU - Le Gleut, R. AU - Radon, K.* AU - Hannes, M. AU - Picasso, F.* AU - Lucke, A.E.* AU - Plank, M.* AU - Kotta, I.C.* AU - Paunovic, I.* AU - Zhelyazkova, A.* AU - Noreña, I.* AU - Winter, S.* AU - Hoelscher, M. AU - Wieser, A.* AU - Küchenhoff, H.* AU - Castelletti, N. C1 - 72159 C2 - 56466 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Understanding the omicron variant impact in healthcare workers: Insights from the prospective COVID-19 post-immunization serological cohort in Munich (KoCo-Impf) on risk factors for breakthrough and reinfections. JO - Viruses VL - 16 IS - 10 PB - Mdpi PY - 2024 SN - 1999-4915 ER - TY - JOUR AB - Hepatitis B virus (HBV) is a major driver of chronic hepatic inflammation, which regularly leads to liver cirrhosis or hepatocellular carcinoma. Immediate innate immune cell response is crucial for the rapid clearance of the infection. Here, natural killer (NK) cells play a pivotal role in direct cytotoxicity and the secretion of antiviral cytokines as well as regulatory function. The aim of this study was to further elucidate NK cell responses triggered by an HBV infection. Therefore, we optimized HBV in vitro models that reliably stimulate NK cells using hepatocyte-like HepG2 cells expressing the Na+-taurocholate co-transporting polypeptide (NTCP) and HepaRG cells. Immune cells were acquired from healthy platelet donors. Initially, HepG2-NTCP cells demonstrated higher viral replication compared to HepaRG cells. Co-cultures with immune cells revealed increased production of interferon-γ and tumor necrosis factor-α by NK cells, which was no longer evident in isolated NK cells. Likewise, the depletion of monocytes and spatial separation from target cells led to the absence of the antiviral cytokine production of NK cells. Eventually, the combined co-culture of isolated NK cells and monocytes led to a sufficient cytokine response of NK cells, which was also apparent when communication between the two immune cell subpopulations was restricted to soluble factors. In summary, our study demonstrates antiviral cytokine production by NK cells in response to HBV+ HepG2-NTCP cells, which is dependent on monocyte bystander activation. AU - Kupke, P.* AU - Brucker, J.* AU - Wettengel, J.M. AU - Protzer, U. AU - Wenzel, J.J.* AU - Schlitt, H.J.* AU - Geissler, E.K.* AU - Werner, J.M.* C1 - 70763 C2 - 55884 TI - Cytokine response of natural killer cells to Hepatitis B virus infection depends on monocyte co-stimulation. JO - Viruses VL - 16 IS - 5 PY - 2024 SN - 1999-4915 ER - TY - JOUR AB - Huge phages have genomes larger than 200 kilobases, which are particularly interesting for their genetic inventory and evolution. We screened 165 wastewater metagenomes for the presence of viral sequences. After identifying over 600 potential huge phage genomes, we reduced the dataset using manual curation by excluding viral contigs that did not contain viral protein-coding genes or consisted of concatemers of several small phage genomes. This dataset showed seven fully annotated huge phage genomes. The phages grouped into distinct phylogenetic clades, likely forming new genera and families. A phylogenomic analysis between our huge phages and phages with smaller genomes, i.e., less than 200 kb, supported the hypothesis that huge phages have undergone convergent evolution. The genomes contained typical phage protein-coding genes, sequential gene cassettes for metabolic pathways, and complete inventories of tRNA genes covering all standard and rare amino acids. Our study showed a pipeline for huge phage analyses that may lead to new enzymes for therapeutic or biotechnological applications. AU - Kallies, R.* AU - Hu, D.* AU - Abdulkadir, N.* AU - Schloter, M. AU - Rocha, U.* C1 - 69039 C2 - 53821 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Identification of huge phages from wastewater metagenomes. JO - Viruses VL - 15 IS - 12 PB - Mdpi PY - 2023 SN - 1999-4915 ER - TY - JOUR AB - Antibody studies analyze immune responses to SARS-CoV-2 vaccination and infection, which is crucial for selecting vaccination strategies. In the KoCo-Impf study, conducted between 16 June and 16 December 2021, 6088 participants aged 18 and above from Munich were recruited to monitor antibodies, particularly in healthcare workers (HCWs) at higher risk of infection. Roche Elecsys® Anti-SARS-CoV-2 assays on dried blood spots were used to detect prior infections (anti-Nucleocapsid antibodies) and to indicate combinations of vaccinations/infections (anti-Spike antibodies). The anti-Spike seroprevalence was 94.7%, whereas, for anti-Nucleocapsid, it was only 6.9%. HCW status and contact with SARS-CoV-2-positive individuals were identified as infection risk factors, while vaccination and current smoking were associated with reduced risk. Older age correlated with higher anti-Nucleocapsid antibody levels, while vaccination and current smoking decreased the response. Vaccination alone or combined with infection led to higher anti-Spike antibody levels. Increasing time since the second vaccination, advancing age, and current smoking reduced the anti-Spike response. The cumulative number of cases in Munich affected the anti-Spike response over time but had no impact on anti-Nucleocapsid antibody development/seropositivity. Due to the significantly higher infection risk faced by HCWs and the limited number of significant risk factors, it is suggested that all HCWs require protection regardless of individual traits. AU - Reinkemeyer, C.* AU - Khazaei, H.* AU - Weigert, M.* AU - Hannes, M.* AU - Le Gleut, R. AU - Plank, M.* AU - Winter, S.* AU - Noreña, I.* AU - Meier, T.* AU - Xu, L.* AU - Rubio-Acero, R.* AU - Wiegrebe, S.* AU - Le Thi, T.G.* AU - Fuchs, C. AU - Radon, K.