Glacier-fed streams (GFS) feature among Earth's most extreme aquatic ecosystems marked by pronounced oligotrophy and environmental fluctuations. Microorganisms mainly organize in biofilms within them, but how they cope with such conditions is unknown. Here, leveraging 156 metagenomes from the Vanishing Glaciers project obtained from sediment samples in GFS from 9 mountains ranges, we report thousands of metagenome-assembled genomes (MAGs) encompassing prokaryotes, algae, fungi and viruses, that shed light on biotic interactions within glacier-fed stream biofilms. A total of 2,855 bacterial MAGs were characterized by diverse strategies to exploit inorganic and organic energy sources, in part via functional redundancy and mixotrophy. We show that biofilms probably become more complex and switch from chemoautotrophy to heterotrophy as algal biomass increases in GFS owing to glacier shrinkage. Our MAG compendium sheds light on the success of microbial life in GFS and provides a resource for future research on a microbiome potentially impacted by climate change.
- MeSH
- Bacteria * genetika klasifikace izolace a purifikace MeSH
- biodiverzita MeSH
- biofilmy růst a vývoj MeSH
- ekosystém MeSH
- geologické sedimenty mikrobiologie MeSH
- houby genetika klasifikace izolace a purifikace MeSH
- ledový příkrov * mikrobiologie MeSH
- metagenom * MeSH
- metagenomika MeSH
- mikrobiota * genetika MeSH
- řeky * mikrobiologie MeSH
- viry genetika klasifikace MeSH
- Publikační typ
- časopisecké články MeSH
Metagenomics is gradually being implemented for diagnosing infectious diseases. However, in-depth protocol comparisons for viral detection have been limited to individual sets of experimental workflows and laboratories. In this study, we present a benchmark of metagenomics protocols used in clinical diagnostic laboratories initiated by the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS). A mock viral reference panel was designed to mimic low biomass clinical specimens. The panel was used to assess the performance of twelve metagenomic wet lab protocols currently in use in the diagnostic laboratories of participating ENNGS member institutions. Both Illumina and Nanopore, shotgun and targeted capture probe protocols were included. Performance metrics sensitivity, specificity, and quantitative potential were assessed using a central bioinformatics pipeline. Overall, viral pathogens with loads down to 104 copies/ml (corresponding to CT values of 31 in our PCR assays) were detected by all the evaluated metagenomic wet lab protocols. In contrast, lower abundant mixed viruses of CT values of 35 and higher were detected only by a minority of the protocols. Considering the reference panel as the gold standard, optimal thresholds to define a positive result were determined per protocol, based on the horizontal genome coverage. Implementing these thresholds, sensitivity and specificity of the protocols ranged from 67 to 100 % and 87 to 100 %, respectively. A variety of metagenomic protocols are currently in use in clinical diagnostic laboratories. Detection of low abundant viral pathogens and mixed infections remains a challenge, implying the need for standardization of metagenomic analysis for use in clinical settings.
- Klíčová slova
- Benchmark, Clinical viral metagenomics, Wet lab protocols,
- MeSH
- benchmarking * MeSH
- lidé MeSH
- metagenomika * metody normy MeSH
- senzitivita a specificita * MeSH
- virové nemoci diagnóza virologie MeSH
- viry * genetika klasifikace izolace a purifikace MeSH
- výpočetní biologie metody MeSH
- vysoce účinné nukleotidové sekvenování metody normy MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- multicentrická studie MeSH
- práce podpořená grantem MeSH
Diphyllin is a natural arylnaphtalide lignan extracted from tropical plants of particular importance in traditional Chinese medicine. This compound has been described as a potent inhibitor of vacuolar (H+)ATPases and hence of the endosomal acidification process that is required by numerous enveloped viruses to trigger their respective viral infection cascades after entering host cells by receptor-mediated endocytosis. Accordingly, we report here a revised, updated, and improved synthesis of diphyllin, and demonstrate its antiviral activities against a panel of enveloped viruses from Flaviviridae, Phenuiviridae, Rhabdoviridae, and Herpesviridae families. Diphyllin is not cytotoxic for Vero and BHK-21 cells up to 100 µM and exerts a sub-micromolar or low-micromolar antiviral activity against tick-borne encephalitis virus, West Nile virus, Zika virus, Rift Valley fever virus, rabies virus, and herpes-simplex virus type 1. Our study shows that diphyllin is a broad-spectrum host cell-targeting antiviral agent that blocks the replication of multiple phylogenetically unrelated enveloped RNA and DNA viruses. In support of this, we also demonstrate that diphyllin is more than just a vacuolar (H+)ATPase inhibitor but may employ other antiviral mechanisms of action to inhibit the replication cycles of those viruses that do not enter host cells by endocytosis followed by low pH-dependent membrane fusion.
