Detection and identification of viruses by electron microscopy

Uncovering the morphological differences between SARS-CoV-2 and SARS-CoV based on transmission electron microscopy images

Comprehending the morphological disparities between SARS-CoV-2 and SARS-CoV viruses can shed light on the underlying mechanisms of infection and facilitate the development of effective diagnostic tools and treatments. Hence, this study aimed to conduct a comprehensive analysis and comparative assessment of the morphology of SARS-CoV-2 and SARS-CoV using transmission electron microscopy (TEM) images. The dataset encompassed 519 isolated SARS-CoV-2 images obtained from patients in Italy (INMI) and 248 isolated SARS-CoV images from patients in Germany (Frankfurt). In this paper, we employed TEM images to scrutinize morphological features, and the outcomes were contrasted with those of SARS-CoV viruses. The findings reveal disparities in the characteristics of SARS-CoV-2 and SARS-CoV, such as envelope protein (E) 98.6 and 102.2 nm, length of spike protein (S) 10.11 and 9.50 nm, roundness 0.86 and 0.88, circularity 0.78 and 0.76, and area sizes 25145.54 and 38591.35 pixels, respectively. In conclusion, these results will augment the identification of virus subtypes, aid in the study of antiviral medications, and enhance our understanding of disease progression and the virus life cycle. Moreover, these findings have the potential to assist in the development of more accurate epidemiological prediction models for COVID-19, leading to better outbreak management and saving lives.

Identification of coronavirus particles by electron microscopy requires demonstration of specific ultrastructural features

With interest we read the publication of Evangelou et al . [1], which studied SARS-CoV-2 induced senescence in severe COVID-19. Immunohistochemistry (IHC) and electron microscopy (EM) were used for in situ detection of SARS-CoV-2 in autopsy tissues. The authors used formalin-fixed and paraffin-embedded (FFPE) autopsy lung of COVID-19 and non-COVID-19 patients to perform re-embedding for EM and ultrastructural analysis. They report detection of SARS-CoV-2 virions within alveolar type 2 cells of representative COVID-19 cases (figure 1c in Evangelou et al. [1]). Three electron micrographs show putative virus particles, indicated by arrows, to document their findings.

Unequivocal detection of ultrastructural features specific to organelles or viruses is required to infer their presence by electron microscopy. This article also provides reference images for the correct identification of coronavirus. https://bit.ly/3IFYDjc

Nanodissection of Selected Viral Particles by Scanning Transmission Electron Microscopy/Focused Ion Beam for Genetic Identification

This study presents the development of a new correlative workflow to bridge the gap between electron microscopy imaging and genetic analysis of viruses. The workflow enables the assignment of genetic information to a specific biological entity by harnessing the nanodissection capability of focused ion beam (FIB). This correlative workflow is based on scanning transmission electron microscopy (STEM) and FIB followed by a polymerase chain reaction (PCR). For this purpose, we studied the tomato brown rugose fruit virus (ToBRFV) and the adenovirus that have significant impacts on plant integrity and human health, respectively. STEM imaging was used for the identification and localization of virus particles on a transmission electron microscopy (TEM) grid followed by FIB milling of the desired region of interest. The final-milled product was subjected to genetic analysis by the PCR. The results prove that the FIB-milling process maintains the integrity of the genetic material as confirmed by the PCR. We demonstrate the identification of RNA and DNA viruses extracted from a few micrometers of an FIB-milled TEM grid. This workflow enables the genetic analysis of specifically imaged viral particles directly from heterogeneous clinical samples. In addition to viral diagnostics, the ability to isolate and to genetically identify specific submicrometer structures may prove valuable in additional fields, including subcellular organelle and granule research.

Best practices for correctly identifying coronavirus by transmission electron microscopy

This guidance provides clear, concise strategies for identifying coronaviruses by transmission electron microscopy of ultrathin sections of tissues or infected tissue cultures. These include a description of virus morphology as well as cell organelles that can resemble viruses. Biochemical testing and caveats are discussed. Numerous references provide information for documentation and further study.

