Virioplankton as an important component of plankton in the Volga Reservoirs

The distribution of virioplankton, abundance and production, frequency of visibly infected cells of heterotrophic bacteria and autotrophic picocyanobacteria and their virus-induced mortality have been studied in mesotrophic and eutrophic reservoirs of the Upper and Middle Volga (Ivankovo, Uglich, Rybinsk, Gorky, Cheboksary, and Sheksna reservoirs). The abundance of planktonic viruses (VA) is on average by 4.6 ± 1.2 times greater than the abundance of bacterioplankton (BA). The distribution of VA in the Volga reservoirs was largely determined by the distribution of BA and heterotrophic bacterioplankton production (PB). There was a positive correlation between VA and BA and between VA and PB. In addition, BA and VA were both positively correlated with primary production of phytoplankton. Viral particles of 60 to 100 µm in size dominated in the phytoplankton composition. A large number of bacteria and picocyanobacteria with viruses attached to the surface of their cells were found in the reservoirs. Viruses as the most numerous component of plankton make a significant contribution to the formation of the planktonic microbial community biomass. The number of phages inside infected cells of bacteria and picocyanobacteria reached 74‒109 phages/cell. Easily digestible organic matter, which entered the aquatic environment as a result of viral lysis of bacteria and picocyanobacteria, could be an additional source of carbon for living bacteria. The results of long-term studies indicate a significant role of viruses in functioning of planktonic microbial communities in the Volga reservoirs.

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Long-term persistence of crAss-like phage crAss001 is associated with phase variation in Bacteroides intestinalis

10.1101/2020.12.02.408625 ◽

2020 ◽

Author(s):

Andrey N Shkoporov ◽

Ekaterina V Khokhlova ◽

Niamh Stephens ◽

Cara Hueston ◽

Samuel Seymour ◽

...

Keyword(s):

Dynamic Equilibrium ◽

Phase Variation ◽

Carrier State ◽

Human Gut ◽

Rapid Phase ◽

Host Interaction ◽

Infected Cells ◽

Phage Sensitivity

The crAss-like phages are ubiquitous and highly abundant members of the human gut virome that infect commensal bacteria of the order Bacteroidales. Although incapable of classical lysogeny, these viruses demonstrate unexplained long-term persistence in the human gut microbiome, dominating the virome in some individuals. Here we demonstrate that rapid phase variation of alternate capsular polysaccharides plays an important role in dynamic equilibrium between phage sensitivity and resistance in B. intestinalis cultures, allowing phage and bacteria to multiply in parallel. The data also suggests the role of concomitant phage persistence mechanisms associated with delayed lysis of infected cells, such as carrier state infection. From an ecological and evolutionary standpoint this type of phage-host interaction is consistent with the Piggyback-the-Winner model, which suggests a preference towards lysogenic or other 'benign' forms of phage infection when the host is stably present at high abundance.

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Patient-individual cancer cell lines and tissue analysis delivers no evidence for a role of DNA virus infection on colorectal cancer oncogenesis

10.21203/rs.2.13448/v1 ◽

2019 ◽

Author(s):

Michael Gock ◽

Marcel Kordt ◽

Stephanie Matschos ◽

Christina S. Mullins ◽

Michael Linnebacher

Keyword(s):

Cell Lines ◽

Molecular Subtypes ◽

Morphological Changes ◽

Tissue Analysis ◽

Oncogenic Viruses ◽

Dna Viruses ◽

Viral Particles ◽

Specific Sequences

Abstract Background Several DNA viruses are highly suspicious to have oncogenic effects in humans. This study investigates the presence of potentially oncogenic viruses such as SV40, JCV, BKV and EBV in patient-derived colorectal carcinoma (CRC) cells typifying all molecular subtypes of CRC. Methods Sample material (gDNA and cDNA) of a total of 49 patient-individual CRC cell lines and corresponding primary material from 11 patients, including normal, tumor-derived and metastasis-derived tissue were analyzed for sequences of SV40, JVC, BKV and EBV using endpoint PCR. In addition, the susceptibility of CRC cells to JCV and BKV was examined using a long-term cultivation approach of patient-individual cells in the presence of viruses. Results No virus-specific sequences could be detected in all specimens. Likewise, no morphological changes were observed and no evidence for viral infection or integration could be provided after long term CRC cell cultivation in presence of viral particles. Conclusions In summary, the presented data suggest that there is no direct correlation between tumorigenesis and viral load and consequently no evidence for a functional role of the DNA viruses included into this analysis in CRC development.

