WEEK 1: VIRAL PROPERTIES Flashcards
Define the following terms:
1. Virion
2. Genome
3. Capsid
4. Nucleocapsid
Virion: Infectious virus particle
Genome: a set of genes
A capsid is a protein shell that encloses the genetic material of a virus.
Nucleocapsid: Genome + capsid.
What is the difference between a virus and a virion?
A virus is an obligate intracellular parasite. Accordingly, it can only survive within a host cell and depends on it for replication and metabolic processes.
Virion: The infective form of a virus when present outside of cells, which consists of DNA or RNA, a protein capsid, and sometimes an envelope.
Started in 1918
H1N1 influenza of avian origin
estimated 25 million deaths.
What virus is this?
Spanish flu
Nipah virus (NiV)
What is meant by a zoonotic virus?
Which animals are reservoirs of this virus?
State 2 main diseases caused by this virus.
- zoonotic virus(it can spread between animals and people.)
- Fruit bats, also called flying foxes, are the animal reservoir.
- Encephalitis and atypical pneumonia
Outbreaks occur almost annually in parts of Asia, primarily Bangladesh and India
Describe HIV.
HIV
retrovirus that infects cells of the human immune system (mainly CD4-positive T-cells and macrophages)
Globally, 39.0 million
630 000 deaths (2022)
Local prevalence: 20.6%
When was the first pandemic of SARS CoV?
How many cases and deaths have been recorded worldwide since December 2019
SARS –CoV
Coronavirus
First pandemic: 2002 to 2003
Guangdong province in China and extended to 29 countries.
COVID19: Wuhan China, December 2019
Over 760 million cases and 6.9 million deaths have been recorded worldwide since December 2019
State the 5 main viral properties.
*Viruses are small: sizes range 20 (parvovirus) - 300 nm (poxvirus)
*Viruses are filterable: Remain infectious after passing through a filter with pores too fine for a bacterium to pass through.
*Obligate intracellular parasites: They rely on the host.
*Genome consists of ONLY one type of nucleic acid: either RNA or DNA.
*Viral genome codes for the few proteins necessary for replication:
Proteins are non-structural e.g., polymerase,
Structural e.g., form part of the virion structure
The virus consists of a genome and an outer cover: capsid or envelope.
What is a capsid?
What is an envelope?
Capsids are either icosahedral or tubular in shape. Describe icosahedral.
Capsid: Protein shell which surrounds and protects the genome. It is made up of multiple sub-units called capsomers.
Envelope: Lipoprotein membrane, derived from the plasma membrane of the host cell.
Viral components are assembled and do not replicate by “division.”
An icosahedron is a polyhedron with 20 faces.
Describe capsid.
State 5 environments in which capsids are stable.
How is it released from the cell?
What is the capsid shape for enveloped viruses? and non-enveloped viruses.
Protein
They are stable in environments:
Temperature
Acid
Proteases
Detergents
Drying
Is released from cell by lysis.
*Helical capsid structure in enveloped viruses.
*Icosahedral capsid structure in nonenveloped viruses and enveloped viruses (all DNA viruses are icosahedral except poxvirus, which has a complex capsid)
What is an envelope?
State the 3 components of envelope.
What does labile mean in medical terms?
State the 4 environments in which envelope is labile under.
What is the function of the envelope in a virus?
What are some surface modifications found on a viral envelope?
- Membrane
*Usually originates from host cell’s plasma membrane when the virion exits the host cell (except Herpesviridae, which acquire their primary envelope from host cell nuclear membranes).
- Lipids
Proteins
Glycoproteins - Rapidly or frequently changing.
- They are labile in the following environment:
Acid
Detergents
Drying
Heat - It protects the genetic material in their life cycle when traveling between host cells. Not all viruses have envelopes.
- Spikes: viral receptor proteins (enables adhesion to host cell)
Sheath and tail fibers: present in bacteriophages
Some viruses do not possess envelopes. These are referred to as nonenveloped viruses (naked viruses).
Give examples of non-enveloped DNA and RNA viruses.
