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Chapter 3
Negative and Positive Staining in Transmission Electron
Microscopy for Virus Diagnosis
Debora Ferreira Barreto-Vieira and
Ortrud Monika Barth
Additional information is available at the end of the chapter
http://dx.doi.org/10.5772/60511
Abstract
Visualization of virus particles and morphological features depends on the resolution
of microscopes. Transmission electron microscopy (TEM) is the starting point for
obtaining the best resolution of images. Two different techniques are available and
described in this paper. Firstly, negative staining of viral suspensions provides
detailed information of virus particles' structure. It is a technique that can be quickly
performed and is able to accommodate the highest magnifications of virus particles.
Secondly, ultra-thin sections of virus-infected tissues or cell cultures, combined with
a positive staining technique can provide information regarding the localization of
viruses inside or around cells. These two complementary techniques for investigating
the structure of a virus and its parasitic life cycle are presented in this paper.
Keywords: transmission electron microscopy, negative staining, positive staining
1. Introduction
High resolution microscopes are essential for visualizing virus particles. A transmission
electron microscope (TEM) fulfils this requirement and is widely used by scientists. Unknown
agents of diseases may be quickly detected by using such a microscope. A recent review on
the value of electron microscopy and virus structures was presented by Zhang et al. [1].
Shortly prior to the recent recognition of mimiviruses [2], orthopoxviruses had been one of the
largest virus particles, in addition to the thin and very long filoviruses. Groups of orthopox‐
© 2015 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons
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and reproduction in any medium, provided the original work is properly cited.
virus particles can be detected when inside infected cells using the highest magnification
available in light microscopy. Nevertheless, an isolated virus particle of ca. 250 nm diameter
remains below the resolution of standard light microscopes. With the advent of TEMs and high
magnifications of over 100 000x, the structural details of virus particles could then begin to be
recognized.
The first demonstration of a viral particle using a TEM was in the form of a member of the
orthopoxvirus genus [3]. Following the introduction of the negative staining technique in the
1960s [4], a variety of viruses has been discovered and classified based on morphological
characteristics such as symmetry, the presence or absence of the envelope or spikes and the
size of these projections [5,6,7,8]. A large number of viruses of medical importance that had
formerly never been described such as adenovirus, enterovirus, orthomyxovirus, reovirus and
paramyxovirus were identified by TEM after isolation in cell cultures inoculated with clinical
specimens [9]. Other viruses like hepatitis B and hepatitis A were detected directly by TEM in
samples such as plasma and faeces, following the failure of attempting to try and isolate them
in cell cultures. The initial classification of many agents was therefore based on a combination
of morphology and genome structure.
Currently, more than 30 000 different viruses comprising 56 families have been identified using
TEM and humans have been found to play host to 21 of the 26 families specific for vertebrates
[10]. The development of other techniques, e.g., immunofluorescence, enzyme-linked immu‐
nosorbent assays (ELISA) and biological molecular methods such as polymerase chain reaction
(PCR) have progressively reduced the importance of TEM in virus diagnosis and microbiology.
However, compared with other diagnostic methods, TEM still benefits from its rapidity and
“open view”, i.e., the capability of detecting all pathogens present in a clinical specimen [11].
Therefore, TEM should be utilized as a frontline method in infectious disease emergencies and/
or in suspected cases of bioterrorism [12]. Electron microscope studies were critical in identi‐
fying the aetiologic agent of severe acute respiratory syndrome (SARS), a coronavirus, during
its 2002/2003 global outbreak [13].
Several methods for specimen preparation have been developed. These can be summarized
into two procedures: the negative staining of vesicular content and viral suspensions, and the
ultra-thin sectioning of infected tissues and cells. Both techniques have been carried out with
complementary results.
2. Negative staining technique
The classic processing of biological specimens observed in a TEM needs fixation, dehydration,
sectioning and a selective “staining” of cell and tissue structures. “Staining”, a means of
receiving coloured images, cannot be effectively used in conjunction with an electron micro‐
scope. Instead, the enhancement of structures for TEM observation is effected, usually by
impregnation with heavy metal salts of plumb, tungstenium and uranium.
