Viruses

How many viral types in 1 kg of marine sediment?

over a million different viral types

How many viral types in 200L of seawater?

about 5000 viral types

How many viruses living in the human gut?

>1000 different viruses

Name some examples of viruses causing pandemics + when

• 1918 - H1N1 virus

• 1957-1958 - H2N2 virus

• 1968 - H3N2 virus

• 2009 - H1N1 virus

• 2020 - covid19

How many deaths in 1918 from H1N1?

over 50 million

How many deaths from 1957-1958 from H2N2?

1.1 million

How many deaths in 1968 from H3N2?

1 million

How many deaths in 2009 from H1N1?

150 - 600 K

How many deaths from covid 19?

over 7 million

What does it mean that a virus is an obligatory parasite?

needs to hijack host metabolic machineries to replicate

How long are bacteria usually?

20 nm to 1 um

What are virus protein coats called? What do these surround?

capsids

nucleic acid genome

Do all viruses have a lipid membrane? What is this called?

no, facultative

envelope

What types of organisms can be infected by living organisms?

→ Archaea

→ Bacteria (bacteriophages)

→ Animals, Plants, Fungi, Protists

→ Viruses (virophages)

Is a virus genome ss or ds? And RNA?

both can be either

How many base pairs usually make up a viral genome ? What explains this size?

2 - 20 Kbp (1.2 Mbp for megaviruses)

minimal info required (hijacks host’s machineries); only specific genes

In terms of size, how do ds and ss compare and DNA and RNA compare? And the organisms housing them?

→ ds > ss; DNA >RNA

organisms will follow, if they have ds or DNA they’ll tend to be larger

What is a viral genome made up of in terms of molecules? What structure does it have?

usually 1 molecule, can be fragmented

To viral genomes tend to be plastic or rigid? How does this relate to their diversity?

plastic = very diverse viruses

What are capsids made up of?

proteins (one or more) called capsomers

What is the structure of capsids?

Self assembly products; highly ordered and symmetrical

Name two types of symmetries found within capsid structures

icosahedral (spherical virus) and helical (rod shaped virus)

Name the structure of the capsids in ebola?

helical (rod shaped virus)

What is the viral envelope made up of?

lipid bilayer with (glyco)proteins from host or virus-encoded

What is the role of the viral envelope ?

Allows entry into host cell (allows fusion/endocytosis) ie allows staying alive

What are some examples of proteins making up the viral envelope in SARS-Cov2?

spike protein = Binds to ACE-2 (modulate angiotensin II activity that increases blood pressure and inflammation)

What do bacteriophages contain in their head? How do they establish contact with host cells?

mixture of icosahedral/filamentous structures

specific proteins/receptors on their feet + contractile tail to inject their genetic material into host

What are2 types of complex viruses? What makes their complexity?

• bacteriophages

• archaea phages

combination of geometry of head/tail/filamentous structures/receptors and proteins etc

What are some examples of Archaea phages?

lemon shape, rod, filament etc

What’s an example of a non symmetrical virus?

poxyviridae (smallpox)

What were some problems associated with virus nomenclatures ie classification?

no standard/unity for how to name them, named after disease, place found, host/sign of disease, their shape, their discoverer, or a combination of the above (Rous Sarcoma virus is who discovered + what it causes)

What is the Baltimore classification reliant on? How many different classes of viruses are there?

1) The nature of the genome RNA/DNA

2) The type of RNA/DNA (ds, ss and polarity)

3) The genome replication mechanism

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What are the 3 classes of virus depending on how they replicate their genome?

