Day 1: Introduction Virology, Virus basics: Entry, replication & exit Flashcards
HC01, 02
Viruses and life forms
Every life form has own viruses: for bacteria, fungi, plants, animals and some viruses themselves
HepD virus and covirus
HepD is a smaller virus which needs other virus to replicate
Is there a kingdom of viruses?
No, viruses did not descend from single prehistoric virus
Bacteriophages
Viruses that specifically infect bacteria
> most abundant virus in surface water
Virome and detection of it
All the viruses in the body or in a certain organ
> detection by high-throughput sequencing
Duration infection with herpesviruses
forever
Classification method viruses
- Type of genome: RNA / DNA
> Symmetry of particle
> Enveloped or non-enveloped
> Genome architecture
» > Single stranded / double stranded
» segmented or not
Viral capsid use
To attach to host cell
> variation in size
Envelope of virus is remaining part of …
the host cell membrane
Capsid spikes go through the …
envelope (is part of the virus particle itself)
+ and - strands in case ssRNA virus
+ strand: like mRNA, directly used for translation
- strand: reverse complement strand, needs to be converted to + strand before translation to make proteins: RNA-dependent RNA polymerase needed (also needed for RNA replication)
Detection envelope for virus?
WIth sequencing > easier than electron microscopy
Viruses seem to not live: they are not self-sustained, although they evolve (need host). Name the practical problems with a virus phylogenetic tree
All types of genomes exist like ssDNA, dsDNA, (+)ssRNA, (-)ssRNA, dsRNA
> no gene is shared between all viruses
Viral properties (components like molecules)
> Made of molecules in living beings: nucleotides, proteins, sugars
can evolve (mutate) and adapt to environment
Viroids
RNA viruses
> very small
> without protein coat, plant pathogens
Virusoids
Even smaller than viroids
> also called satellites
> circular ssRNA dependent on plant viruses for replication and encapsidation
only known human satellite
Hepatitis delta virus (HDV)
> small RNA virus which relies on HBV for encapsidation
> replicates by diverting host DNA dependent RNA polymerases to use RNA as template
Largest known virus
Megaviridae family
> linear dsDNA (> 1 Mb)
> largest human infecting virus: herpesvirus
RNA viruses character
- Very large viruses cannot have RNA genome due to instability of large RNA molecules
> largest RNA viruses infecting humans: coronaviruses
> also: infidelity of RNA replication
> higher mutation rate, no proofreading
> often segmented
Origins viruses: Butterfly vision
Virus infection transform cells into virus factories
> maybe cellular phase of the virus is the real life form (virus particles are just the seeds)
> viruses belong to domain of life
Most viruses infect bacteria and plants, but some infect humans. General characteristics:
- Mostly pathogenic
> interfere with metabolism of the cell and/or invoke a devastating immune response
Smallpox virus
Variola virus (VARV) causes smallpox
> genus orthopoxviruses: large viruses as well including VARV and mpox virus
do viruses belong to domain of life?
yes
VARV characteristics
- Poxviridae family, genus orthopoxvirus
- Poxviridae are enveloped unsegmented large dsDNA viruses
> unlike many dsDNA viruses that replicate in the host, they encode own replication machinery and therefore replicate in cytoplasm - human-specific, no animal reservoir
Infection smallpox route
After upper respiratory tract infection, virus reaches skin where it replicates to cause widespread vesiculapustular rash, with later scarring especially on face
Two forms of smallpox
- Variola major: serious illness with high mortality rate in unvaccinated population
- Variola minor: milder infection
> different strains of VARV
Death from smallpox
Secondary to coagulopathy: bleeding because clotting impairment > hypotension and multi-organ failure
> infants, the eldery and pregnant women had the highest fatality rate
Complications smallpox
- Keratitis and corneal ulcerations leading to blindness
- Secondary bacterial skin infections
- Viral arthritis and osteomyelitis
- Bacterial pneumonia
- Orchitis (acute inflammation of testis)
- Encephalitis
VARV eradication
First eradicated virus
> Proteins on outside of VARV and cowpox virus are much alike
> vaccine based on horsepox: Vaccinia virus (VACV) replaced the cowpox as smallpox vaccine
> global eradication in 1979
> other orthopoxviruses also exist within family poxviridae
Return of smallpox or related virus
Mpox
> endemic in DRC (democratic republic of Congo)
> immunologic niches created because vaccinations stopped because of money issues > more susceptibility for the disease in these countries like Australia, Africa and South America
Mpox was declared a …. in 2022, which ended in 2023 but returned in 2024
PHEIC: Public Health Emergency of International Concern
Rabies death source
99% human rabies deaths because of dogs infected
Novel infectious threats
- Less territory wild animals: increasing number lifestock to feed increasing population
- More contact
- Zoonosis risks
- More international travel: pathogen spread through flying
- Climate change contributes to pathogen transmission like West Nile Virus in Europe
- Flying is a great way to disperse pathogens over large distances: plane, bat, bird
HC02: Viruses replication and dependency
Dependent on host cells to replicate: need cellular machinery to complete replication cycle
> No protein synthesis on themselves: does not code for rRNA and does not contain ribosomal proteins
» do contain some ribosomal protein and tRNA genes to speed up process, but not enough to do it themselves
> need to get into host cell to use cell’s facilities
> sometimes they code for own polymerases
The body of the host is well protected against invaders by the largest organ: the skin. How do they enter?
