1.

0 Virus Structure
1.1 Characteristics of Capsids
1.1.1 Definitions
• Capsid: rigid, symmetrical container composed of viral protein
• Nucleocapsid: Capsid WITH enclosed genome
• Virion: complete, infectious virus particle, possibly including an envelope
### 1.1.2 Morphology
• Diverse: from complex and multi-component to filamentous to amorphous
• All are smaller then the shortest wavelength of visible light
• Capsids can assembly in an energy reliant or spontaneous fashion
– Often composed of identical subunits - contributes to an economic
genome; thus also giving rise to the symmetry of virions ####
1.1.2.1 Icosahedral Symmetry
• Icosahedron: a shape with 20 triangular phases with five, three, or twofold
rotational axes; complex yet capable of spontaneous assembly
• Interactions may be symmetrical or quasi-equivalent (multiple distinct bio-
chemical interactions between identical subunits)
– Represents that the proteins must have some flexibility to allow for
these interactions - topologically
• May also have spike proteins and additional subunits such as hexons and
pentons #### 1.1.2.2 Helical Symmetry
• Helical: tubes composed of identical repeating subunits #### 1.1.2.3
Miscellaneous
• Filamentous viruses, cone shaped, amorphous, pyramids, teardrop, bullet
shaped, gemini, all possible

1.2 Virus Envelopes

• Composed of host lipid bilayer and viral glycoproteins
– Can adopt a variety of shapes
• Obtained by budding
– First send viral glycoproteins to the membrane
– Then nucleocapsids associate with the glycoproteins and are exocy-
tosed
– Alternatively may also be assembled via organelle membranes; very
distinct lipid structures
• Resulting structure is very unstable outside of moist environments
– Rigid proteinaceous capsid is better in the external environment
– Therefore enveloped viruses must travel through aerosols or bodily
fluids
∗ Thus enveloped viruses only found in animal hosts
• Examples
– Influenza virus envelope proteins
– Spike proteins are the HA and NA proteins (used to describe variants

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 such as h1n1)
∗ On the cytoplasmic side are the matrix proteins (M) that binds
to the spike proteins. Then the RNP that binds M.
∗ These all come together and bud off carrying the genome in 8
discrete segments
–

1.3 Virion Assembly

• Factors that influence mode of assembly
– Size of virion
– Shape and complexity of capsid
– Genomic composition
• Assembly modes
– Spontaneous
– Energetic: scaffold requiring, chaperones
• Scaffolding proteins
– Proteins that assist with formation of a pro-capsid, and are not part
of the final, mature virion
• Genomic integration
– Packaging signals can be used to either replicate genomic content
directly into a capsid or post-replication
– Packaging signals are sequences that is recognized by a protein
– May be accompanied with core proteins ## 1.4 Disassembly Mech-
anisms
• Proteolytic cleavage of capsid proteins
– Ex/ the non-canonic furin cleavage site
• Unspooling of genome into cell - In which case the capsid does not enter
the host
• Interaction of genome with cytoplasmic components

2.0 Virus Classification

Basis
• Molecular architecture
• Genetic relatedness
• Host organism
– Distinct conventions and schemes then further developed for different
domains of virology ## Evolutionary Origin
• The RNA world
– posited that because RNA is biochemically active, catalytic, and ca-
pable of forming 3D structures, life likely originated with RNA as an
information storing molecule
– Then as protein and peptide synthesis arose, RNA no longer needed

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 for biochemical functions and DNA was used as a more reliable infor-
mation storage molecule
– This hypothesis requires reverse transcriptase to convert RNA into
DNA
∗ Found in viruses; evidence towards viruses as a life precursor?
∗ Not testable
• Viruses
– Transition to the DNA-based world gave rise to retroviruses
– Small and medium DNA viruses arisen as independently replicating
genetic elements.
– Large DNA viruses evolved from cellular forms
• Krupovic et al. explains viral evolution
– 1. Viruses predate cellular life
– 2. Regression of cells to viruses
– 3. Selfish genetic elements escaped cells with some proteins
∗ Some hybrid is correct ala biochemical evidence
· Precellular things existed and some were stealing from hosts
and viruses evolved from different states along life’s evolution

