Analysis of virus-infected cells by flow cytometry

Characterization and genomic analysis of an oceanic cyanophage infecting marine Synechococcus reveal a novel genus

Cyanophages play a crucial role in the biogeochemical cycles of aquatic ecosystems by affecting the population dynamics and community structure of cyanobacteria. In this study, a novel cyanophage, Nanhaivirus ms29, that infects Synechococcus sp. MW02 was isolated from the ocean basin in the South China Sea. It was identified as a T4-like phage using transmission electron microscopy. Phylogenetic analysis demonstrated that this cyanophage is distinct from other known T4-like cyanophage, belonging to a novel genus named Nanhaivirus within the family Kyanoviridae, according to the most recent classification proposed by the International Committee on Taxonomy of Viruses (ICTV). The genome of this novel cyanophage is composed of 178,866 bp of double-stranded DNA with a G + C content of 42.5%. It contains 217 potential open reading frames (ORFs) and 6 tRNAs. As many as 30 auxiliary metabolic genes (AMGs) were identified in the genome, which related to photosynthesis, carbon metabolism, nutrient uptake and stress tolerance, possibly reflecting a genomic adaption to the oligotrophic environment. Read-mapping analysis showed that Nanhaivirus ms29 mainly distributed in temperate and tropical epipelagic waters. This study enriches of the virus gene database of cyanophages and provides valuable insights into the phylogeny of cyanophages and their interactions with their hosts.

Synthesis of fluorescence labelled aptamers for use as low-cost reagents in HIV/AIDS research and diagnostics

Aptamers are nucleic acids selected by systematic evolution of ligands by exponential enrichment. They have potential as alternatives to antibodies in medical research and diagnostics, with the advantages of being non-immunogenic and relatively inexpensive to produce. In the present study, gp120 aptamers conjugated with fluorescein isothiocyanate (FITC) were generated, which could interact with HIV-1 gp120. A previously isolated gp120 aptamer, CSIR 1.1, was conjugated with FITC by incubation with 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide and imidazole. The conjugation and binding to the glycoprotein were confirmed by flow cytometry. FITC conjugated aptamers showed an increase in fluorescence emission 24-fold higher than baseline, and this difference was statistically significant (P=0.0016). Compared with a commercially available biotinylated anti-gp120 antibody, detected using FITC conjugated streptavidin, the emission of fluorescence obtained from the FITC-conjugated aptamer was 8-fold higher, suggesting a stronger interaction with gp120. In addition, the FITC conjugated aptamer neutralized HIV-1 pseudoviruses with an average IC₅₀ of 21.3 nM, similar to the parent aptamer that had an IC₅₀ of 19.2 nM. However, the difference in inhibition between the two aptamers was not statistically significant (P=0.784). These results indicate that the FITC-conjugated aptamer generated in the present study could potentially be used as a low-cost reagent in HIV/AIDS research and diagnostics.

Dengue Fever, COVID-19 (SARS-CoV-2), and Antibody-Dependent Enhancement (ADE): A Perspective

SARS-CoV-2 pandemic and recurrent dengue epidemics in tropical countries have turned into a global health threat. While both virus-caused infections may only reveal light symptoms, they can also cause severe diseases. Here, we review the possible antibody-dependent enhancement (ADE) occurrence, known for dengue infections, when there is a second infection with a different virus strain. Consequently, preexisting antibodies do not neutralize infection, but enhance it, possibly by triggering Fcγ receptor-mediated virus uptake. No clinical data exist indicating such mechanism for SARS-CoV-2, but previous coronavirus infections or infection of SARS-CoV-2 convalescent with different SARS-CoV-2 strains could promote ADE, as experimentally shown for antibodies against the MERS-CoV or SARS-CoV spike S protein. © 2020 International Society for Advancement of Cytometry.

A flow cytometric granularity assay for the quantification of infectious virus

A flow cytometry-based assay was developed to assess the infective titer of two recombinant viruses: a recombinant herpes simplex type 2 (rHSV-2) and a recombinant canary pox (rALVAC.gfp). This method uses granularity of infected Vero and QT-35 cells, respectively, and correlates this to the infectious titer of virus samples. The percent of the cell populations with a high level of granularity could accurately be correlated to viral titers obtained through a traditional plaque assay, with R² values greater than 0.8 using a semi-logarithmic scale. This approach offers a rapid, high-throughput method for infectious virus titration with similar accuracy to a traditional plaque assay.

