SARS-CoV-2 Flashcards
(31 cards)
Transmission of viruses
Expelled on large droplets or fine aerosols
Airborne transmission - particle cut off size 30-100 micrometres
Affected by environment, temperature, humidity, air flow
Short range transmission of viruses (primary transmission)
Droplets - > 5 micrometres that fall on the ground
Aerosols - 5 micrometers suspended in the air
Direct (physical) contact
Indirect contact (fomite (inatimate objects))
Long-range transmission of viruses (primary transmission)
-Aerosol
-Indirect contact (fomite - inatimate objects)
How to prevent transmission
Viral RNA decays slowly over time - sensitive to heat (highly stable at low temperatures).
Droplet transmission is more important that aerosol transmission - good ventilation is cruical to lower secondary transmission
Main sources of transmission from humans
Directly from respiratory tract
Poor hand hygiene
Vertical Transmission (from mother to offspring)
IgM does not cross the placenta due to its size -seen in fetuses as a result of fetal immunologic response to pathogens, an ability that is acquired early in the first trimester of pregnancy..?
Breast milk can contain vRNA – no reported cases
Very Rarely occurs
Faecal-Oral/ Faecal Aerosol transmission
High number of ACE2 receptors in the bowel
vRNA is in faeces but it is not infectious
No evidence in humans
Sexual Transmission
Semen can contain vRNA
Vaginal fluids negative for vRNA except in very rare cases
Not infectious
Bloodborne transmission
Virus is in the periphery..?perhiperal nervous system???
No documented cases of bloodborne transmission
Pets and Animals transmission
Reports of cats, ferrets and dogs
No documented case of transmission from pet to humans
Non-Alcohol based Hand-sanitiser - Example and how it works
-Benzalkonium chloride – commonly used disinfectant
-Disrupts bacterial cell membranes
-Hydrogen peroxide kills bacterial spores
Alcohol based Hand-sanitiser - examples and mechanism
Isopropyl alcohol and ethanol
Dissolves viral envelope proteins and the nucleocapsid
Exposes the vRNA/ genetic material for degradation
Disrupts viral entry and transmission
Ethanol is very effective against enveloped viruses
Virology of Coronavirus
Family: Coronviridae
Subfamily: Coronavirinae
Four genera:
– Alphacoronavirus, Betacoronavirus (humans and mammals)
– Gammacoronavirus and Deltacoronavirus (birds and fish, some mammals)
Alphacoronavirus (α-CoV 229E and NL63)
Betacoronavirus (β-CoV OC43 and HKU1)
Highly pathogenic and virulent subtypes: Betacoronavirus
SARS-CoV-1, (10 % mortality)
MERS (36 % mortality)
SARS-CoV-2 (3.8 % mortality globally) – 79 – 82 % genome sequence identity
Non-Structural protein (NSP1) is identified in Alpha and Beta.
Components of SARS-CoV-2 Virus
Structural proteins:
Nucleocapsid , Membrane Protein, Envelope Protein , Spike Glycoprotein (24-40 proteins)
Positive sense single stranded RNA of 30,000 nt
13-15 open reading frames
12 expressed proteins
ORF NS proteins 1a = replicase
ORF NS proteins 1b = protease – 96 % similarity
Mechanism of SARS-CoV-2
Virus prevents cellular mRNA from exiting the nucleus – blocking the immune response system – NSp1 prevents interferon from being activated
Mechanism of SARS-CoV-2 - role of spike glycoprotein
- Glycosylated Type I membrane protein
- Trimeric pre-fusion form
- Host furin protease – cleaves the S protein into S1 and S2 units
- N Terminal S1 contains receptor binding domain (RBD)
- Host - Angiotensin converting enzyme 2 receptor (ACE2) – 2-4 x strength
- Further cleavage by host serine protease TMPRSS2 of S2 unit triggers entry
- In vitro – exists as pre and post fusion forms
-ACE2 - enzyme cleaves angiotensin I into 1-9 and angiotensin II into 1-7
~ 600 plasma and sera samples identified majority nAb to the RBD
TMPRSS2 role
Causes further viral cleavage of S2 to trigger viral entry.
Highly expressed in several tissues
-Co-expressed with ACE2 in nasal epithelial cells, lungs and bronchial branches
-Cathepsin L and Furin involved alongside TMPRSS2
-SARS-CoV-2 receptor RBD
What happens inside a host cell after viral entry for viral replication inside host
Viral entry triggers the translation of ORF1a and ORF1b
Produces pp1a and pp1ab - forms the replication complex
Exocytosis is through Golgi pathway or lysosomes – slow and inefficient but persistent
Exit includes five aa – proline, arginine, arginine, alanine and arginine – host furin clips it – essential for lung cell entry
SARS-CoV-2 RdRp
RdRp Used for replication of its genome and the transcription of its genes.
Composed of a catalytic subunit known as NSP 12 - Accessory units are NSP8 and NSP7
Unique RdRp contains long protruding extended RNA regions in NSP8
NSP12 subunit binds to the vRNA between fingers and thumb
Active site is on the palm
The vRNA exits as a duplex from the NSP12
It is unknown how vRNA strands are separated during transcription of viral genes
Why do we see variants?
Poor public health infrastructure
Poor education and understanding of infection and disease
Increased infections of other infectious diseases
Lower vaccination rate
Anti-vaxxers and mis-information
Immunocompromised individuals - Weak immune protection More susceptible to infection Chronic infections
Immunodominance -
Is the consistent feature of the human immune response against a wide array of small and complex pathogens
Study of 650 individuals - 90 % of plasma and serum Ab target the RBD (receptor binding domain)
-nAb block viral protein conformational changes or interactions with entry receptors
-S2 subunit is protected by glycan shielding and immunogenicity is not fully understood
Four classes of RBD-binding neutralising antibodies (nAb)
Class 1 – bind the spike protein in open conformation
Class 2 – ACE2 blocking antibodies – bind RBD in open and closed formation
Class 3 – do not block ACE2 – bind the RBD in open and closed conformation
Class 4 – bind outside the ACE2 site and only in RBD open conformation
Virus escape mutants -
specific mutations helping to achieve the process of immune escape.
Virus escape mutants - Antigenic change examples
Amino acid substitutions – altering the viral epitope
Substitutions in the receptor binding domain (RBD) – increases ACE2 affinity
Glycosylation – the glycan shield – masking
Deletions and insertions – alters the epitope conformation – blocking ab
Allosteric effects outside the epitope – alters the protein confirmation
Virus escape mutants - Antigenic change examples in Cov- 2
two mutations per month in the global population between Dec 2019 and october 2020:Amino acid substitutions within the spike receptor binding motif - Enhancing binding of the ACE2 receptor and reduceing neutralising antibodies.
-B.1.1.298 lineage has the Y453F mutation and a Δ69-70 deletion – alters the conformation of an exposed amino terminal domain loop – increases infectivity