Difficulties in Differentiating Coronaviruses from Subcellular Structures in Human Tissues by Electron Microscopy

Efforts to combat the coronavirus disease (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have placed a renewed focus on the use of transmission electron microscopy for identifying coronavirus in tissues. In attempts to attribute pathology of COVID-19 patients directly to tissue damage caused by SARS-CoV-2, investigators have inaccurately reported subcellular structures, including coated vesicles, multivesicular bodies, and vesiculating rough endoplasmic reticulum, as coronavirus particles. We describe morphologic features of coronavirus that distinguish it from subcellular structures, including particle size range (60–140 nm), intracellular particle location within membrane-bound vacuoles, and a nucleocapsid appearing in cross section as dense dots (6–12 nm) within the particles. In addition, although the characteristic spikes of coronaviruses may be visible on the virus surface, especially on extracellular particles, they are less evident in thin sections than in negative stain preparations.

Morphometry of SARS-CoV and SARS-CoV-2 particles in ultrathin plastic sections of infected Vero cell cultures

SARS-CoV-2 is the causative of the COVID-19 disease, which has spread pandemically around the globe within a few months. It is therefore necessary to collect fundamental information about the disease, its epidemiology and treatment, as well as about the virus itself. While the virus has been identified rapidly, detailed ultrastructural analysis of virus cell biology and architecture is still in its infancy. We therefore studied the virus morphology and morphometry of SARS-CoV-2 in comparison to SARS-CoV as it appears in Vero cell cultures by using conventional thin section electron microscopy and electron tomography. Both virus isolates, SARS-CoV Frankfurt 1 and SARS-CoV-2 Italy-INMI1, were virtually identical at the ultrastructural level and revealed a very similar particle size distribution with a median of about 100 nm without spikes. Maximal spike length of both viruses was 23 nm. The number of spikes per virus particle was about 30% higher in the SARS-CoV than in the SARS-CoV-2 isolate. This result complements a previous qualitative finding, which was related to a lower productivity of SARS-CoV-2 in cell culture in comparison to SARS-CoV.

Ultrastructure of cell trafficking pathways and coronavirus: how to recognise the wolf amongst the sheep

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has resulted in an urgent need to understand the pathophysiology of SARS-CoV-2 infection, to assist in the identification of treatment strategies. Viral tissue tropism is an active area of investigation, one approach to which is identification of virus within tissues by electron microscopy of post-mortem and surgical specimens. Most diagnostic histopathologists have limited understanding of the ultrastructural features of normal cell trafficking pathways, which can resemble intra- and extracellular coronavirus; in addition, viral replication pathways make use of these trafficking pathways. Herein, we review these pathways and their ultrastructural appearances, with emphasis on structures which may be confused with coronavirus. In particular, we draw attention to the fact that, when using routine fixation and processing, the typical 'crown' that characterises a coronavirus is not readily identified on intracellular virions, which are located in membrane-bound vacuoles. In addition, the viral nucleocapsid is seen as black dots within the virion and is more discriminatory in differentiating virions from other cellular structures. The identification of the viral replication organelle, a collection of membranous structures (convoluted membranes) seen at a relatively low scanning power, may help to draw attention to infected cells, which can be sparse. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.

A Cell-Based Capture Assay for Rapid Virus Detection

Routine methods for virus detection in clinical specimens rely on a variety of sensitive methods, such as genetic, cell culture and immuno-based assays. It is imperative that the detection assays would be reliable, reproducible, sensitive and rapid. Isolation of viruses from clinical samples is crucial for deeper virus identification and analysis. Here we introduce a rapid cell-based assay for isolation and detection of viruses. As a proof of concept several model viruses including West Nile Virus (WNV), Modified Vaccinia Ankara (MVA) and Adenovirus were chosen. Suspended Vero cells were employed to capture the viruses following specific antibody labeling which enables their detection by flow cytometry and immuno-fluorescence microscopy assays. Using flow cytometry, a dose response analysis was performed in which 3.6e4 pfu/mL and 1e6 pfu/mL of MVA and WNV could be detected within two hours, respectively. When spiked to commercial pooled human serum, detection sensitivity was slightly reduced to 3e6 pfu/mL for WNV, but remained essentially the same for MVA. In conclusion, the study demonstrates a robust and rapid methodology for virus detection using flow cytometry and fluorescence microscopy. We propose that this proof of concept may prove useful in identifying future pathogens.