* AU - Paunovic, I.* AU - Janke, C.* AU - Wieser, A.* AU - Küchenhoff, H.* AU - Hoelscher, M.* AU - Castelletti, N. C1 - 68051 C2 - 54529 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - The prospective COVID-19 post-immunization serological cohort in Munich (KoCo-Impf): Risk factors and determinants of immune response in healthcare workers. JO - Viruses VL - 15 IS - 7 PB - Mdpi PY - 2023 SN - 1999-4915 ER - TY - JOUR AB - Bacteriophage therapy holds promise in addressing the antibiotic-resistance crisis, globally and in Germany. Here, we provide an overview of the current situation (2023) of applied phage therapy and supporting research in Germany. The authors, an interdisciplinary group working on patient-focused bacteriophage research, addressed phage production, phage banks, susceptibility testing, clinical application, ongoing translational research, the regulatory situation, and the network structure in Germany. They identified critical shortcomings including the lack of clinical trials, a paucity of appropriate regulation and a shortage of phages for clinical use. Phage therapy is currently being applied to a limited number of patients as individual treatment trials. There is presently only one site in Germany for large-scale good-manufacturing-practice (GMP) phage production, and one clinic carrying out permission-free production of medicinal products. Several phage banks exist, but due to varying institutional policies, exchange among them is limited. The number of phage research projects has remarkably increased in recent years, some of which are part of structured networks. There is a demand for the expansion of production capacities with defined quality standards, a structured registry of all treated patients and clear therapeutic guidelines. Furthermore, the medical field is still poorly informed about phage therapy. The current status of non-approval, however, may also be regarded as advantageous, as insufficiently restricted use of phage therapy without adequate scientific evidence for effectiveness and safety must be prevented. In close coordination with the regulatory authorities, it seems sensible to first allow some centers to treat patients following the Belgian model. There is an urgent need for targeted networking and funding, particularly of translational research, to help advance the clinical application of phages. AU - Willy, C.* AU - Bugert, J.J.* AU - Classen, A.Y.* AU - Deng, L. AU - Düchting, A.* AU - Gross, J.* AU - Hammerl, J.A.* AU - Korf, I.H.E.* AU - Kühn, C.* AU - Lieberknecht-Jouy, S.* AU - Rohde, C.* AU - Rupp, M.* AU - Vehreschild, M.J.G.T.* AU - Vogele, K.* AU - Wienecke, S.* AU - Witzenrath, M.* AU - Würstle, S.* AU - Ziehr, H.* AU - Moelling, K.* AU - Broecker, F.* C1 - 67513 C2 - 54078 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Phage therapy in Germany-update 2023. JO - Viruses VL - 15 IS - 2 PB - Mdpi PY - 2023 SN - 1999-4915 ER - TY - JOUR AB - The highly virulent Newcastle disease virus (NDV) isolates typically result in severe systemic pathological changes and high mortality in Newcastle disease (ND) illness, whereas avirulent or low-virulence NDV strains can cause subclinical disease with no morbidity and even asymp-tomatic infections in birds. However, understanding the host’s innate immune responses to infection with either a highly virulent strain or an avirulent strain, and how this response may contribute to severe pathological damages and even mortality upon infection with the highly virulent strain, remain limited. Therefore, the differences in epigenetic and pathogenesis mechanisms between the highly virulent and avirulent strains were explored, by transcriptional profiling of chicken embryonic visceral tissues (CEVT), infected with either the highly virulent NA-1 strain or the avirulent vaccine LaSota strain using RNA-seq. In our current paper, severe systemic pathological changes and high mortality were only observed in chicken embryos infected with the highly virulent NA-1 strains, although the propagation of viruses exhibited no differences between NA-1 and LaSota. Furthermore, virulent NA-1 infection caused intense innate immune responses and severe metabolic disorders in chicken EVT at 36 h post-infection (hpi), instead of 24 hpi, based on the bioinformatics analysis results for the differentially expressed genes (DEGs) between NA-1 and LaSota groups. Notably, an acute hyperinflammatory response, characterized by upregulated inflammatory cytokines, an uncontrolled host immune defense with dysregulated innate immune response-related signaling pathways, as well as severe metabolic disorders with the reorganization of host–cell metabolism were involved in the host defense response to the CEVT infected with the highly virulent NA-1 strain compared to the avirulent vaccine LaSota strain. Taken together, these results indicate that not only the host’s uncontrolled immune response itself, but also the metabolic disorders with viruses hijacking host cell metabolism, may contribute to the pathogenesis of the highly virulent strain in ovo. AU - Cheng, S.* AU - Liu, X.* AU - Mu, J.* AU - Yan, W.* AU - Wang, M.* AU - Chai, H.* AU - Sha, Y.* AU - Jiang, S.* AU - Wang, S.* AU - Ren, Y.* AU - Gao, C.* AU - Ding, Z.* AU - Stöger, T. AU - Tseren-Ochir, E.O.* AU - Dodovski, A.* AU - Alfonso, P.* AU - Mingala, C.N.* AU - Yin, R.