Coronaviruses: Genes and Proteins

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Questions and Answers

What is the structure of coronaviruses' enveloped virions?

They contain complex nucleocapsids

They contain icosahedral nucleocapsids

They contain spherical nucleocapsids

They contain helical nucleocapsids (correct)

Which genera are based on genome homologies within the family Coronaviridae?

Theta-, iota-, and kappa coronaviruses

Lambda-, mu-, and nu coronaviruses

Delta-, epsilon-, and zetacoronaviruses

Alpha-, beta-, and gammacoronaviruses (correct)

What is the mode of entry for coronaviruses into cells?

Entry by pinocytosis

Entry by endocytosis

Entry by exocytosis

Entry by fusion (correct)

What type of RNA viruses are coronaviruses?

<ul> <li>sense RNA viruses</li> </ul> Signup and view all the answers

What is the role of template switching in the process described?

It may help with genome repair and/or generate new viral strains/variants Signup and view all the answers

What is the function of ERGIC in the assembly of virions?

Transport, processing, and modification of proteins Signup and view all the answers

What is the role of M and E proteins in the formation of virus envelopes?

They play important roles in forming virus envelopes by budding Signup and view all the answers

How are mature virions packaged before being targeted to the plasma membrane for release?

They are packaged into vesicles and targeted to the plasma membrane for release Signup and view all the answers

What is the consequence if polymerase fails to find another template after dissociation?

Transcription will abort, which can lead to template switch Signup and view all the answers

What happens as virus particles progress through Golgi membranes?

They become smaller and more uniformly dense, while envelope proteins undergo glycosylation Signup and view all the answers

Which protein is responsible for viral entry and tropism in coronaviruses?

Spike (S) protein Signup and view all the answers

What is the composition of the replicase gene (gene 1) in coronaviruses?

ORF1a and ORF1b Signup and view all the answers

What activities are involved in coronavirus replication?

RNA helicase and nucleoside triphosphatase activities Signup and view all the answers

Where are replication complexes commonly observed in coronavirus-infected cells?

Double membrane vesicles Signup and view all the answers

How are subgenomic mRNAs transcribed in coronaviruses?

Transcription from subgenomic negative-strand mRNA templates made by discontinuous transcription Signup and view all the answers

What is the structure of nucleocapsids in coronaviruses?

Viral N-protein bound to viral RNA in a spherical core structure formed via the M-protein Signup and view all the answers

Which of the following is true about the genome of coronaviruses?

Coronaviruses have a positive-sense RNA genome Signup and view all the answers

What is the most common natural reservoir of CoV, according to the text?

Bats Signup and view all the answers

What is the primary role of spikes in coronaviruses?

Facilitate virus entry into cells Signup and view all the answers

Which family does the SARS coronavirus belong to?

Coronaviridae Signup and view all the answers

What is the primary role of the M and E proteins in the formation of virus envelopes in coronaviruses?

Assisting in the budding of virus particles into the lumen of intracellular membranes Signup and view all the answers

What is the consequence if polymerase fails to find another template after dissociation during coronavirus replication?

Transcription will abort, leading to template switch Signup and view all the answers

Where are replication complexes commonly observed in coronavirus-infected cells?

Perinuclear region of the cell Signup and view all the answers

What is the function of ERGIC in the assembly of virions in coronaviruses?

Transport, processing, and modification of proteins involved in virion assembly Signup and view all the answers

What activities are involved in coronavirus replication?

Formation of RNA-RNA hybrids at 5’ TRS and glycosylation process during transit through Golgi membranes Signup and view all the answers

What happens as virus particles progress through Golgi membranes?

They acquire donut-shaped cores and become smaller and more uniformly dense Signup and view all the answers

What is the mode of entry for coronaviruses into cells?

Receptor-mediated endocytosis followed by membrane fusion Signup and view all the answers

Which one is true about the genome of coronaviruses?

It contains multiple subgenomic ‘-‘ strands used to make ‘+’ strand mRNA for protein synthesis Signup and view all the answers

What is the primary role of the spike protein in coronaviruses?

Facilitating viral entry and tropism Signup and view all the answers

What is the composition of the replicase gene (gene 1) in coronaviruses?

ORF1a and ORF1b Signup and view all the answers

What is the function of the M-protein in coronaviruses?

Forming the spherical core structure Signup and view all the answers

What is the role of RNA helicase in coronavirus replication?

Unwinding double-stranded RNA Signup and view all the answers

Where are replication complexes commonly observed in coronavirus-infected cells?

