General Virology

General Characteristics of viruses

• Virus:- a minute infectious agent which is not resolved by
the light microscope.
• Lacks independent metabolism.
able to replicate only with in a living host cell 
obligate parasite
•Causes a number of important disease such as:
Genital herpes Hepatitis
Influenza
•Vary considerably in size, shape and chemical composition.
• The method used in their cultivation and detection are
completely different from other micro organisms.
•Most viruses infect specific host cells. 1
All viruses consist of two basic components:

1. A core nucleic acid called the genome

either DNA or RNA, but not both.
2. A surrounding coat of protein known as the capsid.
• The capsid gives shape to the viruses.
• The capsid is subdivided in to individual protein sub
units Capsomere.
• The number of capsomers is characteristic for particular
virus.
E.g. 162 capsomers in genital herpes
252 capsomers in adnoviruses
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 Basic virus structure
DNA
Capsid Naked
or + Nucleocapsid =
protein capsid virus
RNA

Lipid membrane,
Nucleocapsid + Enveloped virus
glycoproteins
 Function of Capsid
• Provides protective covering for the genome because
the chemical construction of capsid resists
temperature, PH and other environmental fluctuation.
• Contains special sites on its surfaces that allow the
virion to attach to host cell.
• Capsid proteins are organized in to enzymes to assist
cell penetration during the replication process.
• The structure stimulates the immune system during
periods of disease  antigencity of the virion.
Capsid + the genome = the nucleocapsid.
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 Properties of naked capsid viruses
• Capsid is resistant to
– Drying
– Heat
– Detergents
– Acids
– Proteases
• Consequences
– Can survive in the gastrointestinal tract
– Retain infectivity on drying
– Survive well on environmental surfaces
_ Spread easily via fomites(Objects or materials which have
been associated with infected persons or animals and
which potentially harbour pathogenic microorganisms)
Adapted from Murray, P.R. Rosenthal K.S., Pfaller, M.A. (2005) Medical Microbiology, 5th edition, Elsevier Mosby, Philadelphia, PA , Box 6-4
 Viral Envelope
• Many viruses are surrounded by a flexible membrane known
as an envelope.
• Composed of lipids and protein and is essentially similar to
the host cell membrane ( * includes viral specified
components).
• Acquired from the host cell during the replication process (*
unique to each type of viruses).
• Some of them contains functional projections known as
spikes which assist the attachment of viruses to the host cells.
E.g. - Influenza - HIV
- Measles
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 Properties of enveloped viruses
• Envelope is sensitive to
– Drying
– Heat
– Detergents
– Acid
• Consequences
– Must stay wet during transmission
– Transmission in large droplets and secretions
– Cannot survive in the gastrointestinal tract

Adapted from Murray, P.R. Rosenthal K.S., Pfaller, M.A. (2005) Medical Microbiology, 5th edition, Elsevier Mosby, Philadelphia, PA Box 6-5
Table. Non enveloped (Naked) Viruses Versus
Enveloped Viruses

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 The Structure of virus
• Viruses are among the smallest agents able to cause disease in living
things.
• They range in size from 20 nm to 250 nm
E.g. Small pox -------------------------------Large 250 nm
Tobaccomosaic ---------------------------------------240 nm
Rabies -------------------------------------------- 150 nm
Influenza----------------------------------------------- 100 nm
Bacteriophage ------------------------------------------95 nm
Common cold ---------------------------------------- 70 nm
Polio ------------------------------------------------------27nm
Parvo viruses --------------------------------------- 25 nm
• Compare with eukaryotic nucleus : 2800 nm while Bacterium E.coli:
2000 nm
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Viruses types and compare with
other cells

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 Viruses may appear in several shapes
• In general, there are four main morphological virus types
1. Icosahedral is the basic capsid shape and looks like a
soccer ball
E.g Herpes simplex virus
2.Helical (helix)
E.g. -Tobacco mosaic virus
-Rabies viruses
3. Enveloped : E.g HIV
4. Bacteriophage

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Bacteriophage

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 Replication of Viruses
• Viruses that infect humans are considered along with the
general class of animal viruses
• viruses that infect bacteria are referred to as
bacteriophages, or phages for short.
• Virus reproduction requires that a virus particle infect a
cell and program the cellular machinery to synthesize the
constituents required for the assembly of new virions.
• Thus, a virus is considered an intracellular parasite. The
infected host cell may produce hundreds to hundreds of
thousands of new virions and usually dies.

