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1.
Biotechnol Bioeng ; 119(3): 743-761, 2022 03.
Article in English | MEDLINE | ID: mdl-34936091

ABSTRACT

For drug products manufactured in mammalian cells, safety assurance practices are needed during production to assure that the final medicinal product is safe from the potential risk of viral contamination. Virus filters provide viral retention for a range of viruses through robust, largely size-based retention mechanism. Therefore, a virus filtration step is commonly utilized in a well-designed recombinant therapeutic protein purification process and is a key component in an overall strategy to minimize the risks of adventitious and endogenous viral particles during the manufacturing of biotechnology products. This study summarizes the history of virus filtration, currently available virus filters and prefilters, and virus filtration integrity test methods and study models. There is also discussion of current understanding and gaps with an eye toward future trends and emerging filtration technologies.


Subject(s)
Viruses , Animals , Biotechnology/methods , Drug Contamination/prevention & control , Filtration , Mammals , Virion
2.
San Salvador; MINSAL; jun. 08, 2022. 22 p. ilus, graf, tab, mapas.
Non-conventional in Spanish | LILACS, BISSAL | ID: biblio-1372436

ABSTRACT

Resumen de eventos de notificación hasta SE 21/2022. Alertas internacionales, situación epidemiológica de dengue, situación epidemiológica de zika y Chikungunya, infección respiratoria aguda, neumonías, situación mundial del 2019-nCov (OMS), vigilancia centinela de influenza y otros virus respiratorios, vigilancia centinela de rotavirus y enfermedad diarreica aguda


Summary of notification events until SE 21/2022. International alerts, epidemiological situation of dengue, epidemiological situation of Zika and Chikungunya, acute respiratory infection, pneumonia, global situation of 2019-nCov (WHO), sentinel surveillance of influenza and other respiratory viruses, sentinel surveillance of rotavirus and acute diarrheal disease


Subject(s)
Epidemiology , Electronic Publications , Infections , Viruses , Surveillance , Notification
3.
San Salvador; MINSAL; jun. 15, 2022. 22 p. ilus, graf, tab, mapas.
Non-conventional in Spanish | LILACS, BISSAL | ID: biblio-1372438

ABSTRACT

Resumen de eventos de notificación hasta SE 22/2022. Alertas internacionales, situación epidemiológica de dengue, situación epidemiológica de zika y Chikungunya, infección respiratoria aguda, neumonías, situación mundial del 2019-nCov (OMS), vigilancia centinela de influenza y otros virus respiratorios, vigilancia centinela de rotavirus y enfermedad diarreica aguda


Summary of notification events until SE 22/2022. International alerts, epidemiological situation of dengue, epidemiological situation of Zika and Chikungunya, acute respiratory infection, pneumonia, global situation of 2019-nCov (WHO), sentinel surveillance of influenza and other respiratory viruses, sentinel surveillance of rotavirus and acute diarrheal disease


Subject(s)
Epidemiology , Electronic Publications , Infections , Viruses , Alert , Notification
4.
BMC Public Health ; 22(1): 1167, 2022 Jun 11.
Article in English | MEDLINE | ID: mdl-35690802

ABSTRACT

BACKGROUND: Lower respiratory tract infections are among the main causes of death. Although there are many respiratory viruses, diagnostic efforts are focused mainly on influenza. The Respiratory Viruses Network (RespVir) collects infection data, primarily from German university hospitals, for a high diversity of infections by respiratory pathogens. In this study, we computationally analysed a subset of the RespVir database, covering 217,150 samples tested for 17 different viral pathogens in the time span from 2010 to 2019. METHODS: We calculated the prevalence of 17 respiratory viruses, analysed their seasonality patterns using information-theoretic measures and agglomerative clustering, and analysed their propensity for dual infection using a new metric dubbed average coinfection exclusion score (ACES). RESULTS: After initial data pre-processing, we retained 206,814 samples, corresponding to 1,408,657 performed tests. We found that Influenza viruses were reported for almost the half of all infections and that they exhibited the highest degree of seasonality. Coinfections of viruses are frequent; the most prevalent coinfection was rhinovirus/bocavirus and most of the virus pairs had a positive ACES indicating a tendency to exclude each other regarding infection. CONCLUSIONS: The analysis of respiratory viruses dynamics in monoinfection and coinfection contributes to the prevention, diagnostic, treatment, and development of new therapeutics. Data obtained from multiplex testing is fundamental for this analysis and should be prioritized over single pathogen testing.