Class I - semiconservative
Class II - classical semiconservative, discard (−) strand
Class VII - transcription followed by reverse transcription

If a virus has a dsDNA genome (classes I and VII) how do they make mRNA?

transcription of minus strand to make positive mRNA

If a virus has a ssDNA (+) virus genome (class II) how do they make mRNA?

first synthesise dsDNA intermediary then transcribe a minus mRNA strand

Which are the most efficient types of RNA viruses?

ssRNA + virus class IV

What is a positive strand of DNA/mRNA?

polarised molecule that can be directly translated into proteins by a host cell

What do all viruses whether RNA or DNA, have to make in order to replicate? What are some strategies for this?

positive mRNA

direct transcription, reverse transcription, intermediary transcription of minus strand

Which class of virus replicates through reverse transcription?

ssRNA + retrovirus class VI

Are viral genomes surrounded by a capsule?

no, by a capsid which is a protein coat

What is the capsid made up of? Can it contain polysaccharides? Lipids?

capsomeres

no! no!

Does the nucelocapsid contain lipids? Nucleic acids?

no

always!

What’s the revolution of the Baltimore classification?

provides a unified set of rules that can be applied to all viruses

Name the events describing the life cycle of a virus in the correct order?

attachment, genome injection, production of nucleic acid and proteins, assembly of virions, release

The life cycle of viruses requires the production of…?

a positive strand of RNA

Name the major components of viral particles

• nucleic acid genome (ds or ss, about 15KBP and 1 fragmented molecule)

• surrounded by a symmetrical capsid (made of capsomers)

• facultative lipid membrane (envelope) - allowing fusion with host

What makes viruses so diverse?

• possibility of mixture of morphological structures

• plastic genomes

• high mutation rates especially in RNA viruses

• can have ds or ss dna or rna

• recombination = viruses exchanging genetic info

What properties of viruses underpin the Baltimore classification?

genome nature (rna or dna)

genome type positive or negative ss ie polarity

how replication occurs ie replication mechanism

Describe the differences between lytic/virulent and temperate bacteriophages

enter host cell then burst out killing it = lysis of host cell

switch between lysogenic and lytic cycles so temperate will either cause an infection called lysogeny or lysis

What type of bacteriophage can switch between lytic and lysogenic cycles? Which doesn’t kill the host cell?

temperate phages

lysogenic cycle

What is HPV2 responsible for?

oncogenic virus that causes warts and cervical cancer

What can adeno-associated virus be used for? Why?

as a vector for gene therapy

bc harmless (adeno-associated virus)

What does reovirus cause? Is it dangerous?

severe gastroenteritis (diarrhoea etc)

deaths in countries where kids don’t have access to good water/hospitals

Is there a vaccine for HPV? For reovirus?

yes !

What does the foot and mouth disease virus cause? Does it affect humans?

blisters, ulcers so die bc can’t eat food

How did the gvt/EU respond to the foot and mouth virus?

EU imposed a worldwide ban on British exports of livestock, meat & animal products, Netherlands slaughtered 100 000 times the nb of animals than the nb of cases

caused mayhem! no six nations, no st patricks day :(

Does the influenza virus have a vaccine? Does it still kill people today?

yes but only effective if taken obvs

200 000 people still!

What does HIV cause? Can you live with it? How many died since the start of the pandemic ?

AIDS

Yes, 40 million live with it but 0.5 to 0.8 million deaths a year still today

40 million - today kept at bay but still devastating and not cured

What are 4 types of viruses?

bacteriophages, animals viruses, plant viruses, Archaea viruses

Describe a virion

specifically refers to the extracellular, infectious form of a virus, which is the particle responsible for initiating new infections

How do DNA viruses replicate?

virion integrated inside the host cell, capsid taken away to make the genetic material accessible

How do retroviruses Group VI replicate? (ssRNA +)

small viral RNA is incorporated into the host DNA which then replicates its self therefore including the viral rna

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How are viral particles packaged?

Encapsidation is coupled with maturation of the replicative genome

How are fragmented genomes packaged ?

specifically 8 fragments of the fragmented genome brought together before encapsidation

How are capsomers assembled?

Electrostatic interactions between basic capsid proteins and RNA genome (acidic) = spontaneous assembly