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 Replication of Bacteriophage
E.g. Bacteriophage has the following steps in replication:
 
• Attachment Phage attaches by tail fibers to host cell
• Penetration Phage lysozyme opens cell wall, tail sheath
contracts to force tail core and DNA into cell

• Biosynthesis Production of phage DNA and proteins

• Maturation Assembly of phage particles
• Release Phage lysozyme breaks cell wall
Lytic cycle: Phage causes lysis and death of host cell
Lysogenic cycle: Prophage DNA incorporated in host DNA

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 Replication of animal viruses
It is similar to bacteriophage, but with some notable
exception:
• The attachment will be on the cell membrane
• Have no tail, so the viral attachment sites are distributed
over the entire surface of the capsid.
• Penetration is also different.
• The replication of viruses in susceptible cells can be
divided into eight stages: attachment, penetration,
uncoating, gene expression and
genome replication, assembly, maturation and exit.
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 Major mechanism of viral entry in to an
animal host cell.
1.Endocytosis
Virus binds to specific receptors on the cell membrane surface.
• Virus – receptor complexes result in invaginate to form
vesicles. Eg. influenza viruses, rubella virus, rabies and
coronaviruses,
2. Fusion
Some enveloped viruses fuses with cytoplasmic membrane
Fusion produce an opening through which the
nucleocapside may pass directly in to the cytoplasm
Eg. measles, HIV-1 and herpesviruses enter by a process called
direct fusion

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3. . Direct penetration
Some non- enveloped viruses may be so
small that they are able to pass directly
through cytoplasmic membrane
• Naked capsid viruses, such as poliovirus,
reovirus, and adenovirus, also appear to enter
the cell by viropexis(Viral entry into the cell by
phagocytosis).

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Replication of animal viruses

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Virus replication: general
Effect of viral infection on the Host cell
• Some viruses appear to replicate in cells with out
causing any obvious damage. Other viruses bring
about a variety of changes, some of which can be
lethal.These alterations or changes are referred to a
cytopathic effects.
• Some viruses cause direct damage: i.e. cell lysis may
result in temporary or permanent loss of function.
E.g. polio virus infection in this case Lysis of motor
neurons leads to lose of function of corresponding
muscle.
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• Some virus infections indirectly affect the function of
tissues or organs in the host.
E.g. 1. Influenza virus damage respiratory epithelium and
ciliary activity is severely affected.=> enhance
multiplication of bacteria in the respiratory tissue
• Death from influenza is often due to pneumonia caused
by:
Staphylococcus aureus
Streptococcus pneumoniae
Hemophilus species
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E.g 2. AIDS virus (HIV)
- affect immune cells (CD4 + helper T4 cells and
macrophages)
- The virus brings about immunological changes
that result in the patient’s dying from
infections caused by other infectious agents.

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Viruses classification could be possible using:

• Type of genetic material

• Shape of capsid
• Number of capsomere
• Presence or absence of an envelope
• Type of host that it infects
• Type of disease it produces
• Target cell
• Immunologic or antigenic properties

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The diversity of viral genomes
(Type of genetic material )

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 Viral Taxonomy:
– Family names end in-viridae
– Genus names end in- virus
– Viral species: A group of viruses sharing the
same genetic information and ecological
niche (host).
Common names are used for species
– Subspecies are designated by a number

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 Exampels of Viral Taxonomy

 
• Herpesviridae * Retriviridae
• Herpesvirus * Lentivirus
• Human herpes * Human Immunodeficiency
Virus 1, HHV 2, Virus 1,
HHV 3 HIV 2