- Klíčová slova
- antiviral activity, cleistanthin B, cytotoxicity, diphyllin, enveloped virus, vacuolar ATPase inhibitor,
- MeSH
- antigeny virové metabolismus MeSH
- antivirové látky chemická syntéza farmakologie MeSH
- buněčné linie MeSH
- glukosidy farmakologie MeSH
- lignany chemická syntéza farmakologie MeSH
- replikace viru účinky léků MeSH
- vakuolární protonové ATPasy antagonisté a inhibitory MeSH
- viabilita buněk účinky léků MeSH
- viry klasifikace účinky léků metabolismus MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- antigeny virové MeSH
- antivirové látky MeSH
- cleistanthin B MeSH Prohlížeč
- diphyllin MeSH Prohlížeč
- glukosidy MeSH
- lignany MeSH
- vakuolární protonové ATPasy MeSH
Instrumental insemination of Apis mellifera L. queens is a widely employed technique used in honeybee breeding that enables the effective control of mating. However, drone semen represents a potential source of honeybee viruses. In this study, 43 semen doses collected from apparently healthy drones, and consequently used in instrumental insemination, were analysed using PCR or RT-PCR to detect the presence of viral genome of 11 honeybee viruses. In 91% of samples, viral infection was detected. The survey revealed genomes of five viruses, namely Deformed wing virus (DWV), Acute bee paralysis virus (ABPV), Black queen cell virus (BQCV), Sacbrood virus (SBV), and A. mellifera filamentous virus (AmFV) in 84%, 19%, 14%, 2%, and 67% of samples, respectively. Single infection (30% of samples) as well as multiple infection (61% of samples) of two, three or four pathogens were also evaluated. To the best of our knowledge, this is the first study describing the presence of the BQCV and SBV genome sequence in drone ejaculate. Phylogenetic analysis of BQCV partial helicase gene sequence revealed the high similarity of nucleotide sequence of described Czech strains, which varied from 91.4% to 99.6%. The findings of our study indicate the possibility of venereal transmission of BQCV and SBV.
- Klíčová slova
- BQCV, SBV, ejaculate, honeybees, instrumental insemination, virus detection,
- MeSH
- biodiverzita * MeSH
- chov metody MeSH
- polymerázová řetězová reakce s reverzní transkripcí MeSH
- polymerázová řetězová reakce MeSH
- sperma virologie MeSH
- včely virologie MeSH
- viry klasifikace genetika izolace a purifikace MeSH
- zvířata MeSH
- Check Tag
- mužské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Members of the family Pleolipoviridae (termed pleolipoviruses) are pseudo-spherical and pleomorphic archaeal viruses. The enveloped virion is a simple membrane vesicle, which encloses different types of DNA genomes of approximately 7-16 kbp (or kilonucleotides). Typically, virions contain a single type of transmembrane (spike) protein at the envelope and a single type of membrane protein, which is embedded in the envelope and located in the internal side of the membrane. All viruses infect extremely halophilic archaea in the class Halobacteria (phylum Euryarchaeota). Pleolipoviruses have a narrow host range and a persistent, non-lytic life cycle. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Pleolipoviridae which is available at www.ictv.global/report/pleolipoviridae.