Subject(s)
Coinfection , Respiratory Tract Infections , Virus Diseases , Viruses , Coinfection/epidemiology , Humans , Infant , Rhinovirus , Virus Diseases/epidemiology
5.
Microbiome ; 10(1): 92, 2022 Jun 14.
Article in English | MEDLINE | ID: mdl-35701838

ABSTRACT

BACKGROUND: Prokaryote-virus interactions play key roles in driving biogeochemical cycles. However, little is known about the drivers shaping their interaction network structures, especially from the host features. Here, we compiled 7656 species-level genomes in 39 prokaryotic phyla across environments globally and explored how their interaction specialization is constrained by host life history traits, such as growth rate. RESULTS: We first reported that host growth rate indicated by the reverse of minimal doubling time was negatively related to interaction specialization for host in host-provirus network across various ecosystems and taxonomy groups. Such a negative linear growth rate-specialization relationship (GrSR) was dependent on host optimal growth temperature (OGT), and stronger toward the two gradient ends of OGT. For instance, prokaryotic species with an OGT ≥ 40 °C showed a stronger GrSR (Pearson's r = -0.525, P < 0.001). Significant GrSRs were observed with the presences of host genes in promoting the infection cycle at stages of adsorption, establishment, and viral release, but nonsignificant with the presence of immune systems, such as restriction-modification systems and CRISPR-Cas systems. Moreover, GrSR strength was increased with the presence of temperature-dependent lytic switches, which was also confirmed by mathematical modeling. CONCLUSIONS: Together, our results advance our understanding of the interactions between prokaryotes and proviruses and highlight the importance of host growth rate in interaction specialization during lysogenization. Video Abstract.


Subject(s)
Proviruses , Viruses , Ecosystem , Prokaryotic Cells , Proviruses/genetics , Temperature , Viruses/genetics
6.
FEBS Open Bio ; 12(6): 1094-1095, 2022 Jun.
Article in English | MEDLINE | ID: mdl-35642596

ABSTRACT

The spread of pathogenic viruses implies host infection, replication, and virus dissemination. In each step, viruses have to overcome the host defenses designed to neutralize the threat they pose. The host-virus relationship represents a constant multistage battle for power as the host/cell does not voluntarily give in to the viral enemy. Upon infection, cells recognize viral pathogen-associated molecular patterns, activating the innate antiviral defenses. As such, during most of the replication cycle, the virus has to deal with the cellular antiviral response. At this point, it should not be forgotten that viruses are obligate intracellular parasites and thus are entirely dependent on the host cell for their replication. This dependency has pushed viruses to evolve unorthodox strategies to subvert and repurpose cellular factors and processes required for efficient replication. Even if a virus has the potential to be successful at each step necessary for its spread, this does not mean it has won the war against the host. Another threat to viruses is represented by antiviral drugs designed to diminish their survival and promote the host's wellbeing. This editorial outlines the contents of this special 'In the Limelight' issue of FEBS Open Bio focused on Virology. The section contains four review articles, each focused on a particular aspect of virus-host interaction, including the antiviral response, subversion of the host translational machinery, repurposing of cellular factors, and the development of antiviral drugs.


Subject(s)
Viruses , Antiviral Agents
7.
Microb Genom ; 8(6)2022 Jun.
Article in English | MEDLINE | ID: mdl-35731570

ABSTRACT

Emerging evidence has identified viral circular RNAs (circRNAs) in human cells infected by viruses, interfering with the immune system and inducing diseases including human cancer. However, the biogenesis and regulatory mechanisms of virus-encoded circRNAs in host cells remain unknown. In this study, we used the circRNA detection tool CIRI2 to systematically determine the virus-encoded circRNAs in virus-infected cancer cell lines and cancer patients, by analysing RNA-Seq datasets derived from RNase R-treated samples. Based on the thousands of viral circRNAs we identified, the biological characteristics and potential roles of viral circRNAs in regulating host cell function were determined. In addition, we developed a Viral-circRNA Database (http://www.hywanglab.cn/vcRNAdb/), which is open to all users to search, browse and download information on circRNAs encoded by viruses upon infection.


