Viruses and Virology (15-22) Flashcards
What is a virus?
The smallest infectious agents
consisting of:
→ a genetic element (nucleus acid, DNA or RNA)
→ surrounded by a protein coat (caspid)
→ cannot replicated independently
→ don’t divide by binary fission
What does viral replication consist of?
→ assembly of pre-formed components into many new viral particles
→ viral components produced (eclipse phase)
→ components assemble to final viral particle
Why do we study viruses?
Technology → used in vaccination, used to deliver specific genes, CRISPR
Drugs → understanding life cycle helps development of antiviral drugs (how to target viruses without effecting our cells)
Protection → helps protect general population
Agriculturel importance
What reasons do you suggest for the delay in discovering viruses?
Very small → too small to see under a light microscope
→ developments made when electron microscope discovered
What are the main differences between bacteria and viruses?
Viruses
→ only invade living cells
→ replicate by inserting genome into host
Bacteria
→ single celled organism
→ can invade living and non-living things (soil, water)
→ divide by binary fission
What are bacteriophages?
Viruses that infect bacteria cells
→ structure: capsized head, neck, tail, tail fibres
How do viruses recognise host cells?
Specific interactions between viral attachment proteins and host cells
What is a virion?
A complete viral particle
containing:
nucleocaspid -
→ caspid (protein coating)
→ DNA or RNA
+ viral envelope
What is encoded for in a viral genome?
Structural proteins → cashed proteions, viral attachment proteins
Non-structural proteins → (viral replication) DNA/RNA polymerase, pathogenesis, transformation, modulation of host defences
What is not coded for in a viral genome?
→ the complete protein synthesis machinery
→ proteins involved in cell wall production or membrane biosynthesis
→ no centromeres or telomeres
What is the caspid?
The protein shell that surrounds a viral genome
→ composed of a number of protein molecules arranged in a precise repetitive pattern
→ made up of capsomeres - subunit of the capsid (smallest morphological unit visible on electron microscope)
→ protects from environmental conditions
How is metastability of viral particles achieved?
Stable structure:
→ symmetrical arrangement of many identical viral proteins subunits - provides maximal contact
→ each subunit has identical bonding contacts with its neighbours - repeated interaction provides symmetric arrangement
Unstable structure:
→ contact not covalent
→ can be dissociated or taken apart once the virus attaches to the host cell to release the genome
What are the 3 types of cashed arrangement?
Helical → e.g. TMV
Icosahedral → e.g. poliovirus
Complex → e.g. bacteriophage
Why are icosahedron caspids stable?
Permins the greatest number of cashmeres to be packed in a regular stable structure
→ easiest way of making a stable structure form the smallest number proteins (60 identical subunits)
→ no need for covalent bonds
What is a viral envelope?
A bilayer phospholipid membrane derived mainly from the host cell
→ viral genome does not encode
→ acquired by budding of the nucleocapsid through a cell membrane
→ enveloped viruses: influenza, coronaviruses
Are enveloped or non-enveloped viruses considered more stable?
Non-enveloped are more stable, only required their cashed to infect host cells
→ lack a lipid bilayer so are more resistant to stress
What are the disadvantages of classifying viruses based on diseases?
Not all viruses cause disease - many missed or ignored
→ a single viruses can cause more than one disease
→ viruses can infect more than one host
What is the main criteria for classifying viruses based on morphology?
Nucleus acid → DNA or RNA, ss or ds (polarity), linear, circular, single
Caspid symmetry → icosahedral, helical, complex
Presence of lipid envelope
What are the characteristics for the International Committee on Taxonomy of Viruses (ICTV)?
Host range → eukaryote, prokaryote, plant, animal
Morphological features
Nature of nucleic acid
Additional features → length of tail, specific genes
Phylogenetic trees
Wha are the seven major categories of virus proposed by Baltimore classification?
I → dsDNA (+&-)
II → ssDNA +ve
III → dsRNA (+&-)
IV → ssRNA +ve
V → ssRNA -ve
VI → ssDNA -ve
VII → incomplete dsDNA
What are viroids?