3.0 Virus Entry

3.1.1 Intro
• Depending on the outer host surface, viruses may uses different entry
mechanisms
– Bacteria, archaea, algae, and plants have though cell walls
– Bacteriophages may puncture proteoglycan cell walls
– Plant viruses have thicker cell walls a cuticle that must be damaged
externally or by insects
∗ After damage, may spread through plasmodesmata
– Many animal viruses may simply fuse with cell wall ## 3.1.2 Pene-
tration Strategies ### Enveloped Viruses
• Fusion and fission of the plasma membrane
• Receptor-mediated endocytosis followed by fusion and fission with the
endosome
– Host surface glycoproteins interacts with virus and induces endocyt-
tosis ### Non-enveloped Viruses
• Receptor-mediated endocytosis
– Occur at clathrin-coated pits, caveolae, lipid rafts
– Endocytosis leads to early endosome
– Low pH of endosome may also be a trigger for maturation and entry
into cytosol
∗ prevents uncoating at inappropriate times
• Genome passage
– Pore, portal, transport proteins create channels in the membrane

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 ### Cell-Cell entry
• Filopodia
• Virological synapse may be formed by viruses
• Syncytia ## Misc.
• Covid is an enveloped virus that can fuse with endosome or plasma mem-
brane - these redundant strategies may be an adaptation against defences
• Once inside the cell, migration may be achieved by using the vesicle and
microtubule transport system
– Some viruses require import into nucleus via importins and karyo-
pherins
• Uncoating not well understood ; mayy occur early or later; in cytosol or
in nucleus

4.0 Fiersviridae: ssRNA Bacteriophages

family Fiersviridae
Characteristics
• ssRNA positive-strand genome
– Contains the maturation protein, coat protein, lysis protein, and
RNA replicase
• Icosahedral capsids from 180 copies of coat protein- Gram-negative bacte-
riophages
• Includes Emesvirus and Quebevirus

Attachment
• Fiersviridae enter the cell by associating with the F+ donor cell at the
pilus. Association with the pilus causes a cleavage of the maturation
protein to release viral RNA, but the exact mechanism of entry is under-
studied.

Translation and Replication

• viral mRNA is positive strand, and thus may already be translated into
protein product
• However the genome must also be replicated to produce new copies for
incoming virions
– These processes must be independent of one another, else they would
interrupt and sabotage the competing process
∗ DNA and RNA replicase starts on the 3’ end proceeds to 5’ (5’
to 3’ product)
∗ Ribosomes translate 5’ to 3’
– RNA spontaneous secondary structure (self complementary) prevents
access of late infection codons

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 ∗ only one start codon is available (encodes coat protein)
• The four protein products of the genome must be produced at different
ratios: 180 coat: 1 maturation
– This ratio will allow more efficiency, thus using less resources from
the host, and producing more virions. More virions means more
potential infected hosts and thus greater fitness

Coat Protein
• Initially, the only start codon available to host ribosomes is the coat start
codon

Replicase Protein
• As the ribosome passes over the MJ sequence while translating the coat
protein, the secondary structure of the replicase start codon is disrupted,
making it available for another ribosome
• Replicase then requires four host proteins (including S1, which associates
with the coat start codon) to initiate replication. Competing sites with
the coat protein translational start codon prevents competition
• Then in converting the negative sense RNA to positive sense, the poly-
merase may replicate the positive strand without extra host factors - thus
less complex and more efficient; also no competition

Lysis Protein
• Once the ribosome completes translation of the coat protein at the coat
stop codon, the ribosome does not immediately dissociate from the RNA.
Instead it may randomly “wobble” and move down the mRNA in either
the 5’ or 3’ direction
• If it encounters another start codon, it will began translation again. If it
goes in the 5’ to 3’ direction, it may encounter the lysis start codon; this
is the only way
– This stochastic event is based on the proximity of the lysis start codon
to the original stop codon