Subject(s)
RNA, Circular , Viruses , Cell Line , Humans , RNA/genetics , RNA/metabolism , RNA, Circular/genetics , Viruses/genetics
8.
BMC Pediatr ; 22(1): 359, 2022 Jun 22.
Article in English | MEDLINE | ID: mdl-35733118

ABSTRACT

BACKGROUND: Febrile seizures are the commonest type of seizure in occurring in the first few years of life, mostly affecting children aged six months to five years old. While largely benign, the incidence of each febrile seizure increases the risk of recurrence, afebrile seizures and epilepsy. Viruses are the most frequent cause of febrile illnesses in which a febrile seizure occurs. Febrile seizure presentation patterns appear to follow a seasonal trend. AIMS: To identify patterns of febrile seizure incidence across different seasons with specific viral activity, and to establish a framework for analysing virus circulation data with common illnesses within a shared region and population. SETTING: Our study was a study of febrile seizure presentations in Victoria, Australia and respiratory virus detection. PARTICIPANTS: We obtained independent datasets of emergency department febrile seizure presentations at Monash Health and all respiratory multiplex PCR tests performed at Monash Health from January 2010-December 2019 to observe common trends in virus circulation and febrile seizure incidence. STUDY DESIGN: Trends were studied temporally through mixed effects Poisson regression analysis of the monthly incidence of febrile seizures and the rate of positive PCR tests. Peak viral seasons (95th centile incidence) were compared to median viral circulation (50th centile incidence) to calculate peak season risk ratios. RESULTS: We found a 1.75-2.06 annual risk ratio of febrile seizure incidence in June-September. Temporal analysis of our data showed this peak in febrile seizures was attributable to circulating viruses in this season, and virus modelling showed correlation with increased rates of positive Influenza A (1.48 peak season risk ratio), Influenza B (1.31 peak season risk ratio), Human metapneumovirus (1.19 peak season risk ratio) and Respiratory Syncytial Virus (1.53 peak season risk ratio) on PCR testing. CONCLUSION: Our ecological study statistically demonstrates the recognised winter peak in febrile seizure incidence and ascribes the seasonal relationship to several viral infections which affect the community, including a novel association with Human metapneumovirus.


Subject(s)
Influenza, Human , Seizures, Febrile , Virus Diseases , Viruses , Child , Humans , Infant , Influenza, Human/complications , Influenza, Human/diagnosis , Influenza, Human/epidemiology , Seizures, Febrile/epidemiology , Seizures, Febrile/etiology , Victoria/epidemiology , Virus Diseases/complications
9.
Front Cell Infect Microbiol ; 12: 928050, 2022.
Article in English | MEDLINE | ID: mdl-35734576

ABSTRACT

Probiotics exert a variety of beneficial effects, including maintaining homeostasis and the balance of intestinal microorganisms, activating the immune system, and regulating immune responses. Due to the beneficial effects of probiotics, a wide range of probiotics have been developed as probiotic agents for animal and human health. Viral diseases cause serious economic losses to the livestock every year and remain a great challenge for animals. Moreover, strategies for the prevention and control of viral diseases are limited. Viruses enter the host through the skin and mucosal surface, in which are colonized by hundreds of millions of microorganisms. The antiviral effects of probiotics have been proved, including modulation of chemical, microbial, physical, and immune barriers through various probiotics, probiotic metabolites, and host signaling pathways. It is of great significance yet far from enough to elucidate the antiviral mechanisms of probiotics. The major interest of this review is to discuss the antiviral effects and underlying mechanisms of probiotics and to provide targets for the development of novel antivirals.


