Virology PDF
Virology PDF
THE ESSENTIALS OF
LIFE SCIENCE RESEARCH
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Table of Contents
This guide contains general technical information for viral growth, propagation, preservation, and
application. Additional information on viral culturing can be requested from ATCC Technical Services at
[email protected] or can be found in A Manual of Basic Virological Techniques¹.
Preservation....................................................15
Cryopreservation..................................................... 15
Lyophilization........................................................... 18
Preservation of Specific Strains.......................... 20
Special Hazards........................................................ 20
Product Sheet
ATCC viral strains are shipped with a product sheet that contains information on the production host and
recommendations for infection. The product sheet and additional information can be found on the ATCC
website or can be requested from the ATCC Technical Service Department.
Viral Taxonomy
Viruses are placed into taxonomic groups based on characteristics including morphology, genome type,
and host organism. Viral agents can significantly vary in size, often
ranging between 20 and 300 nanometers in diameter. They also vary
in structure, including helical, icosahedral, prolate, enveloped,
and complex morphologies.
In addition to unique morphological structures, viruses also vary in
genomic structure. Unlike other microorganisms that have double
stranded DNA as genomic material, viral genomes can be composed
of double-stranded DNA, single-stranded DNA, double-stranded
RNA, or single-stranded RNA. Single-stranded RNA viruses can be
further described as positive sense, negative sense, or ambisense. Influenza ultra-structure courtesy of Jordan
For more detailed information on the various morphological and Douglas, CDC
genomic types, please refer to the glossary.
Changes in taxonomy or further analysis of viral strains may lead to a change in nomenclature. Taxonomic
nomenclature as well as the common name can be found on the product sheet. Further information on viral
nomenclature is available online at http://ictvonline.org/.
Viral Replication
Viruses are pathogenic intracellular organisms requiring living cells in order to multiply. The virus life-
cycle can be divided into three major steps: attachment, assembly, and release. Generally, infection is
established when the virus binds to a specific cellular receptor and enters the host cell. Upon cellular entry,
host proteins are recruited to assist with viral replication. Once viral structural proteins are generated, new
viruses assemble within the cell. Depending on the nature of the viral agent, the replication and assembly
process can vary in cellular location and process. Following viral assembly, new infectious particles either
remain cell-associated or exit the cell via lysis or virus shedding.
the virus
Remove growth
insulation andmedium for virus propagation as
inner vial with
forceps, gently raise cotton plug
noted on the product sheet. Viral growth medium
is usually supplemented with a lower percentage
of serum than cell growth medium, often ranging
between 2-10% depending on the virus (See NOTE
1). Ensure that both the cell and viral growth media
are equilibrated for temperature and pH.
2. Initiate the recommended production host, and
Propagation of Feline infectious peritonitis virus (ATCC® No. VR-2004™) in CRFK cells (ATCC®
No. CCL-94™). The panel on the left are uninfected CRFK cells. The panel on the right are
infected CRFK cells exhibiting CPE.
Optimal
Product Name Egg Age (Days) Inoculation Route Incubation (Days) Death of Embryo
Temperature (˚C)
Influenza A virus 10-11 Allantoic 2-3 33-35 -
Influenza B virus 10-11 Allantoic 2-3 33-35 -
Sendai virus 10-11 Allantoic 2-3 35-37 +
Rabies virus 7 Yolk 9-10 36.5 -
Media Supplements
The growth media recommended for host propagation may require the addition of components not
already available in the base medium. These components may include hormones, growth factors, or serum.
After supplements have been added to the base medium, the shelf life of the medium should be determined
on a case-by-case basis. Media containing serum, antibiotics, and/or antimycotics tend to degrade faster
than base media alone. Media containing supplements should not be frozen as this may cause certain
compounds to precipitate out of solution; media should be stored at 2°C to 8°C. For additional information
regarding the preparation, storage, or usage of specific additives, contact your local supplier or consult with
the manufacturer’s product information sheet.
Serum
Serum can serve as a source of growth factors, proteins, vitamins, hormones,
carbohydrates, lipids, amino acids, minerals, and trace elements. The exact
composition of serum is unknown and varies from lot to lot, although lot-
to-lot consistency has improved in recent years.
