CLIN PHARM 114: Pharmaceutical Microbiology and Parasitology Laboratory

VIROLOGY
Professor ENJT/ACPU/JMD | Reviewed: FEB 25, 2025 | Last Edited: FEB 26, 2025

THERAPY
OUTLINE
SUMMARY OF REPLICATION PROCESS OF COVID
VIRUS
DMITRI IWANOWSKI
WENDELL M. STANLEY VIRAL LIKE AGENTS
SATELLITES
GENERAL CHARACTERISTICS OF VIRUSES VIROID
HOST RANGE HEPATITIS DELTA VIRUS (HDV)
VIRUSES AS TREATMENT PRIONS
VIRUSES AS TREATMENT: OBSTACLES DISEASES CAUSED BY PRIONS
VIRAL STRUCTURE
VIRION VIRAL SURVIVAL AND SUSCEPTIBILITY
NUCLEIC ACID
ssRna virus
CAPSID
Shapes
LEGEND
PHOSPHOLIPID ENVELOPE
Naked vs Enveloped ●​ black = from laboratory manual
Advantages vs Disadvantages ●​ red = notes from professor
ENZYMES ●​ green = powerpoint notes

DNA VIRUSES DMITRI IWANOWSKI

ENVELOPED OR NAKED ●​ Wanted to isolate the cause of tobacco mosaic disease
REPLICATE ENVELOPE ●​ Filtered the sap of disease tobacco plants, but the
pathogen passed through the filter
ICOSAHEDRAL
○​ But in the end, wala siyang nafilter and the pathogen
DOUBLE STRANDED
passed through the filter
●​ Healthy plants injected with the filtered fluid -> tobacco
RNA VIRUSES mosaic disease
ENVELOPED ○​ This means that there must be a causative agent that
REPLICATION IN CYTOPLASM is very small, even smaller than your bacterial cells
HELICAL
SINGLE STRANDED

VIRAL REPLICATION
PERMISSIVENESS
FACTORS THAT AFFECT THE
PERMISSIVENESS OF HOST CELLS
PROCESS OF VIRAL REPLICATION
ATTACHMENT (ADSORPTION)
PENETRATION/ ENTRY
UNCOATING*
SYNTHESIS
Figure 1. Dmitri Iwanowski
DNA Viruses (occurs in nucleus)
RNA Viruses (occurs in cytoplasm) WENDELL M. STANLEY
ASSEMBLY & RELEASE ●​ Isolated the tobacco mosaic disease virus
○​ In the end, he was able to isolate the causative agent
HOST CELL OUTCOME in a mosaic disease, but they initially believe that they
DEATH are bacterial in nature
TRANSFORMATION ○​ After conducting chemical studies, they were able to
determine that the causative agent is living differently
LATENT INFECTION
compared to the bacteria, characterizing the
CHRONIC INFECTION
causative agent as a virus
HIV SCREENING & EARLY ANTIRETROVIRAL ●​ Led the chemical and structural studies on a purified virus

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 ■​ Ex. When intracellular environment becomes
favorable for viral multiplication, the virus can
survive and thrive in the host cell

Are all viruses harmful? NO.

They are some that can help the environment.

Tulip mosaic virus

●​ Causes viral infection on the tulip
●​ Alters plant cell development leading to
the complex color patterns of the petals
○​ This is a mechanism done to
attract more pollinators that is
Figure 2. Wendell M. Stanley good for the ecosystem
●​ Other benefits: Significant factor in
GENERAL CHARACTERISTICS OF VIRUSES ecosystems, Vaccines, treatment option,
●​ Viruses are NOT living organisms because they are used in the development of seeds
acellular NOTE
●​ Acellular
○​ No plasma, cytosol, & organelles
●​ Small
○​ 20 to 1000 nm in length

Figure 4. Tulip mosaic virus

VIRUSES AS TREATMENT
●​ Phage Therapy
○​ Use of bacteriophage to treat bacterial infections
Figure 3. Comparison of sizes of viruses, bacterium (E. coli), ○​ Ongoing clinical trials – first approval in 2019
and RBC ○​ Technique to combat AMR

●​ They are much smaller compared to bacterium cell

●​ Oncolytic Viruses
●​ Obligate Intracellular parasites
○​ Infects and kills cancer cells
○​ No enzymes for protein synthesis & metabolism, only
○​ Ongoing clinical trials for > 9 virus groups
for nucleic acid synthesis (preformed enzymes: DNA
polymerase, reverse transcriptase)
○​ They need a host to multiply and survive
●​ Has one type of nucleic acid
○​ Has DNA or RNA, but never both

