Coronaviridae Basic Flashcards by B RB

Family of SARS-CoV-2

Coronaviridae

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SubFamily of SARS-CoV-2?

Coronavirinae

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Alphacoronavirus that infects Humans

HCoV-229E and HCOV-NL63

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Betacoronavirus that infects human

-HCoV-0C43
-HCOV-HKU1
-SARS-CoV
-SARS-CoV-2
-MERS-CoV

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Animals that can be infected by Betacoronavirus Genus

-Mice
-Bat
-Pig
-Dog
-Cows
-Horses
-Humans
-etc

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Primary Host Cell Receptor of HCoV-229E

Aminopeptidase N (APN)

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Primary Host Cell Receptor HCoV-NL63

Angiotensin-converting enzyme 2 (ACE2)

Potential Additional Receptors: Heparan sulfate, CD209L

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Primary Host Cell Receptor of
HCoV-OC43

Sialic acid (multiple receptors) and Neuropilin-1as a secondary probably receptor

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Primary Host Cell Receptor of HCoV-HKU1

9-O-Acetyl-sialic acid

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Primary Host Cell Receptor of SARS-CoV-1

ACE2

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Primary Host Cell Receptor of MERS-CoV

Dipeptidyl peptidase 4 (DPP4)

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Primary Host Cell Receptor of SARS-COV-2

ACE2

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All seven CoV that infects human has Spike protein?

Yes

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Type of DNA of all Coronaviridae species

Positive-sense
Single-stranded
RNA

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Define the characteristics of the Betacoronavirus genus

Enveloped, positive-sense single-stranded RNA, spike glycoproteins in S1 and S2 subunits.

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Briefly describe the clinical symptoms caused by SARS-CoV

Fever, cough, shortness of breath, pneumonia

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SARS-CoV-2: higher affinity for ACE2 because…?

Has a furin cleavage site

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What is the furin cleavage site?

specific sequence of amino acids found in the spike protein and plays a crucial role in viral entry and infectivity.

Cleaved by an enzyme called furin activates the spike protein,enabling it to fuse with the host cell membrane

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SARS-COV-1 has furin cleavage site?

No, only SARS-CoV-2

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How does MERS-CoV differ from other Betacoronaviruses in terms of transmission?

MERS-CoV primarily transmitted through direct contact with dromedary camels, while SARS-CoV and SARS-CoV-2 mainly through respiratory droplets.

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How does the virus gain entry into the host cell?

Spike protein binds to a host cell receptor, followed by membrane fusion and viral entry.

What is the role of RNA-dependent RNA polymerase (RdRp) in replication?

Synthesizes new copies of viral RNA using the existing RNA as a template

Briefly describe the function of the spike protein

Mediates attachment,entry,and fusion with the host cell membrane.

What are the two subunits of the spike protein, and what is their significance?

S1:receptor binding; S2:membrane fusion.Mutations in S1 can affect host range and transmissibility.

Describe the function of the nucleocapsid protein (N).

Encapsulates the viral RNA genome, protecting it and facilitating replication

What is the role of non-structural proteins (Nsps) in replication?

Diverse functions, including RNA processing, immune evasion, and modifying host cell machinery for viral benefit.

What are the main types of antivirals used against Betacoronaviruses?

Direct-acting antivirals (DAAs) and nucleoside analogs.

How do Direct-acting antivirals (DAAs) work?

Inhibit specific viral proteins critical for replication, such as RdRp or proteases.

Explain the mechanism of action of nucleoside analogs antivirals

Mimic natural building blocks of RNA, incorporated into viral RNA, leading to chain termination and impaired replication.

Briefly describe the concept of viral proofreading and its relevance to antiviral resistance

Viruses lack robust proofreading mechanisms, leading to higher mutation rates and potential for resistance development.

What are the roles of the envelope (E), membrane (M), and nucleocapsid (N) proteins in SARS-CoV-2?

E: virion assembly and budding; M: virion shape and integrity; N: encapsulates RNA genome.

Briefly explain the functions of non-structural proteins (Nsps) 10 and 12 in SARS-CoV-2 replication.

Nsp10: suppresses host protein synthesis; Nsp12: aids RNA synthesis and proofreading.

Briefly describe the process of virion assembly and release in SARS-CoV-2.

Occurs in the endoplasmic reticulum-Golgi complex, involving interactions between viral proteins and host membranes.

Which FDA-approved drugs are currently used to treat COVID-19 caused by SARS-CoV-2?

Paxlovid, Molnupiravir, Remdesivir (with limitations).

Explain the mechanism of action of Paxlovid against SARS-CoV-2.

Inhibits the viral protease Mpro, essential for viral replication. main protease (Mpro), also known as the 3-chymotrypsin-like protease (3CLpro), is another crucial enzyme in the life cycle

How does Remdesivir exert its antiviral effect against SARS-CoV-2?

Acts as a nucleotide analog, interfering with viral RNA synthesis

Front: What is the composition of the SARS-CoV-2 viral envelope?

Lipid bilayer derived from host cell membranes, embedded with viral proteins like spike, E, and M.

How does the lipid composition of the SARS-CoV-2 envelope influence its infectivity and immune evasion?

May contribute to viral fusion with host cells and potentially modulate immune response.

What is the genome sequence identity shared between SARS-CoV-2 and SARS-CoV?

SARS-CoV-2 shares ~80% genome sequence identity with SARS-CoV.

How much genome sequence identity does SARS-CoV-2 share with MERS-CoV?

SARS-CoV-2 shares 50% genome sequence identity with MERS-CoV

What are the structural genes of SARS-CoV-2?

The structural genes of SARS-CoV-2 are spike (S), envelope (E), membrane (M), and nucleocapsid (N).

What is the name of the International Committee of Viruses

International Committee on Taxonomy of Viruses (ICTV)

Which species of bat shares the highest genome sequence identity with SARS-CoV-2?

Rhinolophus affinis shares the highest genome sequence identity with SARS-CoV-2 among bats.

What are the two bat coronaviruses closely related to SARS-CoV-2, besides RaTG13?

RmYN02 and bat coronaviruses ZC45 and ZXC21 are closely related to SARS-CoV-2.

What is the full size of the S protein of SARS-CoV-2?

The full size of the S protein of SARS-CoV-2 is 1,273 amino acids.

Which enzyme participates in the cleavage of the S protein and activates the entry of SARS-CoV-2?

Host proteases, including transmembrane protease serine protease 2 (TMPRSS2), cathepsin L, and furin, participate in the cleavage of the S protein and activate the entry of SARS-CoV-2.

What are the structural domains of the S1 subunit of SARS-CoV-2?

The S1 subunit of SARS-CoV-2 consists of two functional domains: an N-terminal domain and a C-terminal domain.

What is the target of neutralizing antibodies in SARS-CoV-2?

The RBD (receptor-binding domain) of the S1 C-terminal domain is the target of neutralizing antibodies in SARS-CoV-2.

Which is the size of SARS-CoV-2 whole genome?

Approximately 30,000 base pairs. 30K

Base pairs of the Spike Protein of SARS-CoV-2?

3,822 base pairs