- Klíčová slova
- Halorubrum pleomorphic virus 1, ICTV, Pleolipoviridae, taxonomy,
- MeSH
- fyziologie virů MeSH
- genom virový MeSH
- hostitelská specificita MeSH
- virové proteiny genetika metabolismus MeSH
- viry klasifikace genetika izolace a purifikace MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- virové proteiny MeSH
Rodents are distributed throughout the world and interact with humans in many ways. They provide vital ecosystem services, some species are useful models in biomedical research and some are held as pet animals. However, many rodent species can have adverse effects such as damage to crops and stored produce, and they are of health concern because of the transmission of pathogens to humans and livestock. The first rodent viruses were discovered by isolation approaches and resulted in break-through knowledge in immunology, molecular and cell biology, and cancer research. In addition to rodent-specific viruses, rodent-borne viruses are causing a large number of zoonotic diseases. Most prominent examples are reemerging outbreaks of human hemorrhagic fever disease cases caused by arena- and hantaviruses. In addition, rodents are reservoirs for vector-borne pathogens, such as tick-borne encephalitis virus and Borrelia spp., and may carry human pathogenic agents, but likely are not involved in their transmission to human. In our days, next-generation sequencing or high-throughput sequencing (HTS) is revolutionizing the speed of the discovery of novel viruses, but other molecular approaches, such as generic RT-PCR/PCR and rolling circle amplification techniques, contribute significantly to the rapidly ongoing process. However, the current knowledge still represents only the tip of the iceberg, when comparing the known human viruses to those known for rodents, the mammalian taxon with the largest species number. The diagnostic potential of HTS-based metagenomic approaches is illustrated by their use in the discovery and complete genome determination of novel borna- and adenoviruses as causative disease agents in squirrels. In conclusion, HTS, in combination with conventional RT-PCR/PCR-based approaches, resulted in a drastically increased knowledge of the diversity of rodent viruses. Future improvements of the used workflows, including bioinformatics analysis, will further enhance our knowledge and preparedness in case of the emergence of novel viruses. Classical virological and additional molecular approaches are needed for genome annotation and functional characterization of novel viruses, discovered by these technologies, and evaluation of their zoonotic potential.
- Klíčová slova
- Diagnostics, High-throughput sequencing, Microarray, PCR, Pathogen, RT-PCR, Rodent, Rolling circle amplification, Workflow, Zoonosis,
- MeSH
- diagnostické techniky molekulární metody MeSH
- hlodavci virologie MeSH
- metagenomika metody MeSH
- techniky amplifikace nukleových kyselin metody MeSH
- virové nemoci epidemiologie veterinární virologie MeSH
- viry klasifikace genetika izolace a purifikace MeSH
- vysoce účinné nukleotidové sekvenování metody MeSH
- zoonózy epidemiologie virologie MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
This study condenses data acquired during investigations of the virological quality of irrigation water used in production of fresh produce. One hundred and eight samples of irrigation water were collected from five berry fruit farms in Finland (1), the Czech Republic (1), Serbia (2), and Poland (1), and sixty-one samples were collected from three leafy green vegetable farms in Poland, Serbia, and Greece. Samples were analyzed for index viruses of human or animal fecal contamination (human and porcine adenoviruses, and bovine polyoma viruses), and human pathogenic viruses (hepatitis A virus, hepatitis E virus, and noroviruses GI/GII). Both index and pathogenic viruses were found in irrigation water samples from the leafy green vegetables production chain. The data on the presence of index viruses indicated that the highest percentage of fecal contamination was of human origin (28.1 %, 18/64), followed by that of porcine (15.4 %, 6/39) and bovine (5.1 %, 2/39) origins. Hepatitis E virus (5 %, 1/20) and noroviruses GII (14.3 %, 4/28) were also detected. Samples from berry fruit production were also positive for both index and pathogenic viruses. The highest percentage of fecal contamination was of human origin (8.3 %, 9/108), followed by that of porcine, 4.5 % (4/89) and bovine, 1.1 % (1/89) origins. Norovirus GII (3.6 %, 2/56) was also detected. These data demonstrate that irrigation water used in primary production is an important vehicle of viral contamination for fresh produce, and thus is a critical control point which should be integrated into food safety management systems for viruses. The recommendations of Codex Alimentarius, as well as regulations on the use of water of appropriate quality for irrigation purposes, should be followed.