HOST RANGE
●​ Spectrum of host cells a virus can infect
○​ Mostly, one virus can only infect one host species
●​ Viruses with wide host range (exception from the ones
mentioned above):
○​ Arbovirus
○​ Rabies virus
○​ Influenza virus
●​ Determined by:
○​ Virus’s requirements for specific attachment to host
cell
■​ Ex. glycoprotein projections: also called “spikes”, Figure 5. Bacteriophages: Viral Plaques
they are specific to most cell receptors. If the VIRUSES AS TREATMENT
spikes can be attached to different types of ●​ Here, you have an agar plate solid media that is
receptors, they can attach and infect the host cell inoculated with both viral and bacterial suspension
○​ Availability of cellular factors needed for viral ●​ After letting it grow, dots appear on the clearing of the
multiplication solid media called plaques

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●​ Plaques are assumed to be the viral growth that inhibits
the growth of bacteria (the clear background surrounding
the plagues in Figure X).

Fighting Infection with Phages

VIRUSES AS TREATMENT: OBSTACLES

●​ High bacterial strain specificity
○​ Since viruses have specific receptors, they only bind
to specific receptors of host cells
●​ Bacteria can evolve different receptors
○​ Bacteria is an evolving organism, hence, there is
antimicrobial resistance, making them resistant to Figure 7. Replication of nucleic acids in virion, following central
certain antibiotics dogma
●​ Difficulty in obtaining patents
○​ General problem as well in generating medicines ssRNA Virus
●​ Negative perception on viruses ●​ (+) sense: can act directly acts as mRNA
○​ The negative perception on viruses is that they can ○​ They can directly undergo translation, and therefore,
only cause disease, they cannot be used as vehicles directly forming your proteins.
in developing treatment ○​ The ribosomes can act upon the positive (+) sense
○​ Because of this perception, these kind of studies are single stranded RNA to form proteins
very limited ●​ (-) sense: acts as template for a complementary (+) sense
mRNA
VIRAL STRUCTURE ○​ You need to make a positive (+) sense mRNA first
VIRION before undergoing translation approach
●​ A complete, fully developed, infectious viral particle
●​ Contains: CAPSID
○​ A nucleic acid (in the form of DNA and RNA, contains ●​ Protein coating that protects the RNA or DNA
the genetic material) ●​ Composed of capsomeres (protein subunits)
○​ Capsid (protein coat, protecting the nucleic acid) ●​ Accounts for the majority of the virus’ mass
○​ +/- Phospholipid envelope: May or may not be
present in the viral structure Shapes
●​ Helical
○​ its shapes makes the RNA enclosed in the helical
capsid
●​ Polyhedral
○​ Icosahedron - polyhedral with 20 triangular faces
■​ Most common shape
●​ Complex

Figure 6. Virion

NUCLEIC ACID
●​ Genetic material or makeup of the virus
●​ Either DNA or RNA
●​ Either single-stranded (ss) or double-stranded (ds)
●​ Can be linear, circular or segmented Figure 8. Capsid Shapes, helical (leftmost), polyhedral
●​ The process of replicating or multiplying of the genetic (middle), and complex (rightmost)
material still follows the central dogma, depending
whether you are starting with RNA (single-stranded) or PHOSPHOLIPID ENVELOPE
DNA (double-stranded). ●​ Phospholipid bilayer
●​ Acquired from the host cell during viral replication or
release
●​ May or may not contain spikes
○​ Surface projections
■​ Found on the envelope
○​ Glycoproteins that attach to specific receptor sites
■​ Will attach to the host cell

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 NAKED VS ENVELOPED Table 1. DNA viruses, classified under presence/absence of
phospholipid envelope
●​ Naked/Non-enveloped (left) ENVELOPED NAKED
○​ Viral DNA or RNA is enclosed in a capsid. The spikes
Herpes Adeno (naked)
may already appear on the capsid.
○​ Glycoprotein projections does not have projections, Hepadna Parvo (naked)
hence they are place onto the capsid Pox Papova (naked)
●​ Enveloped (right)
○​ Its spikes are found on the envelope. Polyoma (naked)

○​ Mnemonics: HAP (read as happy)