* C1 - 65041 C2 - 52371 TI - Intense innate immune responses and severe metabolic disorders in chicken embryonic visceral tissues caused by infection with highly virulent newcastle disease virus compared to the avirulent virus: A bioinformatics analysis. JO - Viruses VL - 14 IS - 5 PY - 2022 SN - 1999-4915 ER - TY - JOUR AB - Viruses are the cause of a considerable burden to human, animal and plant health, while on the other hand playing an important role in regulating entire ecosystems. The power of new sequencing technologies combined with new tools for processing "Big Data" offers unprecedented opportunities to answer fundamental questions in virology. Virologists have an urgent need for virus-specific bioinformatics tools. These developments have led to the formation of the European Virus Bioinformatics Center, a network of experts in virology and bioinformatics who are joining forces to enable extensive exchange and collaboration between these research areas. The EVBC strives to provide talented researchers with a supportive environment free of gender bias, but the gender gap in science, especially in math-intensive fields such as computer science, persists. To bring more talented women into research and keep them there, we need to highlight role models to spark their interest, and we need to ensure that female scientists are not kept at lower levels but are given the opportunity to lead the field. Here we showcase the work of the EVBC and highlight the achievements of some outstanding women experts in virology and viral bioinformatics. AU - Hufsky, F.* AU - Abecasis, A.* AU - Agudelo-Romero, P.* AU - Bletsa, M.* AU - Brown, K.* AU - Claus, C.* AU - Deinhardt-Emmer, S.* AU - Deng, L.* AU - Friedel, C.C.* AU - Gismondi, M.I.* AU - Kostaki, E.G.* AU - Kuhnert, D.* AU - Kulkarni-Kale, U.* AU - Metzner, K.J.* AU - Meyer, I.M.* AU - Miozzi, L.* AU - Nishimura, L.* AU - Paraskevopoulou, S.* AU - Perez-Cataluna, A.* AU - Rahlff, J.* AU - Thomson, E.* AU - Tumescheit, C.* AU - van der Hoek, L.* AU - Van Espen, L.* AU - Vandamme, A.* AU - Zaheri, M.* AU - Zuckerman, N.* AU - Marz, M.* C1 - 65884 C2 - 52566 TI - Women in the European virus bioinformatics center. JO - Viruses VL - 14 IS - 7 PY - 2022 SN - 1999-4915 ER - TY - JOUR AB - Human endogenous retrovirus (HERVs), normally silenced by methylation or mutations, can be reactivated by multiple environmental factors, including infections with exogenous viruses. In this work, we investigated the transcriptional activity of HERVs in human A549 cells infected by two wild-type (PR8M, SC35M) and one mutated (SC35MΔNS1) strains of Influenza A virus (IAVs). We found that the majority of differentially expressed HERVs (DEHERVS) and genes (DEGs) were up-regulated in the infected cells, with the most significantly enriched biological processes associated with the genes differentially expressed exclusively in SC35MΔNS1 being linked to the immune system. Most DEHERVs in PR8M and SC35M are mammalian apparent LTR retrotransposons, while in SC35MΔNS1, more HERV loci from the HERVW9 group were differentially expressed. Furthermore, up-regulated pairs of HERVs and genes in close chromosomal proximity to each other tended to be associated with immune responses, which implies that specific HERV groups might have the potential to trigger specific gene networks and influence host immunological pathways. AU - Liu, H.* AU - Bergant, V.* AU - Frishman, G. AU - Ruepp, A. AU - Pichlmair, A.* AU - Vincendeau, M. AU - Frishman, D.* C1 - 65829 C2 - 52536 TI - Influenza A virus infection reactivates human endogenous retroviruses associated with modulation of antiviral immunity. JO - Viruses VL - 14 IS - 7 PY - 2022 SN - 1999-4915 ER - TY - JOUR AB - Flavivirus outbreaks require fast and reliable diagnostics that can be easily adapted to newly emerging and re-emerging flaviviruses. Due to the serological cross-reactivity among fla-vivirus antibodies, neutralization tests (NT) are considered the gold standard for sero-diagnostics. Here, we first established wild-type single-round infectious virus replicon particles (VRPs) by packaging a yellow fever virus (YFV) replicon expressing Gaussia luciferase (Gluc) with YFV structural proteins in trans using a double subgenomic Sindbis virus (SINV) replicon. The latter expressed the YFV envelope proteins prME via the first SINV subgenomic promoter and the capsid protein via a second subgenomic SINV promoter. VRPs were produced upon co-electroporation of replicon and packaging RNA. Introduction of single restriction enzyme sites in the packaging construct flanking the prME sequence easily allowed to exchange the prME moiety resulting in chimeric VRPs that have the surface proteins of other flaviviruses including dengue virus 1-4, Zika virus, West Nile virus, and tick-borne encephalitis virus. Besides comparing the YF-VRP based NT assay to a YF reporter virus NT assay, we analyzed the neutralization efficiencies of different human anti-fla-vivirus sera or a monoclonal antibody against all established VRPs. The assays were performed in a 96-well high-throughput format setting with Gluc as readout in comparison to classical plaque reduction NTs indicating that the VRP-based NT assays are suitable for high-throughput analyses of neutralizing flavivirus antibodies. AU - Lücke, A.C.* AU - Vom Hemdt, A.* AU - Wieseler, J.* AU - Fischer, C.* AU - Feldmann, M.* AU - Rothenfußer, S. AU - Drexler, J.F.* AU - Kümmerer, B.M.