MICROBIOLOGY II WEEK 1 (30/03/2021) MORAL, JRC

○ Individual structural proteins ➔ subunits ➔ 5

BASIC CONCEPTS IN VIROLOGY protomers ➔ pentamer capsomeres ➔
Viruses procapsid or capsid
● Smallest filterable agents ○ Capsid and Envelope: for protection, packaging,
● Obligate intracellular parasites delivery, and spread
● Could be living or nonliving ○ Destruction could result to infectivity
● Mode of replication: ● Nucleic acid (DNA or RNA)
○ Assembly of individual components ○ Nucleocapsid
● Lack the capacity: ● Replication enzymes (i.e. viral polymerase)
○ Make energy substrates Types or capsid
○ Replicate their genome independently ● Helical capsid (eg tobacco mosaic virus)
● Must adapt to the biochemical rules of the cell in order to ● Icosahedral capsid (eg adenovirus)
successfully use the cell’s biosynthetic machinery; ● Multiple helical capsids, spherical viral envelope (eg
Hijacking to produce virions influenza virus)
● Infect only cellular forms ● Complex capsid: icosahedral head, helical tail (eg
○ Eukaryotes bacteriophage)
○ Prokaryotes
● Important causes of human disease Envelope Naked Capsid
○ Common colds
Component Membrane Protein
○ Lethal rabies Lipids
○ Causes some cancer (oncogenic viruses: e.g. Proteins
Human papilloma viruses - Cervical cancer; Glycoproteins
Human herpesvirus 8 - Kaposi’s sarcoma)
Properties Is environmentally labile Is environmentally stable
● Also affects the wellbeing of societies
—disrupted by the following: to the following:
○ E.g. Smallpox, Covid-19 pandemic ● Acid ● Temperature
● Some viruses are studied for their usefulness and ● Detergents ● Acid
applications in medicine and in the industry ● Drying ● Proteases
● Heat ● Detergents
○ Phage typing of bacteria Modifies cell membrane during ● Drying
○ Sources of enzymes in molecular biology replication
(reverse transcriptase from retroviruses and Released from cell by lysis
Released by budding and cell
RNA polymerases from phages) lysis
○ Pesticides (baculoviruses and myxoma virus)
○ Antibacterial agents – phage therapy to treat Consequence Must stay wet Can be spread easily (on
infections s fomites, from hand to hand,
Cannot survive the GIT by dust, by small droplets)
○ Anti-cancer agents
○ Gene vectors Spreads in large droplets, Can dry out and retain
● They have genes – DNA or RNA enclosed in a protein secretions, organ transplants, infectivity
and blood transfusions
coat
Can survive the adverse
○ Viruses could only have EITHER Does not need to kill the cell to conditions of the gut
○ Can be dsDNA, ssDNA, dsRNA, or ssRNA spread
Can be resistant to
May need antibody and detergents and poor
cell-mediated immune response for sewage treatment
protection and control
Antibody may be sufficient
Elicits hypersensitivity and for immunoprotection
inflammation to cause
immunopathogenesis

Replication
1. Recognition of the target cell mediated by viral attachment
proteins (VAPs) otherwise known as adhesion molecules
on the envelope/capsids
a. Viruses exhibit tropism
2. Attachment
3. Penetration
a. Naked viruses: penetrate through receptor
mediated endocytosis or viropexis
b. Enveloped viruses: viral envelope fuses with
membrane of target cell, nucleocapsid is
delivered inside (non-endocytic route)
Structure
4. Uncoating
● Unit of measurement for virion sizes: nm
a. Uncoating can be triggered by attachment to cell
● Clinically important viruses range from 18nm-300nm
surface receptors, acidic environment, or
proteases
Typical structure of a naked and enveloped virion
b. Capsid is uncoated to deliver the nucleic acids
● Envelope with glycoprotein spikes (no envelope for
into the site of replication
naked)
c. DNA is transported to nucleus
● Capsid
d. RNA remains in cytoplasm
○ Has attachment proteins
5. Macromolecular synthesis (transcription and translation)
○ Capsomeres - forms to make the capsid
a. Early mRNA ➔ nonstructural proteins synthesis
b. Replication of the genome
MICROBIOLOGY II WEEK 1 (30/03/2021) MORAL, JRC
c. Late mRNA ➔ structural protein synthesis
d. Posttranslational modification of proteins
6. Assembly
a. Capsid assemble first as empty structures and
then filled with genome; or
b. Some assemble around the genome
c. Viral glycoproteins delivered into the cell
membrane ➔ capsid associates with it through
budding ➔ enveloped viruses
7. Release
a. Lysis of the cell
b. Exocytosis
c. Budding