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What is in a Viral Stock: Perspectives and Current Limitations of Flow Virometry

10.20944/preprints202011.0409.v1 ◽

2020 ◽

Author(s):

Timothy K. Soh ◽

Jens B. Bosse

Keyword(s):

Flow Cytometry ◽

Full Potential ◽

Multiple Objects ◽

Virus Particles ◽

Viral Particles ◽

Viral Stock ◽

Infected Cells ◽

A Minor ◽

Unique Capability

Herpesviruses produce a plethora of pleomorphic and heterogeneous particle populations. The composition and biological role of these is not understood. Detailed analysis has been challenging due to the lack of multidimensional identification and purification methodologies. Fluorescence-activated cell sorting (FACS), originally developed to sort objects with at least ten thousand-fold larger volumes, has recently been applied to cellular exosomes as well as viral particles and has been dubbed nanoscale flow cytometry or “flow virometry”. In comparison to other nanoparticles, herpesvirus concentrations can be measured with high precision using simple culturing methods. Here, we used this unique capability to evaluate a standard FACS sorter. We demonstrate that detection and separation capabilities were insufficient to distinguish infectious fluorescent viral populations from populations lacking fluorescence and infectivity. Moreover, fluorescent populations did not contain single virus particles but mostly aggregates. On top, analysis of viral samples by flow cytometry was confounded by swarm detection, as multiple objects are measured simultaneously and interpreted as a single object. Despite these technical difficulties, comparison of crude supernatant to gradient purified HCMV revealed that infectious virus is a minor proportion of the particles released from infected cells. Our data stress the need for a set of standardized controls and protocols when applying FACS to biological nanoparticles and highlights technical challenges that need to be solved before flow virometry can achieve its full potential.

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Flow Cytometry Analysis of HIV-1 Env Conformations at the Surface of Infected Cells and Virions: Role of Nef, CD4, and SERINC5

Journal of Virology ◽

10.1128/jvi.01783-19 ◽

2019 ◽

Vol 94 (6) ◽

Cited By ~ 3

Author(s):

Isabelle Staropoli ◽

Jérémy Dufloo ◽

Anaïs Ducher ◽

Pierre-Henri Commere ◽

Anna Sartori-Rupp ◽

...

Keyword(s):

Neutralizing Antibodies ◽

Cellular Proteins ◽

Viral Infectivity ◽

Viral Particles ◽

Immunodeficiency Virus ◽

Infected Cells ◽

Env Protein ◽

The Impact ◽

Hiv 1

ABSTRACT The HIV-1 Env protein is exposed at the surface of virions and infected cells. Env fluctuates between different closed and open structural states and these conformations influence both viral infectivity and sensitivity to antibody binding and neutralization. We established a flow virometry assay to visualize Env proteins at the surface of human immunodeficiency virus type 1 (HIV-1) virions. The assay is performed on ultracentrifuged fluorescent viral particles that are stained with a panel of broadly neutralizing antibodies (bNAbs) and nonneutralizing antibodies (nnAbs) that probe different epitopes of Env. We used this assay to compare Env at the surface of producer cells and viral particles and to analyze the effect of Nef, CD4, and SERINC5 on Env accessibility to antibodies. We studied the laboratory-adapted strain NL4-3 and two transmitted/founder viruses, THRO and CH058. We confirm that antibody accessibility varies between viral strains and show that Nef, CD4, and SERINC5 additively impact Env conformations. We further demonstrate that the Env accessibility profile on virions is globally similar to that observed on HIV-1-infected cells, with some noticeable differences. For instance, nnAbs bind to virions more efficiently than to producer cells, likely reflecting changes in Env conformational states on mature viral particles. This test complements other techniques and provides a convenient and simple tool for quantifying and probing the structure of Env at the virion surface and to analyze the impact of viral and cellular proteins on these parameters. IMPORTANCE HIV-1 Env conformation is one of the key parameters determining viral infectivity. The flow virometry-based assay developed in this study allows for the characterization of proteins incorporated in HIV-1 particles. We studied the conformation of HIV-1 Env and the impact that the viral protein Nef and the cellular proteins CD4 and SERINC5 have on Env accessibility to antibodies. Our assay permitted us to highlight some noticeable differences in the conformation of Env between producer cells and viral particles. It contributes to a better understanding of the actual composition of HIV-1 particles.