* C1 - 64336 C2 - 52184 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - High-throughput platform for detection of neutralizing antibodies using flavivirus reporter replicon particles. JO - Viruses VL - 14 IS - 2 PB - Mdpi PY - 2022 SN - 1999-4915 ER - TY - JOUR AB - Antibiotic resistance causes around 700,000 deaths a year worldwide. Without immediate action, we are fast approaching a post-antibiotic era in which common infections can result in death. Pseudomonas aeruginosa is the leading cause of nosocomial infection and is also one of the three bacterial pathogens in the WHO list of priority bacteria for developing new antibiotics against. A viable alternative to antibiotics is to use phages, which are bacterial viruses. Yet, the isolation of phages that efficiently kill their target bacteria has proven difficult. Using a combination of phages and antibiotics might increase treatment efficacy and prevent the development of resistance against phages and/or antibiotics, as evidenced by previous studies. Here, in vitro populations of a Pseudomonas aeruginosa strain isolated from a burn patient were treated with a single phage, a mixture of two phages (used simultaneously and sequentially), and the combination of phages and antibiotics (at sub-minimum inhibitory concentration (MIC) and MIC levels). In addition, we tested the stability of these phages at different temperatures, pH values, and in two burn ointments. Our results show that the two-phages-one-antibiotic combination had the highest killing efficiency against the P. aeruginosa strain. The phages tested showed low stability at high temperatures, acidic pH values, and in the two ointments. This work provides additional support for the potential of using combinations of phage-antibiotic cocktails at sub-MIC levels for the treatment of multidrug-resistant P. aeruginosa infections. AU - Aghaee, B.L.* AU - Khan Mirzaei, M. AU - Alikhani, M.Y.* AU - Mojtahedi, A.* AU - Maurice, C.F.* C1 - 61447 C2 - 50255 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Improving the inhibitory effect of phages against Pseudomonas aeruginosa isolated from a burn patient using a combination of phages and antibiotics. JO - Viruses VL - 13 IS - 2 PB - Mdpi PY - 2021 SN - 1999-4915 ER - TY - JOUR AB - Coronavirus disease 2019 (COVID-19), caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), comprises mild courses of disease as well as progression to severe disease, characterised by lung and other organ failure. The immune system is considered to play a crucial role for the pathogenesis of COVID-19, although especially the contribution of innate-like T cells remains poorly understood. Here, we analysed the phenotype and function of mucosal-associated invariant T (MAIT) cells, innate-like T cells with potent antimicrobial effector function, in patients with mild and severe COVID-19 by multicolour flow cytometry. Our data indicate that MAIT cells are highly activated in patients with COVID-19, irrespective of the course of disease, and express high levels of proinflammatory cytokines such as IL-17A and TNFα ex vivo. Of note, expression of the activation marker HLA-DR positively correlated with SAPS II score, a measure of disease severity. Upon MAIT cell-specific in vitro stimulation, MAIT cells however failed to upregulate expression of the cytokines IL-17A and TNFα, as well as cytolytic proteins, that is, granzyme B and perforin. Thus, our data point towards an altered cytokine expression profile alongside an impaired antibacterial and antiviral function of MAIT cells in COVID-19 and thereby contribute to the understanding of COVID-19 immunopathogenesis. AU - Deschler, S.* AU - Kager, J.* AU - Erber, J.* AU - Fricke, L.* AU - Koyumdzhieva, P.* AU - Georgieva, A.* AU - Lahmer, T.* AU - Wiessner, J.R.* AU - Voit, F.* AU - Schneider, J.* AU - Horstmann, J.* AU - Iakoubov, R.* AU - Treiber, M.* AU - Winter, C.* AU - Ruland, J.* AU - Busch, D.H.* AU - Knolle, P.A.* AU - Protzer, U. AU - Spinner, C.D.* AU - Schmid, R.M.* AU - Quante, M.* AU - Böttcher, K.* C1 - 61343 C2 - 50172 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Mucosal-associated invariant T (MAIT) cells are highly activated and functionally impaired in COVID-19 patients. JO - Viruses VL - 13 IS - 2 PB - Mdpi PY - 2021 SN - 1999-4915 ER - TY - JOUR AB - The hepatitis C virus (HCV) is capable of spreading within a host by two different transmission modes: cell-free and cell-to-cell. However, the contribution of each of these transmission mechanisms to HCV spread is unknown. To dissect the contribution of these different transmission modes to HCV spread, we measured HCV lifecycle kinetics and used an in vitro spread assay to monitor HCV spread kinetics after a low multiplicity of infection in the absence and presence of a neutralizing antibody that blocks cell-free spread. By analyzing these data with a spatially explicit mathematical model that describes viral spread on a single-cell level, we quantified the contribution of cell-free, and cell-to-cell spread to the overall infection dynamics and show that both transmission modes act synergistically to enhance the spread of infection. Thus, the simultaneous occurrence of both transmission modes represents an advantage for HCV that may contribute to viral persistence. Notably, the relative contribution of each viral transmission mode appeared to vary dependent on different experimental conditions and suggests that viral spread is optimized according to the environment. Together, our analyses provide insight into the spread dynamics of HCV and reveal how different transmission modes impact each other. AU - Durso-Cain, K.* AU - Kumberger, P.* AU - Schälte, Y. AU - Fink, T.* AU - Dahari, H.* AU - Hasenauer, J. AU - Uprichard, S.L.* AU - Graw, F.* C1 - 62667 C2 - 50922 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - HCV spread kinetics reveal varying contributions of transmission modes to infection dynamics. JO - Viruses VL - 13 IS - 7 PB - Mdpi PY - 2021 SN - 1999-4915 ER - TY - JOUR AB - Many recent studies highlight the fundamental importance of viruses. Besides their important role as human and animal pathogens, their beneficial, commensal or harmful functions are poorly understood. By developing and applying tailored bioinformatical tools in important virological models, the Marie Skłodowska-Curie Initiative International Training Network VIROINF will provide a better understanding of viruses and the interaction with their hosts. This will open the door to validate methods of improving viral growth, morphogenesis and development, as well as to control strategies against unwanted microorganisms. The key feature of VIROINF is its interdisciplinary nature, which brings together virologists and bioinformaticians to achieve common goals. AU - Goettsch, W.