Infectious Diseases Week 8

What family do coronaviruses belong to

Family Coronaviridae

When were coronaviruses first identified

In the 1950s

What are the viral properties of coronaviruses

Enveloped

SSRNA (+)

~31 kb – among the largest known RNA viruses

How long did it take to identify the host receptor for SARS-CoV

10 years

How long did it take to identify the host receptor for MERS-CoV

1 year

How long did it take to identify the host receptor for SARS-CoV-2

2 months

how many coronavirus strains can infect humans and cause mild to severe disease

7

when and where was SARS-CoV identified

March 2003 in Guandong province, China

How many cases and deaths did SARS-CoV cause

8,096 cases and 774 deaths (9.6% case fatality rate)

When was SARS-CoV contained

July 2003

How was SARS-CoV contained

Through regular containment measures – e.g., travel restrictions, quarantine, self-isolation

Is there a vaccine or antiviral available for SARS-CoV

No vaccine or antiviral available

What are the reservoirs for SARS-CoV

bats and civets

How many SARS-related coronaviruses have been discovered in bats

50+ SARS-related coronaviruses

What does MERS stand for

Middle East respiratory syndrome coronavirus

When and where did MERS-CoV emerge

In the Middle East in 2012-2013

How many people did MERS-CoV infect

Approximately 2.6K infections in 27 countries (943 deaths)

Where did MERS-CoV spread

Within the Middle East, with a small number of cases in Europe and the UK due to travel. South Korean outbreak in 2015

What does MERS-CoV cause

Acute respiratory infection/respiratory distress

Is there a vaccine or antiviral treatment for MERS-CoV

No vaccine or antiviral treatment developed

What are the reservoirs for MERS-CoV

Dromedary camels and bats

What receptor does MERS-CoV bind to

CD26 (also known as DPP4 receptors)

Does MERS-CoV bind to ACE2

No. MERS-CoV does not bind ACE2 (which is the SARS-CoV receptor)

What does the MERS-CoV RBD domain require

The specific receptor CD26/DPP4

When and where was SARS-CoV-2 (COVID) identified

End of 2019 Wuhan China

what was SARS-CoV-2 originally designated

2019-nCoV

How many cases were there worldwide by 2024

>776M cases worldwide (12M in Australia)

Does SARS-CoV-2 spread outside of the lung

Yes. It appears to spread outside of the lung – e.g., ocular transmission

What other clinical symptoms can SARS-CoV-2 cause

Blood clots, stroke, diabetes, cardiac injury, liver damage, kidney failure, skin rashes

Are there vaccines and antiviral treatments for SARS-CoV-2

Yes. Vaccine and antiviral treatment developed

What is the reservoir for SARS-CoV-2

Currently unknown, but bats and pangolins are thought to be involved

What is the spike protein of SARS-CoV-2 coated in

Sugar molecules, or glycans

What do the glycans do

Disguise the spike protein from the immune system

How many points can the spike protein hinge at on the stalk

Three points – giving it flexibility

What are the regions of the spike protein

Receptor-binding domain

S1 subunit

S2 subunit

stalk (with hip, knee, and ankle regions)

glycan coating

What does the SARS-CoV-2 spike protein bind to on the host cell

ACE2 (angiotensin-converting enzyme 2)

What enzyme cleaves the spike protein

TMPRSS2 (host molecule)

What does TMPRSS2 cleavage expose

Parts of the spike that fuse the viral membrane with that of the host

What happens after the spike protein is cut

The spike glycoprotein folds back onto itself, like a zipper, forcing the viral and cell membranes to fuse

What hydrophobic amino acids are exposed

Hydrophobic amino acids in the spike that rapidly embed themselves into the nearest membrane – that of the host cell

What happens in Stage 2 of SARS-CoV-2 life cycle: Inside the cell

Viral RNA is translated into non-structural proteins (NSPs) that quickly suppress the translation of host messenger RNAs in favour of those belonging to the virus

What happens in Stage 3: Remodelling the cell

The virus transforms the cell's ER into bubble-like structures called double-membrane vesicles (DMVs). These might provide a safe haven for more viral RNA to be replicated and translated

What happens in Stage 4: Exit

Once the newly made molecules assemble into a complete virus particle, it leaves the cell through an organelle called the Golgi apparatus, or perhaps through lysosomes

What happens in Stage 5: The last slice

A host enzyme named furin makes a crucial cut at a site of five amino acids on the spike protein. This prepares the virus to strike another cell

Do variants have a higher proportion of snipped spike proteins

Yes. Variants have a higher proportion of snipped spike proteins, helping them to infect cells more efficiently