DNA viruses, e.g., Papillomaviridae, Adenoviridae, Parvoviridae, Polyomaviridae
RNA viruses, e.g., Caliciviridae, Picornaviridae, Reoviridae, Hepeviridae
Other
State 4 shapes of viruses
- Helical: spiral shape
- Icosahedral: is a geometric shape with 20 sides
- Spherical
- Polyhedral: Is a three-dimensional shape with flat polygonal faces, straight edges and sharp corners or vertices.
- Complex: complex architecture
Which of the following is the most common capsid shape of the virus?
a) Cone
b) Icosahedron
c) Cube
d) Rod
b
Arrange the following.
Family, Species, Genus, Order, Sub family
- Order
- Family
3.Subfamily - Genus
- Species
Describe the nomenclature of HHV 1according to the following:
1. Order
2. Family
3.ubfamily
4. Genus
5. Species
Order: Caudovirales
Family: Herpesviridae
Subfamily: Alphaherpesvirinae
Genus: Simplexvirus
Species: Human herpesvirus 1
Name the 7 classes of Baltimore classification Viruses.
Class I: Double-stranded DNA (dsDNA) viruses.
Class II: Single-stranded DNA (ssDNA) viruses.
Class III: Double-stranded RNA (dsRNA) viruses.
Class IV: Single-stranded RNA (ssRNA) viruses.
Class V: Single-stranded RNA (ssRNA) viruses.
Class VI: Positive sense ssRNA reverse transcriptase viruses.
Class VII: Double-stranded DNA (dsDNA) reverse
Describe the virus replication process.
- Recognition of the target cell
- Attachment
- Penetration:
*The mechanism of internalization depends on the virion structure and cell type.
*Nonenveloped viruses enter the cell by receptor-mediated endocytosis
*Enveloped viruses fuse their membranes with cellular membranes to deliver the nucleocapsid or genome directly into the cytoplasm - Uncoating:
*Uncoating process maybe initiated by
attachment to the receptor
*Promoted by the acidic environment
*Proteases found in an endosome or lysosome
This process leads to release of the genome into the host cell.
- Macromolecular synthesis
*Early messenger RNA (mRNA) and nonstructural protein synthesis: genes for enzymes and nucleic acid–binding proteins
6. Assembly of virus
7. Budding of enveloped viruses
8. Release of virus
Target cell is Receptor specific.
Susceptible target cell defines the tissue tropism e.g., neurotropic, lymphotropic.
What is tropism?
What receptor is targeted by the Epstein Barr virus?
What receptor is targeted by Human immunodeficiency virus?
Receptor specific
*A tropism is the innate ability of an organism to turn or move in response to a stimulus.
*Epstein-Barr virus (EBV): has a very limited host range and tropism because it binds to the C3d receptor (CR2) expressed on human B cells
*Human immunodeficiency virus: Helper T cell CD4 molecule and chemokine coreceptor
State the receptors used by the following viruses for attachment.
- CMV
2.EBV
3.HIV
Parvovirus B19
Rabies virus
Rhinovirus
SARS-C-o-V-2
Viruses Receptors
CMV Integrins (e.g., heparan sulfate)
EBV CD21
HIV CD4, CXCR4, CCR5
Parvovirus B19 P antigen on erythrocytes
Rabies virus Nicotinic acetylcholine receptor
Rhinovirus ICAM-1
SARS-CoV-2 ACE2
What are the Baltimore classification groups for DNA viruses?
Occurs in the nucleus, using host cell polymerases for viral mRNA synthesis.
EXCEPT which viruses?
Incorporation of viral DNA to host DNA
Name the enzyme responsible for transcription of DNA to mRNA.
What translates mRNA into proteins?
What does DNA replication require?
Replication is initiated at a unique DNA sequence of the genome called the __________.
Viral DNA synthesis is semiconservative, and viral and cellular DNA polymerases require a ______ to initiate synthesis of the DNA chain.
Baltimore classification group I and II: dsDNA, ssDNA
Occurs in the nucleus, using host cell polymerases for viral mRNA synthesis (EXCEPT poxviruses)
Incorporation of viral DNA to host DNA.