Sera from fetal bovine sources are commonly used to maintain cell cultures
in preparation for viral infection. Fetal serum is a rich source of growth
factors and is appropriate for the growth of fastidious cells. It is often
supplied at a concentration of 2-10%. (See NOTE 5)
Unfortunately, naturally derived products from animals, such as sera, may
contain adventitious microorganisms. All reputable suppliers routinely
test their products for infectious viruses by several methods including NOTE 5:
Fo r v i r a l i n o c u l a t i o n , ATCC
fluorescent antibody labeling, cytopathic effect, and hemadsorption. recommends decreasing the
These products are also screened for the standard microbial contaminants percentage of serum to 2% as it can
such as bacteria, fungi, and mycoplasma. To reduce the risk of any possible interfere with viral attachment. This
can vary from strain to strain, and is
contamination, ATCC recommends that all serum should be triple filtered not applicable for influenza viruses.
through 0.1 µm sterile filters before use.
ATCC offers the following types of animal sera:
• Fetal Bovine Serum (also known as fetal calf ) – ATCC® No. 30-2020
• Fetal Bovine Serum qualified for embryonic stem cells – ATCC® No. SCRR-30-2020
• Iron-supplemented Calf Bovine Serum – ATCC® No. 30-2030
• Horse Serum – ATCC® No. 30-2040
These products are rigorously tested for adventitious infective agents and sourced only from U.S. herds.
Further, each lot is tested for its ability to support cell culture growth and is the same sera used in ATCC labs.
A. Storage
Do not store serum at temperatures above -20°C for any length of time. Avoid any repeated freeze-
thaws by dispensing and storing sera in aliquots. Additionally, ensure that sera are stored away
from direct light.
Cryopreservation
Overview
Freezing a viral suspension often results in a decrease in viability and titer¹¹, ¹². For cell-associated pathogens,
such as Chlamydia and Rickettsia, as the suspension is cooled below the freezing point, ice crystals begin to
form and the concentration of solutes in the suspension increases resulting in damage of host cell structures.
This can be minimized if water within the cells is allowed to escape by osmosis during the cooling process;
a slow cooling rate, generally -1˚C to -10˚C per minute, facilitates this progression. However, as host cells
lose water, they shrink in size and will quickly lose viability if they surpass a minimum threshold volume.
The addition of cryoprotectant agents, such as glycerol or dimethylsulfoxide (DMSO), will mitigate these
effects¹³, ¹⁴.
The viability of viruses that are not cell-associated is best maintained by rapid freezing. In this method,
samples are quickly frozen in a dry ice slurry and stored in liquid nitrogen vapor or within a mechanical
freezer at -80°C.
Overall, there are numerous factors that can affect the viability of recovered viruses. These critical parameters
can include the composition of the cryoprotectant and the viral titer. For cell-associated viruses, obtain
optimal cell viability upon recovery by modifying the cryopreservation procedure for each viral strain.
Contact ATCC for more information on the cryopreservation of viral strains.
Freeze Medium
Glycerol and DMSO are the most common cryoprotectant agents. To preserve viral strains, ATCC commonly
uses a mixture of FBS and DMSO or glycerol. When employing these cryoprotectants, use only reagent-
grade DMSO or glycerol. Store both in aliquots protected from light. ATCC offers DMSO (ATCC® No. 4-X) that
has been thoroughly tested for use.
Equipment
A. Cryopreservation vials
There are two materials to choose from for cryopreservation vials: glass or plastic. Glass vials are
more difficult to work with: they need to be sterilized before use, they need to be sealed with a
hot flame, and they can be difficult to open. However, they are considered fail-safe once properly
sealed.
If cryopreservation in glass ampoules is not possible, plastic vials can be used. Plastic vials come in
two varieties: those with an internal thread and silicone gasket, and those with an external thread.
Vials with an internal-thread were the first commercially available, but have some disadvantages
over the external-thread version. For example, while the silicone gasket provides an excellent seal,
it needs to be tightened just right; the vial will leak if the seal is too tight or too loose.
B. Controlled-rate freezing chambers
For cell-associated viruses, there are several means to achieve a cooling rate of -1˚C per minute.
The best method involves the use of a computer controlled, programmable electronic freezing
unit (such as Thermo Scientific* CryoMed Freezers), which rigorously maintains this rate of cooling.
This is the method used exclusively at ATCC. Such equipment is relatively expensive and necessary
for only the most sensitive strains.
A less costly approach is to place the cryopreservation vials into an insulated chamber and cool
for 24 hours in a mechanical freezer at -70˚C or colder. There are several commercially available
freezing chambers, which achieve a cooling rate very close to the ideal -1˚C per minute (CoolCell®
LX; ATCC® ACS-6000). Alternatively, the vials can be placed into a polystyrene box, with 15 mm
(3/4 inch) thick walls and 1 L capacity that is packed with paper, cotton wool, or foam peanuts for
insulation.
