Basic Virology Flashcards
1
Q
what are viruses and where do they replicate?
A
- Infectious, acellular (non-living) agents
- live and reproduce inside host cells (obligate intracellular parasites)
2
Q
what is the structure of a viral genome?
A
DNA or RNA genome (never both) surrounded by a protein capsid; some also have a lipid envelope with glycoproteins.
3
Q
can viruses reproduce on their own?
A
No — they lack necessary genes and must use the host cell’s machinery
4
Q
what is the relative size comparison of viruses, bacteria and eukaryotic cells?
A
viruses are small relative to them and their organelles
5
Q
what are the components of a viral partical?
A
- Genome
- Capsid
- Spikes
- Envelope
- Matrix Proteins
- Tegument
- Non-Structural Proteins
6
Q
what are the types of genome STRUCTURES?
A
Circular: Forms a loop (commonly seen in some DNA viruses).
Linear: A straight strand (either DNA or RNA).
Segmented: The genome is split into multiple pieces
7
Q
what are the viral genome types for DNA and RNA?
A
DNA Viruses:
Double-stranded DNA (dsDNA)
Single-stranded DNA (ssDNA)
RNA Viruses:
Double-stranded RNA (dsRNA)
Single-stranded RNA (ssRNA)
8
Q
what are the different types of polarity for ssRNA viruses?
A
+ sense: same sequence as mRNA
- sense: complementary to mRNA
ambisense: contains both + and - sense regions
9
Q
what is encoded in a viral genome?
A
gene products and regulatory signals required for:
- replication
- assembly and packaging
- regulation/kinetics of replication cycle
- modulation of host defense
- spread to other cells and host
10
Q
what is a capsid?
A
protein shell that protects and surrounds the genome and introduces the viral genome into the host cell
11
Q
what are the three viral shapes of a capsid?
A
- helical
- icosahedral
- complex
12
Q
what is a capsomere?
A
the individual protein subunit that join together in a specific pattern to form the complete capsid
13
Q
what is a nucleocapsid?
A
the combination of the viral genome (nucleic acid) and the capsid that surrounds it
14
Q
what are peplomers (spikes)?
A
Glycoprotein structures that project from the viral envelope or capsid and bind specific receptors on host cells to help the virus attach and enter host cells
15
Q
what are two examples of viruses with peplomers?
A
Orthomyxoviruses (influenza virus)
Adenoviruses (non-enveloped)
16
Q
what is a viral envelope (enveloped viruses only)?
A
A lipid bilayer derived from the host cell membrane during replication, surrounds the capsid or nucleocapsid and is embedded with spikes (viral glycoproteins)
17
Q
what are matrix proteins?
A
link the envelope to the nucleocapsid and help maintain structural integrity during viral assembly
18
Q
what is the tegument?
A
A space between the envelope and nucleocapsid that contains regulatory proteins, such as transcription/translation factors
19
Q
what are non-structural proteins?
A
polymerases, enzymes, and regulatory proteins packaged within the virion that help the virus replicate inside the host
20
Q
what are the main functions of non-structural proteins?
A
- establishment of infection
- escape host defense mechanisms
- transcription of viral genome
- replication
21
Q
What is viral classification and taxonomy based on?
A
Viruses are grouped by:
- Genetic material (DNA or RNA)
- Chemical properties
- Shape and structure (morphology)
- How they replicate (mechanism of multiplication)
22
Q
what is the Baltimore Classification System?
A
a method used to categorize viruses based on how they generate messenger RNA (mRNA) to produce proteins in a host cell
23
Q
what are the groups of the Baltimore Classification System?
A
Group I: Double-stranded DNA (dsDNA)
Group II: Single-stranded DNA (ssDNA)
Group III: Double-stranded RNA (dsRNA)
Group IV: Positive-sense single-stranded RNA (+ssRNA)
Group V: Negative-sense single-stranded RNA (-ssRNA)
Group VI: Positive-sense ssRNA with reverse transcription
Group VII: Double-stranded DNA with reverse transcription
24
Q
what is the common strategy for viral propagation?
A
- viruses package their genetic material in a protective shell (a viral particle) so they can move from one host to another
- the virus’s genome has all the instructions needed to infect a suitable (permissive) cell and make more viruses
- to survive long-term, viruses must keep spreading and establish themselves in the population.