Subject(s)
Probiotics , Viruses , Animals , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , Immune System , Intestines , Probiotics/pharmacology , Probiotics/therapeutic use
10.
J Phys Chem B ; 126(24): 4411-4414, 2022 Jun 23.
Article in English | MEDLINE | ID: mdl-35734854
11.
J Hazard Mater ; 436: 129159, 2022 08 15.
Article in English | MEDLINE | ID: mdl-35643009

ABSTRACT

The microbial community in seriously contaminated environment were not well known. This research investigated the community reassemblies in microcosms made of two distinct mangrove sediments amended with high levels of hexabromocyclododecanes (HBCDs). After eight months of contamination, the transformation of HBCDs yielded various lower brominated products and resulted in acidification (pH ~2). Therefore, the degraders and dehalogenase homologous genes involved in transformation of HBCDs only presented in low abundance to avoid further deterioration of the habitats. Moreover, in these deteriorated habitats, 1344 bacterial, 969 archaeal, 599 eukaryotic (excluded fungi), 187 fungal OTUs, and 10 viral genera, were reduced compared with controls. Specifically, in two groups of microcosms, Zetaproteobacteria, Deinococcus-Thermus, Spirochaetes, Bacteroidetes, Euryarchaeota, and Ascomycota, were positively responding taxa to HBCDs. Caloneis (Bacillariophyta) and Ascomycota turned to the dominant eukaryotic and fungal taxa. Most of predominant taxa were related to the contamination of brominated flame retardants (BFRs). Microbial communities were reassembled in divergent and sediment-dependent manner. The long-term contamination of HBCDs leaded to the change of relations between many taxa, included some of the environmental viruses and their known hosts. This research highlight the importance of monitoring the ecological effects around plants producing or processing halogenated compounds.


Subject(s)
Flame Retardants , Hydrocarbons, Brominated , Viruses , Environmental Monitoring/methods , Eukaryota , Flame Retardants/analysis , Hydrocarbons, Brominated/analysis
13.
PLoS Comput Biol ; 18(6): e1010228, 2022 06.
Article in English | MEDLINE | ID: mdl-35675415

ABSTRACT

Viruses play diverse and important roles in ecosystems. In recent years, trade-offs between host and virus traits have gained increasing attention in viral ecology and evolution. However, microbial organism traits, and viral population parameters in particular, are challenging to monitor. Mathematical and individual-based models are useful tools for predicting virus-host dynamics. We have developed an individual-based evolutionary model to study ecological interactions and evolution between bacteria and viruses, with emphasis on the impacts of trade-offs between competitive and defensive host traits on bacteria-phage population dynamics and trait diversification. Host dynamics are validated with lab results for different initial virus to host ratios (VHR). We show that trade-off based, as opposed to random bacteria-virus interactions, result in biologically plausible evolutionary outcomes, thus highlighting the importance of trade-offs in shaping biodiversity. The effects of nutrient concentration and other environmental and organismal parameters on the virus-host dynamics are also investigated. Despite its simplicity, our model serves as a powerful tool to study bacteria-phage interactions and mechanisms for evolutionary diversification under various environmental conditions.


Subject(s)
Bacteriophages , Viruses , Bacteria , Biodiversity , Biological Evolution , Ecosystem , Population Dynamics
14.
J Exp Med ; 219(7)2022 Jul 04.
Article in English | MEDLINE | ID: mdl-35670811

ABSTRACT

Autosomal recessive IRF7 deficiency was previously reported in three patients with single critical influenza or COVID-19 pneumonia episodes. The patients' fibroblasts and plasmacytoid dendritic cells produced no detectable type I and III IFNs, except IFN-ß. Having discovered four new patients, we describe the genetic, immunological, and clinical features of seven IRF7-deficient patients from six families and five ancestries. Five were homozygous and two were compound heterozygous for IRF7 variants. Patients typically had one episode of pulmonary viral disease. Age at onset was surprisingly broad, from 6 mo to 50 yr (mean age 29 yr). The respiratory viruses implicated included SARS-CoV-2, influenza virus, respiratory syncytial virus, and adenovirus. Serological analyses indicated previous infections with many common viruses. Cellular analyses revealed strong antiviral immunity and expanded populations of influenza- and SARS-CoV-2-specific memory CD4+ and CD8+ T cells. IRF7-deficient individuals are prone to viral infections of the respiratory tract but are otherwise healthy, potentially due to residual IFN-ß and compensatory adaptive immunity.