Lyophilization
Overview
Freeze-drying is a process where water and other solvents are removed from a frozen product via
sublimation¹⁵. Sublimation occurs when a frozen liquid goes directly to a gaseous state without entering a
liquid phase. The freeze-drying process results in a stable, readily rehydrated product. This process consists
of three steps: pre-freezing the product to form a frozen structure, primary drying to remove most water,
and secondary drying to remove bound water.
During the initial freezing process, ice crystals begin to form and the concentration of solutes in the
suspension increases. The method used during freezing can greatly affect the ability to freeze-dry the
material. Slow cooling rates are recommended as this will result in the formation of vertical ice crystal
structures and allow for more efficient water sublimation from the frozen product.
Freeze-dried products are hygroscopic and must be protected from moisture during storage. Additionally,
these products are sensitive to other factors including oxygen and temperature, which can significantly
decrease the shelf life. It is important to store freeze-dried material in a manner that protects the product
from exposure to moisture and oxygen and at refrigerated temperatures (4°C).
Generally, the lyophilization of viruses is not currently used by ATCC. This is because the methods for
lyophilization vary depending on the type of virus, and some viruses cannot be successfully preserved by
freeze-drying due to loss of viability. Strongly cell-associated viruses, including certain members of the
herpes virus family, such as varicella-zoster, lose viability outside the host. Therefore, these viruses cannot
be preserved by this method. Though ATCC does not currently freeze-dry any virus preparations, it was
done fairly extensively in the past. The methods of lyophilization that were previously used by ATCC are
described below. For additional information, contact ATCC technical services.
Equipment
A. Lyophilization Vials
For the storage of lyophilized viruses, ATCC uses sterile funnel-tipped glass ampoules (Wheaton)
and glass serum vials. Generally, during the lyophilization process, material is freeze-dried in a
glass ampoule, disinfected, and sealed.
B. Lyophilization Apparatuses
For the lyophilization of viruses, ATCC previously employed a commercial freeze-dryer. In this
freeze-drying procedure, samples are mixed with a suitable preservative, dispensed into the
appropriate ampoule, and allowed to slowly freeze into a solid mass. The preservative used for
lyophilization can vary between viral agents; several examples are listed below in Table 4. Once
Special Hazards
Care must be taken during the cryopreservation or lyophilization of animal viruses. Problems such as
contamination, breakage of glass ampoules during handling and storage, dispersal of freeze-dried virus
when opening glass ampoules, and the handling of liquid nitrogen must all be considered. To prevent
contamination and the dispersal of viruses, aseptic technique must be followed. This can include the
decontamination of all equipment and vials as well as performing all preparations in a biological safety
cabinet. Additionally, protective clothing should be worn during preparation to prevent contamination as
well as to guard against harm due to contact with liquid nitrogen.
Biosafety
The need for precautions when experimenting with viral cultures depends upon the source and nature
of the biological material, the experimental procedure, and the laboratory/containment conditions. Since
every situation is different, the risks need to be identified for each individual strain and the appropriate
precautions need to be taken before any work begins.
More information on risk assessment and precautions can be found in the Center for Disease Control
(CDC) publication Biosafety in Microbiological and Biomedical Laboratories¹⁷. The text of this publication is
available in its entirety online at www.cdc.gov.
A biosafety level (BSL) is assigned to each viral strain for the purposes of packaging for safe shipment. ATCC
follows federal biosafety guidelines and takes several factors into consideration when assessing a potential
hazard, and in some cases the ATCC assigned biosafety level is more restrictive. Generally, ATCC only ships
and stores viruses with a biosafety level assignment of 1, 2, or 3.
Biosafety Level 1
• Work involving well-characterized viral strains not known to consistently cause disease in
immunocompetent adult humans.
• Work can be conducted on the bench top using aseptic technique, no special containment equipment
or facility is required.
Biosafety Level 2
• Work involving viral strains that pose a moderate hazard to health adult humans.
• Work should be conducted in designated biological safety cabinets within laboratories with restricted
access.
Biosafety Level 3
• Work involving indigenous or exotic agents that may cause serious or potentially lethal disease via
inhalation.
• Work should be conducted in biological safety cabinets localized inside a specialized BSL-3 containment
facility within laboratories with restricted access.
As the recipient of an ATCC virus, take into account not only the nature of the material but also the
manipulations employed during its handling when assessing the potential laboratory risk. Keep in mind
that there will be situations where the intended use of an agent may require more stringent precautions
than associated with the assigned biosafety level¹⁷.