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Viral burst size of heterotrophic prokaryotes in aquatic systems

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s002531540601352x ◽

2006 ◽

Vol 86 (3) ◽

pp. 613-621 ◽

Cited By ~ 92

Author(s):

Verónica Parada ◽

Gerhard J. Herndl ◽

Markus G. Weinbauer

Keyword(s):

Large Scale ◽

Burst Size ◽

Aquatic Systems ◽

The Past ◽

Number Of Factors ◽

Transmission Electron ◽

Viral Particles ◽

Infected Cells ◽

Heterotrophic Prokaryotes

Viral burst size (BS), i.e. the number of viruses released during cell lysis, is a critical parameter for assessing the ecological and biogeochemical role of viruses in aquatic systems. Burst size is typically estimated by enumerating the viral particles in bacteria using transmission electron microscopy. Here, we review the average BS reported for different aquatic systems, present several hypotheses on the control of the BS and evaluate whether there are relationships between BS and bacterial activity parameters across systems. Based on reports from a variety of different aquatic environments, we calculated a mean BS of 24 and 34 for marine and freshwater environments, respectively. Generally, the BS increased with the trophic status of the environment and with the percentage of infected cells in marine populations. When diel dynamics were investigated or averages from large-scale environments were used, BS was positively related to bacterial production but no trend was detectable across systems. The across systems' finding that BS was significantly related to the frequency of infected cells (FIC) could be due to co-infection or superinfection. At any given site, BS seems to be influenced by a number of factors such as the size of the host cell and the viruses, the metabolic activity of the host and phage and host diversity. Thus, based on the available data collected over the past two decades on a variety of aquatic systems, some relations between BS and bacterial variables were detectable.

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Patient-individual cancer cell lines and tissue analysis delivers no evidence of sequences from DNA viruses in colorectal cancer cells

10.21203/rs.2.13448/v4 ◽

2020 ◽

Author(s):

Michael Gock ◽

Marcel Kordt ◽

Stephanie Matschos ◽

Christina S. Mullins ◽

Michael Linnebacher

Keyword(s):

Cell Lines ◽

Morphological Changes ◽

Tissue Analysis ◽

Oncogenic Viruses ◽

Dna Viruses ◽

Viral Particles ◽

Colorectal Cancer Cells ◽

Specific Sequences

Abstract Background: Several DNA viruses are highly suspicious to have oncogenic effects in humans. This study investigates the presence of potentially oncogenic viruses such as SV40, JCV, BKV and EBV in patient-derived colorectal carcinoma (CRC) cells typifying all molecular subtypes of CRC. Methods: Sample material (gDNA and cDNA) of a total of 49 patient-individual CRC cell lines and corresponding primary material from 11 patients, including normal, tumor-derived and metastasis-derived tissue were analyzed for sequences of SV40, JVC, BKV and EBV using endpoint PCR. In addition, the susceptibility of CRC cells to JCV and BKV was examined using a long-term cultivation approach of patient-individual cells in the presence of viruses. Results: No virus-specific sequences could be detected in all specimens. Likewise, no morphological changes were observed and no evidence for viral infection or integration could be provided after long term CRC cell cultivation in presence of viral particles. Conclusions: In summary, the presented data suggest that there is no direct correlation between tumorigenesis and viral load and consequently no evidence for a functional role of the DNA viruses included into this analysis in CRC development.

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Patient-individual cancer cell lines and tissue analysis delivers no evidence of sequences from DNA viruses in colorectal cancer cells

BMC Gastroenterology ◽

10.1186/s12876-020-01404-x ◽

2020 ◽

Vol 20 (1) ◽

Cited By ~ 1

Author(s):

Michael Gock ◽

Marcel Kordt ◽

Stephanie Matschos ◽

Christina S. Mullins ◽

Michael Linnebacher

Keyword(s):

Cell Lines ◽

Morphological Changes ◽

Tissue Analysis ◽

Oncogenic Viruses ◽

Dna Viruses ◽

Viral Particles ◽

Colorectal Cancer Cells ◽

Specific Sequences

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Role of PACS-1 in Trafficking of Human Cytomegalovirus Glycoprotein B and Virus Production

Journal of Virology ◽

10.1128/jvi.77.20.11105-11113.2003 ◽

2003 ◽

Vol 77 (20) ◽

pp. 11105-11113 ◽

Cited By ~ 50

Author(s):

Colin M. Crump ◽

Chien-Hui Hung ◽

Laurel Thomas ◽

Lei Wan ◽

Gary Thomas

Keyword(s):

Envelope Glycoprotein ◽

Secretory Pathway ◽

Virus Production ◽

Viral Proteins ◽

Glycoprotein B ◽

Efficient Production ◽

Viral Particles ◽

Infected Cells ◽

Golgi Network

ABSTRACT The final envelopment of herpesviruses during assembly of new virions is thought to occur by the budding of core viral particles into a late secretory pathway organelle, the trans-Golgi network (TGN), or an associated endosomal compartment. Several herpesvirus envelope glycoproteins have been previously shown to localize to the TGN when expressed independently from other viral proteins. In at least some cases this TGN localization has been shown to be dependent on clusters of acidic residues within their cytoplasmic domains. Similar acidic cluster motifs are found in endogenous membrane proteins that also localize to the TGN. These acidic cluster motifs interact with PACS-1, a connector protein that is required for the trafficking of proteins containing such motifs from endosomes to the TGN. We show here that PACS-1 interacts with the cytoplasmic domain of the HCMV envelope glycoprotein B (gB) and that PACS-1 function is required for normal TGN localization of HCMV gB. Furthermore, inhibition of PACS-1 activity in infected cells leads to a decrease in HCMV titer, whereas an increase in expression of functional PACS-1 leads to an increase in HCMV titer, suggesting that PACS-1 is required for efficient production of HCMV.