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 Major diseases caused by human viruses
"Group" Family Human pathogens (disease)
dsDNA
Poxviridae Variola (smallpox); Orf (pustular dermatitis); Molluscum contagiosum (pustular dermatitis)
Herpesviridae Herpes simplex 1,2 (oral, genital herpes); Varicella-zoster (chickenpox); Epstein-Barr (mononucleosis);
Cytomegalovirus (neonatal abnormalities); HHV6 (roseola); HHV8 (Kaposi's sarcoma)
Adenoviridae Adenovirus (respiratory infection, conjunctivitis)
Polyomaviridae Polyomavirus (benign kidney infection, respiratory disease, leukoencephalopathy)
Papillomaviridae Papillomavirus (warts, genital carcinoma)
ssDNA
Anellovirus Unknown
Parvoviradae B-19 (fifth disease, fetal death)
Retro
Hepadnaviridae Hepatitis B ("serum" hepatitis)
Retroviridae HIV (aids); HTLV (leukemia)
dsRNA
Reoviridae Rotavirus (infantile gastroenteritis)
ssRNA (-)
Rhabdoviridae Rabies virus (rabies)
Filoviridae Ebola virus (ebola)
Paramyxoviridae Parainfluenza virus (respiratory infection); Mumps virus (mumps);
Respiratory syncytial virus (respiratory infection); Measles virus (measles)
Orthomyxoviridae Influenza virus (influenza)
Bunyaviridae Hantaan virus (hemorrhagic fever with renal syndrome)
Arenaviridae Lassa fever virus (hemorrhagic fever)
Deltavirus Hepatitis D (fulminant acute hepatitis)
ssRNA (+)
Picornaviridae Poliovirus (polio), rhinovirus (URI), Hepatitis A ("infectious" hepatitis)
Calciviridae Norwalk (gastroenteritis)
Hepevirus Hepatitis E (acute hepatitis)
Astroviridae Astrovirus (gastroenteritis)
Coronaviridae Coronavirus (respiratory infection)
Flaviviridae Yellow fever virus (yellow fever); Hepatitis C (hepatitis)
Togaviridae Eastern Equine encephalitis virus (encephalitis); Rubella virus (rubella)
Animal viruses can be cultured in variety of
ways

• Live animals such as mice, rabbits, guinea pigs

• Animal models are used for diagnostic
purposes.
• Cell cultures
• Suspension cell culture
• Embryonated eggs
Convenient and cheap
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• Virion:- a completely assembled virus out side its host cell.
• Viroids:- consist short, naked fragments of single stranded
RNA. They cause plant diseases
No animal diseases have been discovered that are
caused by viroids.
• Prions: small infectious proteins that apparently cause
fatal neurologic diseases in animals.
E.g Bovine spongiform
encephalopathy: mad cow disease( Creutzfeldt-Jakob
disease).

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 General Mycology
Mycology is the study of fungi
• Over the course of time, more than 100,000 species
of fungi have been recognized and described.
• Fewer than 500 of these species have been
associated with human disease
• No more than 100 are capable of causing infection
in otherwise normal individuals.
• The remainder are only able to produce disease in
hosts that are debilitated or immunocompromised.

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 WHAT ARE FUNGI?

• Fungi are not plants. Fungi form a separate group of

higher organisms, distinct from both plants and
animals
 fungal cells are encased within a rigid cell wall,
mostly composed of chitin and glucan.
• These features contrast with animals, which have no
cell walls, and plants, which have cellulose as the
major cell wall component.

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 fungi are heterotrophic.
This means that they are lacking in chlorophyll
and cannot make their organic food as plants
can, through photosynthesis.
• They are saprotrophic.
Saprotroph :An organism which obtains its
nutrients from non-living organic matter
commonly dead and decaying plant or animal
matter) by absorbing soluble organic compound.
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• They may produce extracellular enzymes(e.g.,
CELLULASES, XYLANASES) which release soluble
components from insoluble materials. Saprotrophs
are important agents of decay and MINERALIZATION,
and are thus essential links in the cycles of matter
(e.g. CARBON CYCLE).
• Some saprotrophs are facultative parasite. (either
SAPROPHYTE or SAPROZOITE.)
• This characteristics that led to their being placed in a
separate kingdom.
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 Fungal Cell Structure and Function
 Fungi are eukaryotic
• are commonly called yeasts, molds, and mushrooms.
• have a complex cell wall.
• Reproduce typically by asexual and sexual mechanisms
A. Fungal cell wall :
• protects cells from osmotic shock and determines shape.
• is composed primarily of polysaccharides, notably chitin, but also glucans
and mannans.
• is antigenic( stimulates the formation of antibodies)
B. Fungal cell membrane
• has a typical eukaryotic bilayered membrane.
• has ergosterol as the dominant sterol rather than cholesterol, which is an
important difference targeted by imidazoles and polyene antifungals.