What do SARS-CoV-2 infected cells create

Large multinucleated respiratory cells (syncytia) filled with up to 20 nuclei

What was generated to identify the host receptor for SARS

Pseudoviruses

What vector was used

Vesicular stomatitis virus (VSV) vector

What are 293T cells

Epithelial-like cells isolated from the kidney of a patient

What does the pseudovirus system encode

The spike protein, and the virion proteins to form a mature virus except the env genes

Why can't mature virions be formed

The absence of Env gene expression means that mature virions cannot be formed

What was shown to be the natural reservoir for SARS

Chinese horseshoe bats

How long after the epidemic was the receptor for SARS discovered

10 years

What does the SARS viral spike protein bind to

Angiotensin-converting enzyme 2 (ACE2)

Where is ACE2 expressed

On endothelial cells of the lower respiratory tract

What does SARS use for S protein priming

the cellular serine protease TMPRSS2

What did the immunofluorescence assay show

Human, civet, and bat ACE2 all support SARS-CoV infection, while control cells with no receptor show no virus

What percentage amino acid identity do SARS-CoV and SARS-CoV-2 share

Approximately 76%

What receptor do both SARS-CoV and SARS-CoV-2 use

ACE2

What protease primes the spike protein for both viruses

TMPRSS2

What is the neutralisation efficiency by SARS convalescent sera for SARS-CoV vs SARS-CoV-2

High for SARS-CoV

Moderate for SARS-CoV-2

What is the cross-reactivity between SARS-CoV and SARS-CoV-2

weak

What is VSV and what does it mean that it is pantropic

Vesicular stomatitis virus – a pantropic virus can infect a wide range of cell types.

Do SARS and SARS-CoV-2 spike proteins facilitate similar patterns of viral uptake in human cell lines

yes – similar patterns in human cell lines but not so much in animal cell lines

What does this suggest about the virus

The virus must have a preference for the human receptor – adapted for human transmission

What cells were used to test receptor specificity for SARS CoV-2

BHK21 cells

What did BHK21 cells lack

A suitable receptor for SARS or SARS-CoV-2

What happened when BHK21 cells were transfected with human or bat ACE2

SARS and SARS-CoV-2 were taken up

What receptor does MERS bind to

hDPP4 (CD26)

Can MERS bind to ACE2 or APN

no

What receptor does 229E-S use

hAPN

Can 229E-S use hACE2 for viral infection

no

What happened when anti-hACE2 antibody was added

SARS and SARS-CoV-2 were inhibited in a dose-dependent manner

What did the native SARS-CoV-2 virus experiment confirm

That SARS-CoV-2 uses hACE2 as its receptor

Why is knowing the receptor important

It guides development of antiviral therapeutics:

(i) Design drugs that target receptor entry

(ii) Vaccine targets

What is the incubation period

The interval between exposure to an infectious agent and the appearance of the first symptoms of the disease

What is the prodromal period

The time when the pathogen has yet to cause disease and onset of first symptoms (fatigue, malaise, mild fever)

What is the illness period

The acute period when disease symptoms are at their peak

What is the decline period

Once symptoms begin to subside

What is the convalescence period

The last period of disease progression where the individual regains strength and returns to normal health

What is incidence

Measures the number of new cases of a specific disease that develop in a population in a specified time period

What is prevalence

Measures the proportion of a population who have a specific disease in a given time period, regardless of when the disease first developed

What symptoms are shared between flu and COVID-19

Fever, cough, fatigue – early symptoms are shared among a number of respiratory infections

What are the complications of flu

Less likely to occur because of immunity built up over time

What are the complications of COVID-19

Severe respiratory complications may come on extremely quickly; gastrointestinal symptoms, clotting → stroke, diabetes, inflammatory skin lesions

What did the SARS-CoV-2 virus cause

A respiratory infection that led to significant acute respiratory distress

What happened in the lungs of infected patients

Fluid accumulated within the lungs, making it difficult to breathe due to reduced oxygen exchange

Has acute respiratory distress been noted for other respiratory viruses

Yes – including influenza A

What is required to control viral infections

Innate and adaptive immune system

What cells arrive at the site of infection

Macrophages and neutrophils arrive and recruit lymphocytes

What do CD8+ T-cells do

Kill viral-infected cells

What do CD4+ T-cells do

Provide help for B-cells → antibody production

What are alveoli

Air sacs where oxygen transfers from the lungs into the bloodstream

What do cytokine molecules stimulate

The movement of cells towards sites of inflammation, infection, and trauma

What is thought to be over-activated in response to SARS-CoV-2 infection

The immune system

What does this over-activation lead to

Massive release of proinflammatory cytokines = cytokine storm

Can a cytokine storm be observed in other conditions

Yes – in some cases of autoimmunity