Subject(s)
COVID-19 , Influenza, Human , Virus Diseases , Viruses , Adult , COVID-19/genetics , Humans , Influenza, Human/genetics , SARS-CoV-2
15.
Adv Food Nutr Res ; 100: 265-286, 2022.
Article in English | MEDLINE | ID: mdl-35659354

ABSTRACT

Foodborne diseases are one of the most serious concerns in public health. It is estimated that around 600 million cases of gastroenteritis occur worldwide each year. At present, more than 200 food-borne diseases are known, which can cause from mild gastroenteritis to syndromes with a fatal outcome, with the added possibility of chronic complications. One of the major etiological agents in foodborne diseases are the food and waterborne viruses, which are attracting a great deal of attention to researchers, food hygienists and policy makers. Several aspects differentiate these pathogens from foodborne pathogenic bacteria: their high capacity for infection and preservation in food environments, and their difficulty for a correct and sensitive detection. In recent years, different initiatives have been carried out to prioritize research in the area of viruses in food, prioritizing different aspects of their detection, epidemiology and control. There is clear evidence that the existing data on their prevalence may be underestimated due to the lack of robust methods for their sensitive detection. It is also necessary to know exactly what the incidence is in the different stages of the food production chain, and particularly in that which is dedicated to the transformation of products of animal origin. Finally, it is also necessary to calibrate the current disinfection procedures in the food industry in order to reliably establish a quantitative evaluation of the viral risk in food.


Subject(s)
Foodborne Diseases , Gastroenteritis , Viruses , Animals , Food Microbiology , Gastroenteritis/epidemiology , Public Health
16.
Front Immunol ; 13: 851642, 2022.
Article in English | MEDLINE | ID: mdl-35663971

ABSTRACT

The rapid evolution of highly infectious pathogens is a major threat to global public health. In the front line of defense against bacteria, fungi, and viruses, antimicrobial peptides (AMPs) are naturally produced by all living organisms and offer new possibilities for next-generation antibiotic development. However, the low yields and difficulties in the extraction and purification of AMPs have hindered their industry and scientific research applications. To overcome these barriers, we enabled high expression of bomidin, a commercial recombinant AMP based upon bovine myeloid antimicrobial peptide-27. This novel AMP, which can be expressed in Escherichia coli by adding methionine to the bomidin sequence, can be produced in bulk and is more biologically active than chemically synthesized AMPs. We verified the function of bomidin against a variety of bacteria and enveloped viruses, including severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), herpes simplex virus (HSV), dengue virus (DENV), and chikungunya virus (CHIKV). Furthermore, based on the molecular modeling of bomidin and membrane lipids, we elucidated the possible mechanism by which bomidin disrupts bacterial and viral membranes. Thus, we obtained a novel AMP with an optimized, efficient heterologous expression system for potential therapeutic application against a wide range of life-threatening pathogens.


Subject(s)
COVID-19 , Viruses , Adenosine Monophosphate , Animals , Antiviral Agents/pharmacology , Cattle , SARS-CoV-2
17.
Curr Opin Virol ; 54: 101231, 2022 Jun.
Article in English | MEDLINE | ID: mdl-35643020

ABSTRACT

Despite the growing interest in the microbiome in recent years, the study of the virome, the major part of which is made up of bacteriophages, is relatively underdeveloped compared with their bacterial counterparts. This is due in part to the lack of a universally conserved marker such as the 16S rRNA gene. For this reason, the development of metagenomic approaches was a major milestone in the study of the viruses in the microbiome or virome. However, it has become increasingly clear that these wet-lab methods have not yet been able to detect the full range of viruses present, and our understanding of the composition of the virome remains incomplete. In recent years, a range of new technologies has been developed to further our understanding. Direct RNA-Seq technologies bypass the need for cDNA synthesis, thus avoiding biases subjected to this step, which further expands our understanding of RNA viruses. The new generation of amplification methods could solve the low biomass issue relevant to most virome samples while reducing the error rate and biases caused by whole genome amplification. The application of long-read sequencing to virome samples can resolve the shortcomings of short-read sequencing in generating complete viral genomes and avoid the biases introduced by the assembly. Novel experimental methods developed to measure viruses' host range can help overcome the challenges of assigning hosts to many phages, specifically unculturable ones.