Weak points
> Eyes
> Mouth
> Vagina
> Anus
> Scratches/injury
> Placenta: from mother to unborn child
Entry into the body: name viruses for the points
- Eyes: Influenza, Rhinovirus
- Mouth: All respiratory viruses, including influenza virus, norovirus, most herpesviruses
- Skin: through arthropods bites: dengue virus, through mammalian bites: rabies virus, through injection: HCV, HBV
- Vagina/Anus: HIV, HSV2, HPV
- Placenta: HIV, CMV, rubella virus
First sign of bird flu
The eyes are infected
Why cervical cancer when HPV infection
Cervix is a barrier and viruses are halted there, mutations and cancer occurs there
Rubella virus character
Rode hond
> dangerous for fetus specifically, blindness and congenital mistakes early age
Difference of cell entry of virus based on:
Cell type: bacterial, animal plant cell
> also cell type within species
> Bacteriophages cannot infect human cells
How does Ad2 virus enter the cell
Clathrin-mediated endocytosis after binding the receptor
> non-oncogenic adenovirus (dsDNA), infects upper respiratory tract
Trojan horse strategy of virus cell entry
Virus pretends to be something else: nutrient, signal: ligand presentation as pretender)
> Binding ligand by receptor and actively transported in the cell
> like HIV to CD4
Virus type and entry mechanism
Enveloped: Receptor-mediated endocytosis or direct membrane fusion
Non-enveloped: receptor mediated endocytosis
Virus entry: Direct membrane fusion
Enveloped viruses
> Envelope with spike proteins was part of the host cell with the original ligand > determines tropism
> Protein interaction induces fusion with the cell membrane: capsid released inside the cell
» cytoplasmic nucleocapsid
Virus entry: endocytosis
Our cells take up a lot of nutrients and viruses can be engulfed as well
> binds a bit to the cell membrane: endocytosis
Envelope of virus
Lipid bilayer taken from cell membrane during virus particle budding, through which viral spike proteins protude
> Influenza virus (ssRNA)
> Epstein-Barr virus (dsDNA)
Naked viruses
Non-enveloped viruses
> do not take lipids from cellular membrane and are often released through cell lysis in culture
> HPV (dsDNA)
> Rotavirus (dsRNA)
Entry steps
- Virus binds molecule in cell membrane: can be an unspecific molecule (liek heparan-sulfate or other carbohydrate structures): attachment factors
- More specific interaction is found afterwards by binding a receptor of the host cell: this interaction initiates conformational changes in virus particle: activate signalling pathways and promote endocytic internalization
Herpes simplex virus (HSV) attachment factors
Heparan-sulfate on host cell
> then search for stable interaction with receptor
> receptor is the protein which will bind the viral spike proteins in enveloped viruses
HIV-1 attachment factors (multiple, used in parallel or succession)
Binding of mannose binding C-type lectin receptor family members, the dendritic cell specific adhesion molecule DC-SIGN or L-SIGN (liver/lymph node)
HIV-1 receptor binding
glycoprotein 120 (gp120) binds CD4 > stable interaction, conformational change > allows virus to associate with co-receptors like CXCR4 and CCR5 chemokine receptors
> membrane fusion
Which viral protein binds to the cell membrane protein
Enveloped > spike glycoproteins (like gp120 in HIV-1)
Naked > structures that bind receptors are projections or indentations in capsid surface
Cellular tropism of virus
Determined by specific cellular protein that a virus binds
> if a ubiquitous, a-specific molecule is used > many types of cell, tissue or host can be infected
» HIV-1 cannot infect CD4 negative cells
Endocytic pathway used by virus: one or multiple
Multiple: because multiple endocytosis systems exist in eukaryotes
HCV (hepatitis C virus) entry
Endocytosis (enveloped)
- Virion attaches to receptors at cell surface
- Virus-receptor complex is taken into cells by endocytosis
- Membrane fusion in the cell: get envelope out so that contents are released (capsid to cytoplasm)
> route is chosen that binds receptors to activate or inactivate signalling routes so that replication and exit is optimalized.