- Klíčová slova
- Food safety, Irrigation water, Molecular detection, Produce, Virological quality,
- MeSH
- kontaminace potravin analýza MeSH
- listy rostlin růst a vývoj virologie MeSH
- ovoce růst a vývoj virologie MeSH
- sladká voda chemie virologie MeSH
- viry klasifikace genetika izolace a purifikace MeSH
- zelenina růst a vývoj virologie MeSH
- zemědělské zavlažování MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Evropa MeSH
AIM: In this study, buccal swabs from patients with the clinical picture of parotitis epidemica in whom mumps virus (MV) infection was not confirmed by direct detection or serologically were tested. The aim was to detect by molecular methods nucleic acids (NAs) of other respiratory viruses possibly involved in salivary gland swelling. At the same time, paired sera, if available, were tested. MATERIAL AND METHODS: The study group consisted of 72 buccal swabs from patients of the Clinic of infectious, tropical, and parasitic diseases, Na Bulovce Hospital. Paired sera were available from ten patients. Samples were collected in 2013 to 2015. Buccal swabs were tested by PCR for the presence of NAs of adenoviruses (AdV), bocaviruses (hBoV), parainfluenza viruses of types 1-4 (HPIV), human metapneumovirus (hMPV), coronaviruses (HCoV: NL63, OC43, HKU1, and 229E), respiratory syncytial virus (RSV), influenza A virus, influenza B virus, and Epstein-Barr virus (EBV). Paired sera were screened by the complement fixation test (AdV and influenza A and B viruses), hemagglutination inhibition test (HPIV types 2 and 3), ELISA (AdV, EBV), and immunofluorescence (EBV). RESULTS: NAs from viruses other than the mumps virus were detected in 27 of 72 patients with clinical symptoms of parotitis epidemica, and serological tests revealed etiological links with parainfluenza viruses in three more cases. Overall, 30 (41.7%) of 72 patients with suspected mumps tested positive for one or more viruses from the study panel. The most commonly detected viruses were AdV 11/72 (15.3%), EBV 9/72 (12.5%), and HPIV 3/72 (4.2%), but influenza A virus (H3N2) 1/72 (1.4%) was also found. Some patients tested positive for more than one virus: 2/72 (3%) for AdV plus hBoV and 1/72 (1.4%) for HPIV plus HCoV. In addition, examination of paired sera revealed HPIV positivity in three more patients. PCR and serology detected etiological link with HPIV in six (8.3%) of 72 patients tested. CONCLUSION: In our study group, nearly 42% of patients with the clinical picture of parotitis epidemica in whom mumps virus (MV) infection was not confirmed by direct detection or serologically tested positive for viruses other than the mumps virus. Thorough laboratory diagnosis of suspected mumps in vaccinated persons is important not only for the treatment of patients and adoption of isolation and other measures, but also for a better understanding of the epidemiology of the disease and outcomes of the immunisation programmes.