Naked viruses – release during lysis

Enveloped viruses – released through budding from the plasma
membrane without killing the cell

Positive sense RNA resembles mRNA ➔ binds to ribosomes ➔

proteins

Negative sense RNA ➔ transcribed to mRNA ➔ proteins

MICROBIOLOGY II WEEK 1 (30/03/2021)
Since their discovery, bacteriophages have been considered
to be potential antibacterial
therapeutics for the treatment of various infectious diseases
in humans.
D’Herelle’s enthusiasm concerning the wide possibilities of
phage therapy led to extensive attempts to isolate
bacteriophages that were active against bacterial agents
found in infected wounds and apply them in treatment. As a
result, phage therapy was used in the USSR ( Union of
Soviet Socialist Republics) during the Finnish Campaign
(1939–1940) and continued during the World War II (
the use of bacteriophages
in the clinical treatment of infected wounds was not stopped
in Eastern Europe and the former
SU, as antibiotic treatment of such infections sometimes
failed, even in cases of antibiotic-sensitive bacteria.
The urgency of the antibiotic resistance crisis has led to
a resurgence of interest in these largely long forgotten
treatments,
Despite the widespread introduction of antibiotics, phage
preparations continued to be used in the USSR and, later,
in the Russian Federation for the prevention of wound
infections and treatment of infectious complications of
surgical
wounds
BACTERIOPHAGE TREATMENT OF WOUND
INFECTIONS AND INFECTIOUS COMPLICATIONS OF
SURGICAL WOUNDS
● Bacteriophages (phages) are viruses that use
the bacterial machinery to infect, replicate, and
kill bacterial cells.
● Viruses exhibit tropism
● bacteriophages that were active against
bacterial agents found in infected wounds and
apply them in treatment.
● It was reported that the mixtures of bacteriophages
active against Clostridium perfringens,
Staphylococcus spp., and Streptococcus spp. were
used for the prevention and treatment of gas
gangrene (Kokin, 1941).
● Phage therapy:
○ Mono therapy - phage administration alone
○ Complex therapy/ treatments - phages +
antibiotics
■ Decreased healing time by
1.2-2.5x
● Pyophage and mono-specific phages
● To improve the efficacy of phage therapy,
● “Pyophage” (a poly-specific cocktail of phages)
was applied initially, and after detection of the
etiologic agents, mono-specific lytic phages were
used (Pokrovskaya et al., 1941; Tsulukidze, 1941;
Krestovnikova, 1947).
○ Staphylococcal infections (69%)
MORAL, JRC
○ Streptococcal infections (50%)
● Course of treatment
○ washings of a wound with a phage
preparation
○ subcutaneous injections of phages from
one to four times per day
○ Five to eight days of therapy were
sufficient for clinical improvement in
the majority of cases
Infected postoperative wounds
● faster cleaning of wounds from purulent masses,
granulation, and healing without deforming scars
● Question remained:
○ Which is better to use: one specific
bacteriophage or a poly-specific phage
cocktail.
● Application of highly specific bacteriophages
(adapted by cultivation on a bacterial strain isolated
from a patient) was more effective than treatment
with poly-specific phage cocktails
●
● However, the adapted phage preparations require
detailed characterization because they may contain
temperate bacteriophages produced by the clinical
bacterial strain.
PHAGE TREATMENT OF INFECTED
BURNS
● Phage therapy could potentially be used to treat
burns and prevent sepsis.
● Burn surfaces are rapidly colonized by bacteria,
which are capable of producing biofilms and are
often resistant to multiple antibiotics
● An interesting feature of some phages is the
possession of genes coding for
exopolysaccharide depolymerases (Figure 2D)
that can degrade the polysaccharidic
component of the extracellular matrix of
biofilms facilitating biofilm dispersion and
access of the phage into the deeper layers of
this structure
● Topical application - time consuming; only for
infections resistant to available antibiotics
○ Topical application of phages led to the
○ elimination of multiple drug resistant
(MDR) P. aeruginosa or successful skin
graft take in 18 of 30 patients with burns,
but the
○ method was time-consuming, and the
authors recommended this therapy only for
infections resistant to available antibiotics
The dosage of phage preparation is believed to
be very important in phage therapy, and the
therapeutic titer should be higher than 10^6