* AU - Beerenwinkel, N.* AU - Deng, L. AU - Dölken, L.* AU - Dutilh, B.E.* AU - Erhard, F.* AU - Kaderali, L.* AU - von Kleist, M.* AU - Marquet, R.* AU - Matthijnssens, J.* AU - McCallin, S.* AU - McMahon, D.P.* AU - Rattei, T.* AU - Van Rij, R.P.* AU - Robertson, D.L.* AU - Schwemmle, M.* AU - Stern-Ginossar, N.* AU - Marz, M.* C1 - 61964 C2 - 50565 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - ITN-VIROINF: Understanding (Harmful) virus-host interactions by linking virology and bioinformatics. JO - Viruses VL - 13 IS - 5 PB - Mdpi PY - 2021 SN - 1999-4915 ER - TY - JOUR AB - BACKGROUND: The SARS-CoV-2 spike protein mediates attachment of the virus to the host cell receptor and fusion between the virus and the cell membrane. The S1 subunit of the spike glycoprotein (S1 protein) contains the angiotensin converting enzyme 2 (ACE2) receptor binding domain. The SARS-CoV-2 variants of concern contain mutations in the S1 subunit. The spike protein is the primary target of neutralizing antibodies generated following infection, and constitutes the viral component of mRNA-based COVID-19 vaccines. METHODS: Therefore, in this work we assessed the effect of exposure (24 h) to 10 nM SARS-CoV-2 recombinant S1 protein on physiologically relevant human bronchial (bro) and alveolar (alv) lung mucosa models cultured at air-liquid interface (ALI) (n = 6 per exposure condition). Corresponding sham exposed samples served as a control. The bro-ALI model was developed using primary bronchial epithelial cells and the alv-ALI model using representative type II pneumocytes (NCI-H441). RESULTS: Exposure to S1 protein induced the surface expression of ACE2, toll like receptor (TLR) 2, and TLR4 in both bro-ALI and alv-ALI models. Transcript expression analysis identified 117 (bro-ALI) and 97 (alv-ALI) differentially regulated genes (p ≤ 0.01). Pathway analysis revealed enrichment of canonical pathways such as interferon (IFN) signaling, influenza, coronavirus, and anti-viral response in the bro-ALI. Secreted levels of interleukin (IL) 4 and IL12 were significantly (p < 0.05) increased, whereas IL6 decreased in the bro-ALI. In the case of alv-ALI, enriched terms involving p53, APRIL (a proliferation-inducing ligand) tight junction, integrin kinase, and IL1 signaling were identified. These terms are associated with lung fibrosis. Further, significantly (p < 0.05) increased levels of secreted pro-inflammatory cytokines IFNγ, IL1ꞵ, IL2, IL4, IL6, IL8, IL10, IL13, and tumor necrosis factor alpha were detected in alv-ALI, whereas IL12 was decreased. Altered levels of these cytokines are also associated with lung fibrotic response. CONCLUSIONS: In conclusion, we observed a typical anti-viral response in the bronchial model and a pro-fibrotic response in the alveolar model. The bro-ALI and alv-ALI models may serve as an easy and robust platform for assessing the pathogenicity of SARS-CoV-2 variants of concern at different lung regions. AU - Rahman, M.* AU - Irmler, M. AU - Keshavan, S.* AU - Introna, M.* AU - Beckers, J. AU - Palmberg, L.* AU - Johanson, G.* AU - Ganguly, K.* AU - Upadhyay, S.* C1 - 63865 C2 - 51630 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Differential effect of SARS-CoV-2 spike glycoprotein 1 on human bronchial and alveolar lung mucosa models: Implications for pathogenicity. JO - Viruses VL - 13 IS - 12 PB - Mdpi PY - 2021 SN - 1999-4915 ER - TY - JOUR AB - Available treatments for hepatitis B can control the virus but are rarely curative. This led to a global initiative to design new curative therapies for the 257 million patients affected. Discovery and development of these new therapies is contingent upon functional in vitro and in vivo hepatitis B virus (HBV) infection models. However, low titer and impurity of conventional HBV stocks reduce significance of in vitro infections and moreover limit challenge doses in current in vivo models. Therefore, there is a critical need for a robust, simple and reproducible protocol to generate high-purity and high-titer infectious HBV stocks. Here, we outline a three-step protocol for continuous production of high-quality HBV stocks from supernatants of HBV-replicating cell lines. This purification process takes less than 6 h, yields to high-titer stocks (up to 1 × 1011 enveloped, DNA-containing HBV particles/mL each week), and is with minimal equipment easily adaptable to most laboratory settings. AU - Wettengel, J.M. AU - Linden, B. AU - Esser, K. AU - Laue, M.* AU - Burwitz, B.J.* AU - Protzer, U. C1 - 62785 C2 - 51061 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Rapid and robust continuous purification of high-titer hepatitis B virus for in vitro and in vivo applications. JO - Viruses VL - 13 IS - 8 PB - Mdpi PY - 2021 SN - 1999-4915 ER - TY - JOUR AB - Several viral factors impact the natural course of hepatitis B virus (HBV) infection, the sensitivity of diagnostic tests, or treatment response to interferon-α and nucleos(t)ide analogues. These factors include the viral genotype and serotype but also mutations affecting the HBV surface antigen, basal core promoter/pre-core region, or reverse transcriptase. However, a comprehensive overview of the distribution of HBV variants between HBV genotypes or different geographical locations is lacking. To address this, we performed an in silico analysis of publicly available HBV full-length genome sequences. We found that not only the serotype frequency but also the majority of clinically relevant mutations are primarily associated with specific genotypes. Distinct mutations enriched in certain world regions are not explained by the local genotype distribution. Two HBV variants previously identified to confer resistance to the nucleotide analogue tenofovir in vitro were not identified, questioning their translational relevance. In summary, our work elucidates the differences in the clinical manifestation of HBV infection observed between genotypes and geographical locations and furthermore helps identify suitable diagnostic tests and therapies. AU - Velkov, S.