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Regulation of Apolipoprotein E Trafficking by Hepatitis C Virus-Induced Autophagy

Journal of Virology ◽

10.1128/jvi.00211-18 ◽

2018 ◽

Vol 92 (14) ◽

Cited By ~ 4

Author(s):

Ja Yeon Kim ◽

Jing-hsiung James Ou

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Apolipoprotein E ◽

Protein Degradation ◽

Envelope Protein ◽

Subgenomic Rna ◽

Viral Particles ◽

Infected Cells ◽

Rna Replicon

ABSTRACTApolipoprotein E (ApoE) plays an important role in the maturation and infectivity of hepatitis C virus (HCV). By analyzing the subcellular localization of ApoE in Huh7 hepatoma cells that harbored an HCV subgenomic RNA replicon, we found that ApoE colocalized with autophagosomes. This colocalization was marginally detected in HCV-infected cells, apparently due to the depletion of ApoE by HCV, as treatment with bafilomycin A1 (BafA1), a vacuolar ATPase inhibitor that inhibits autophagic protein degradation, partially restored the ApoE level and enhanced its colocalization with autophagosomes in HCV-infected cells. The role of HCV-induced autophagy in the degradation of ApoE was further supported by the observations that nutrient starvation, which induces autophagic protein degradation, led to the loss of ApoE in HCV subgenomic RNA replicon cells and that the knockdown of ATG7, a protein essential for the formation of autophagic vacuoles, increased the ApoE level in cells with productive HCV replication. Interestingly, the inhibition of autophagy by ATG7 knockdown reduced the colocalization of ApoE with the HCV E2 envelope protein and the HCV titers released from cells. In contrast, the treatment of cells with BafA1 enhanced the colocalization of ApoE and HCV E2 and increased both intracellular and extracellular HCV titers. These results indicated that autophagy played an important role in the trafficking of ApoE in HCV-infected cells. While it led to autophagic degradation of ApoE, it also promoted the interaction between ApoE and HCV E2 to enhance the production of infectious progeny viral particles.IMPORTANCEHepatitis C virus (HCV) is one of the most important human pathogens. Its virion is associated with apolipoprotein E (ApoE), which enhances its infectivity. HCV induces autophagy to enhance its replication. In this report, we demonstrate that autophagy plays an important role in the trafficking of ApoE in HCV-infected cells. This leads to the degradation of ApoE by autophagy. However, if the autophagic protein degradation is inhibited, ApoE is stabilized and colocalized with autophagosomes. This leads to its enhanced colocalization with the HCV E2 envelope protein and increased production of infectious progeny viral particles. If autophagy is inhibited by suppressing the expression of ATG7, a gene essential for the formation of autophagosomes, the colocalization of ApoE with E2 is reduced, resulting in the reduction of progeny viral titers. These results indicate an important role of autophagy in the transport of ApoE to promote the production of infectious HCV particles.

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Investigation of Extracellular Vesicles From SARS-CoV-2 Infected Specimens: A Safety Perspective

Frontiers in Immunology ◽

10.3389/fimmu.2021.617042 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yury O. Nunez Lopez ◽

Anna Casu ◽

Richard E. Pratley

Keyword(s):

Disease Progression ◽

Extracellular Vesicles ◽

Research Needs ◽

Scientific Communities ◽

Safety Measures ◽

Enveloped Viruses ◽

Viral Particles ◽

Viremic Phase ◽

Infected Cells

The coronavirus disease 2019 (COVID-19) pandemic, caused by the SARS-CoV-2 virus, is wreaking havoc around the world. Considering that extracellular vesicles (EVs) released from SARS-CoV-2 infected cells might play a role in a viremic phase contributing to disease progression and that standard methods for EV isolation have been reported to co-isolate viral particles, we would like to recommend the use of heightened laboratory safety measures during the isolation of EVs derived from SARS-CoV-2 infected tissue and blood from COVID-19 patients. Research needs to be conducted to better understand the role of EVs in SARS-CoV-2 infectivity, disease progression, and transmission. EV isolation procedures should include approaches for protection from SARS-CoV-2 contamination. We recommend the EV and virology scientific communities develop collaborative projects where relationships between endogenous EVs and potentially lethal enveloped viruses are addressed to better understand the risks and pathobiology involved.

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