Single stranded circular RNA molecule
→ infectious pathogens to plants
→ unlike viruses, have no protein competent - no caspid
→ smallest self-replicating pathogen
→ appear as rod-shaped or dumb-bell-shaped
e.g. potato spindle tuber viroid (PSTVd) pathogen of potatoes
What must viruses do in order to replicate?
- get into the cell
- make more virus (produce viral proteins)
- get out of the cell (to infect others)
What are the steps of viral replication?
- attachment to target cell
- penetration into cell
- uncoating (removal of caspid)
- biosynthesis
- assembly (complete viral particle)
- release
How can viruses recognise cellular receptors on the host cell?
Through their VAPs - viral attachment proteins
→ interaction between VAPs and host cellular receptors is very specific and determines the host cell and species range
What is viral tropism?
The specificity of a virus to a specific host
How do enveloped viruses enter a host cell?
Fusion with plasma membrane (e.g. Herpes, HIV)
Via endosomes at low pH (e.g. influenza) - destabilises membrane
How do non-enveloped viruses enter a host cell?
Endocytosis
Entry directly across plasma membrane (e.g/ poliovirus)
What is uncoating?
Removal of the protein caspid
→ digestion of caspid by cellar enzymes releases viral genome
Where is viral nucleic acid delivered to?
DNA → into the nucleus (except poxvirus)
RNA → into the cytoplasm (except HIV, influenza)
What happens during biosynthesis of viral life cycle?
Protein and NA synthesis → mRNA is translated into proteins, nucleic acid is replicated
→ NA + proteins packaged into viral caspid
How do dsDNA viruses produce their mRNA?
Transcription with host RNA polymerase
What is required for replication of RNA viruses?
RNA-dependant RNA polymerase (RdRp) replicase
→ cells have to RdRp
→ RNA virus genome has to encode it
What is the difference between in vivo and in vitro culture systems?
In vivo → grows virus in host
e.g. animal, plant, bacteria, chicken eggs
In vitro → grows virus in isolated tissues/cells obtained from host - cell culture
How can viruses be cultivated in chicken eggs?
Different compartments can culture different viruses
Chorioallontoic membrane inoculation → herpes, poxvirus
Amniotic inoculation → influenza, mumps
Yolk sac inoculation → herpes
Allantoic inoculation → influenza, mumps, again adenovirus
How are viruses cultivated in cell cultures?
- individual cells isolated from tissue
- suspended in liquid culture medium in a petri dish
- cells stop dividing due to contact inhibition
- cells transferred to new medium - secondary cell culture
How are continuous cell cultures obtained?
Usually originate from naturally occurring tumours
→ heteroploid cells that will divide for ever
→ can be passaged or sub-cultured many time
→ have lost their contact inhibition
What is the HeLa cell line?
HeLa cells were the first continuous tissue-culture cell line
→ from Henrietta Lacks (31) diagnosed with cervical carcinoma
→ used to establish tissue culture important for research
→ discoveries related to polio, cancer and AIDS
What are cyto pathic effects of viral infections?
Distinct observable cell abnormalities/changes in the cells due to viral infections
e.g. shrinking → poliovirus
What is hemadsorption?
Cells infected with certain viruses acquire the ability to bind to and absorb red blood cells
→ some viruses produce no cytopathic effects so hemadsorption can be used to detect e.g. influenza, measles, mumps
What is the purpose of virus titration?
Research for studying viruses and their effects
Therapeutic → effective at reducing viral load
How can the number of viral particles be measured?
Electron micropscy
→ cons: time consuming, expensive, requires skilled personnel
How can the amount of viral proteins be measures?
Enzyme-linked immunosorbent assay (ELIZA)
Immunofluorescence (IMF)
How can the number of viral nucleic acids copies be measures?
PCR
→ determine how many viral nucleic acid copies in a sample
How can cytopathic viruses be quantified?
Plaque assay
→ virus added to monolayer of cultured cells
→ agar added onto to prevent dilution
1 plaque = 1 plaque forming unit
→ serial dilution of sample
What is pathogenicity assay?
Used to determine the infectious titre
What is a haemagglutination assay?
Some viruses can bind to red blood cells (haemagglutinin)
→ they cross link the erythrocytes
→ serial dilution of sample + fixed number of red blood cells, wait 45 mins
→ titre - the highest dilution producing visible haemagglutination
simple, quick, economical
What are the phases of bacterial cell growth curve?