○​ 4 naked, 3 enveloped

REPLICATE ENVELOPE
●​ DNA viruses usually replicate in nucleus
○​ Enter the nucleus of the host cell first before they
Figure 9. Naked/Non-enveloped (Left) vs. Enveloped (Left) undergo replication
●​ Except: Pox
Table 1. Advantages and Disadvantages of Phospholipid ○​ Enters the Cytoplasm instead
Envelope ○​ Exemption is Poxviridae wherein its replication
ADVANTAGES DISADVANTAGES happens in cytoplasm
Helps evade immune Easily damaged by ICOSAHEDRAL
response environmental conditions that ●​ DNA viruses are generally icosahedral
destroy membranes ●​ Except Pox
(They can be easily killed by ○​ They are brick-shaped
harsh conditions, such as ○​ Exemption is Poxviridae wherein its capsid shape is
chemical disinfectants that brick-shaped
target the envelope of the
virus) DOUBLE STRANDED
●​ DNA viruses are generally double stranded
Helps virus infect new cells Naked viruses – more
●​ Except Parvo
virulent, capsid is more
○​ They are ssDNA
resistant and remains intact
○​ Exemption is Parvoviridae wherein it is
(The absence of the envelope
single-stranded
helps it to be more virulent
because the capsid is more
RNA VIRUSES
resistant and it remains intact
better than the envelope) ENVELOPED
●​ DNA viruses are generally enveloped
●​ Exceptions (they are naked RNA viruses):
QUESTION: Which can survive better? Your ○​ Picorna
envelope of naked virus? ○​ Calici
ANSWER: Naked viruses are more resistant to ○​ Reo
harmful conditions. ■​ Exemption: PRC (mnemonics) which are naked
●​ Absence of the envelope helps the viruses
NOTE
naked virus be more virulent since the REPLICATE IN CYTOPLASM
capsid is more resistant and it remains ●​ DNA viruses generally replicate on cytoplasm
intact better than than the enveloped ●​ Exceptions (they replicate into the nucleus):
●​ This also means that naked viruses ○​ Retro
are more virulent ○​ Orthomyxo

HELICAL
ENZYMES
●​ In terms of shape of the capsid, generally RNA viruses
●​ Some viruses have pre-formed enzymes
are helical
○​ Polymerases - synthesize DNA & RNA
●​ Exceptions
○​ Replicase - copy RNA
○​ Picorna - icosahedral
○​ Reverse transcriptase - synthesize DNA from RNA
○​ Reo - icosahedral
■​ Ex. Retrovirus
○​ Calici - icosahedral
●​ Viruses completely lack genes for synthesis of metabolic
○​ Flavi - icosahedral
enzymes
○​ Retro - varying
■​ Some are polyhedral in shape close to being
DNA VIRUSES spherical
ENVELOPED OR NAKED ○​ Toga - icosahedral
●​ These mentioned below are the most notable DNA
viruses

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 SINGLE-STRANDED ○​ If the attachment sites of the virus and receptor sites
●​ In terms of shape of the capsid, generally RNA viruses on the host cell are not compatible, attachment will
are helical not occur
●​ Exception: Reo ●​ Glycoprotein spikes or other attachment molecules
○​ Composed of a double-stranded RNA (sRNA) ●​ Receptor sites are inherited characteristics of the host
●​ Viruses usually have tissue specificities (tropisms)
VIRAL REPLICATION ○​ Hepatitis B – liver
●​ Viruses need host in order for them to multiply because ■​ Hepatitis B virus is specific to liver tissue
they are obligate, intracellular parasites ○​ Mumps virus – salivary glands
●​ Viruses have genes for structural components ○​ Viruses are usually highly specific
○​ Codes for basic structural components such
as capsid and envelopes in the glycoprotein
spikes
●​ No genes to code for enzymes
○​ No genes for enzymes used in metabolism
●​ Virus needs to invade a host cell and invade its
metabolic machinery
○​ To take advantage of the metabolic
machinery that happens in host cells so they
can replicate and multiply and produce more
viral particles