Increasing Type 1 Poliovirus Capsid Stability by Thermal Selection

Poliomyelitis is a highly infectious disease caused by poliovirus (PV). It can result in paralysis and may be fatal. Integrated global immunization programs using live-attenuated oral (OPV) and/or inactivated (IPV) PV vaccines have systematically reduced its spread and paved the way for eradication. Immunization will continue posteradication to ensure against reintroduction of the disease, but there are biosafety concerns for both OPV and IPV. They could be addressed by the production and use of virus-free virus-like particle (VLP) vaccines that mimic the "empty" capsids (ECs) normally produced in viral infection. Although ECs are antigenically indistinguishable from mature virus particles, they are less stable and readily convert into an alternative conformation unsuitable for vaccine purposes. Stabilized ECs, expressed recombinantly as VLPs, could be ideal candidate vaccines for a polio-free world. However, although genome-free PV ECs have been expressed as VLPs in a variety of systems, their inherent antigenic instability has proved a barrier to further development. In this study, we selected thermally stable ECs of type 1 PV (PV-1). The ECs are antigenically stable at temperatures above the conversion temperature of wild-type (wt) virions. We have identified mutations on the capsid surface and in internal networks that are responsible for EC stability. With reference to the capsid structure, we speculate on the roles of these residues in capsid stability and postulate that such stabilized VLPs could be used as novel vaccines.

IMPORTANCE

Poliomyelitis is a highly infectious disease caused by PV and is on the verge of eradication. There are biosafety concerns about reintroduction of the disease from current vaccines that require live virus for production. Recombinantly expressed virus-like particles (VLPs) could address these inherent problems. However, the genome-free capsids (ECs) of wt PV are unstable and readily change antigenicity to a form not suitable as a vaccine. Here, we demonstrate that the ECs of type 1 PV can be stabilized by selecting heat-resistant viruses. Our data show that some capsid mutations stabilize the ECs and could be applied as candidates to synthesize stable VLPs as future genome-free poliovirus vaccines.

Rapid and reliable detection of bacterial endospores in environmental samples by diagnostic electron microscopy combined with X-ray microanalysis

Diagnostic negative staining electron microscopy is a front-line method for the rapid investigation of environmental and clinical samples in emergency situations caused by bioterrorism or outbreaks of an infectious disease. Spores of anthrax are one of the diagnostic targets in case of bioterrorism, because they have been used as a bio-weapon in the past and their production and transmission are rather simple. With negative staining electron microscopy bacterial spores can be identified based on their morphology at the single cell level. However, because of their particular density, no internal structures are visible which sometimes makes it difficult to distinguish spores from particles with a similar size and shape that are frequently present in environmental samples. Spores contain a high concentration of calcium ions besides other elements, which may allow a proper discrimination of spores from other suspicious particles. To investigate this hypothesis, negative staining electron microscopy, using either transmission or scanning electron microscopes, was combined with energy dispersive X-ray microanalysis, which reveals the element content of individual nanoparticles. A peak pattern consisting of calcium, sulphur and phosphorus was found as a typical signature within the X-ray spectrum of spores in various Clostridium and Bacillus species, including all strains of anthrax (Bacillus anthracis) tested. Moreover, spores could be reliably identified by this combined approach in environmental samples, like household products, soil or various presumed bioterrorist samples. In summary, the use of X-ray spectroscopy, either directly in the transmission electron microscope, or in a correlative approach by using scanning electron microscopy, improves the emergency diagnostics of suspicious environmental samples.

Detection limit of negative staining electron microscopy for the diagnosis of bioterrorism-related micro-organisms

Aims:  To determine the detection limit of diagnostic negative staining electron microscopy for the diagnosis of pathogens that could be used for bioterrorism.