- Klíčová slova
- mumps - epidemiology - PCR - differential diagnosis.,
- MeSH
- diferenciální diagnóza MeSH
- dospělí MeSH
- kojenec MeSH
- lidé MeSH
- mladý dospělý MeSH
- polymerázová řetězová reakce MeSH
- předškolní dítě MeSH
- virové nemoci diagnóza epidemiologie virologie MeSH
- virové vakcíny aplikace a dávkování imunologie MeSH
- viry klasifikace izolace a purifikace MeSH
- Check Tag
- dospělí MeSH
- kojenec MeSH
- lidé MeSH
- mladý dospělý MeSH
- mužské pohlaví MeSH
- předškolní dítě MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- virové vakcíny MeSH
DNA cruciform structures play an important role in the regulation of natural processes including gene replication and expression, as well as nucleosome structure and recombination. They have also been implicated in the evolution and development of diseases such as cancer and neurodegenerative disorders. Cruciform structures are formed by inverted repeats, and their stability is enhanced by DNA supercoiling and protein binding. They have received broad attention because of their important roles in biology. Computational approaches to study inverted repeats have allowed detailed analysis of genomes. However, currently there are no easily accessible and user-friendly tools that can analyse inverted repeats, especially among long nucleotide sequences. We have developed a web-based server, Palindrome analyser, which is a user-friendly application for analysing inverted repeats in various DNA (or RNA) sequences including genome sequences and oligonucleotides. It allows users to search and retrieve desired gene/nucleotide sequence entries from the NCBI databases, and provides data on length, sequence, locations and energy required for cruciform formation. Palindrome analyser also features an interactive graphical data representation of the distribution of the inverted repeats, with options for sorting according to the length of inverted repeat, length of loop, and number of mismatches. Palindrome analyser can be accessed at http://bioinformatics.ibp.cz.
- MeSH
- DNA bakterií analýza genetika MeSH
- DNA virů analýza genetika MeSH
- DNA analýza genetika MeSH
- Escherichia coli genetika MeSH
- genom bakteriální genetika MeSH
- genom virový genetika MeSH
- internet * MeSH
- křížová struktura DNA analýza genetika MeSH
- obrácené repetice genetika MeSH
- oligonukleotidy analýza genetika MeSH
- reprodukovatelnost výsledků MeSH
- sekvence nukleotidů MeSH
- viry klasifikace genetika MeSH
- výpočetní biologie metody MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- DNA bakterií MeSH
- DNA virů MeSH
- DNA MeSH
- křížová struktura DNA MeSH
- oligonukleotidy MeSH
A wide range of viral agents is associated with the development of acute myocarditis and its possible chronic sequela, dilated cardiomyopathy (DCM). There is also increasing evidence that Borrelia burgdorferi (Bb) is associated with DCM in endemic regions for Bb infection. This study sought to use electron microscopy to prospectively analyze the presence of viruses and Bb within the myocardium of 40 subjects with preserved left ventricular (LV) ejection fraction and 40 patients with new-onset unexplained DCM during the same time period. Virus particles were found within the myocardium of 23 subjects (58%) of both cohorts studied, yet there was no statistically significant difference in virus family presence between those with DCM versus those with preserved LV systolic function. In contrast, Bb was detected only in those subjects with DCM (0 versus 5 subjects; p ˂ 0.05). Polymerase chain reaction was performed on samples from patients who were positive for Bb according to electron microscopy, and Bb was confirmed in 4 out of 5 individuals. Our results demonstrate that the prevalence of viral particles does not differ between subjects with preserved LV systolic function versus those with DCM and therefore suggests that the mere presence of a viral agent within the myocardium is not sufficient to establish a clear link with the development of DCM. In contrast, the presence of Bb was found only within myocardial samples of patients with DCM; this finding supports the idea of a causal relationship between Bb infection and DCM development.
- MeSH
- antivirové látky škodlivé účinky terapeutické užití MeSH
- Borrelia burgdorferi genetika izolace a purifikace fyziologie ultrastruktura MeSH
- dilatační kardiomyopatie mikrobiologie patofyziologie virologie MeSH
- elektronová mikroskopie MeSH
- funkce levé komory srdeční MeSH
- krevní tlak MeSH
- lidé středního věku MeSH
- lidé MeSH
- lymeská nemoc klasifikace mikrobiologie patofyziologie MeSH
- myokard ultrastruktura MeSH
- prospektivní studie MeSH
- senioři MeSH
- srdce mikrobiologie patofyziologie virologie MeSH
- virové nemoci komplikace farmakoterapie virologie MeSH
- viry klasifikace genetika izolace a purifikace ultrastruktura MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- antivirové látky MeSH