PERMISSIVENESS
Figure 10. Attachment on the process of viral replication
●​ Ability of host cell to support full viral replication
○​ The more permissive a host cell, the more it can ●​ This animation shows that once a single glycoprotein
support the replication of the virus spike has attached to one receptor site of the cell →
cascade of other attachments will follow → forming an
FACTORS THAT AFFECT THE PERMISSIVENESS OF enclosure to the virus
HOST CELLS
●​ Receptors PENETRATION/ ENTRY
○​ Receptors of host cells must be able to attract the ●​ Direct Penetration (Naked Viruses)
viral glycoprotein spikes
○​ If the receptors is not compatible to the viral
glycoprotein spikes then it will not support the
replication process of the virus
●​ Infected cell must survive until replication is completed
○​ Once the cell detects that it is being invaded by a
pathogen/foreign body, it will undergo apoptosis or
programmed cell death, therefore not completing the
viral replication process
●​ Adequate environment for viral replication
○​ Necessary conditions for viral replication inside the Figure 11. Attachment on the process of viral replication
host cell is there for viral replication to occur
○​ The naked virus attaches to the cell membrane →
PROCESS OF VIRAL REPLICATION capsid will sink into the cell membrane → creates a
●​ Viral replication usually takes 8 to 36 hours pore → releases genetic material into the cell (leaving
●​ Mnemonic: APUSAR the capsid in the cell membrane surface without
1.​ Attachment of virions to the host cell uncoating)
2.​ Penetration/Entry of virion or its genome to the host
cell ●​ Membrane Fusion (Enveloped Virus)
3.​ Uncoating* to release the viral genome
○​ * = not all viruses undergo the uncoating process
4.​ Synthesis of new nucleic acids and viral proteins by
the host cell
5.​ Assembly of new virions within the host cell
6.​ Release of new virions

ATTACHMENT (ADSORPTION)
●​ Dependent on the chemical attraction between the
attachment sites of the virus and receptor sites on the
host cell

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 ○​ Once the viral DNA is replicated inside the nucleus, it
will go outside of the nucleus to undergo translation
forming proteins in the ribosomes of the host cells
○​ DNA replication happens in the nucleus while
protein synthesis happens in the cytoplasm
●​ Exception: Poxviridae – all components are synthesized in
the cytoplasm
○​ They do not enter the nucleus for DNA replication

RNA Viruses (occurs in the cytoplasm)

●​ +ssRNA, dsRNA
○​ +ssRNA is directly translated by ribosomes into viral
proteins
○​ Positive-sense single-stranded RNA serves as the
○​ Envelope virus attaches to cell membrane →
template for translation in the ribosomes
envelope of the virus fuses/merge with the cell
○​ +ssRNA acts as an mRNA for ribosomes to directly
membrane of the host cell → the envelope will open
encode and form viral proteins)
releasing the capsid and viral genome → capsule
●​ Retrovirus RNA (+ssRNA)
enters, and capsid undergoes uncoating inside the
○​ Use of reverse transcriptase to transcribe provirus
cytoplasm
DNA from +ssRNA
○​ +ssRNA serves as the template for DNA synthesis
●​ Endocytosis (Naked or Enveloped Virus)
■​ Not directly translated
■​ Provirus DNA will undergo the same DNA
replication/synthesis in the host cell
●​ -ssRNA
○​ Has RNA-dependent RNA polymerase
■​ RNA polymerase converts negative-sense
single-stranded RNA to a positive-sense
single-stranded RNA
○​ Transcription from -ssRNAto +ssRNA
■​ +ssRNA will serve as a template to be encoded
by the ribosomes into viral proteins

○​ The naked or enveloped virus attaches to the cell

membrane → whole virus (including the envelope) is
engulfed by the host cell → whole virus enters the
cytoplasm → capsid containing the genome is
released → capsid undergoes uncoating to release
viral genome (viral DNA/RNA)

UNCOATING*
●​ Not all have this
●​ For viruses that penetrate a host cell with intact capsids
Figure 12.Viral Synthesis for RNA Viruses
●​ Separation of the viral nucleic acid from its protein coat
●​ Occurs via different means in different viruses
○​ Uncoated within vesicles or within cytosol

SYNTHESIS
DNA Viruses
●​ Replication of DNA occurs in the nucleus
○​ Proteins migrate into the nucleus and combine with
DNA
■​ DNA of virus fuses with the host cell DNA
undergoing the same process of DNA
replication/synthesis happening in the host cell
Figure 13. Summary of RNA viruses and DNA viruses
●​ After the host cell DNA is transcribed and
translated, the viral DNA will also be affected ●​ DNA viruses undergo the usual central dogma that we
●​ Synthesis of capsid and other proteins in the cytoplasm know

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 actively dividing; latent infection phase can take up to
ASSEMBLY & RELEASE 3-10 years
●​ Assembly of capsid
●​ Envelope protein is encoded by viral genes and CHRONIC INFECTION
incorporated into the plasma membrane ●​ Cause disease after years of latent infection
●​ Envelope develops around the capsid through budding or ●​ Eg. AIDS (progression from HIV)
exocytosis → viruses are gradually shed (out of the host ○​ The host can appear healthy, but the virus has been
cell) multiplying in inside of them, so after years it will
●​ Non-enveloped viruses (first accumulate in the host cell cause reactivation of the virus that will now lead to
then) are released through rupture in the host plasma AIDS
membrane → host cell death
HIV SCREENING & EARLY ANTIRETROVIRAL THERAPY
●​ Hence, it is recommended to conduct HIV screening to
have early detection to increase patient’s chance for
survival
●​ This initiates early therapy (antiretroviral medicines) to
prevent progression to chronic infection (AIDS)