On double membrane vesicles Signup and view all the answers

What is the structure of subgenomic mRNAs in coronaviruses?

Contain overlapping sequences on their 3' end Signup and view all the answers

What is the consequence if polymerase fails to find another template after dissociation?

Increased mutation rate Signup and view all the answers

What activities are involved in coronavirus replication?

RNA helicase, nucleoside triphosphatase, and exonuclease activities Signup and view all the answers

What is the role of membrane association in coronavirus replication?

Common among '+ strand RNA viruses of eukaryotes Signup and view all the answers

What is the primary function of nucleocapsids in coronaviruses?

Contain viral N-protein bound to viral RNA in a helical fashion Signup and view all the answers

Which cellular component undergoes rearrangement during coronavirus infection?

Subcellular architecture and membrane structures Signup and view all the answers

What is the primary role of spikes in coronaviruses?

Facilitate virus entry into host cells by binding to receptors Signup and view all the answers

Which family does the SARS coronavirus belong to?

Coronaviridae Signup and view all the answers

Where are coronaviruses commonly found in nature?

Bats Signup and view all the answers

What is the mode of entry for coronaviruses into cells?

Entry by fusion Signup and view all the answers

During coronavirus replication, polymerase can pause and dissociate at any of the TRSs. What is the consequence if polymerase fails to find another template after dissociation?

Transcription will abort, leading to template switch Signup and view all the answers

What is the primary role of the M and E proteins in the formation of virus envelopes in coronaviruses?

Assist in budding of virus particles Signup and view all the answers

Where are virions packaged into vesicles before being targeted to the plasma membrane for release?

Golgi apparatus Signup and view all the answers

What is the function of ERGIC in the assembly of virions in coronaviruses?

Transport, processing, and modification of proteins Signup and view all the answers

What is the mode of assembly for enveloped virus-like particles when only M and E proteins are expressed?

$M$ and $E$ proteins interact with each other to form the particles Signup and view all the answers

What is the primary role of nucleocapsids in coronaviruses?

Protection of viral RNA from degradation Signup and view all the answers

What happens as virus particles progress through Golgi membranes?

They undergo glycosylation of envelope proteins Signup and view all the answers

What is the role of template switching in coronavirus replication?

It may help with genome repair and generate new viral strains/variants Signup and view all the answers

What is the primary function of the spike protein in coronaviruses?

Facilitates viral entry and tropism Signup and view all the answers

What is the composition of the replicase gene (gene 1) in coronaviruses?

ORF1a and ORF1b Signup and view all the answers

Where are replication complexes commonly observed in coronavirus-infected cells?

On double membrane vesicles Signup and view all the answers

What is the structure of coronaviruses' enveloped virions?

'+ strand RNA viruses Signup and view all the answers

What is the role of subgenomic mRNAs in coronaviruses?

Transcribed from subgenomic negative-strand mRNA templates made by discontinuous transcription Signup and view all the answers

What activities are involved in coronavirus replication?

RNA helicase, nucleoside triphosphatase activities, and RNA exonuclease with proofreading activity Signup and view all the answers

What is the consequence if polymerase fails to find another template after dissociation during coronavirus replication?

Incomplete synthesis of viral genome Signup and view all the answers

What is the primary role of nucleocapsids in coronaviruses?

Formed from viral N-protein bound to viral RNA in a helical fashion Signup and view all the answers

What is the function of the M-protein in coronaviruses?

Forms the spherical core structure via the M-protein. Signup and view all the answers

What is the mode of entry for coronaviruses into cells?

Spike proteins bind to a variety of cellular receptors for entry. Signup and view all the answers

What is the primary mode of entry for coronaviruses into cells?

Direct membrane fusion Signup and view all the answers

Which genera are based on genome homologies within the family Coronaviridae?

Alpha-, beta-, and gammacoronaviruses Signup and view all the answers

What is the most common natural reservoir of CoV where SARS was found?

Bats Signup and view all the answers

What is the structure of virions in coronaviruses?

Enveloped virions containing helical nucleocapsids Signup and view all the answers

What is the primary role of template switching in coronavirus replication?

Generating new viral strains/variants through recombination Signup and view all the answers

What is the function of the C-terminal cytoplasmic tail of the M protein in coronaviruses?

Interacting with packaging signals in N to ensure only full-length viral RNA gets packaged into virions Signup and view all the answers

Where does the assembly of virions take place in coronaviruses?