* AU - Protzer, U. AU - Michler, T. C1 - 60638 C2 - 49513 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Global occurrence of clinically relevant hepatitis B virus variants as found by analysis of publicly available sequencing data. JO - Viruses VL - 12 IS - 11 PB - Mdpi PY - 2020 SN - 1999-4915 ER - TY - JOUR AB - Hepatitis B is a major global health problem, with an estimated 257 million chronically infected patients and almost 1 million deaths per year. The causative agent is hepatitis B virus (HBV), a small, enveloped, partially double-stranded DNA virus. HBV has a strict species specificity, naturally infecting only humans and chimpanzees. Sodium taurocholate co-transporting polypeptide (NTCP), a bile acid transporter expressed on hepatocytes, has been shown to be one of the key factors in HBV infection, playing a crucial role in the HBV entry process in vitro and in vivo. Variations in the amino acid sequence of NTCP can inhibit HBV infection and, therefore, contributes, in part, to the species barrier. This discovery has revolutionized the search for novel animal models of HBV. Indeed, it was recently shown that variations in the amino acid sequence of NTCP represent the sole species barrier for HBV infection in macaques. Here, we review what is known about HBV entry through the NTCP receptor and highlight how this knowledge has been harnessed to build new animal models for the study of HBV pathogenesis and curative therapies. AU - Wettengel, J.M. AU - Burwitz, B.J.* C1 - 59854 C2 - 49073 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Innovative HBV animal models based on the entry receptor NTCP. JO - Viruses VL - 12 IS - 8 PB - Mdpi PY - 2020 SN - 1999-4915 ER - TY - JOUR AB - Avian orthoavulavirus 13 (AOAV-13), also named avian paramyxovirus 13 (APMV-13), has been found sporadically in wild birds around the world ever since the discovery of AOAV-13 (AOAV-13/wild goose/Shimane/67/2000) in a wild goose from Japan in 2000. However, there are no reports of AOAV-13 in China. In the present study, a novel AOAV-13 virus (AOAV-13/wild goose/China/Hubei/V93-1/2015), isolated from a wild migratory waterfowl in a wetland of Hubei province of China, during active surveillance from 2013 to 2018, was biologically and genetically characterized. Phylogenetic analyses demonstrated a very close genetic relationship among all AOAV-13 strains, as revealed by very few genetic variations. Moreover, pathogenicity tests indicated that the V93-1 strain is a low virulent virus for chickens. However, the genome of the V93-1 virus was found to be 16,158 nucleotides (nt) in length, which is 12 nt or 162 nt longer than the other AOAV-13 strains that have been reported to date. The length difference of 12 nt in strain V93-1 is due to the existence of three repeats of the conserved sequence, "AAAAAT", in the 5 '-end trailer of the genome. Moreover, the HN gene of the V93-1 virus is 2070 nt in size, encoding 610 aa, which is the same size as the AOAV-13 strain from Japan, whereas that of two strains from Ukraine and Kazakhstan are 2080 nt in length, encoding 579 aa. We describe a novel AOAV-13 in migratory waterfowl in China, which suggests that diversified trailer region sequences and HN gene lengths exist within serotype AOAV-13, and highlight the need for its constant surveillance in poultry from live animal markets, and especially migratory birds. AU - Fei, Y.* AU - Liu, X.* AU - Mu, J.* AU - Li, J.* AU - Yu, X.* AU - Chang, J.* AU - Bi, Y.* AU - Stöger, T. AU - Wajid, A.* AU - Muzyka, D.* AU - Sharshov, K.* AU - Shestopalov, A.* AU - Amonsin, A.* AU - Chen, J.* AU - Ding, Z.* AU - Yin, R.* C1 - 56622 C2 - 47215 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - The emergence of avian orthoavulavirus 13 in wild migratory waterfowl in China revealed the existence of diversified trailer region sequences and HN gene lengths within this serotype. JO - Viruses VL - 11 IS - 7 PB - Mdpi PY - 2019 SN - 1999-4915 ER - TY - JOUR AB - Dromedary camels (Camelus dromedarius) are now known to be the vertebrate animal reservoir that intermittently transmits the Middle East respiratory syndrome coronavirus (MERS-CoV) to humans. Yet, details as to the specific mechanism(s) of zoonotic transmission from dromedaries to humans remain unclear. The aim of this study was to describe direct and indirect contact with dromedaries among all cases, and then separately for primary, non-primary, and unclassified cases of laboratory-confirmed MERS-CoV reported to the World Health Organization (WHO) between 1 January 2015 and 13 April 2018. We present any reported dromedary contact: direct, indirect, and type of indirect contact. Of all 1125 laboratory-confirmed MERS-CoV cases reported to WHO during the time period, there were 348 (30.9%) primary cases, 455 (40.4%) non-primary cases, and 322 (28.6%) unclassified cases. Among primary cases, 191 (54.9%) reported contact with dromedaries: 164 (47.1%) reported direct contact, 155 (44.5%) reported indirect contact. Five (1.1%) non-primary cases also reported contact with dromedaries. Overall, unpasteurized milk was the most frequent type of dromedary product consumed. Among cases for whom exposure was systematically collected and reported to WHO, contact with dromedaries or dromedary products has played an important role in zoonotic transmission. AU - Conzade, R. AU - Grant, R.