- lag phase → no increase
- log phase → exponential
- stationary phase → plateau
- death phase → decrease
What are the phases of viral growth curve?
- inoculation → decline as virus binds to cells
- eclipse → virions penetrate cells
- burst → host cells release many viral particles
- burst size → (stationary) number of visions released per bacterium
What is a susceptible cell?
A cell that expressed the specific receptors that are recognised by a specific virus through its VAPs
→ virus can bind + enter
What is a permissive cell?
A cell that contains the proteins and molecules within it necessary for viral replication to occur
→ cells must be susceptible and permissive for viral infection
What are the common portals on entry for viruses?
Conjunctiva
GI tract
Respiratory tract
Skin
Congenital infection
Genital tract
How do viruses enter through the respiratory tract?
Middle-sized droplets are inhaled and transmit infection rapidly via Respiratory tract
→ viruses contained in larger droplets are deposited in the upper Respiratory tract
→ smaller aerosolised particles or liquids are able to travel into the lower Respiratory tract
What conditions of the GI tract prevents infection?
Stomach acidity
Low pH
Digestive enzymes
Bile in intestines
→ inactivate most viruses
What are the local barrier of the genital tract?
e.g. mucus and low pH of the vagina
How can viruses enter through the skin?
Trauma or inoculation
Medical procedures → sharing needles
Insects or animals bites (rabies, yellow fever)
What are the 3 types of vertical viral transmission?
In utero → during pregnancy (e.g. rubella, CMV)
Perinatal → during birth (e.g. neonatal HSV)
Postnatal → after birth (e.g. HIV)
What is viermia?
The presence of virus in the blood e.g. HIV, hepatitis
→ transmitted through blood
What is uraemia?
The presence of virus within the urine e.g. Hantavirus
→ transmitted to people through aerosolise or virions
What are localised infections?
Replicate at the initial site of infection
What is pathogenesis?
The ability/capacity of the virus to cause disease
→ measured quantitatively by virulence
How can virulence be quantified?
Virus titre
Mean time to death
Mean time to appearance of disease
Measurement of fever, weight loss
Measurement of pathological lesions (poliovirus)
Reduction if CD4 T cell (HIV)
Case:fatality ratio / hospitalisation rate
What are the mechanisms of viral injury and disease?
Direct cytotoxicity of the virus
Virus-induced immunopathogensis
Virus-induced immune suppression
Virus-induced transformation
What is direct virus killing?
Damage to he host
→ may be a consequence of virus replication
e.g. poliovirus kills neurones
Ebola virus damages vascular endothelial cells causing haemorrhage
What is virus-induced immunopathogenesis?
Tissue injury may reflect host defence mechanisms that include apoptosis or immune responses that target virus-infected cells
What is virus-induced immune suppression?
Some viruses can specifically target and infect cells on the immune system causing immunodeficiency
→ HIV most prominent infection, causes AIDS
What can virus-induced transformation cause?
Cancer → indirect effects from viral infection like immune suppression + HIV infection
Chronic inflammation → associated with HBV or HCV infection
Viral infection directly promotes tumour development
What is HIV?
Human Immunodeficiency Virus
→ retrovirus
→ enveloped
→ two surface glycoproteins: gp120, gp41
How does HIV replicate?
Recognised by interaction between VAP gp120 and host CD4 + entry
→ RNA genome released from caspid
→ synthesis of proteins + assembly
What are the 3 stages of the pathogenesis of HIV?
- acute phase
- chronic phase
- AIDS phase
What is the acute stage of HIV?
Characterised by infection of activated CD4+ T cells in mucosal lymphoid tissues and death of many infected cells
What is the chronic stage of HIV?
Virus spreads throughout the body to helper T cells, macrophages, dendritic cells
→ may last for many years
→ virus contained without lymphoid tissues
→ patients are asymptomatic or suffer minor infections
What is the AIDS stage of HIV?
Lymph nodes and the spleen are sites of continuous HIV replication
→ cell destruction and the number of blood CD4+ T cells declines
→ eventually continuous cycle of virus infection and T cell death and new infection meds to loss od CD4+ T cells
What are the cytopathic effects of HIV?