Some biological elements are very small and as a result, sectioning reveals aspects of its content
but not about its global surface structure. The result is a bi-dimensional image. Nevertheless,
Microbiology in Agriculture and Human Health
46
when observed as a whole using the negative staining technique, these elements reveal a tri-
dimensional image.
To prepare small biological specimens such as bacteria, viruses, phages, micoplasma, filaments
and cell membranes, or even nucleic acids and protein filaments for TEM observation, the
special technique of “negative contrast” was developed [4]. Instead of applying a more or less
strong positive contrast of structures (“staining”), in this instance, contrast is not applied to
the object but to its environment, using heavy metal salts. The electron beam can cross
biological material easier than the surrounding space. The result resembles an inverted
traditional TEM image (Figures 2, 4-7).The standard staining solution used today is an aqueous
1% phosphotungstic acid with pH 7.2.
Essentially, a fixed or unfixed drop of viral suspension is applied onto a formvar- or collodium-
covered electron microscope grid for a few seconds; the liquid is absorbed by a filter paper,
then a drop of the staining solution is applied and few seconds later also absorbed (Figure 1).
After drying, the specimen is ready to be introduced into the electron beam.
Figure 1. Negative staining procedure. Forceps, grid and white filter paper are the primary tools.
This unbelievably simple technique, at the outset rejected by the scientific community,
eventually became a revolutionary approach for studying primarily viral morphology as
emphasized by viral diagnostics [14]. Extremely detailed images were obtained and published,
revealing substructures and macromolecules as viral antibodies and virus particle spines [5,
9, 15, 16, 17, 18, 19, 20].
Negative and Positive Staining in Transmission Electron Microscopy for Virus Diagnosis
http://dx.doi.org/10.5772/60511
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In order to gain additional information about small structured elements, several technical steps
in sample processing were developed such as immune-electron microscopy (Figure 5), solid-
phase-electron microscopy, ammonium-sulphate precipitation, gradient fraction contrasting
and particle concentration by diffusion in an agarose layer [21].
Contrasting solutions show a large spectrum of possibilities. Selection must be in accordance
with the pH and electrical charge of the sample, of the contrasting solution and of the EM grid
Figure 2. Orthopoxvirus particle, Brazilian Cantagalo strain (negative staining). This virus particle was isolated from a
milker's hand nodule, macerated using a drop of distilled water and applied onto a collodium-covered EM-copper
grid, then stained using a drop of 2% phosphotungstic acid in distilled water.
Figure 3. Ultra-thin section of a Vero cell infected with the same strain of virus demonstrated in Figure 2 (positive
staining).
Microbiology in Agriculture and Human Health
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Figure 4. Group of seven adenovirus particles and numerous small adeno-associated virus particles. A drop of clari‐
fied faeces from a patient suffering from gastroenteritis was processed as described in Figure 1.
Figure 5. A group of rotavirus particles. Clarified faeces from a patient suffering from gastroenteritis was incubated
with a specific antibody prior to being submitted to the negative staining procedure and processed as described in
Figure 1. Both several empty and RNA-filled virus particle can be distinguished.
Negative and Positive Staining in Transmission Electron Microscopy for Virus Diagnosis
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or support [19, 22]. Resulting precipitates and a lack of spreading of the sample are the most
common inconveniences. For better spreading and adsorption of virus particles onto a
formvar-carbon coated grid, polylysine (poly-L-lysine) is currently being used in our labora‐
tory (Figures 6 to 7).
Figure 6. Hepatitis B antigen. One drop of a gradient virus suspension was applied directly onto an electron micro‐
scope grid and in sequence stained with 1% alcoholic uranyl acetate. Virus particles are joined together into very dark
groups.
Figure 7. Hepatitis B antigen. One drop of the same virus suspension as shown in Figure 6 was applied to an electron
microscope grid formerly coated with polylysine and in sequence stained with 1% alcoholic uranyl acetate. Virus parti‐
cles are spread all over the grid.
Microbiology in Agriculture and Human Health
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An overview of the negative staining technique development and application was presented
by Biel & Gelderblom [6], Harris et al. [23] and more recently, by Schramlová et al. [24]. Benefits
or deception are always surprising factors when the electron beam reveals a TEM image inside
a dark room.