ERGIC (endoplasmic reticulum Golgi intermediate compartment) Signup and view all the answers

What is the primary role of the M and E proteins in the formation of virus envelopes in coronaviruses?

Playing important roles in forming the virus envelopes by budding Signup and view all the answers

What is the structure where helical nucleocapsids containing genome RNA are delivered for packaging?

ERGIC (endoplasmic reticulum Golgi intermediate compartment) Signup and view all the answers

Which protein is responsible for interacting with packaging signals to ensure only full-length viral RNA gets packaged into virions?

M protein Signup and view all the answers

Where do mature virions get packaged before being targeted to the plasma membrane for release?

Secretory vesicles Signup and view all the answers

What is the role of subgenomic mRNAs in coronaviruses?

Acting as templates for protein synthesis during translation Signup and view all the answers

What is the primary function of the nucleocapsid protein in coronaviruses?

Forming the structure for viral RNA in a helical fashion Signup and view all the answers

What is the role of the HE (hemagglutinin esterase) protein in some coronaviruses?

Facilitating viral entry into host cells Signup and view all the answers

What is the function of the RNA helicase in coronavirus replication?

Assisting in genome replication Signup and view all the answers

What is the primary function of the E (envelope) protein in coronaviruses?

Forming ion channels that contribute to virus pathogenesis Signup and view all the answers

What is the mode of assembly for enveloped virus-like particles when only M and E proteins are expressed?

Formation of virus-like particles with M and E proteins incorporated into their envelopes Signup and view all the answers

What is the structure of subgenomic mRNAs in coronaviruses?

Contain overlapping sequences on their 3' end Signup and view all the answers

What is the consequence if polymerase fails to find another template after dissociation during coronavirus replication?

Generation of defective subgenomic mRNAs Signup and view all the answers

What activities are involved in coronavirus replication?

RNA helicase and nucleoside triphosphatase activities, and RNA exonuclease with proofreading activity Signup and view all the answers

Where are genome replication complexes commonly observed during coronavirus infection?

On convoluted membranes within infected cells Signup and view all the answers

What is the structure of coronaviruses' enveloped virions?

Spherical core structures formed via the M-protein with spike proteins embedded within them Signup and view all the answers

What is the diameter of naked icosahedral capsid of Picornaviruses?

~30nm Signup and view all the answers

How many copies of each of the three to four proteins are present in a mature Picornavirus virion?

60 copies Signup and view all the answers

What is covalently bound to the 5’ end of the RNA in Picornaviruses?

VPg Signup and view all the answers

How is the genome of Picornaviruses structured?

<ul> <li>sense ssRNA genome</li> </ul> Signup and view all the answers

What is the primary function of the Flavivirus E protein?

Directs receptor binding and membrane fusion Signup and view all the answers

What is the consequence of antibody-dependent enhancement (ADE) in flaviviruses?

Causes more severe diseases like dengue hemorrhagic fever Signup and view all the answers

Where does the synthesis of non-structural proteins establish active RNA replicase complexes in flaviviruses?

On membranes in the cytoplasm Signup and view all the answers

What is the role of the precursor membrane protein (prM) in flaviviruses?

Associates with the E protein to form a heterodimer, protecting E from premature conformational changes Signup and view all the answers

What is the mode of entry for flaviviruses into cells?

Mediated by endocytosis within clathrin-coated vesicles Signup and view all the answers

What is the primary symptom range caused by Togaviruses in animals and humans?

Rashes, high fever, joint pain, encephalitis Signup and view all the answers

What is the function of the internal ribosome entry site (IRES) in the 5’ NCR of a viral genome?

To allow translation initiation without a 5’ cap Signup and view all the answers

What is the consequence of Picornavirus infection on cap-dependent translation?

Proteolytic cleavage of eIF-4G abolishes cap-dependent translation Signup and view all the answers

What is the role of IRES elements in viral RNA translation?

To imitate translation at the correct spot near AUG Signup and view all the answers

What is the primary mode of binding for virions to cellular receptors?

'Canyons' or loop regions on their surface Signup and view all the answers

What is the consequence of Picornavirus proteins being made as a single precursor polyprotein that is autocatalytically cleaved?

Generation of functional viral proteins Signup and view all the answers

What is involved in Picornavirus RNA replication after protein synthesis?

A multi-protein complex bound to cellular vesicles Signup and view all the answers

How does poliovirus RNA enter the cytoplasm?

Major rearrangement forming a channel in the cell membrane Signup and view all the answers

What is involved in Flavivirus virion assembly?