Production of viral proteins including gb41 and gp120 in the plasma membrane increase plasma membrane permeability
→ influx of lethal amounts of calcium, induces apoptosis
→ osmotic lysis of the cell caused by influx of water
→ viral production can interfere with cellular protein synthesis leading to cell death
What are some viral virulence genes?
Gene/s that:
→ affect viral replication
→ encode toxins
→ encode modulators of the immune system
→ enable virus to spread in the host
What is the concept of vaccination underpinned by?
Infection often leads to life-long immunity
The virulence of different strains of a pathogen may vary → infection with a low-virulence strain (causing mild or no disease) may lead to resistance to a high-virulence strain which would cause severe disease
What is the smallpox vaccine?
Late 18th century by Edward Jenner
→ milkmaid cowpox - immune to smallpox
→ deliberately inoculated 8yo boy with cowpox-infected material
What is a vaccine?
A biological product that can be used to safely induce an immune response that confers protection against infection and/or disease on subsequent exposure to a pathogen
What is a live attenuated vaccine?
Contains the whole virus that has been weakened or attenuated - replicating but doesn’t cause disease
→ produces an immune response similar to that seen during natural infection
e.g. MMR, rotavirus, oral polio, infuenza
features: tend to create a strong lasting immune response, may not be suitable for immunocompromised individuals
What is a killed/inactivated vaccine?
Contain whole virus which has been killed or have been altered so that they cannot replicate
e.g. inactivated polio vaccine or IPV, inactivated flu, Hep A, rabies
features: don’t create a string and lasting immune response, may be suitable for immunocompromised individuals
What is a subunit vaccine?
Do not contain the whole virus at all
→ they contain one or more specific component/unit/antigens usually from the surface of the virus
e.g. Hep B, human papilloma virus
features: don’t create a strong and lasting immune response, may be suitable for immunocompromised individuals
What is a nucleus acid/genetic vaccine?
Do not provide the viral protein/antigen. Instead they provide the genetic instructions/genes that encode for that specific viral antigen to host cells
→ these genes are the expressed by the host cells to produce the viral antigen, which stimulated an immune response
e.g. RNA: Pfizer, moderna / DNA
features: quick and easy to develop, provide significant promise for the development of vaccines in the future
Why are vaccination programmes required?
In order to control a disease
→ must be effective vaccine + program must be effective
UK doctors paid bonus if they have high vaccination
effective vaccination programmes must be: cheap, safe and acceptable
What are antiviral drugs?
Antivirals can stop infection once it has started
→ vaccines can prevent viral disease - they have limited or no therapeutic effect if someone is already infected
→ about 100 antiviral drugs are available - against HIV, HCV, Herpes
What do antiviral drugs target?
Most target enzymes
→ polymerases, protease, integrase, NS5A, other virus, host
75% target virus, 25% target host
Why do we have a limited number of antiviral drugs?
Many compounds that interfere with virus growth cause effects in the host
→ side effects common (unacceptable)
→ every step in viral replication cycle engage host functions
Some medically important viruses can’t be propagated, have no animal models or are dangerous
→ HPV, HBV, smallpox, Ebola virus, lassa virus
Must be potent-completely inhibit viral replication
Many acute viral infections are short-lived
What are antiviral-binding inhibitors?
Maraviroc - anti-HIV
→ mode of action: blocks the chemokine receptor CCR5 - blocks binding
What are antiviral-entry inhibitors?
Amantadine & rimantadine - anti-influenza
→ mode of action: inhibits entry and NA release - blockage of the M2 ion channel
Why did hydroxychloroquine failed for SARS Cov-2?
Licensed drug (for Malaria)
→ known to inhibit replication of multiple viruses by inhibiting acidification of endomsomal acidification
→ found to inhibit SARS Cov-2 replication in cell culture
→ given emergency approval by FDA - but then failed
doesn’t inhibit SARS Cov-2 - doesn’t enter through pH dependant
What are inhibitors of viral polymerases?
Oral and genenital herpes-HSV-1/2
What are neuraminidase inhibitors influenza?
Neuraminidase - allows new viruses produced to escape
→ inhibits release of viruses prevents infecting other cells
Neuraminidase (NA) Tamiflu