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C. Fungal cellular components:
• include eukaryotic nuclei, mitochondria, and numerous vacuoles.
• do not include chloroplasts.
D. Fungal forms
1.Hyphae
– are filamentous subunits of molds and mushrooms.
– may lack septa (cross-walls); these forms are referred to as nonseptate,
aseptate (without regularly occurring cross-walls), or coenocytic
(multinucleate)
– may be septate (cross-walls).
– may be dematiaceous (dark colored) or hyaline (colorless).
– grow apically. A mass (or colony) of hyphae is a mycelium; an organized body
of hyphae is a fruiting body (e.g., a mushroom).

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2. Yeasts:
– are single-celled fungi, generally round to oval shaped.
– generally reproduce by budding (blastoconidia).
– may have a capsule (e.g., Cryptococcus).
– of the genus Candida may elongate to develop into
pseudohyphae.
– The yeast cells of Candida albicans (found on human
epithelium) also germinate, forming sprout-like projections
called germ tubes that extend to form true hyphae. Along
with pseudohyphae, true hyphae are found in infected
tissues.

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3.Dimorphic fungi
– are capable of converting from a yeast or yeast-like
form to a filamentous form and vice versa.
– are stimulated to convert by environmental conditions
such as temperature and availability of nutrients.
– usually exist in the yeast or yeast-like form in a
mammalian body and as the filamentous form in the
environment
– include the major pathogens Blastomyces,
Histoplasma, Coccidioides, and Sporothrix .

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4.Pseudohyphae
– are a series of elongated budding yeasts that remain
attached to each other and form a hyphal-like structure, but
with constrictions at the septations .
– are characteristic of most Candida species
5.Fungal spores
– may be formed either asexually (without nuclear fusion) or
by a sexual process involving nuclear fusion and then
meiosis. Most important in clinical isolates are the asexual
spores
• Collective functions of mold spore are; Production,
dissemination, and protection of the species against adverse
environmental conditions 43
Fungal structure

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Microscopic morphology of mold
Psuedohyphae
(a) septate hyphae (b) aseptate hyphae
Figure. Hyphae and mycelia.

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 Comparison between bacteria and fungi
Fungi Bacteria
   

Eukaryotic Prokaryotic
Generally larger than bacteria to (1 - 30 µm.) Smaller in size(0.1 to 10 µm)

Sterols(ergosterol) present in cell membrane Sterols absent, except in Mycoplasma

Cell wall made up of Glucons, mannana; chitin Peptidoglycan

(non - peptidoglycan)

Produce a wide variety of sexual and asexual Endospores (not for reproduction); some asexual reproductive spores
reproductive spores

Limited to heterotrophic; aerobic, facultatively Heterotrophic,chemoautotrophic,photoautrophic,aerobic,

anaerobic

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 Classifications of fungi

• Fungus classified in to five categories based on

» spore types
» morphology of hyphae,
» sexual cycles.

• These groups are:

1. Oomycetes
2.zygomycetes
3.Ascomycetes
4.Basidiomycetes
5.Deuteromycetes(imperfect fungi).
• Except for the deutermycetes, all fungi produce sexual spores‘

• Most fungi reproduce by sexual sporulation.

• asexual spores that are generally responsible for initiating human infection.
 Morphological classification

a- Filamentous fungi (molds)

Grow as threads (hyphae)
Interlace to form mycelium
b-Yeasts:
single cells, reproduce by budding
separate : Cryptococcus neoformans
attached : Candida albicans
c- Dimorphic :
exist in two forms (Histoplasma capsulatum)
Yeasts (at 37 °C) Or Molds (at 27 °C)
Mycelial phase
Yeast phase

Histoplasma capsulatum

Paracoccidioides brasilensis
Morphology of frequently isolated systemic
(dimorphic) fungi
Mycelial phase Yeast phase

Blastomyces dermatitidis

Coccidioides immitis
Dimorphism
 Clinical classification
(Fungal infection)
Medical Mycology: Is the study of fungi that infect human
• Fungi cause some of the most persistent and disfiguring disease still
prevalent through out the world.
• Diseases caused by fungi are collectively called mycoses (singular,
mycosis).
• The incidence of the disease (infection) is related to the degree of
exposure to fungi in living conditions, occupation, and leisure
activities and to immune status.
• Most mycotic agents are soil saprophytes and mycotic diseases are
generally not communicable from person-to-person (occasional
exceptions: Candida and some dermatophytes).

