Coronaviruses

Question 1

How many human coronaviruses have been identified?

Answer 1

• 7
• mostly associated with the common cold
• not well studied before SAR-CoV-2
• can be alpha, beta, delta or gamma

Question 2

What kind of virus is coronavirus?

Answer 2

• ssRNA positive sense
• nidovirales

Question 3

What are the 4 main genes in a coronavirus genome?

Answer 3

• structural (S)
• N protein
• M protein
• E protein
• many accessory proteins

Question 4

What are some of the roles of the structural protein in the coronavirus genome?

Answer 4

• form large spikes on the virion surface
• bind specific cellular receptors
• induces fusion of the viral envelope with the cell membrane
• induces neutralising Abs and cell mediated immunity

Question 5

What is the role of the N protein of coronavirus?

Answer 5

• binds viral RNA and aids in its synthesis
• forms the nucleocapsid
• also involved in cell-mediated immunity

Question 6

What is the role of the M protein in the coronavirus genome?

Answer 6

• determines budding site
• triggers viral assembly
• forms the shell of the internal viral core

Question 7

What is the role of the E protein of coronavirus?

Answer 7

• triggers particle assembly
• associates with the viral envelope to form an ion channel
• may cause host cell apoptosis

Question 8

What are the roles of accessory proteins encoded on the coronavirus genome?

Answer 8

• avoiding host immune responses
• deleting these doesnt affect replication in culture but may in animals

Question 9

How does coronavirus enter the cell?

Answer 9

• receptor binding and endosome entry
• or fusion with the cell membrane
• proteases cleave the spike proteins from the surface as/before the cell enters

Question 10

How can coronavirus shield itself from the host immune response while building up metabolites/components needed for replication?

Answer 10

• some viral proteins induce double membrane vesicles derived from the ER
• contain intermediates of RNA replication and have a pore through which the viral genome can interact while staying protected

Question 11

How does a frameshift came into coronavirus replication?

Answer 11

• not just 1 long ORF like many viruses
• translation of ORF1 occurs
• ribosome reaches a complex RNA structure that 5% of the time causes it to slip back 1 nucleotide, miss the stop codon and translate the rest
• acts as a way to regulate proteins needed in lower quantities such as viral replication proteins

Question 12

What cleaves the polyproteins produced in coronavirus replication?

Answer 12

• viral encoded proteases
• NSP5 cleaves ORF1
• PLpro also involved

Question 13

What proteins are encoded in the coronavirus genome? nae 6

Answer 13

• RNA dependent polymerase
• helicase
• RNA capping enzymes
• endo+exo nucleases
• NSP3+4 induce double membrane vesicles
• NSP1 shuts down host translation

Question 14

Describe the role of subgenomic RNAs in the coronavirus genome

Answer 14

• produce the accessory proteins
• made as a result of discontinuous transcription

Question 15

How does discontinuous transcription lead to the production of subgenomic RNAs?

Answer 15

• replication-translation complex reaches specific TRS elements on the genome
• RTC jumps to the 5’ end and produces sgRNA -> sgmRNA -> accessory proteins

Question 16

What is the role of continuous transcription?

Answer 16

• to produce full-length negative sense RNA internediates that act as a template for genome replication

Question 17

What is the genome size of a coronavirus compared to other positive sense RNA viruses?

Answer 17

• much larger
• has proof-reading enzymes while others dont
• lower accuracy of others may impose an upper limit on the size of their genomes

Question 18

What are the main ORFs seen in coronaviruses?

Answer 18

• ORF1a = genome expression
• ORF1b = genome replication
• 3’ ORFs = virus dissemination

Question 19

How does coronavirus evade the innate immune response? (5)

Answer 19

• encode many proteins to:
• inhibit interferon signalling or production (NSP1 can stop their translation)
• inhibiting antiviral proteins like PKR
• structural proteins like N can interfere with host defense machinery
• inhibition of inflammasomes
• inhibition of NK cells

Question 20

What are 3 of the most commonly known and well studied coronaviruses?

Answer 20

• SARS-CoV
• MERS-CoV
• SARS-CoV2

Question 21

Describe same clinical difference and similarities between SARS-CoV, MERS-CoV and SARS-CoV2

Answer 21

Question 22

How are MERS-CoV and SARS-CoV-2 spread?

Answer 22

• droplets
• aerosol spread
• contaminated surfaces

Question 23

Where does SARS-CoV-2 replicate + what is immunity like>

Answer 23

• throughout the respiratory tract
• unknown duration of immunity

Question 24

Where do SARS-CoV and MERS-CoV replicate + what is immunity like>

Answer 24

• in the lower respiratory tract
• long-lived memory T cell response proportional to disease

Question 25

What happens once SARS-CoV-2 enters the lungs?

Answer 25

- destruction of cells leads to inflammatory response - in some, excessive infiltration of monocytes, macrophages and T cells leads to widespread inflammation, organ damage and cytokine storm - in a healthy immune response the virus is cleared here or doesn't even make it to the lungs

Question 26

Where did human SARS-CoV + MERS-CoV come from?

Answer 26

- camels -> bats - bats -> civets and other traded animals - civets or camels -> humans - mixture of cross-species and zoonotic transmission

Question 27

Where did human SARS-CoV-2 come from?

Answer 27

- bats -> unsure intermediate host (bats?) -> humans - mixture of cross-species and zoonotic transmission

Question 28

What is the vaccine situation for coronavirus?

Answer 28

- 12 used worlwide and many in development for SARS-CoV- 2 - 3 candidates for MERS targeting the S protein

Question 29

How did civet-infecting SARS-CoV move to infect humans?

Answer 29

- spike protein binds ACE-2 with a receptor binding motif - civet and humans have similar ACE-2 - motif only needs a 2 amino acid shift to have high affinity to both ACE-2s

Question 30

What kinds of issues have hampered coronavirus vaccine development in the past?

Answer 30

- some trials enhanced disease - used to have a lack of understanding of the immune response to SARS - animals cant fully recapitulate human disease

Question 31

How has SARS-CoV-2 adapted to increase infection rate?

Answer 31

- acquired an extra furin cleavage site in the spike protein - spike gets cleaved before leaving the host cell priming it for entry to the next one - this mutation destabilises the virus but further mutations fixed this - also allows binding to a wider variety of respiratory tract cells

Question 32

What do we know about immunity to coronavirus?

Answer 32

- little - immunity wanes rapidly - poor understanding of how prior infection with other coronaviruses affects later infections

Question 33

What is antigenic cartography>

Answer 33

- mapping relationships between antigenic variants of a virus - provides a quantitative + visual summary of antigenic differences - can see evolution of the virus and how existing treatments might fare against now/other strains

Question 34

What antivirals are available for coronavirus?

Answer 34

- repurposed drugs - mostly inaffective at reducing mortality, need for assisted ventilation or duration of hostpital stays