pfu/ml.
○ concentration of infectious vector
● It is possible that the result of phage therapy
depends on both phage titer and a number of other
reasons, including sensitivity and accessibility of
bacterial host to the phage, routes of phage
MICROBIOLOGY II WEEK 1 (30/03/2021)
administration, duration of phage treatment course,
and so on.
PHAGE THERAPY OF PATIENTS WITH
INFECTED ULCERS
● Chronic trophic ulcers occur as a complication
of some disorders
● Phage therapy could be an alternative to antibiotics
or, at least, a supplementary approach to the
treatment of infected ulcers.
● It is believed that the rate of healing of ulcers
depends on the concurrent infection;
● S. aureus and P. aeruginosa were found to be
predominant and the most pathogenic species
commonly persisting in chronic wounds (Wolcott et
al., 2016), and their elimination would lead to
improvement and wound healing in the majority of
cases.
● needed. In fact, phage therapies, biocontrol agents,
● PhagoBioDerm (a biodegradable wound dressing
impregnated with the phage cocktail Pyophage)
○ degrade slowly and release active
antimicrobials, including phage particles,
for a long time.
○ Reduced number of treatments
○ Helps prevent microbial infections in
wounds
● The use of PhagoBioDerm reduced the number of
treatments and hence, injuring of wounds;
therefore, this type of material is promising for both
therapy and prevention of microbial infections in
wounds
●
● The main difficulty in treating of wounds infected
with several pathogenic bacteria was the inability to
quickly select phages against all identified bacterial
agents
● Different schemes and routes of phage
administration have been applied, varying from oral
or intravenous applications to multiple topical
treatments. Wound dressings, and subcutaneous
injections
An interesting feature of some phages is the possession of
genes coding for exopolysaccharide depolymerases (Figure
2D) that can degrade the polysaccharidic component of the
extracellular matrix of biofilms facilitating biofilm dispersion
and access of the phage into the deeper layers of this
structure
Fernández, L., Gutiérrez, D., García, P., & Rodríguez, A.
(2019). The Perfect Bacteriophage for Therapeutic
Applications-A Quick Guide. Antibiotics (Basel, Switzerland),
8(3), 126. https://doi.org/10.3390/antibiotics8030126
MORAL, JRC
Bacteriophage Applications for Food Production and
Processing
● Foodborne illnesses remain a major cause of
hospitalization and death worldwide despite many
advances in food sanitation techniques and
pathogen surveillance.
● bacteriophage biocontrol, a green and natural
method that uses lytic bacteriophages isolated
from the environment to specifically target
pathogenic bacteria and eliminate them from (or
significantly reduce their levels in) foods.
Application of Bacteriophages in Nanotechnology
● Numerous applications of phages became
possible thanks to phage display—a method
connecting the phenotype and genotype, which
allows for selecting specific peptides or
proteins with affinity to a given target.
● One could think that phages are useful only in
applications when bacteria detection/identification is
sensors for bacteria detection, and antibacterial
materials constitute important fields of study
providing solutions for vital problems of the current
world. However, phages proved to be useful and
monodispersed building blocks and templates in
nanotechnology, physical chemistry, and material
science, due to their abundance corresponding to
the variety of morphologies, robustness, ease of
preparation, and ease of modification. The Nobel
awarded phage-display technique caused an
explosion of new and exciting examples of phage
utilization
Bacteriophages--potential for application in wastewater
treatment processes
● Phage treatments have the potential to control
environmental wastewater process problems such
as: foaming in activated sludge plants; sludge
dewaterability and digestibility; pathogenic bacteria;
and to reduce competition between nuisance
bacteria and functionally important microbial
populations.
Application of bacteriophages in sensor development
● Bacteriophage-based bioassays are a promising
alternative to traditional antibody-based
immunoassays. Bacteriophages, shortened to
phages, can be easily conjugated or genetically
engineered. Phages are robust, ubiquitous in
nature, and harmless to humans.
MICROBIOLOGY II WEEK 1 (30/03/2021) MORAL, JRC