SUMMARY OF REPLICATION PROCESS OF COVID VIRUS

Explainer: How the coronavirus (SARS-CoV-2) infects h…

VIRAL LIKE AGENTS

SATELLITES
●​ Small, single-stranded RNA molecules that lack genes for
their own replication
●​ Require a helper virus
●​ Found in plants (along with viroids)
Figure 14. Assembly and Release

1.​ Viral capsid is formed VIROID

2.​ It goes to the cell membrane ●​ Infectious RNA particle smaller than a virus
3.​ It forms an envelope and budding will occur ●​ Does not require a helper virus
4.​ The formed bud will separate from host cell ●​ Found in plants (along with viroids)
5.​ Envelope virion is released to the environment
HEPATITIS DELTA VIRUS (HDV)
HOST CELL OUTCOME ●​ Animal virus
DEATH ●​ Similar to satellites
●​ Host cell’s own function shuts down due to virion ●​ Require the HBV as its helper virus
replication leading to cell death ○​ Can only be found in a patient who is already infected
●​ Since there have been changes in the host cell, there can with hepatitis B to undergo replication
be alterations in the processes and cause the cell to shut
down leading to cell death PRIONS
●​ Proteinaceous infectious particles
TRANSFORMATION
●​ Abnormal, transmissible, pathogenic agents
●​ Activation or introduction of oncogenes
○​ Convert cellular proteins into prions
●​ Uncontrolled and uninhibited cell growth
○​ The presence of prions are usually found in the brain,
○​ This can cause cancers since there have been
leading to cognitive impairment or diseases related to
alterations in the genetic material, cell synthesis
the brain
processes could be altered hence can cause
●​ Resistant to heat, radiation, enzymes that digest DNA or
uncontrollable cell growth
RNA
○​ This is because prions are usually resistant to usual
LATENT INFECTION agents used for disinfection (radiation, heat) that
●​ Phase of infection where there are no apparent clinical allow digestion of RNA and DNA, since they are
signs and symptoms but the virus is essentially alive and proteins in nature and they do not have genetic
replicating inside the host material with them
●​ Virus in sleeping state ●​ Sensitive to protein denaturing agents
●​ Virus survives but no clinical infection
●​ Various factors can lead to viral reactivation DISEASES CAUSED BY PRIONS
○​ Change in the health of the host ●​ Bovine spongiform encephalopathy (BSE) or mad cow
●​ Eg. HIV - first the host is infected then they will present disease
with flu-like symptoms then eventually subside, but does ○​ Found in cattles
not mean that HIV virus is killed, it can be inside and

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 ○​ Results to loss of motor function, metal degeneration,
and even death
○​ The spongiform appears as if there are holes at the
brain of the cattle/cow, hence it becomes spongy in
appearance
●​ Creutzfeldt-Jakob disease
○​ Diseases presenting in humans similar to BSE
○​ Contracted by humans when they eat cattle or
infected cows with prions or the BSE, presenting the
same symptoms in BSE (motor function, metal
degeneration, and even death)
●​ Kuru
○​ Loss of voluntary motor control
○​ Usually presented in the tribes in the New Guinea
area as a result of their practice of eating the brains
of dead family members as one of their funeral

VIRAL SURVIVAL AND SUSCEPTIBILITY

●​ Importance: We must know them or appreciate them to
know what are the ways to kill your viruses
●​ Factors that affect the viral survival and susceptibility
○​ Can be influenced by temperature, pH,
disinfectants, radiation
○​ Enveloped viruses are susceptible to detergents and
solvents
■​ Since enveloped viruses have a phospholipid
envelope, detergents can destroy the envelope
of the virus, and eventually killing the virus
○​ No single temperature-time to eliminate all types of
viruses
■​ Common practice is to expose the virus at 60C
for 1 to 10 hours
○​ Varying sensitivity to extreme pH
■​ Common practice to make the virus be killed is to
have an acidic pH for 6 hours
■​ However, some viruses can survive acidic pH
such as enteroviruses (contracted by fecal-oral
route), with a stomach in acidic pH
○​ Susceptible to UV light

Figure 15. Activity and required contact time for disinfectants

acting on enveloped and nonenveloped viruses.
●​ don’t memorize this tabLE

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