• There are four general categories on the basis of the primary tissue
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affinity of the pathogen.
 1. Superficial mycoses
– Are fungal infections confined to the outer most dead
layers of skin, hair and nails

– symptoms - discoloration, scaling, or de-pigmentation of

the skin.

– Do not elicit a cellular response from the host.

– Infections are generally painless.

E.g Tinea versicolor
 2. Cutaneous Mycoses
• Restricted to keratinized layer of the skin (epidermis), hair, or
nails.

• Elicit an inflammatory response, resulting in more serious skin

diseases with uncomfortable painful and sometimes even
crippling symptoms.

• Symptoms - include
• Itching, Scaling or ring like patches of the skin;
• Brittle or broken hairs;
• Thick discolored nails.
E.g Dermatophytes
 3. Subcutaneous mycoses

 Are infections confined to :

 The subcutaneous tissue (dermis or fatty tissues)

 The deeper layer of the skin

 Symptoms include :
 Ulcers, that progress and do not heal and the
presence of draining sinus tracts.
E.g Mycotic mycetoma, Chromomycosis,
Sporotrichosis
 4. Systemic mycoses
• Are caused by pathogenic and/or opportunistic fungi affect
internal organs or tissues of the body.

• Symptoms
• very general as fever, and fatigue;
• a chronic cough and chest pain.

• Are infections caused by a group of fungi which cause

infections in patients who are immunocompromised
E.g Histoplasmosis, Blastomycosis
 Others Fungal diseases
5-Opportunistic diseases:
The opportunistic mycoses are caused by ubiquitous
saprophytes and occasional pathogens that invade the
tissues of those patients who have:
1) Predisposing disease (diabetes, cancer, leukemia, etc.) or

2) Predisposing conditions (agammaglobulinemia, steroid or

antibiotic therapy).

E.g Candidosis, Cryptococcosis, Aspergillosis

6-Toxic fungal diseases:
Aflatoxin of Aspregillus flavus grown on seeds
exotoxin formed in share between fungus and medium
Mycotismus: the fungal flesh is toxic(black mushroom)
7-Allergic fungal diseases:
Fungal spores are inhalant allergens
Aspregillus hay fever(type ) or farmer’s lung(typeIII)
* A single fungus can cause more than one clinical
category

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 Clinical diseases
* Dermatophytes lesions
Circular (ring-worm), active edge (extending), healing centers

* Anatomical site of lesion:

Tinea corporis (Trunk)

Tinea Capitis (Scalp)
Tinea pedis (Foot)
Candida albicans
 Laboratory diagnosis

Specimens:
Skin scales : scraping skin at the advanced edge
Infected nail: clipping
Hair : stumps of broken hair

Thick keratinised samples dissolved in 5-20 % KOH

 Laboratory diagnosis
1- Microscopic examination:
- Presence of hyphal septa
- Shape, number, and arrangement of spores
-- Conidia:asexual spores formed on the outside of a specialized piece of
hyphae
– Blastoconidia: buds from a mother yeast cell
– Arthroconidi:conidia formed by the fragmentation (joint formation) of the hyphal
strand

- Shape of yeasts and presence of pseudohyphae

2- Culture:
- Sabouraud’s dextrose agar+chloramphincol+cyclohexamide
Cyclohexamide inhibits many saprophytic contaminating fungi,
while the CAF is inhibitery for most bacteria
- Specimen implanted on surface and partially submerged
- Incubation at 20-30°C for 2 weeks
- For yeasts: brain-heart infusion agar
- Macroscopical examination of mold colony is essential
 Laboratory diagnosis
3- Biochemical reactions:
a- Sugar fermentation
b- Germ tube formation on cultivation in serum (2-6 hs)
c- Chlamydospore formation on corn agar
d- Urease test

4- Cutaneous delayed type hypersensitivity tests:

- Histoplasmin test

5-Serological tests: useful in deep fungal infection