Methods and Results:  Suspensions of vaccinia poxvirus and endospores of Bacillus subtilis were used at defined concentrations as a model for poxviruses and spores of anthrax (Bacillus anthracis), both of which are pathogens that could be used for bioterrorist attacks. Negative staining electron microscopy was performed directly or after sedimentation of these suspensions on to the sample supports using airfuge ultracentrifugation. For both virus and spores, the detection limit using direct adsorption of a 10‐μl sample volume onto the sample support was 10⁶ particles per ml. Using airfuge ultracentrifugation with a sample volume of 80 μl, the detection limit could be reduced to 10⁵ particles per ml for spores and to 5 × 10⁴ particles per ml for poxviruses. The influence on particle detection of incubation time, washing and adsorption procedures was investigated.

Conclusions:  The reproducibility and sensitivity of the method were acceptable, particularly considering the small sample volume and low particle number applied onto the sample support.

Significance and Impact of the Study:  Diagnostic negative staining electron microscopy is used for the diagnosis of pathogens in emergency situations because it allows a rapid examination of all particulate matter down to the nanometre scale. This study provides precise detection limit for the method, an important factor for the validation and improvement of the technique.

Modern uses of electron microscopy for detection of viruses

Electron microscopy, considered by some to be an old technique, is still on the forefront of both clinical viral diagnoses and viral ultrastructure and pathogenesis studies. In the diagnostic setting, it is particularly valuable in the surveillance of emerging diseases and potential bioterrorism viruses. In the research arena, modalities such as immunoelectron microscopy, cryo-electron microscopy, and electron tomography have demonstrated how viral structural components fit together, attach to cells, assimilate during replication, and associate with the cellular machinery during replication and egression. These studies provide information for treatment and vaccine strategies.

Biophysical characterization of influenza virus subpopulations using field flow fractionation and multiangle light scattering: Correlation of particle counts, size distribution and infectivity

Adequate biophysical characterization of influenza virions is important for vaccine development. The influenza virus vaccines are produced from the allantoic fluid of developing chicken embryos. The process of viral replication produces a heterogeneous mixture of infectious and non-infectious viral particles with varying states of aggregation. The study of the relative distribution and behavior of different subpopulations and their inter-correlation can assist in the development of a robust process for a live virus vaccine. This report describes a field flow fractionation and multiangle light scattering (FFF-MALS) method optimized for the analysis of size distribution and total particle counts. The FFF-MALS method was compared with several other methods such as transmission electron microscopy (TEM), atomic force microscopy (AFM), size exclusion chromatography followed by MALS (SEC-MALS), quantitative reverse transcription polymerase chain reaction (RT Q-PCR), median tissue culture dose (TCID(50)), and the fluorescent focus assay (FFA). The correlation between the various methods for determining total particle counts, infectivity and size distribution is reported. The pros and cons of each of the analytical methods are discussed.

Identification of the orthopoxvirus p4c gene, which encodes a structural protein that directs intracellular mature virus particles into A-type inclusions

The orthopoxvirus gene p4c has been identified in the genome of the vaccinia virus strain Western Reserve. This gene encodes the 58-kDa structural protein P4c present on the surfaces of the intracellular mature virus (IMV) particles. The gene is disrupted in the genome of cowpox virus Brighton Red (BR), demonstrating that although the P4c protein may be advantageous for virus replication in vivo, it is not essential for virus replication in vitro. Complementation and recombination analyses with the p4c gene have shown that the P4c protein is required to direct the IMV into the A-type inclusions (ATIs) produced by cowpox virus BR. The p4c gene is highly conserved among most members of the orthopoxvirus genus, including viruses that produce ATIs, such as cowpox, ectromelia, and raccoonpox viruses, as well as those such as variola, monkeypox, vaccinia, and camelpox viruses, which do not. The conservation of the p4c gene among the orthopoxviruses, irrespective of their capacities to produce ATIs, suggests that the P4c protein provides functions in addition to that of directing IMV into ATIs. These findings, and the presence of the P4c protein in IMV but not extracellular enveloped virus (D. Ulaeto, D. Grosenbach, and D. E. Hruby, J. Virol. 70:3372-3377, 1996), suggest a model in which the P4c protein may play a role in the retrograde movement of IMV particles, thereby contributing to the retention of IMV particles within the cytoplasm and within ATIs when they are present. In this way, the P4c protein may affect both viral morphogenesis and processes of virus dissemination.