Viability Testing
Cytopathic effects (CPE)
For tissue-culture adapted viruses, viability is primarily monitored by
NOTE 6:
observing host cell appearance. During the synthesis of viral components, During early viral infection, cells
the host cell undergoes morphological and biochemical changes. These may become rounded or appear
deviations often result in degenerative changes known as cytopathic more refractive. More severe
CPE include focal degeneration,
effect. The degree of visible cell damage varies between viral species and vacuolization, cellular fusion, or
host cell lines. Some viruses cause little to no CPE in host cells, while others host cell death.
can destroy the host cell population. Characteristic CPE is best observed by
analyzing cultures daily¹⁸. (See NOTE 6)
Propagation of Human herpes virus 1 (ATCC® No. VR-260™) in Vero cells (ATCC® No. CCL-
81™). The left panel depicts uninfected CCL-81™ cells. The right panel depicts infected CCL-
81™ cells exhibiting CPE.
Hemagglutination
Many viruses can attach to molecules present on the surface of Direct Hemagglutination
red blood cells. At certain concentrations, a viral suspension may Positive Reation:
cause red blood cells to clump together. This natural phenomenon,
known as hemagglutination, prevents red blood cells from settling
out of suspension and has been adapted for use in viability testing Hemagglutinating virus Red blood cells Agglutination
and CEID viral titering. In a hemagglutination assay, chicken red Negative Reation:
Viral Authentication
Sequencing
The ATCC Virology collection utilizes sequencing to authenticate
our holdings as they are accessioned or come up for replenishment.
ATCC sequences approximately ≥500 bp of the viral genome that is
characteristic of the species or virus type.
Enzyme Linked Immunosorbant Assay
All viruses have at least one unique surface antigen. Through an
enzyme-linked immunosorbant assay (ELISA), these antigens can
be used as a biological marker to authenticate a viral species.
There are two forms of this assay, the direct and indirect ELISA.
Both assays employ enzyme-conjugated monoclonal detection antibodies that tightly bind a specific viral
antigen. With a direct ELISA, one is testing for the presence of the virus, while an indirect ELISA assay detects
specific viral antibody rather than the virus itself. The presence of a specific virus is analyzed by assessing
the conjugated enzyme activity via incubation with a substrate that is converted into a measurable colored
product. When using an ELISA for authentication purposes, a colorimetric change indicates the viral sample
was correctly identified.
Cell Transformation
Cancerous cells emerge due to discrete changes in the cellular genome. These genomic deviations can
arise due to viral transformation. During the infection of non-permissive cells, viral genetic material can
become covalently integrated into the host genome. If viral integration induces the aberrant expression of
a proto-oncogene, cell growth can become unrestricted, resulting in an immortal cell state.
This natural process has been adapted by cell biologists for use in the immortalization of mammalian cells
in tissue culture. Immortalized cell lines offer the possibility of an inexhaustible supply of cells, allowing for
more consistent and reproducible research. Viral genes such as the simian virus 40 (SV40) T antigen have
been used as a simple, reliable agent for the immortalization of a variety of cell types¹⁹, ²⁰. SV40 is believed
to induce immortalization by suppressing the transcription of p53, a tumor suppressor protein responsible
for initiating apoptosis following cell damage.
In addition to their use in cell immortalization, viral strains can be used to introduce nucleic acids into cells.
This process, termed transduction, allows scientists to analyze the function of specific genes, to examine
the effects of gene silencing, or to introduce therapeutic genes.
Phage Therapy
Bacteriophages are viruses that infect bacterial cells, often resulting
in the lysis and subsequent death of the bacterial host. Since the
early 20th century, European scientists have taken advantage of this
natural process to treat bacterial infections in a process known as
phage therapy. Because the host range of a bacteriophage is very
narrow, often specific to one species, they are considered more
effective than antibiotic treatment and result in less harm to the
human microflora²². Though phage therapy has many benefits, it
was abandoned by many countries due to the antigenic properties
and unpredictable behavior of bacteriophages in addition to the
wide-spread production and use of antibiotics. However, with the recent emergence of antibiotic-resistant
bacteria, scientists are now forced to re-evaluate the beneficial properties of the application of phage
therapy²³.
Nanotechnology
Cancer treatments have commonly employed surgery, radiation, chemotherapy, and hormone therapy²⁴.
Though these treatments have helped millions of patients go into remission, they come at a cost. Most
cancer treatments attack both healthy and cancerous cells, often leaving patients nauseous, fatigued, and
immunocompromised. To combat these negative side effects, viral nanoparticles are being engineered and
analyzed as a potential form of drug delivery.
Viral nanoparticles are viruses whose genomic material has been removed and replaced with therapeutic
drugs. Because viruses have naturally evolved the ability to cross the host cell membrane, they are an ideal
candidate for drug packaging and targeted delivery. To minimize toxic side effects, infection, and induced
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