25
what are the steps to the viral life cycle?
attachment/entry
uncoating
expression
replication
assembly
release
26
what happens during the attachment/entry step of the Viral Life Cycle?
Virus binds to specific receptors on the surface of a host cell and enters the cell
* some viruses need co-receptors for full entry
27
what are the uncoating strategies of viruses?
1. At Plasma Membrane: Some enveloped viruses fuse their envelope with the host cell membrane right at the surface
2. Within Endosomes: Many viruses enter cells by endocytosis and the acidic environment triggers uncoating
3. At The Nuclear Pore: uncoating occurs at the nuclear pore so the genome can enter the nucleus
28
give an example of a virus for each uncoating strategy
1. Plasma Membrane: Respiratory syncytial virus
2. Endosome: influenza
3. Nuclear Pore: adenovirus, herpes
29
what are the three main strategies that viruses use for expression (mRNA and protein production)?
1. polyprotein
2. subgenomic mRNAs
3. mRNA splicing
30
what occurs during the polyprotein strategy?
Many positive-sense RNA viruses make one long polyprotein from their genome, which is then cut by a viral protease into separate functional proteins to form mature polypeptides
31
what occurs during the subgenomic mRNA strategy?
the full-length viral genome is copied into a negative-sense intermediate, and then shorter “subgenomic” plus-sense mRNAs are transcribed from specific segments of that negative template. These subgenomic RNAs each encode different parts of the viral proteome, allowing the virus to generate multiple distinct proteins from one genomic RNA at different points in time
32
what occurs during mRNA splicing?
virus produces one primary mRNA, but then splices it differently to create multiple protein variants
33
what are the replication strategies for DNA viruses?
ssDNA viruses → dsDNA using DNA-dependent DNA polymerase (DdDp) then → mRNA using DNA-dependent RNA polymerase (DdRp)
dsDNA viruses → mRNA directly using host or viral DNA-dependent RNA polymerase (DdRp)
34
what are the replication strategies for RNA Viruses?
+ ssRNA viruses → use RNA-dependent RNA polymerase (RdRp) to make a –ssRNA template → then make more +ssRNA or used +ssRNA directly to make mRNA
– ssRNA viruses → use RNA-dependent RNA polymerase (RdRp) to make +ssRNA (mRNA) for translation → then make mRNA
dsRNA viruses→ use RNA-dependent RNA polymerase (RdRp) to transcribe +ssRNA (mRNA) from one strand → use that for translation and replication
35
what are the replication stratigies for Reverse-Transcribing Viruses (Retroviruses)?
+ssRNA → use reverse transcriptase (RT) to convert RNA to RNA:DNA → to dsDNA, which integrates into the host genome → Host machinery makes mRNA
dsDNA → transcribed into RNA:DNA, then reverse-transcribed into mRNA
36
give an example of a ssDNA virus and dsDNA virus
Parvovirus
Herpesvirus
37
give an example of +ssRNA viruses, –ssRNA viruses and dsRNA viruses
Poliovirus
Influenza, Measles, Rabies
Rotavirus
38
where do a majority of DNA viruses replicate and what is the exception?
- most replicate in the nucleus through host cell DNA-dependent RNA polymerase to synthesize the viral mRNA
**Poxviruses replicate in the cytoplasm and therefore they carry their own polymerase within the virus particles
39
where do a majority of RNA viruses replicate and what is the exception?
most undergo their entire cycle in the cytoplasm
* retrovirus (HIV) and orthomyxoviruses (influenza), have a replicative step in the nucleus
40
All RNA viruses encode what polymerase? what is the exception?
RNA-dependent RNA polymerase
* exception is Retroviruses that encode an RNA-
dependent DNA polymerase
41
why are RNA viruses so diverse?
1. High mutation rates (misincorporation of nucleotides)
2. Segment reassortment and RNA recombination
3. RNA Editing
42
what causes the high mutation rates of RNA virus genomes?
RNA-dependent RNA polymerases (RdRp), which copy viral RNA, do not have proofreading abilities and as a result, mutations occur frequently (1 mistake per 1,000 to 100,000 bases copied)
43
how does Segment Reassortment & RNA Recombination occur in viral genomes?