Travel to nucleus
For most DNA viruses and some RNA viruses
> replicate in nucleus, need RNA polymerase
> must traverse the nuclear membrane through nuclear pores
> or wait for nuclear membrane to disintegrate during cell division
Retrovirus in nucleus or cytosol?
Nucleus: pastes DNA into genomic DNA
Why can RNA viruses stay in the cytosol?
They just need to be translated and maybe converted by own encoded enzymes
Cell-to-cell transport of viruses beside budding or exocytosis of virions
Mechanisms are created so that no novel attachment of virions to cells is needed:
> cell-to-cell fusion: giant cells (syncytia): virus can move freely in those cells
> after uptake by e.g. macrophages or DCs some viruses can survive degradation in the endosomes and be presented as whole virions to e.g. CD4+ T-cells or between CD4+ T-cells (for HIV-1)
Virus replication
- Replication in cytosol or nucleus
> replication of genome mostly by virus-encoded enzymes
> transcription (when DNA virus) done by host polymerases (RNAP-2)
> translation of viral RNA into proteins by host ribosomes
» viruses can form own subcellular section in the cell for viral replication
Exit of virus
- Enveloped viruses: budding: take viral glycoproteins on cell membrane with them: spike proteins
> Signal peptides present on these glycoproteins to direct them for translocation to cell surface so that they are released with enveloped virus - Cell lysis: naked viruses: (only in vitro??, unknown)
- Vesicles: naked viruses
Hep A virus (HAV) characteristics
- Picornavirus: (+) ssRNA
- 7,5 kb
- Sole species of genus Hepatovirus
- Infects via fecal-oral route and is shed in feces as a naked (nonenveloped) particle, but circulates in blood cloaked in an envelope derived from host cell membranes
Extracellular vesicles and virus particles
- Extracellular vesicles (like exosomes, microvesicles) are natural lipid particles released by many cell types
> Exosomes: lipid bilayer extracellular vesicles that are secreted from various cell types and act as mediators of intercellular communication by delivering function proteins, mRNA and miRNA to recipient cells
» general mechanism to release viral capsids (naked)
HEV, poliovirus and rhinovirus all released through
Extracellular vesicles
> capsids of HEV particles are individually covered by a lipid membrane that resembles exosome membrane, similar to enveloped viruses (without spikes!), and are released from infected cells via exosomal pathway
HEV infection
- (+) ssRNA
- Orthohepevirus genus of hepeviridae family
- causive agent of hepatitis E: occurs as waterborne infection in developing countries and zoonotic infection in industrialized countries
Exit virus from a host
By excretions mainly
> mouth and respiratory system: sneezing, saliva
> GI system: vomit, feces, urine
> Sexual: vaginal epithelium, semen
> Blood: blood sucking insects, needles, cuts
> Organ transplantation, blood transfusion included
Survival viruses between hosts
- Difference in eveloped and non-enveloped virions
- Lipid bilayer of envelope is relatively sensitive to heat and detergents: easy to sterilize, have limited survival outside hosts and normally transfer directly from host to host (like HIV)
» lose spike proteins, not infectious anymore - Non-enveloped viruses: more stable outside hosts: norovirus virions can survive for yeats outside the host