Outbreaks of acute gastroenteritis associated with Norwalk-like viruses in campus settings

Norwalk-like viruses (NLVs) are transmitted by fecally contaminated food, water, fomites, and person-to-person contact. They are a leading cause of acute gastroenteritis epidemics in industrialized countries. NLV outbreaks are characterized by a 12- to 48-hour incubation period; nausea, vomiting, and diarrhea for 24 to 72 hours; and high secondary attack rates. NLV infections spread rapidly on college and university campuses because of close living quarters, shared bathrooms and common rooms, many food handlers, popular self-service salad bars in dining halls, and person-to-person contact through sports and recreational activities. The illness is generally mild and self-limited but an outbreak can strain the resources of campus health services and cause high absenteeism among both students and staff. Treatment is primarily through antiemetic medication and oral rehydration. Prevention and control of NLV outbreaks rests on promoting hand washing; enforcement of strict hygiene in all food preparation areas; and prompt, rigorous cleaning of potentially contaminated areas where someone has been ill.

Transmission of Norwalk virus during a football game

BACKGROUND

During a college football game in Florida, diarrhea and vomiting developed in many of the members of a North Carolina team. The next day, similar symptoms developed in some of the players on the opposing team.

METHODS

We interviewed those who ate the five meals served to the North Carolina team before the game and some of the players on the opposing team who became ill. Patients with primary cases were members or staff of the team who had vomiting or diarrhea at least 10 hours after but no more than 50 hours after eating a box lunch served the day before the game. Patients with secondary cases had a later onset of symptoms or had symptoms without having eaten the box lunch. Stool samples were examined by electron microscopy and by a reverse-transcription-polymerase-chain-reaction (RT-PCR) assay.

RESULTS

The two football teams shared no food or beverages and had no contact off the playing field. Of five meals served to the North Carolina team before the game, only the box lunch was associated with a significant risk of illness (relative risk of illness, 4.1; 95 percent confidence interval, 1.6 to 10.0). The rate of attack among those who ate the box lunch was 62 percent. There were 11 secondary cases among the members and staff of the North Carolina team and 11 such cases among the Florida players. All four stool samples obtained from North Carolina patients were positive for Norwalk-like virus on electron microscopy. All four samples as well as one of two stool samples from players on the Florida team were positive for a Norwalk-like virus of genogroup I on RT-PCR assay; the RT-PCR products had identical sequences.

CONCLUSIONS

This investigation documents person-to-person transmission of Norwalk virus among players during a football game. Persons with acute gastroenteritis should be excluded from playing contact sports.

Identification of viral infection by confocal microscopy

Confocal microscopy is a valuable adjunct to electron microscopy in the fields of diagnostic and investigative virology. Confocal imaging can be used to examine large amounts of tissue stained by a variety of methods for evidence of viral infection. Areas thus identified can then be processed for ultrastructural study, allowing a highly focused search for viral pathogens. With the possible exception of the vibrating microtome, all of the equipment and reagents necessary for the preparation of specimens for confocal scanning are available in any well-stocked histology laboratory. Although originally developed to facilitate viral diagnosis by EM, the methods described herein can be applied to the ultrastructural study of any focal pathologic process.

Special techniques in diagnostic electron microscopy

The power of electron microscopy as a diagnostic tool can be amplified considerably by the application of ancillary preparative and analytic methods. Subcellular chemistry and structure can be examined by various forms of microprobe analysis and by special staining methods, including cytochemical, immunocytochemical, and negative staining. Qualitative ultrastructural examination can be augmented by morphometric analysis. Correlative microscopic survey methods can be used as a means of targeting ultrastructural investigations. This article provides an overview of the use of these special techniques in the diagnosis and classification of tumors and other selected pathologic processes.

Identification of focal viral infections by confocal microscopy for subsequent ultrastructural analysis

A correlative microscopy method for the ultrastructural analysis of focal viral tissue infections is presented. Using a confocal scanning laser microscope, foci of infection are identified in tissue sections prior to embedment; a variety of techniques can be employed for viral detection, including staining with standard histochemical reagents and fluorescently labeled antibodies. Areas of infection identified using confocal microscopy are excised from the tissue sections, embedded, and examined by transmission electron microscopy. Applications of this technique in both diagnostic and basic research settings are described.