High sensitivity detection and sorting of infectious human immunodeficiency virus (HIV-1) particles by flow virometry

Detection of viruses by flow cytometry is complicated by their small size. Here, we characterized the ability of a standard (FACSAria II) and a sub-micron flow cytometer (A50 Micro) to resolve HIV-1 viruses. The A50 was superior at resolving small particles but did not reliably distinguish HIV-1, extracellular vesicles, and laser noise by light scatter properties alone. However, single fluorescent HIV-1 particles could readily be detected by both cytometers. Fluorescent particles were sorted and retained infectivity, permitting further exploration of the functional consequences of HIV-1 heterogeneity. Finally, flow cytometry had a limit of detection of 80 viruses/ml, nearly equal to PCR assays. These studies demonstrate the power of flow cytometry to detect and sort viral particles and provide a critical toolkit to validate methods to label wild-type HIV-1; quantitatively assess integrity and aggregation of viruses and virus-based therapeutics; and efficiently screen drugs inhibiting viral assembly and release.

High-throughput fluorescence-activated nanoscale subcellular sorter with single-molecule sensitivity

Recent single-cell and single-molecule studies have shown that a variety of subpopulations exist within biological systems, such as synaptic vesicles, that have previously been overlooked in common bulk studies. By isolating and enriching these various subpopulations, detailed analysis with a variety of analytical techniques can be done to further understand the role that various subpopulations play in cellular dynamics and how alterations to these subpopulations affect the overall function of the biological system. Previous sorters lack the sensitivity, sorting speed, and efficiency to isolate synaptic vesicles and other nanoscale systems. This paper describes the development of a fluorescence-activated nanoscale subcellular sorter that can sort nearly 10 million objects per hour with single-molecule sensitivity. Utilizing a near-nanoscale channel system, we were able to achieve upward of 91% recovery of desired objects with a 99.7% purity.

Detection of infective poliovirus by a simple, rapid, and sensitive flow cytometry method based on fluorescence resonance energy transfer technology

The rapid and effective detection of virus infection is critical for clinical management and prevention of disease spread during an outbreak. Several methods have been developed for this purpose, of which classical serological and viral nucleic acid detection are the most common. We describe an alternative approach that utilizes engineered cells expressing fluorescent proteins undergoing fluorescence resonance energy transfer (FRET) upon cleavage by the viral 2A protease (2A(pro)) as an indication of infection. Quantification of the infectious-virus titers was resolved by using flow cytometry, and utility was demonstrated for the detection of poliovirus 1 (PV1) infection. Engineered buffalo green monkey kidney (BGMK) cells expressing the cyan fluorescent protein (CFP)-yellow fluorescent protein (YFP) substrate linked by a cleavage recognition site for PV1 2A(pro) were infected with different titers of PV1. After incubation at various time points, cells were harvested, washed, and subjected to flow cytometry analysis. The number of infected cells was determined by counting the number of cells with an increased CFP-to-YFP ratio. As early as 5 h postinfection, a significant number of infected cells (3%) was detected by flow cytometry, and cells infected with only 1 PFU were detected after 12 h postinfection. When applied to an environmental water sample spiked with PV1, the flow cytometry-based assay provided a level of sensitivity similar to that of the plaque assay for detecting and quantifying infectious virus particles. This approach, therefore, is more rapid than plaque assays and can be used to detect other viruses that frequently do not form clear plaques on cell cultures.

Quantitative measurement of varicella-zoster virus infection by semiautomated flow cytometry

Varicella-zoster virus (VZV; human herpesvirus 3) is the etiological cause of chickenpox and, upon reactivation from latency, zoster. Currently, vaccines are available to prevent both diseases effectively. A critical requirement for the manufacturing of safe and potent vaccines is the measurement of the biological activity to ensure proper dosing and efficacy, while minimizing potentially harmful secondary effects induced by immunization. In the case of live virus-containing vaccines, such as VZV-containing vaccines, biological activity is determined using an infectivity assay in a susceptible cellular host in vitro. Infectivity measurements generally rely on the enumeration of plaques by visual inspection of an infected cell monolayer. These plaque assays are generally very tedious and labor intensive and have modest throughput and high associated variability. In this study, we have developed a flow cytometry assay to measure the infectivity of the attenuated vaccine strain (vOka/Merck) of VZV in MRC-5 cells with improved throughput. The assay is performed in 96-well tissue culture microtiter plates and is based on the detection and quantification of infected cells expressing VZV glycoproteins on their surfaces. Multiple assay parameters have been investigated, including specificity, limit of detection, limit of quantification, range of linear response, signal-to-noise ratio, and precision. This novel assay appears to be in good concordance with the classical plaque assay results and therefore provides a viable, higher-throughput alternative to the plaque assay.

Short hairpin RNA-mediated inhibition of HSV-1 gene expression and function during HSV-1 infection in Vero cells

AIM

To evaluate the efficiency of 3 short hairpin RNA (shRNA) interfering with the herpes simplex virus type 1 (HSV-1) gene coding glycoprotein D (gD) for inhibiting the gD expression and virus replication in vitro.

