2. Viruses

Learning Outcomes: L3

• Explain why the virus is not a life form
• Describe general features of viral replication
• Use hepatitis C, human immunodeficiency virus (HIV) and influenza viruses to illustrate specific aspects of virus replication
• Use terminology correctly
• Compare bacteria and viruses
• Outline challenges in fighting infectious disease

Features of a virus

• Viruses and prions are non-living organisms- prions do not have genetic info and are thought to consist of single protein:
• Small- need e microscope to visualise- makes research harder= less antiviral drugs
• Varied shapes- filamentous, icosahedron (symmetrical, 20 faces that each consist of proteins that self-assemble, not a life form)
• Obligate intracellular parasites- uses host cell, virus must be infectious to endure nature (maintain itself and have selection pressure)
• Depend on biochemical machinery of host cell to replicate- use host processes to produce their components
• Can't make energy or proteins independent of host- non-living
• Replication is by self-assembly of individual viral components: NA, capsid
• Genome is DNA or RNA

Virus Structure

• 
• Naked virus:
• Viral genome: DNA/RNA, ss/ds
• Capsid: composed of capsomeres#
• Nucleocapsid= capsid + genetic info
• Enveloped virus:
• Nucleocapsid surrounded by envelope derived from host cell when virus buds off
• Spike proteins (glycoproteins) involved in contact with host cell
• Virion- infective viral particle:
• Enveloped= nucleocapsid + envelope
• Non-enveloped= nucleocapsid is virion

Naked vs Enveloped

• Naked: eg Polio
• More stable when under environmental stress- more problematic as don't have to remain wet to be stable due to no membrane
• Spreads more easily
• Survives gut, poor water treatment
• Enveloped: Influenza, HIV, ebola
• Must be wet to stay infectious- lipids not stable when dry out, airborne transmission less likely
• Very sensitive to detergents
• Spread through large droplets (coughing)
• Doesn't need to kill cell to spread (buds off instead)

Viral Genome

• 
• Legenda: How virus is replicated depends on the identity of the NA and strategy of genome replication (lifecycle)

Viral Replication

• Assembly of new viral particles requires:
• Copies of the viral genome
• Viral proteins- make mRNA (+RNA) to be translated, DNA -> mRNA -> protein (mRNA/+RNA is made from DNA or -RNA)
• Viral genome must code proteins for all processes not provided by host:
• Proteins for progeny viral particles (capsid, spikes)
• Enzymes for genome replication
• Proteins for interference with host immune defence (immunomodulatory)

Making mRNA for Translation into Protein

• 
• dsDNA= transcription to mRNA
• +RNA= ready for translation (already mRNA)
• -RNA= virus encoded enzyme that copies to complementary stand
• Retrovirus= already has +RNA in capsid but has evolved to go through DNA phase +RNA -> -DNA -> dsDNA -> mRNA
• Red arrows= viral protein needed

Making new Viral Genome Copies

• 
• Has to go through complementary intermediate phase in host

Making the Viral Particle for ssRNA(-)

• Start= -RNA (intermediate = +RNA)
• Making genome copies= -RNA-> +RNA -> -RNA
• Making proteins= -RNA -> +mRNA (transcription) -> protein (translation)
• Polymerases made to make genetic info
• Once all components are made= self-assembly
• 

Stages of Infectious (Productive) Cycle

• Find host cell with specific receptors to attach to (tissue specificity)
• Penetration of cell
• Uncoating of virus particle
• Replication (gene expression)- location specific to each virus (nucleus or not)
• Assembly
• Release- budding/lysis

Penetration/Entry for a Enveloped Virus

• 1st Strategy: immediate membrane fusion
• Fusion of virus envelope with host cell membrane and insert nucleocapsid
• Site of virus entry formed by receptor( and coreceptor for some eg HIV)
• 2nd Strategy(active): Initial entry of complete virus
• Initial entry by endocytosis
• Followed by escape involving fusion with endosomal membrane
• All virus have in common: virus particle is assembled intracellularly