Concerted use of immunologic and ultrastructural analyses in diagnostic medicine: immunoelectron microscopy and correlative microscopy

Electron microscopy (EM) is a valuable tool in diagnostic medicine, and in some cases, can be enhanced by immunological methods. A major medical application of EM, diagnostic virology, can frequently be augmented by employment of immunological reagents. Three immunoelectron microscopy (IEM) methods, aggregation, coating, and gold labeling, provide means for serotyping viruses; aggregation by antibody can also be used to concentrate viruses in dilute suspension or to serotype them. As a research tool, IEM can be useful in studying the relationship of various pathogen proteins to the infected cells or tissues. Delineating the subcellular location of viral components can yield information about how virions are constructed, and hence, suggest methods and compounds for inhibiting that process. Conversely, labeling virus-infected cells with antibodies against various cell receptors and proteins can yield information about the association of the proteins with budding virions. Another research example is the identification by immunological staining of virus-infected cells for subsequent ultrastructural identification of the specific cell type involved. Electron microscopy and immunolabeling methods are also useful in the diagnosis of immune complex disorders, including various forms of postinfectious immune complex glomerulonephritis. Precise analysis of immune complex deposits can be accomplished by using EM to pinpoint their location and immunohistology to probe their composition. Finally, a variety of optical microscopic techniques, including some involving immunofluorescent labeling, can be used to identify areas of interest in inhomogeneous tissues for further study by EM.

An electron-lucent region within the virion distinguishes HIV-1 from HIV-2 and simian immunodeficiency virus

Ultrastructural comparisons of immature or budding particles of human immunodeficiency virus (HIV) types 1 and 2 and simian immunodeficiency virus of macaques (SIVmac) revealed no significant difference between these genetically distinct, but related, viruses. However, a region encompassing the core of mature HIV-1 virions was found to be more electron lucent than that observed in HIV-2 and SIVmac. This ultrastructural distinction cannot be attributed to HIV-1-specific vpu, HIV-2/SIV-specific vpx, or virion-associated vpr gene products.

Characterization of a variant strain of Norwalk virus from a food-borne outbreak of gastroenteritis on a cruise ship in Hawaii

A gastroenteritis outbreak affecting at least 217 (41%) of 527 passengers on a cruise ship was caused by a variant strain of Norwalk virus (NV) that is related to but distinct from the prototype NV strain. Consumption of fresh-cut fruit served at two buffets was significantly associated with illness (P < or = 0.01), and a significant dose-response relationship was evident between illness and the number of various fresh-cut fruit items eaten. Seven (58%) of 12 paired serum specimens from ill persons demonstrated at least fourfold rises in antibody response to recombinant NV capsid antigen. A 32-nm small round-structured virus was visualized by electron microscopy in 4 (29%) of 14 fecal specimens, but none of the 8 specimens that were examined by an enzyme immunoassay for NV antigen demonstrated antigen. Four (40%) of 10 fecal specimens were positive by reverse transcriptase-PCR by using primer pairs selected from the polymerase region of NV. In a 145-bp region, the PCR product shared only 72% nucleotide sequence identity with the reference NV strain and 77% nucleotide sequence identity with Southampton virus but shared 95% nucleotide sequence identity with UK2 virus, a United Kingdom reference virus strain. In addition, the outbreak virus was serotyped as UK2 virus by solid-phase immune electron microscopy. The genetic and antigenic divergence of the outbreak strain from the reference NV strain highlights the need for more broadly reactive diagnostic assays and for improved understanding of the relatedness of the NV group of agents.

Viral infections in the acquired immunodeficiency syndrome

The following communication is a tripartite synopsis of the role of viral infection in the acquired immunodeficiency syndrome (AIDS). The first section describes the impact of viral opportunistic infection in AIDS; for each virus, clinical presentation and diagnosis, laboratory diagnostic approaches (with emphasis on electron microscopy), and therapeutic interventions attempted to date are discussed. The second segment explores current theories on the pathogenesis of AIDS, and describes diagnostic and therapeutic approaches to the syndrome itself. The final section catalogues ultrastructural anomalies in the cells of AIDS patients, many of which have been mistakenly identified as etiologic agents.