METHODS

Vero cells were selected for an in vitro model of infection. Three shRNA sequences (shRNAgD1, -gD2, and -gD3) targeting specifically the gD gene of HSV-1 were selected for evaluating the antiviral effects. The antiviral effects of shRNA in the cells infected with HSV-1 were evaluated by cytopathic effect (CPE) observations and plaque assays. The transcription level of viral RNA and the gD expression were studied by RT-PCR, Western blotting, and flow cytometry.

RESULTS

With the 3 shRNA at a final concentration of 120 nmol/L, a significant inhibition of CPE in the HSV-1-infected cells was observed. The ED50 of shRNA-gD1, gD2, and gD3 were 48.74+/-2.57, 57.13+/-3.24, and 114.64+/-5.12 nmol/L, respectively. The gD gene decreased significantly after viral infection in the Vero cells pretreated with shRNA compared to the virus group. The expressions of the gD protein, determined by Western blotting and flow cytometry, were also drastically decreased in shRNA-transfected cells.

CONCLUSION

Exogenous shRNA molecules can suppress the HSV-1 gD expression. They are inhibitors of HSV replication during infection in Vero cells.

Establishment of a cell-based assay for screening of compounds inhibiting very early events in the cytomegalovirus replication cycle and characterization of a compound identified using the assay

To simplify the detection of infectious human cytomegalovirus (HCMV), we generated a cell line that produced luciferase in a dose-dependent manner upon HCMV infection. Using this cell line, we identified anti-HCMV compounds from a diverse library of 9,600 compounds. One of them, 1-(3,5-dichloro-4-pyridyl)piperidine-4-carboxamide (DPPC), was effective against HCMV (Towne strain) infection of human lung fibroblast cells at a 50% effective concentration of 2.5 microM. DPPC also inhibited the growth of clinical HCMV isolates and guinea pig and mouse cytomegaloviruses. Experiments using various time frames for treatment of the cells with DPPC demonstrated that DPPC was effective during the first 24 h after HCMV infection. DPPC treatment decreased not only viral DNA replication but also IE1 and IE2 expression at mRNA and protein levels in the HCMV-infected cells. However, DPPC did not inhibit the attachment of HCMV particles to the cell surface. DPPC is a unique compound that targets the very early phase of cytomegalovirus infection, probably by disrupting a pathway that is important after viral entry but before immediate-early gene expression.

Virus assay using antibody-functionalized peptide nanotubes

Robust trace-level detection of viruses is crucial to meet urgent needs in fighting the spread of disease or detecting bioterrorism events. We report a new method for rapid and highly sensitive detection of viruses utilizing fluorescent antibody nanotubes. When viral pathogens were mixed with these antibody nanotubes, the nanotubes rapidly aggregated around the viruses to form a networking structure. Trace quantities of viruses such as herpes simplex virus type 2, adenovirus, vaccinia and influenza type B were detected on attomolar order by changes in fluorescence and light scattering intensities associated with aggregation of dye-loaded antibody nanotubes around viruses. High specificity of each antibody nanotube toward its targeted virus was demonstrated by quantifying concentrations of two different viruses in mixtures. This antibody nanotube assay detects targeted pathogens within 30 minutes after incubation with antibody nanotubes. This antibody nanotube assay could fill a pressing need to detect and quantify viruses both rapidly and sensitively.

Flow cytometry-based assay for titrating dengue virus

Plaque assays for titrating dengue virus (DENV) are time-consuming and not suitable for strains that do not plaque. Fluorescence-activated cell sorting (FACS) has been used to detect DENV-infected cells. Here we describe a FACS-based assay for titrating DENV. We determined that at 24 h postinfection, the number of infected cells detected by FACS represented the first round of infection and therefore could be used as a readout of the number of infectious particles in the inoculum. When the titers of different laboratory and clinical strains of DENV were compared using FACS, plaque, and endpoint dilution assays, for most strains the FACS titers were comparable to titers obtained by plaque or endpoint dilution assays. The FACS assay is an improvement over the plaque assay because the infection period is reduced from 5 to 7 days to 24 h and the assay can be used to titrate clinical isolates that frequently do not form clear plaques on cell monolayers. The novel FACS-based methods described here will facilitate laboratory studies of dengue.

A Lys49 phospholipase A(2) homologue from Bothrops asper snake venom induces proliferation, apoptosis and necrosis in a lymphoblastoid cell line

Lys49 phospholipase A(2) homologues are abundant in viperid snake venoms. These proteins have substitutions at the calcium-binding loop and catalytic center which render them enzymatically inactive; however, they display a series of toxic activities, particularly cytotoxicity upon various cell lines in vitro. In this study we explored whether myotoxin II (MT-II), a Lys49 phospholipase A(2) homologue from the venom of the snake Bothrops asper, is capable of inducing various effects in a single cell type, using the lymphoblastoid B cell line CRL-8062 as a model. Cells were incubated with varying concentrations of MT-II for 24 and 48 h, time intervals that are more prolonged than the usual incubation times previously used in the characterization of this toxin. Results indicate that MT-II induces proliferation at low concentrations (0.5-5.0 microg/mL). Apoptosis was predominant at higher toxin levels (5-25 microg/mL), whereas necrosis, associated with overt plasma membrane disruption, occurred at concentrations > or =25 microg/mL, and was the predominant effect at higher MT-II concentrations (50 microg/mL). It is concluded that a single phospholipase A(2) homologue can induce markedly different effects on a single cell line, depending on the concentration used, an observation that may have implications for the action of this type of venom component in vivo.