* AU - Malik, M.R.* AU - Elkholy, A.* AU - Elhakim, M.* AU - Samhouri, D.* AU - Ben Embarek, P.K.* AU - Van Kerkhove, M.D.* C1 - 54207 C2 - 45402 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Reported direct and indirect contact with dromedary camels among laboratory-confirmed MERS-CoV cases . JO - Viruses VL - 10 IS - 8 PB - Mdpi PY - 2018 SN - 1999-4915 ER - TY - JOUR AB - Chronic hepatitis B virus (HBV) infection puts more than 250 million people at a greatly increased risk to develop end-stage liver disease. Like all hepadnaviruses, HBV replicates via protein-primed reverse transcription of a pregenomic (pg) RNA, yielding an unusually structured, viral polymerase-linked relaxed-circular (RC) DNA as genome in infectious particles. Upon infection, RC-DNA is converted into nuclear covalently closed circular (ccc) DNA. Associating with cellular proteins into an episomal minichromosome, cccDNA acts as template for new viral RNAs, ensuring formation of progeny virions. Hence, cccDNA represents the viral persistence reservoir that is not directly targeted by current anti-HBV therapeutics. Eliminating cccDNA will thus be at the heart of a cure for chronic hepatitis B. The low production of HBV cccDNA in most experimental models and the associated problems in reliable cccDNA quantitation have long hampered a deeper understanding of cccDNA molecular biology. Recent advancements including cccDNA-dependent cell culture systems have begun to identify select host DNA repair enzymes that HBV usurps for RC-DNA to cccDNA conversion. While this list is bound to grow, it may represent just one facet of a broader interaction with the cellular DNA damage response (DDR), a network of pathways that sense and repair aberrant DNA structures and in the process profoundly affect the cell cycle, up to inducing cell death if repair fails. Given the divergent interactions between other viruses and the DDR it will be intriguing to see how HBV copes with this multipronged host system. AU - Schreiner, S. AU - Nassal, M.* C1 - 51158 C2 - 43076 CY - Basel TI - A role for the host DNA damage response in Hepatitis B Virus cccDNA formation-and beyond? JO - Viruses VL - 9 IS - 5 PB - Mdpi Ag PY - 2017 SN - 1999-4915 ER - TY - JOUR AB - Chronic infection with the hepatitis B virus (HBV) can lead to liver failure and can cause liver cirrhosis and hepatocellular carcinoma (HCC). Reliable means for detecting and monitoring HBV infection are essential to identify patients in need of therapy and to prevent HBV transmission. Nanomaterials with defined electrical, optical, and mechanical properties have been developed to detect and quantify viral antigens. In this review, we discuss the challenges in applying nanoparticles to HBV antigen detection and in realizing the bio-analytical potential of such nanoparticles. We discuss recent developments in generating detection platforms based on gold and iron oxide nanoparticles. Such platforms increase biological material detection efficiency by the targeted capture and concentration of HBV antigens, but the unique properties of nanoparticles can also be exploited for direct, sensitive, and specific antigen detection. We discuss several studies that show that nanomaterial-based platforms enable ultrasensitive HBV antigen detection. AU - Shevtsov, M.* AU - Zhao, L. AU - Protzer, U. AU - Klundert, M.A.A. C1 - 51629 C2 - 43325 CY - Basel TI - Applicability of metal nanoparticles in the detection and monitoring of hepatitis B virus infection. JO - Viruses VL - 9 IS - 7 PB - Mdpi Ag PY - 2017 SN - 1999-4915 ER - TY - JOUR AB - Hepatitis B virus (HBV) infection remains a major public health problem worldwide with more than 240 million individuals chronically infected. Current treatments can control HBV replication to a large extent, but cannot eliminate HBV infection. Cytokines have been shown to control HBV replication and contribute to HBV cure in different models. Cytokines play an important role in limiting acute HBV infection in patients and mediate a non-cytolytic clearance of the virus. In this review, we summarize the effects of cytokines and cytokine-induced cellular signaling pathways on different steps of the HBV life cycle, and discuss possible strategies that may contribute to the eradication of HBV through innate immune activation. AU - Xia, Y.* AU - Protzer, U. C1 - 50818 C2 - 42758 CY - Basel TI - Control of hepatitis B virus by cytokines. JO - Viruses VL - 9 IS - 1 PB - Mdpi Ag PY - 2017 SN - 1999-4915 ER - TY - JOUR AB - The human immunodeficiency virus type 1 (HIV-1) protein Vpu is encoded exclusively by HIV-1 and related simian immunodeficiency viruses (SIVs). The transmembrane domain of the protein has dual functions: it counteracts the human restriction factor tetherin and forms a cation channel. Since these two functions are causally unrelated it remains unclear whether the channel activity has any relevance for viral release and replication. Here we examine structure and function correlates of different Vpu homologs from HIV-1 and SIV to understand if ion channel activity is an evolutionary conserved property of Vpu proteins. An electrophysiological testing of Vpus from different HIV-1 groups (N and P) and SIVs from chimpanzees (SIVcpz), and greater spot-nosed monkeys (SIVgsn) showed that they all generate channel activity in HEK293T cells. This implies a robust and evolutionary conserved channel activity and suggests that cation conductance may also have a conserved functional significance. AU - Greiner, T.