Variable Yield+Speed of Viral Replication

• Host cell properties and viral properties combined define how many and how fast new particles are released:
• Attachment to host cell surface- right interaction
• Replication- host cell metabolic activity
• Affects lab experiments- data dependent on animal/tissue model system may delay research of some viruses

Retrovirus Life Cycle: HIV

• Attachment, co-receptor binding, fusion...
• Upon fusion, viral RNA released from capsid
• Genome is RNA- requires viral enzyme reverse transcriptase to make DNA
• Viral genome integrates into host cell chromosomal DNA via integrase= persistent infection (cant get out without damaging DNA)
• Transcribed into mRNA and transported from nucleus to cytoplasm
• Translation to polypeptide which is cleaved to produce functional viral proteins
• Assemble at cell membrane and budding
• 

+RNA Virus: Hepatitis C (+ssRNA infects)

• Entire life cycle is extra-nuclear:
• Host receptors bind glycoproteins, membrane fusion, release of nucleocapsid
• +RNA immediately translated to polypetide and cleaved to make viral proteins (including viral polymerase)
• Viral polymerase participates in trasncription of -RNA (acts as template to make +RNA copies)
• Self-assembly and fusion of membrane, budding
• Blood-borne virus that causes liver disease
• 

-RNA Virus: Ebola, Influenza -ssRNA infects

• Carry unique enzymes in capsids that facilitate replication (to kickstart process)
• Entire lifecycle is extra-nuclear but influenza transcription occurs in the nucleus
• Virus released by budding
• Influenza spike glycoproteins:
• HA= Hemagglutinin - recognised and binds siaalic acid containing receptor on host cell (erythrocytes + upper respiratory tract cells)
• NA= Neuraminidase- exosialidase, cleaves sialic acid from adjacent sugar residue in glycoprotein and is involved with release of virus from cell

Roles of NA

• Helps the virus approach target cells= cleavage of sialic acids from respiratory tract mucins
• Assists in fusion of viral and cell membranes
• Facilitates budding of new virions by preventing their aggregation HA of one of interacting with sialylated glycans of the second one
• Structure of the neuraminidase active site is strictly conserved and inhibitors are used as drugs

Virus Specific Challenges

• Influenza: HA and NA are susceptible to antigenic drift (mutation) and shift (recombination)
• New strains and subtypes of influenza emerge
• Pandemics/ epidemics as a result
• Eg H7N9 HA evolved mutations to make it similar to human proteins= immune camouflage
• HIV: viral reverse transcriptase is highly error prone
• Many genomic variants made every time RNA is reverse transcribed to DNA
• All HIV particles are slightly different, can get some more effective than others so selection pressure leads to rapid evolution
• Few effective anti-viral drugs are available:
• ​​​​​​​Viruses use our machinery so we can target few things: entry, uncoating, genome regulation

Why viral infections are problematic

• Few drugs available and drug resistance
• High mutagenic rates
• Emerging infectious disease
• Latent and persistent infections
• latent = virus doesnt lead to disease but can be re-awakened eg coldsore
• Chronic= results in chronic illness
• Can initiate cancer- integrates into genome and makes oncogenes
• Re-emerging infectious diseases (polio)
• Public health issues/ transmission: clean water, upheaval, education

Transmission routes: Virus specific

• Food and water bourne
• Human to human: air/aerosols eg sneezing, oral/fecal, exhcange bodily fluids
• Vector eg mosquito
• Foodbourne bacterial pathogens:
• EHEC- transmission from cow to human host
• Listeria monocytogenes- transmission from animal to human via milk and dairy, meat or transmission from plants to human (effects pregnant women, immunocompromised, children, elderly)
• Waterbourne bacterial pathogen:
• Vibrio cholera- unclean water (chitin) to human