Transcription of DNA to mRNA by host DNA-dependent RNA polymerase II
mRNA is translated by host cell ribosomes into proteins.
DNA replication and requires a DNA-dependent DNA polymerase
Replication is initiated at a unique DNA sequence of the genome called the origin (ori).
Viral DNA synthesis is semiconservative, and viral and cellular DNA polymerases require a primer to initiate synthesis of the DNA chain.
What is the Baltimore class for RNA virus?
Where does replication occur?
The RNA virus genome must code for RNA-dependent RNA polymerases (replicases and transcriptase’s)
RNA polymerases work at a fast pace but are also error prone leading to frequent mutations.
+ssRNA is similar to mRNA, translation occurs directly from this template.
-ssRNA is transcribed to mRNA
+ssRNA: RNA-dependent RNA polymerase produces a ___________, and this template is used to generate more mRNA and to replicate the genome.
-ssRNA: _____________must be produced by the viral polymerase to act as a template to generate more copies of the genome.
Baltimore class IV, V: +ssRNA, -ssRNA
Replication occurs in the cytoplasm.
The RNA virus genome must code for RNA-dependent RNA polymerases (replicases and transcriptase’s)
RNA polymerases work at a fast pace but are also error prone leading to frequent mutations.
+ssRNA is similar to mRNA, translation occurs directly from this template.
-ssRNA is transcribed to mRNA
+ssRNA: RNA-dependent RNA polymerase produces a negative strand, and this template is used to generate more mRNA and to replicate the genome.
-ssRNA: positive-strand RNA must be produced by the viral polymerase to act as a template to generate more copies of the genome.
What Baltimore classis dsRNA?
Describe the life cycle of dsRNA virus.
Baltimore class III: Reovirus
*The reovirus RNA polymerase is part of the inner capsid core.
*Individual mRNA units are transcribed from each of the 10 or more segments of the genome while they are still in the core.
*The mRNAs are released into the cytoplasm:
where they direct protein synthesis
*Are sequestered into new cores which produce more viral RNA
What Baltimore classification are retroviruses?
Describe the lifecycle of retroviruses.
Baltimore classification: VI
No means for replication of the RNA in the cytoplasm.
Instead, they have two transfer RNA (tRNA) molecules, and an RNA-dependent DNA polymerase (reverse transcriptase)
The tRNA is used as a primer for synthesis of a circular complementary DNA (cDNA) copy of the genome.
The cDNA is synthesized in the cytoplasm travels to the nucleus and is then integrated into the host nucleus and undergo transcription and translation.
Viral RNA copies are made by differential splicing of this RNA.
What is the class of SARS CoV 2 according to Baltimore classification?
Class IV: +ss RNA virus
Assembly of the virus is initiated by sufficient structural protein synthesis.
Assembly of the DNA nucleocapsid for viruses other than poxviruses occurs in the _________and requires transport of the virion proteins into the nucleus.
Where does RNA virus and poxvirus assembly occur?
Capsid viruses may be assembled empty structures (procapsids) to be filled with the genome (e.g., picornaviruses).
They may be assembled around the genome.
This process is initiated by sufficient structural protein synthesis.
Assembly of the DNA nucleocapsid for viruses other than poxviruses occurs in the nucleus and requires transport of the virion proteins into the nucleus.
RNA virus and poxvirus assembly occurs in the cytoplasm.
Capsid viruses may be assembled empty structures (procapsids) to be filled with the genome (e.g., picornaviruses).
They may be assembled around the genome.
State the 2 mechanisms of release of the virus form the host cell.
Enveloped viruses: released via budding.
Nonenveloped viruses: released via host cell lysis.
Describe the 4 factors influencing pathogenesis of virus.
- Tissue Tropism: Viral affinity for specific body tissues. This determines the disease the virus causes.
- Direct cell damage and death from viral replication and release.
- Indirect cell damage can result from host immune response.
- The virus ability to spread to other sites.
