Viral replication

Stages of viral replication [9]

Recognition, attachment, penetration, uncoating, transcription, protein synthesis, replication, assembly, lysis and release

Virus host movement

virus movement is driven by Brownian forces, diffusion, electrostatic interactions

how viruses attach to host cells?

viral attachment proteins (VAP) bind to certain cellular surface proteins

What molecules can be receptors for viruses

proteins, carbohydrates, glycolipids, glycoproteins

Define affinity in terms of virus binding

strength of interaction between a single receptor and a singel virus attachment protein (one to one)

Define avidity in terms of virus binding

measure of overall binding of receptor with ligand, involving multiple binding sites

The change in strength of binding

at first the affinity is low, then due to VAPs and receptors results in high avidity interaction

Penetration of enveloped viruses

fusion of envelope with cell membrane

Enveloped viruses which fuse at the membrane

HIV, herpes virus

Enveloped viruses which fuse after receptor mediated endocytosis

influenza

Penetration of non-enveloped viruses

viropexis - direct entry

viropexis

hydrophobic viral protein interacts directly with membrane and injects the genome through the membrane

HIV-1 receptor binding, two proteins [2]

gp120 - mediates binding to the viral receptors, an antigenic target for antibodies gp41 - mediates fusion

DNA from DNA viruses is transported to

the nucleus

RNA from RNA viruses is transported to

the cytoplasm

Where can synthesis of nucleic acids also occur (not in the nucleus or the cytoplasm)

partially assembled capsids

Viruses which replicate in partially assembled capsids [4]

reovirus, poxvirus, retrovirus, hepadnavirus

Why does the virus uncoats?

to initiate viral gene expression, and replication of viruses

DNA virus cellular characteristics [2]

replication and transcription occurs in the nucleus, uses cellular enzymes and proof-reading mechanisms

DNA virus non-cellular characteristics [3]

no histones episomal circular DNA frame shifts

What is ori

origin of replication typically on circular DNA viruses such as polyomavirus

Rolling circle replication

a DNA replication mechanism in which one strand is nicked and unrolled for use as a template to synthesize a complementary strand

Which viruses replicate by rolling circle?

herpes viruses

All DNA viruses replicate in the nucleus except

Poxvirus

Main enzyme for RNA replicatio

RdRp (RNA dependent RNA polymerase)

Which RNA virus does not replicate in the cytoplasm?

orthomyxovirus

+ RNA replication

Can be directly translated into proteins Synthesized negative strand serves for genome replication

+RNA strand is the same as mRNA?

yes

VPg function

Viral protein genome-linked acts as a primer during RNA synthesis

-RNA virus replication

• RNA is synthesized acts as a template for mRNA synthesis and production of new genome

In the cytoplasm, what proteins associate with the synthesized genome to form the nucleocapsid?

N, L and NS proteins

Which protein associates with the G protein modified membrane

the matrix protein

retrovirus replication

have their own enzymes for transcription use cellular enzymes for replication form viral dsDNA in the nucleus

Which viruses produce polyproteins

RNA viruses polyproteins are processed by viral and cellular proteases

What is the nucleocapsid composed of

DNA or RNA + structural proteins (capsid)

Virus assembly general steps [6]

formation of a structural units of the protein shell

assembly of the protein shell via interaction of units

selective packaging of the nucleic acid genome and other virion components

acquisition of an envelope (only for enveloped viruses)

release from host cell virion

maturation (only for some viruses)

Define virion

a completely assembled, infectious virus outside its host cell

Virus assembly cellular machineries [2]

ER -> Golgi -> PM secretory pathway transport viral glycoproteins nuclear import and export

machinery moves viral proteins and nucleic acids

How do viruses localize their proteins [5]

nuclear localization sequences signal sequences,

CHO-,

lipid modifications

ER retention signals

interactions with microtubules, actin filaments

Virus which forms an icosahedral particle

poliovirus

5S structural unit is composed of

VP1, VP2, VP3, VP4

Complete icosahedral particle is composed of

12 pentamers (5S) and RNA

Viral scaffolding proteins

• Establish transient intermediate structures

• Viral proteases packaged in these intermediate structures become activated to finalize structure

Where is the nucleocapsid with scaffolding proteins assembled

in the nucleus

How is viral genome identified during packaging

Via packaging signals on the genome which are recognized by structural proteins. Binding of one structural protein initiates subsequent binding.

How does poliovirus achieve genome specificity

packaging of viral proteins and RNA synthesis are coupled

Enveloped virus assembly (idk man)

viral membrane proteins are co translationally translocated into the ER membrane they become processed and glycosylated for by viral and cellular chaperones and transported out to the PM then they travel to the site of viral budding lateral interactions build a matrix of proteins which often excludes cellular proteins

Viral budding strategies [4]

Alphaviruses - envelope glycoproteins and capsid drive budding retroviruses - internal matrix or capsid proteins drive budding coronavirus - envelope proteins drive budding matrix proteins and additional glycoproteins or RNP drive budding efficiently and accurately

Maturation of viruses include

virion components are processed to make them infectious

Viruses which require viral or/and cellular proteases

HIV, poxvirus, HCV

Viruses which process sialic acids

influenza