Maturation Protein
• Once replicase creates a new positive sense strand, rather than going into
the final stable, equilibrium secondary structure, there is an intermediate
structure that forms.
• This structure is the only one with the maturation protein shine-dalgarno
sequence available
• Thus ribosomes may only produce maturation protein once there is nascent
mRNA, that has not reached its equilibrium folding state
– requires replicase protein to have been produced, which itself requires
coat protein

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5.0 Microviridae: ssDNA Bacteriophages
General Morphology
• Naked Icosahedral capsids with 12 spikes
– 33 nm diameter

Taxonomy
• Two subfamilies
– Gokushovirinae
∗ Viruses of obligate intracellular parasitic bacteria
– Bullavirinae
∗ Viruses of free living bacteria
∗ Case study: PhiX174
· First genome ever sequenced

PhiX174 Genome
• circular ssDNA 4.4-6.1 kb in length
• Genes overlapped each other
– Highlights genomic economy and coding capacity
∗ x amounts of genome encodes x product
∗ Smaller genome; more replication; more fitness
∗ Mutation can affect multiple genes, more likely to be deleterious
• 11 proteins
– 2 DNA replication/packaging proteins
– 2 Scaffolding proteins
– 4 virion structural proteins
– 1 Lysis proteins

PhiX174 Proteins
1. A
1. Replicase; needs conservation
2. A*
1. Non-essential
3. B
1. Internal Scaffold; highly flexible
4. C
1. Packaging
5. D
1. External Scaffold
6. E
1. Lysis
7. F

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 1. Major Capsid
8. G
1. Major Spike
9. H
1. DNA delivery
10. J
1. DNa Packaging
11. K
1. Non-essential
[[Pasted image 20230928152031.png]]

PhiX174 Regulation
• 3 Transcriptional promoters and 4 terminators
• Multiple promoters produce different transcripts. However, because it is
polycistronic, these transcripts carry the same genes. The genes towards
the 3’ end are in more transcripts and thus are produced more often
– overlapping open reading frames
• Overlapping genes
– genes that need to be highly conserved by be kept alone, or paired
with genes that are non-essential and/or highly flexible
∗ therefore, mutations in important gene can be conserved and
other genes not affected
• This allows for genomic economy but allows keeps the capacity for evolu-
tion - so it may participate in the co-evolutionary arms arce

PhiX174 Attachment
• Capsid protein F binds glucose (other microviruses may bind proteins)
• Genome injected through spikes via protein H ## PhiX174 Replication
### Stage I Replication
• ssDNA uncoated, but cannot be transcribed until it is dsDNA (fundamen-
tals)
• host single strand binding protein (SSB), and primosome complex stabi-
lizes ssDNA and RNA Polymerase synthesizes the okazaki fragments, Pol1
and ligase makes the double strand DNA
– Hairpin region on genome is site for primosome assembly
– the minus-strand is formed, which hybridizes with the viral positive
strand ### Stage II Replication
• Now the replicative form dsDNA may be replicated to form more viral
genomes
– dsDNA itself is also the template for transcription
• A protein (viral protein) cooperates with host proteins to replicate via
rolling circle mechanism
– produces more plus-strand circular ssDNA

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 • Host and viral proteins work as a helicase
Stage 3 replication is the same process, but viral protein J participates to pack-
age the nascent strand into the procapsid via pores ## PhiX174 Assembly -
Multi-step, energetic process - subunits are labelled with S; svedberg units of
sedimentation coefficient (centrifugation properties) - Step 1 is to assemble the
procapsid via scaffolding proteins - Coat is made of 9S (coat) and 6S (spike)
subunits that dimerize into the 12S subunit via internal scaffolding protein B
- 12S units are packaged with external scaffolding protein D - Forms the pro-
capsid, which is porous and thus allows DNA packaging - Here, DNA may be
packaged to form the provirion - Protein A and C forms the DNA packaging
complex. DNA rolling replication to export ssDNA into procapsid with pro-
tein J - DNA packages as they are synthesized; stage 3 DNA replication - This
process changes internal structure of the procapsid to become the provirion; In-
ternal scaffold protein B leaves - Protein D (external scaffolding) is removed to
form the mature virion - Scaffolding proteins - Flexible structure and multiple
conformations allow for multiple interactions and ability to evolve -