Subject(s)
Bacteriophages , Viruses , Bacteriophages/genetics , Metagenome , Metagenomics/methods , RNA, Ribosomal, 16S/genetics , Virome , Viruses/genetics
18.
Curr Opin Virol ; 54: 101232, 2022 Jun.
Article in English | MEDLINE | ID: mdl-35644066

ABSTRACT

Picobirnaviruses are small double-stranded RNA viruses first discovered in 1988 in stool samples from patients with diarrhea. It has generally been assumed that picobirnaviruses infect animal hosts and that they are potential agents of diarrhea, but there is still no direct evidence demonstrating that picobirnaviruses infect animals. In the metagenomic era, virome studies have broadened our understanding of picobirnavirus genetic diversity and genome organization, expanded the types of animals in which they have been detected, and identified novel associations with human disease. Most importantly, from the wealth of new sequencing data and comparative genomic analyses, a provocative new hypothesis has emerged that picobirnaviruses may not infect animals, but rather that they may infect evolutionarily simpler denizens of the gastrointestinal tract: bacteria and/or fungi. Depending on whether the true hosts of picobirnaviruses are animals, fungi, or bacteria, the mechanisms by which they impact animal biology will vary dramatically.


Subject(s)
Picobirnavirus , RNA Virus Infections , Viruses , Animals , Bacteria/genetics , Diarrhea , Feces , Fungi/genetics , Humans , Phylogeny , Picobirnavirus/genetics , RNA Virus Infections/veterinary , Viruses/genetics
19.
Virulence ; 13(1): 980-989, 2022 12.
Article in English | MEDLINE | ID: mdl-35658809

ABSTRACT

One of the greatest achievements of the last century is the development of vaccines against viral diseases. Vaccines are essential for battling infectious diseases and many different formulations are available, including live attenuated vaccines. However, the use of live attenuated vaccines has the potential for adverse effects, including reversion of pathogenicity, recombination, and functional complementation in the host. Marek's disease is a serious disease in poultry controlled by live attenuated vaccines that has resulted in increased virulence over the decades. Recombination between circulating field viruses or vaccines is a proposed mechanism for the increase in virulence, however, complementation between vaccines and field strains has not been demonstrated in chickens. Here, we describe functional complementation of vaccines with virulent virus to functionally complement transmission and spread in the host. Using the natural virus-host model of Marek's disease in chickens, our results show dual infection of target cells in chickens with vaccine and virulent virus providing the opportunity for recombination or complementation to transpire. Interestingly, our controlled results showed no evidence of recombination between vaccine and virulent virus, but functional complementation occurred in two independent experiments providing proof for complementation during natural infection in vaccinated individuals. These results suggest complementation as a potential mechanism for vaccine-mediated viral evolution and the potential for complementation should be taken into consideration when developing novel vaccines.


Subject(s)
Coinfection , Marek Disease , Poultry Diseases , Viral Vaccines , Viruses , Animals , Chickens , Marek Disease/prevention & control , Vaccines, Attenuated/genetics , Viral Vaccines/genetics
20.
BMC Genomics ; 23(1): 433, 2022 Jun 10.
Article in English | MEDLINE | ID: mdl-35689184

ABSTRACT

BACKGROUND: Shotgun metagenomics yields ever richer and larger data volumes on the complex communities living in diverse environments. Extracting deep insights from the raw reads heavily depends on the availability of fast, accurate and user-friendly biodiversity analysis tools. RESULTS: Because environmental samples may contain strains and species that are not covered in reference databases and because protein sequences are more conserved than the genes encoding them, we explore the alternative route of taxonomic profiling based on protein coding regions translated from the shotgun metagenomics reads, instead of directly processing the DNA reads. We therefore developed the Unipept MetaGenomics Analysis Pipeline (UMGAP), a highly versatile suite of open source tools that are implemented in Rust and support parallelization to achieve optimal performance. Six preconfigured pipelines with different performance trade-offs were carefully selected, and benchmarked against a selection of state-of-the-art shotgun metagenomics taxonomic profiling tools. CONCLUSIONS: UMGAP's protein space detour for taxonomic profiling makes it competitive with state-of-the-art shotgun metagenomics tools. Despite our design choices of an extra protein translation step, a broad spectrum index that can identify both archaea, bacteria, eukaryotes and viruses, and a highly configurable non-monolithic design, UMGAP achieves low runtime, manageable memory footprint and high accuracy. Its interactive visualizations allow for easy exploration and comparison of complex communities.


Subject(s)
Metagenomics , Viruses , Algorithms , Bacteria/genetics , Sequence Analysis, DNA , Software , Viruses/genetics
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