Which of the following phase determines the specificity of the virus?
a) Uncoating
b) Release
c) Attachment
d) Penetration
C
A virus attaches to a specific receptor site on the host cell membrane through attachment proteins in the capsid or via glycoproteins embedded in the viral envelope. The specificity of this interaction determines the host—and the cells within the host—that can be infected by a particular virus.
Describe the following laboratory diagnosis of viruses.
- Antibody assays:
- Direct demonstration of virus:
- Culture
- Molecular techniques
- Antibody assays:
*Enzyme-Linked Immune Sorbent Assay (ELISA) technique
*Lateral flow assays: AB-AG
Basically, it is a simple to use diagnostic device used to confirm the presence or absence of a target analyte, such as pathogens or biomarkers in humans or animals, or contaminants in water supplies, foodstuffs, or animal feeds.
- Direct demonstration of virus:
*Electron microscopy
Not ideal for routine laboratory testing - Culture
*Viral culture is a laboratory technique in which samples of a virus are placed to different cell lines which the virus being tested for its ability to infect.
If the cells show changes, known as cytopathic effects, then the culture is positive.
- Molecular techniques
Nucleic acid amplification techniques such as Polymerase Chain Reaction (PCR)
Anti- virals inhibit a certain stage of the virus replication cycle.
State the 4 main stages inhibited.
*Viral attachment and/or entry.
*Replication of the viral genome.
*Synthesis of specific viral protein(s).
*Assembly or release of new infectious virions
What does Acyclovir interfere with to inhibit DNA replication?
Acyclovir interferes with DNA polymerase to inhibit DNA replication.
Innate immunity involves Physical, biological, and chemical defenses.
Describe the innate immune response mechanisms of the host against viral infections.
*Keratinocytes are impermeable to viruses
*Mucociliary clearance of respiratory tract (transports viruses towards the throat)
*Production of acid and viral replication inhibitors by commensal organisms
*RNA interference (only against RNA viruses)
*Natural killer cells
*Complement system
*Interferon: IFN-alpha and IFN-beta
Produced by infected cells
Triggers damage and death of infected cells
Inhibit viral replication and viral protein synthesis
*RNA endonucleases: cleave phosphodiester bonds between nucleotides.
*Phosphorylation of protein kinases → inactivation of eIF2 → inhibition of protein synthesis
Describe the adaptive immune response against viral infections.
*Immunoglobulins
*T cells
Describe 3 mechanisms by which viruses cause infection in the host.
- Cytolysis: viral replication results in the destruction of host cell → release of virus
Seen with nonenveloped viruses.
Some enveloped viruses. - Immunopathological host reactions: cellular immune response to the invading virus is triggered by cytotoxic T cells → destruction of infected cells (e.g., HBV); the virus, however, is not cytopathogenic.
3.Transfer of genetic material: bacteriophages may transfer virulence factors (e.g., exotoxins)
Describe the course of viral infection.
- Abortive (no viral replication or cell damage)
- Acute
- Chronic
- Persistent
Latent viral infection (virus is inactive; no replication): virus remains dormant in infected cells.
Productive viral infection (viral replication occurs, dormant infection with few or no signs of infection)
Transforming viral infection (virus may or may not replicate): triggers malignant transformation (e.g., EBV, HPV)
The genome of the virus consists either of
DNA
RNA
State the 4 characteristics of DNA.
State 4 characteristics of RNA.
The genome of the virus consists either of
DNA
RNA
The DNA can be
Single
Double stranded
Linear
Circular
The RNA can be either
Positive sense (+) (like messenger RNA[mRNA])
Negative sense (−) (analogous to a photographic negative)
Double stranded (+/−)
The RNA genome may also be segmented into pieces, with each piece encoding one or more genes.
Outline routes of viral transmission.
Mechanisms of Viral Transmission
Aerosols
Food, water
Fomites (tissues, clothes)
Direct contact with secretions
(Saliva, semen)
Sexual contact, birth
Blood transfusion or organ
transplant
Zoonosis (animals, insects
[arboviruses])
Genetic (vertical)
(retroviruses