* AU - Bolduan, S. AU - Hertel, B.* AU - Groß, C.* AU - Hamacher, K.* AU - Schubert, U.* AU - Moroni, A.* AU - Thiel, G.* C1 - 50241 C2 - 42248 CY - Basel TI - Ion channel activity of Vpu proteins is conserved throughout evolution of HIV-1 and SIV. JO - Viruses VL - 8 IS - 12 PB - Mdpi Ag PY - 2016 SN - 1999-4915 ER - TY - JOUR AB - Posttranslational modifications (PTMs) of proteins include enzymatic changes by covalent addition of cellular regulatory determinants such as ubiquitin (Ub) and small ubiquitin-like modifier (SUMO) moieties. These modifications are widely used by eukaryotic cells to control the functional repertoire of proteins. Over the last decade, it became apparent that the repertoire of ubiquitiylation and SUMOylation regulating various biological functions is not restricted to eukaryotic cells, but is also a feature of human virus families, used to extensively exploit complex host-cell networks and homeostasis. Intriguingly, besides binding to host SUMO/Ub control proteins and interfering with the respective enzymatic cascade, many viral proteins mimic key regulatory factors to usurp this host machinery and promote efficient viral outcomes. Advanced detection methods and functional studies of ubiquitiylation and SUMOylation during virus-host interplay have revealed that human viruses have evolved a large arsenal of strategies to exploit these specific PTM processes. In this review, we highlight the known viral analogs orchestrating ubiquitin and SUMO conjugation events to subvert and utilize basic enzymatic pathways. AU - Wimmer, P.* AU - Schreiner, S. C1 - 46818 C2 - 37872 SP - 4854-4877 TI - Viral mimicry to usurp ubiquitin and sumo host pathways. JO - Viruses VL - 7 IS - 9 PY - 2015 SN - 1999-4915 ER - TY - JOUR AB - The host cell protein tetherin can restrict the release of enveloped viruses from infected cells. The HIV-1 protein Vpu counteracts tetherin by removing it from the site of viral budding, the plasma membrane, and this process depends on specific interactions between the transmembrane domains of Vpu and tetherin. In contrast, the glycoproteins (GPs) of two filoviruses, Ebola and Marburg virus, antagonize tetherin without reducing surface expression, and the domains in GP required for tetherin counteraction are unknown. Here, we show that filovirus GPs depend on the presence of their authentic transmembrane domains for virus-cell fusion and tetherin antagonism. However, conserved residues within the transmembrane domain were dispensable for membrane fusion and tetherin counteraction. Moreover, the insertion of the transmembrane domain into a heterologous viral GP, Lassa virus GPC, was not sufficient to confer tetherin antagonism to the recipient. Finally, mutation of conserved residues within the fusion peptide of Ebola virus GP inhibited virus-cell fusion but did not ablate tetherin counteraction, indicating that the fusion peptide and the ability of GP to drive host cell entry are not required for tetherin counteraction. These results suggest that the transmembrane domains of filoviral GPs contribute to tetherin antagonism but are not the sole determinants. AU - Gnirß, K.* AU - Fiedler, M.* AU - Krämer-Kühl, A.* AU - Bolduan, S. AU - Mittler, E.* AU - Becker, S.* AU - Schindler, M. AU - Pöhlmann, S.* C1 - 31053 C2 - 34147 CY - Basel SP - 1654-1671 TI - Analysis of determinants in filovirus glycoproteins required for tetherin antagonism. JO - Viruses VL - 6 IS - 4 PB - Mdpi Ag PY - 2014 SN - 1999-4915 ER - TY - JOUR AB - Human endogenous retroviruses (HERVs) represent approximately 8% of our genome. HERVs influence cellular gene expression and contribute to normal physiological processes such as cellular differentiation and morphogenesis. HERVs have also been associated with certain pathological conditions, including cancer and neurodegenerative diseases. As HTLV-1 causes adult T-cell leukemia and HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) and has been shown to modulate host gene expression mainly through the expression of the powerful Tax transactivator, herein we were interested in looking at the potential modulation capacity of HTLV-1 Tax on HERV expression. In order to evaluate the promoter activity of different HERV LTRs, pHERV-LTR-luc constructs were co-transfected in Jurkat T-cells with a Tax expression vector. Tax expression potently increased the LTR activity of HERV-W8 and HERV-H (MC16). In parallel, Jurkat cells were also stimulated with different T-cell-activating agents and HERV LTRs were observed to respond to different combination of Forskolin, bpV[pic] a protein tyrosine phosphatase inhibitor, and PMA. Transfection of expression vectors for different Tax mutants in Jurkat cells showed that several transcription factors including CREB appeared to be important for HERV-W8 LTR activation. Deletion mutants were derived from the HERV-W8 LTR and the region from −137 to −123 was found to be important for LTR response following Tax expression in Jurkat cells, while a different region was shown to be required in cells treated with activators. Our results thus demonstrated that HTLV-1 Tax activates several HERV LTRs. This raises the possibility that upregulated HERV expression could be involved in diseases associated with HTLV-1 infection. AU - Toufaily, C.* AU - Landry, S.* AU - Leib-Mösch, C. AU - Rassart, E.* AU - Barbeau, B.* C1 - 6748 C2 - 29204 SP - 2146-2159 TI - Activation of LTRs from different human endogenous retrovirus (HERV) families by the HTLV-1 tax protein and T-cell activators. JO - Viruses VL - 3 IS - 11 PB - MDPI AG PY - 2011 SN - 1999-4915 ER -