3. Positive staining technique
The positive staining technique has been used since the late 50s and the early 60s for enhancing
the contrast of biological samples (tissues and cell structures, viruses, etc.). Using this techni‐
que, as well as negative staining, the samples are incubated in heavy metal salt solutions that
react with cellular structures. Uranyl acetate [25] and lead citrate [26] are the most commonly
used salts today. Grids containing ultra-thin sections of a sample are incubated for 15 minutes
in uranyl acetate; this procedure should be performed in an environment protected from light.
Following on, the grids are washed in distilled water and incubated in lead citrate at four to
five minutes in an environment free of CO2. NaOH tablets are used to keep the environment
free from reacting with CO2 (Figure 8). At the end of the procedure the grids are washed in
distilled water, air dried and observed with a TEM [27, 28].
Figure 8. Positive staining. The grid held with a forceps contains ultra-thin sections of a sample (arrow). In the Petri
dish, there are two drops of the staining solution beside two tablets of NaOH (Barreto-Vieira et al. 2010).
3.1. Specimen preparation
Cells. Monolayers were fixed in 1% glutaraldehyde in a cacodylate buffer (0.2 M, pH 7.2) and
post-fixed with 1% buffered osmium tetroxide, dehydrated in acetone, embedded in epoxy
resin and polymerized at 600C for three days [28, 29]. The blocks were cut into ultra-thin
Negative and Positive Staining in Transmission Electron Microscopy for Virus Diagnosis
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sections 50 to 70 nm thick using a diamond knife adapted to an ultramicrotome (Figure 9). The
sections were placed onto copper grids and stained with uranyl acetate and lead citrate and
observed in a TEM (Figure 10).
Figure 9. Ultramicrotomy: a) silicone support filled with resin blocks (arrow) containing fragments of tissues; b) ultra-
thin sectioning using a diamond knife and a copper grid (arrow) to collect sections.
Figure 10. Dengue virus particles (arrow) isolated in the Aedes albopictus mosquito cell line (C6/36) from the serum of
infected BALB/c mice. Positive staining using lead citrate (arrow) emphasizes viral RNA, while cytoplasmic proteins
are emphasized using uranyl acetate.
Fragments of tissues. Glutaraldehyde at 2% in a cacodylate buffer (0.2M, pH 7.2) was routinely
used to fix tissue fragments, then post-fixed by immersion in a 1% buffered osmium tetroxide,
dehydrated in acetone, embedded in epoxy resin and polymerized at 600C for three days [28,
29]. Semi-thin 0.5 μm thick sections were cut using a diamond knife. These sections were
stained with a methylene blue/azure II solution [30] and observed using a photonic micro‐
Microbiology in Agriculture and Human Health
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scope. Ultra-thin sections were placed onto copper grids and stained with uranyl acetate and
lead citrate and observed in a TEM.
Tissue fragments from experimentally infected animals. In our experiments, the infected animals
(mice) were peritoneally anaesthetized and fixed by perfusion with a 4% paraformaldeyde in
a sodium phosphate buffer (0.2M, pH 7.2) for 30 min. The tissues were carefully collected in
sequence and the fragments post-fixed by immersion in 2% glutaraldehyde in cacodylate
buffer (0.2M, pH 7.2), post-fixed with 1% buffered osmium tetroxide, dehydrated in acetone,
embedded in epoxy resin and polymerized at 600C for three days [28, 29]. Ultra-thin sections
were obtained and processed as described above (Figure 11).
Figure 11. Hepatic tissue of BALB/c mice infected with the dengue virus. Note the numerous lipidic inclusions (L) and
a pyknotic nucleus (N). Positive staining emphasizes the chromatin of the hepatocyte nucleus using lead citrate and
cytoplasmic proteins using uranyl acetate.
4. Advantages and disadvantages of the TEM
Virus diagnosis via TEM, when compared to other techniques such as immunofluorescence,
PCR and ELISA have both advantages and disadvantages.