Reassortment happens in segmented viruses when two related viruses infect the same cell, they can swap entire RNA segments, creating new viral combinations
Recombination involves mixing of sequences between two RNA molecules within a cell, resulting in a new, blended RNA strand
44
what occurs during RNA editing in the viral genome?
Viruses can intentionally change their RNA after it's made by:
- inserting non-templated nucleotides
- altering existing bases
45
what is anti-genetic drift?
Small, gradual changes (mutations) in the viral genome anti-genetic binding site due to errors in replication
46
what is anti-genetic shift?
sudden, major change in the viral genome caused by reassortment of gene segments when two different viruses infect the same cell
47
how are enveloped viruses released?
budding, MVB (multivesicular body) pathway, autophagic pathway and lysosomal pathway
48
how are non-enveloped viruses released
lytic egress
49
HIV Life Cycle
Attachment: HIV binds to CD4 and a coreceptor (CCR5 or CXCR4) on the host immune cell and fuses with the membrane.
Uncoating: HIV releases its RNA and enzymes into the host cell.
Reverse Transcription: viral RNA is converted into DNA by reverse transcriptase.
Integration: viral DNA enters the nucleus and is integrated into the host genome by the enzyme integrase.
Transcription & Translation (Expression): host cell makes viral RNA and proteins from the integrated viral DNA.
Assembly: New viral RNA and proteins are brought together at the cell surface to form an immature HIV particle.
Release & Maturation: new virus buds off from the host cell and matures with the help of HIV protease, becoming fully infectious
50
what are the early immune responses to a viral infection?
fever
inflammation
interferons
cytokines
51
what are type-I interferons?
proteins released by virus-infected cells to warn nearby uninfected cells and trigger those cells to enter an "antiviral state" to fight off infection *major antiviral response
52
Explain the Cell-Mediated Immunity (Early Response)
First line of defense against virus-infected cells that acts before antibodies appear and involves:
- Natural Killer (NK) cells
- Cytotoxic T cells (CD8⁺)
- Macrophages and other innate immune cells
53
Explain the Antibody-Mediated Immunity (Later Response)
Kicks in later during infection and antibodies help by:
- activating complement → leads to destruction of infected cells
- tagging infected cells for destruction by immune cells
54
how do viruses evade the nucleic sensing pathways?
Our immune system can detect viral RNA or DNA inside cells using sensors like TLRs, RLRs, cGAS, and STING but viruses make proteins that block or break these signals, so the immune system can’t detect or respond to the virus properly
55
how do viruses evade the Type I Interferon Signaling pathway?
blocking the Interferon-stimulating genes ability to produce proteins that help fight infections
56
what is molecular mimicry?
when a pathogen (like a virus or bacteria) makes proteins that look similar to the body’s own proteins
57
what are the outcomes when a virus infects a cell?
abortive infection
productive infection
latency
transformation
58
what is abortive infection?
The virus enters the cell, but can’t complete its life cycle, no new viruses are made, the cell usually survives, but the infection fails
59
what are defective viruses?
viruses that are missing part of their genome or lack essential genes needed to complete their life cycle and need helper viruses
60
what is malignant transformation?
process where normal or benign neoplastic tissue becomes a cancer
61
what are tumor suppressor proteins?
protective proteins in your cells that prevent uncontrolled growth
62
what are viral oncogenes?
gene from a virus that can disrupt normal cell regulation and promote cancer that may turn on growth signals, block cell death, or interfere with tumor suppressor proteins
63
what is the purpose of membrane filters in virus isolation?
used to separate viruses from larger cells (like bacteria or animal cells) in a solution by using filters with tiny pores that allow only particles smaller than the pore size to pass through
64
what are the three systems in which viruses are grown?
animals
embryonated eggs
cell and organ cultures
65
what are the steps for the cultivation of viruses in cell cultures?
- Inoculation: cells are placed into a flask or petri dish that contains a nutrient-rich growth medium.
- Cell Growth: cells divide and form a monolayer, covering the surface of the flask or dish
- Virus Introduction: virus is added to the culture, and it infects the cells
66
what are the common methods used to detect virsues?
- Hemagglutination assay
- Cell culture
○ cytopathic effect (CPE)
○ Vacuolization, inclusion bodies, Syncytia
○ immunofluorescence
- ELISA
- Nucleic Acid Amplification Test
67
What is a Hemagglutination Assay?
a test used to detect viruses that can bind to red blood cells (RBCs) through hemagglutinin proteins, causing clumping (agglutination) of the RBCs.
