The nature of viruses Flashcards
Properties of viruses (6)
1) small size - 20-2300 nm
2) Obligate intracellular parasites
3) Composition - nucleic acid and protein, sometimes lipid and carbohydrate too
4) Unique mode of replication (has an eclipse phase)
5) Diversity - all species are infected by viruses, and may cause plagues (which occurs when they jump between species) or be asymptomatic
6) Numerous with around 1x10^31 viruses
Structure of viruses
a) possible symmetry of capsid
b) composition
a) capsid is a protein cell surrounding nucleic acid genome. Can be helical or icosahedral (see image)
b) Nucleocapsid. Lipid envelope - some viruses have a lipid envelope surrounding the capdis, derived from the host cell often by budding of the nucleocapsid through the cell membrane. Carbohydrate (lipid envelope embedded with virus proteins, which may be glycosylated, may have spikes protruding (branch to the next cell it will infect)
Define
a) virion
b) genome
c) capsid
d) nucelocapsid
e) envelope
f) envelope protein
g) structural protein
h) non-structutal protein
a) virus particle
b) virus nucleic acid
c) protein coat (built from capsomers)
d) capsid + genome
e) virus membrane
f) virus protein in the envelope
g) protein in the virion
h) virus protein not in the virion (eg subversion from host immunity)
Examples of virus structures
a) Tobacco mosaic virus
b) Poliovirus
c) Influenza virus
d) Herpes simplex virus
a) Helical, no envelope
b) Icodahedral, no envelope
c) Helical, has envelope
d) Icosahedral, has envelope
Overview of viral genomes
Can have DNA or RNA. Can be linear or circular. Can be monopartile or segmented. Can be ds or ss. If ss, can have +ve polarity (mRNA, so can be translated immediately into protein in the host) or -ve polarity (must be converted to mRNA in host prior to translation). Size range 3-1500kb
Examples of viral genomes (size, DNA/RNA, ss/ds, no. of segments)
a) Polio virus
b) Measles virus
c) Influenza virus
d) Rotavirus
e) HIV
f) Hepatitis B virus
g) Parvovirus
h) Herpes simplex virus
a) 7.5kb, RNA, ss+ve, 1 segment
b) 15.9kb, RNA, ss-ve, 1 segment
c) 13.6kb, RNA, ss-ve, 8 segments
d) 18.5kb, RNA, ds, 11 segments
e) 10kb, RNA, ss+ve, 1 diploid segment
f) 3.2kb, DNA, ds (partial), 1 circular segment
g) 5kb, DNA, ss, 1 segment
h) 152kb, DNA, ds, 1 segment
RNA virus genomes and sizes
Range between 3-32kb. RNA dependent RNA polymerases (RdRp) are error prone and lack proof reading capacity. Therefore, many mutations are made every replication cycle, which is an advantage for genetic diversity (more likely to evolve to be resistant to a selective pressure). But, for genomes >20kb, there are too many mutations made, so the genome is non-viable, hence larger genomes must have proof reading. eg coronaviruses have RNA genome of 30kb, RdRp still makes errors, but these are corrected by viral protein nsp14
Protein coding capacity of viral genomes
Is used efficiently. The genes are densely packed. There are small intergenic spaces and few non-coding spaces. They have overlapping reading frames, meaning more than 1 protein can be made from the same nucleic acid. They also use RNA splicing
Parameters for viral classification (7)
1) type of disease (smallpox, chickenpox)
2) mode of transmission (eg arboviruses)
3) structure (capsid type, lipid envelope)
4) immunological relatedness
5) nucleic acid sequence
6) protein structure
7) mode of replication
a) ways of measuring viruses (6)
b) The plaque assay
a) i) observing disease in host ii) electon microscopy iii) PCR (just measuring genome, not infectivity) iv) haemagglutination (when virus is diluted enough, no agglutination of RBCs)
v) immunological evidence of infection vi) plaque assay (infectivity)
b) Infection of susceptible host cell, replication, release and infection of new cells. Area of killed cells is large enough to be seen - a plaque (1 plaque is considered 1 viral particle). Titres expressed as plaque-forming units/ml (pfu/ml). Note, not all viruses can be titrated by plaquee assay (eg HBV)
Viral replication
a) The one-step growth curve
b) Overview of stages of replication
a) (see image)
b) i) Binding to host cell ii) Penetration, getting through the cell membrance iii) Eclipse phase, expression of virus proteins, replication of nucleic acid iv) assembly of new infectious particles v) release, by cell lysis or budding
Viral replication
a) Binding
b) Penetration of enveloped viruses (2 mechanisms)
c) Penetration of non-enveloped viruses
a) Binding between virus protein and cell receptors. (eg. HIV protein gp120 to CD4. Influenza haemagglutinin, HA to sialic acid. Sars-cov-2 spike protein to angiotensin converting enzyme II, ACE-2). Antibodies can neutralise viral protein binding by binding to the protein and block virus infection
b) Fusion between virus and cell membranes. 1) fusion at cell surface (eg HIV and measles). Occurs at a neutral pH (see image) 2) fusion with acidified intracellular vesicles. Dependent on acidification (see image)
c) After binding, there is a conformational change of the virus, leading to a disruption of membrane integrity, then the transfer of viral nucleic acid or capsid into the host cytosol. eg poliovirus, FMDV. Bacteriophage T4 (in E. coli) tail plate binding to host cell wall causes coiling of its sheath, causing the DNA to be injected into the cell through the core.
Viral replication - the eclipse phase
Virus particles have been disassembled, so no infectious particles are present. Expression of virus proteins (highly regulated, temporal and quantitative). Replication of virus nucleic acid (requires virus to encode its own nucleic acid polymerase or exploit/modify a host enzyme)
Grouping of viruses according to how they form mRNA
Group I (dsDNA) - can directly transcribe mRNA with host enzymes. eg herpes, pox, adeno, papova
Group II (ssDNA,+ve/-ve) - must first convert to ds DNA, then transcribe mRNA, eg parvo
Group III (dsRNA) - template must be copied by an enzyme in the virus particle. eg rota, blue tongue
Group IV (ssRNA, +ve) - is mRNA. eg picorna, flavi, corona, alpha
Group V (ssRNA, -ve) - must be converted to mRNA by enzyme in viral particle
Group VI (ssRNA, +ve) - use reverse transcription to first form dsDNA, then transcribed to mRNA. eg retro