Advantages:1) TEM is the only technique that allows for direct visualization of an aetiologic
agent of very small diameter, e.g., viruses; all other diagnostic techniques show indirect results;
2) samples can be processed and analysed quickly. Following simple and rapid negative
staining, TEM “open view” allows for rapid morphological identification and a differential
diagnosis of various infectious agents present in a specimen. Likely, intact virions observed
with TEM may be indicative of an infectious virus, whereas the detection of antigens or nucleic
Negative and Positive Staining in Transmission Electron Microscopy for Virus Diagnosis
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acid may not always indicate the presence of viable infectious virus particles [31]; 3) TEM is
valuable for differential diagnoses, for example, in patients with vesicular dermatitis, so as to
exclude smallpox; 4) TEM assists in elucidating unknown aetiologic agents in outbreaks,
epidemics or pandemics, since it is not necessary to use specific reagents. The causative agents
of the recent SARS pandemic and the outbreak of human monkey pox in the USA were quickly
identified using TEM [13].
Disadvantages:1) TEM is of low diagnostic sensitivity compared to other diagnostic methods.
It requires a high concentration of virus particles (>105 particles per mL), both in suspensions
and in tissues or cells; 2) the evaluation of samples cannot be automated with TEM and should
be performed by an experienced professional; 3) TEM is not an appropriate method for
screening a large number of samples as in a viral outbreak, due to the high cost of TEM
maintenance and the availability of trained personal.
Acknowledgements
Financial support: research fellowship of the Conselho Nacional de Desenvolvimento Cientí‐
fico e Tecnológico (CNPq), process numbers 301525/2009-9 and 304067/2014-18 (second
author).
Author details
Debora Ferreira Barreto-Vieira * and Ortrud Monika Barth
*Address all correspondence to: barreto@ioc.fiocruz.br
Laboratory of Morphology and Virus Morphogenesis, Instituto Oswaldo Cruz, Fundação
Oswaldo Cruz, Rio de Janeiro, Brazil
References
[1] Zhang Y, Hung T, Song J D, He JS. Electron microscopy: essentials for viral structure,
morphogenesis and rapid diagnosis. Science China Life Sciences 2013;56: 421-430.
[2] Saadi H, Pagnier I, Colson P, Cherif J K, Beji M, Boughalmi M, Azza S, Armstrong N,
Robert C, Fournous G, La Scola B, Raoult D. First Isolation of Mimivirus in a patient
with pneumonia. Clinical Infectious Disease 2013;57: e127-134.
[3] Von Borries B, Ruska E, Ruska H. Bakterien und Virus in übermikroskopischer Auf‐
nahme, Klinische Wochenschrift 1938;17: 921-925.
Microbiology in Agriculture and Human Health54
[4] Brenner S, Horne RW. A negative staining method for high resolution electron mi‐
croscopy of viruses. Biochimica et Biophysica Acta 1959;34:103.
[5] Hayat MA, Miller SE. Negative Staining. McGraw Hill Publishing Company, NY,
253p; 1990.
[6] Biel SS, Gelderblom HR. Diagnostic electron microscopy is still a timely and reward‐
ing method. Journal of Clinical Virology 1999; 13: 105-119.
[7] Flewett TH, Bryden AS, Davies H. Virus particles in gastroenteritis. Lancet
1973;2:1497.
[8] Tyrrell DAJ, Almeida J. Direct electron-microscopy of organ culture for the detection
and characterization of viruses. Archive of Virology 1967;22: 417-425.
[9] Madeley CR, Field AM. Virus Morphology, 2nd ed., Churchill Livinstone. 295p;1988.
[10] Van Regenmortel MHV, Fauquet CM, Bishop DHL, Carsten EB, Estes MK et al. Virus
taxonomy: classification and nomenclature of viruses, 7th Report of the International
Committee on Taxonomy of Viruses, Academic Press, San Diego. 1167 p; 2000.
[11] Gentile M, Gelderblom HR. Rapid viral diagnosis: role of electron microscopy. New
Microbiology 2005;28: 1-12.
[12] 12] Schatzmayr HG, Barth OM. Bioterrorismo e microorganismos patogênicos. His‐
tória, Ciências, Saúde – Manguinhos 20: 1735-1749;2013.
[13] Goldsmith CS, Tatti KM, Ksiazek TG, Rollin PE, Comer JA, Lee WW, Rota PA, Bank‐
amp B, Bellini WJ, Zaki SR. Ultrastructural characterization of SARS coronavirus.