68
What does a red dot in the center of the well indicate in a hemagglutination assay?
No agglutination; RBCs sink to the bottom and form a central dot (negative result).
69
What does a diffuse red color across the well mean in a hemagglutination assay?
Hemagglutination occurred; RBCs are evenly dispersed due to virus-mediated clumping (positive result).
70
What is hemagglutination inhibition in a hemagglutination assay?
When virus-specific antibodies bind to the virus, blocking its ability to agglutinate RBCs, resulting in a red dot (inhibition = negative result).
71
What is CPE (Cytopathogenic Effect)?
visible damage in host cells occurs due to the accumulation of viral products inside infected cells and replication, is commonly observed in cell culture and can also be used diagnostically in biopsied or autopsied tissues
72
what is Vacuole Formation (Vacuolization) ?
a type of viral induced change caused by infected cell producing large, clear spaces (vacuoles) in the cytoplasm
73
what are Inclusion Bodies?
a type of viral induced change that causes areas in the nucleus or cytoplasm to stain differently because these are sites where viral proteins or nucleic acids are being made or assembled
74
what is Syncytia?
a type of viral induced change that occurs when the plasma membranes of multiple infected cells fuse to form one large, multinucleated cell
75
What is Immunofluorescence?
lab technique used to detect specific viral proteins (antigens) in cells or tissues by using fluorescently labeled antibodies that bind to the antigens
76
What is Enzyme Immunoassay?
test used to detect the presence of a virus or viral antigen (such as a protein) in a patient sample using antibodies and enzymes
77
What are the steps of Enzyme Immunoassay?
1. apply patient sample to membrane filter
2. add antibody with enzyme conjugate where the antibody will bind to the antigen if present
3. wash to remove unattached conjugate
4. add substrate
78
what are Nucleic Acid Amplification Tests (NAATs)?
lab techniques used to detect viruses by identifying their unique genetic material (DNA or RNA) in a sample—like blood, tissue, or fluid
79
what is PCR (Polymerase Chain Reaction)?
detects viral DNA in the patient’s sample by amplifying (makes millions of copies of) a specific DNA region to make it easy to detect
80
what is RT-PCR (Reverse Transcriptase PCR)?
detects viral RNA (e.g., SARS-CoV-2, flu) by using reverse transcriptase (RT) to turn RNA → DNA (called cDNA) where regular PCR then amplifies the cDNA.
81
what are the current licensed antiviral vaccines?
1. Live attenuated viral vaccines
2. Inactivated whole viral vaccines Inactivated by heat, UV, or chemical
3. Subunit vaccines
4. Recombinant viral proteins
5. Virus-like particles (VLPs)
82
what are the next-generation strategies for making vaccines that are not currently licensed?
1. Viral Vector (attenuated virus or bacterium is used to introduce microbial DNA to host cells)
2. DNA Vaccines
3. RNA Vaccines
4. Antigen-Presenting Cells (APCs)
83
What is an mRNA Vaccine?
use a piece of genetic code (mRNA) to teach your cells how to make a viral protein—usually the spike protein of SARS-CoV-2. Your immune system then learns to recognize and fight the real virus
84
what are Vector-based Vaccines?
harmless virus is used to deliver genetic instructions (DNA) from the target virus
85
what are the targets for antiviral drugs?
- virus polymerase
- reverse transcriptase
- HIV proteases
- virus replication
- RNA mutagen
- Viral neuraminidase
- hemagglutinin/matrix protein
86
what is HPV?
small, non-enveloped DNA virus with a capsid made of 72 building blocks and includes two key proteins L1 and L2 that infects skin and mucosal areas, like the genitals and throat.
87
what does the HPV Vaccine target?
targets the L1 protein of the capsid to prevent infection
88
what is Anti-retroviral Therapy ART (HIV)?
1. Fusion Inhibitors: Block HIV from entering the cell
2. Reverse Transcriptase Inhibitors: Stop HIV from copying its RNA into DNA
3. Integrase Inhibitors: Prevent HIV DNA from entering the host cell’s DNA
4. Protease Inhibitors: Block the virus from maturing properly