High-power blue/UV light-emitting diodes as excitation sources for sensitive detection

With advances in III-V nitride manufacturing processes, high-power light-emitting diode (LED) chips in the blue and UV wavelengths are now commercially available at reasonable cost and can be used as excitation sources in optical sensing. We describe the use of these high-power blue and UV LEDs for sensitive fluorescence detection, including chip-based flow cytometry, capillary electrophoresis (CE), and single-molecule imaging. By using a blue LED with a focusable power of approximately 40 mW as the excitation source for fluorescent beads, we demonstrate a simple chip-based bead sorter capable of enriching the concentration of green fluorescent beads from 63% to 95%. In CE experiments, we show that a mixture of analyte solution containing 30 nM 6-carboxyrhodamine 6G and 10 nM fluorescein can be separated and detected with excellent signal-to-noise ratio (approximately 17 for 10 nM fluorescein) using the collimated emission from a blue LED; the estimated mass detection limit was approximately 200 zmol for fluorescein. We also demonstrated ultrasensitive fluorescence imaging of single rhodamine 123 molecules and individual lambda-DNA molecules. At a small fraction of the cost of an Ar+ laser, high-power blue and UV LEDs are effective alternatives for lasers and arc lamps in fluorescence applications that demand portability, low cost, and convenience.

A polysaccharide fraction from medicinal herb Prunella vulgaris downregulates the expression of herpes simplex virus antigen in Vero cells

Herpes simplex viruses (HSV) are pathogenic. With the emergence of drug-resistant strains of HSV, new antiviral agents, especially those with different modes of action, are urgently needed. Prunella vulgaris L. (Labiatae), a perennial plant commonly found in China and Europe, has long been used as a folk medicine to cure ailments. In this study, a polysaccharide fraction was prepared from Prunella vulgaris (PPV), and its effects on the expressions of HSV-1 and HSV-2 antigens in their host Vero cells were investigated with flow cytometry. The HSV antigen increased time-dependently in the infected cells, and PPV reduced its expression. The effective concentrations of PPV with 50% reductions of the HSV-1 and HSV-2 antigens were 20.6 and 20.1 microg/ml, respectively. The novelty of PPV is that it also reduces the antigen expression of acyclovir-resistant strain of HSV-1. After incubations with 25-100 microg/ml of PPV the HSV antigen-positive cells were reduced by 24.8-92.6%, respectively, showing that this polysaccharide fraction has a different mode of anti-HSV action from acyclovir. Results from this study show that PPV is effective against both the HSV-1 and HSV-2 infections, and flow cytometry offers a quantitative and highly reproducible anti-HSV drug-susceptibility assay.

Biosafety concerns for shared flow cytometry core facilities

Many researchers who need flow cytometry for their projects have neither sufficient funds nor the work volume to justify the purchase of an analytic cytometer or cell sorter. In shared flow cytometry facilities, costs for instrument purchases, cytometer maintenance, and personnel are pooled to provide economic services for a multitude of users when they are required. Owing to the diverse nature of the samples that are submitted to core facilities, the biohazard potential of the samples can vary dramatically. For the safety of facility personnel and users, it is critical that information about hazards contained in the samples be transmitted to instrument operators before flow cytometry experiments are started. During 1999 the former Biosafety Committee of the International Society for Analytical Cytology formulated a framework biosafety questionnaire for shared facilities designed to request information about the hazard potential of experimental samples from investigators who wish to use the facility. In this report we review safety issues that are pertinent to flow cytometry core facilities by discussing the individual components of this biosafety questionnaire.

High-speed cell sorting: fundamentals and recent advances

Cell sorters have undergone dramatic technological improvements in recent years. Driven by the increased ability to differentiate between cell types, modern advances have yielded a new generation of cytometers, known as high-speed cell sorters. These instruments are capable of higher throughput than traditional sorters and can distinguish subtler differences between particles by measuring and processing more optical parameters in parallel. These advances have expanded their use to facilitate genomic and proteomic discovery, and as vehicles for many emerging cell-based therapies. High-speed cell sorting is becoming established as an essential research tool across a broad range of scientific fields and is poised to play a pivotal role in the latest therapeutic modalities.