Emerging Infectious Disease 2004;10: 320-326.
[14] Gelderblom HR. Electron microscopy in diagnostic Virology. Bioforum 2001;5: 64-67.
[15] Horne RW. The examination of small particles. Negative staining methods. In DH
KAT, Techniques for Electron Microscopy, Blackwell Scientific Publications, Oxford,
2nd ed, p. 311-355;1965.
[16] Nermut MV. Methoden der Negativkontrastierung. Meth Samml EM Wiss Verl, Stutt‐
gart, 3.1.2.3, 22p;1973.
[17] Almeida JD, Atanasiu P, Bradley DW, Gardner PS, Maynard J, Schuurs AW, Voller
A, Yolken RH. Manual for rapid laboratory viral diagnosis. World Health Organiza‐
tion Publication 1979;47: 7-10.
[18] Doane FW, Anderson N. Electron Microscopy in Diagnostic Virology. Cambridge
University Press, Cambridge. p.178;1987.
[19] Barth OM. Estudos sobre a contrastação negativa de suspensões virais. Revista Brasi‐
leira de Biologia 1984; 44: 71-80.
Negative and Positive Staining in Transmission Electron Microscopy for Virus Diagnosis
http://dx.doi.org/10.5772/60511
55
[20] Barth OM, Schatzmayr HG. Classificação e características gerais dos vírus patogêni‐
cos para o homem. In JR Coura, Dinâmica das Doenças Infecciosas e Parasitárias. Segun‐
da edição, Editora Guanabara Koogan, Rio de Janeiro, p.1680-1694; 2013.
[21] Barth OM. Contrastação Negativa. In W de Souza, Manual Sobre Técnicas Básicas em
Microscopia Eletrônica. Vol. I. Técnicas Básicas. Sociedade Brasileira de Microscopia
Eletrônica, Rio de Janeiro, p.60-73;2007.
[22] Barth OM. The use of polylysine during negative staining of viral suspensions. Jour‐
nal of Virological Methods 1985; 11: 23-27.
[23] Harris JR, Bhella D, Adrian M. Recent developments in negative staining for trans‐
mission electron microscopy. The Americas Microscopy and Analysis 2006;78: 5-9.
[24] Schramlová J, Arientová S, Hulínská D. The role of electron microscopy in the rapid
diagnosis of viral infections – review. Folia Microbiology 2010;55: 88-101.
[25] Watson ML. Staining of tissue sections for electron microscopy with heavy metals. II.
Application of solutions containing lead and barium. The Journal of Biophysical and
Biochemical and Cytology 1958;4: 727-730.
[26] Reynolds. The use of lead citrate at high pH as an electron opaque stain in electron
microscopy. Journal of Cell Biology 1963;17: 208-212.
[27] Attias M. Desidratação, inclusão, ultramicrotomia e constrastação. In W de Souza,
Manual Sobre Técnicas Básicas em Microscopia Eletrônica. Vol. I. Técnicas Básicas.
Sociedade Brasileira de Microscopia Eletrônica, Rio de Janeiro, p.44; 2007.
[28] Barreto-Vieira DF, Barth-Schatzmayr OM, Schatzmayr HG. Modelo animal experi‐
mental para o estudo da patogênese dos vírus dengue sorotipos 1 e 2, manual de
técnicas. Interciência, Rio de Janeiro, 82 p.;2010.
[29] Sesso A. Fixação de sistemas biológicos. In W de Souza, Manual Sobre Técnicas Básicas
em Microscopia Eletrônica. Vol. I. Técnicas Básicas. Sociedade Brasileira de Microsco‐
pia Eletrônica, Rio de Janeiro, p.13-21;2007.
[30] Humprey CD, Pittman EE. A simple methylene blue-azure-II basic fuchsin for epoxy-
embedded tissue sections. Stain Technology 1974;49: 9.
[31] Curry A. Electron microscopy and the investigation of a new infectious diseases. In‐
ternat J Infect Dis 7: 251-258. Doane FW, Anderson N 1987. Electron Microscopy in
Diagnostic Virology, Cambridge University Press, 178p;2003.
Microbiology in Agriculture and Human Health
56