Cleavage of VP0 to VP2 plus VP4, assembling into protomers and provirion Signup and view all the answers

What is induced by Picornavirus infection in host cells?

Cytoplasmic vesicles and alteration of intracellular transport pathways Signup and view all the answers

How are Flavivirus envelope proteins arranged?

With icosahedral symmetry Signup and view all the answers

What does Flavivirus genome organization most resemble?

Picornaviruses, translated into a single, long polyprotein that undergoes proteolytic processing Signup and view all the answers

Study Notes

Coronavirus Structure and Replication Process

Nucleocapsids in coronaviruses are formed from viral N-protein bound to viral RNA in a helical fashion, resembling '-' strand RNA viruses, and some may have a spherical core structure formed via the M-protein.
Corona virions contain multiple envelope proteins: spike (S), membrane (M), envelope (E), nucleocapsid (N), and in some cases, HE (hemagglutinin esterase) protein.
Spike protein, a major surface transmembrane glycoprotein, is responsible for viral entry and tropism, and it generally forms trimers.
Spike proteins bind to a variety of cellular receptors, with different coronaviruses utilizing different receptors for entry.
The replicase gene (gene 1) in coronaviruses is composed of ORF1a and ORF1b, which are translated into polyproteins that are processed by viral proteinases.
RNA helicase and nucleoside triphosphatase activities, as well as RNA exonuclease with proofreading activity, are involved in coronavirus replication.
Membrane association of viral RNA synthesis is common among '+ strand RNA viruses of eukaryotes, and replication complexes are the site of viral RNA synthesis.
Coronavirus-induced membrane alterations involve the rearrangement of subcellular architecture, with replication complexes commonly observed on double membrane vesicles.
Genome replication proceeds via a full-length negative-strand intermediate, used to direct synthesis of full-length '+' strand genomes, and subgenomic mRNAs are transcribed from subgenomic negative-strand mRNA templates.
Subgenomic mRNAs contain overlapping sequences on their 3' end and are transcribed from subgenomic negative-strand mRNA templates made by discontinuous transcription.
Rearrangement of subcellular architecture and membrane association of viral RNA synthesis are observed in coronavirus-infected cells, involving double membrane vesicles and convoluted membranes.
The replicase gene in coronaviruses is composed of ORF1a and ORF1b, which are translated into polyproteins that are processed by viral proteinases.

Coronavirus Structure and Replication Process

Nucleocapsids in coronaviruses are formed from viral N-protein bound to viral RNA in a helical fashion, resembling '-' strand RNA viruses, and some may have a spherical core structure formed via the M-protein.
Corona virions contain multiple envelope proteins: spike (S), membrane (M), envelope (E), nucleocapsid (N), and in some cases, HE (hemagglutinin esterase) protein.
Spike protein, a major surface transmembrane glycoprotein, is responsible for viral entry and tropism, and it generally forms trimers.
Spike proteins bind to a variety of cellular receptors, with different coronaviruses utilizing different receptors for entry.
The replicase gene (gene 1) in coronaviruses is composed of ORF1a and ORF1b, which are translated into polyproteins that are processed by viral proteinases.
RNA helicase and nucleoside triphosphatase activities, as well as RNA exonuclease with proofreading activity, are involved in coronavirus replication.
Membrane association of viral RNA synthesis is common among '+ strand RNA viruses of eukaryotes, and replication complexes are the site of viral RNA synthesis.
Coronavirus-induced membrane alterations involve the rearrangement of subcellular architecture, with replication complexes commonly observed on double membrane vesicles.
Genome replication proceeds via a full-length negative-strand intermediate, used to direct synthesis of full-length '+' strand genomes, and subgenomic mRNAs are transcribed from subgenomic negative-strand mRNA templates.
Subgenomic mRNAs contain overlapping sequences on their 3' end and are transcribed from subgenomic negative-strand mRNA templates made by discontinuous transcription.
Rearrangement of subcellular architecture and membrane association of viral RNA synthesis are observed in coronavirus-infected cells, involving double membrane vesicles and convoluted membranes.
The replicase gene in coronaviruses is composed of ORF1a and ORF1b, which are translated into polyproteins that are processed by viral proteinases.

Coronavirus Structure and Replication Process

Nucleocapsids in coronaviruses are formed from viral N-protein bound to viral RNA in a helical fashion, resembling '-' strand RNA viruses, and some may have a spherical core structure formed via the M-protein.
Corona virions contain multiple envelope proteins: spike (S), membrane (M), envelope (E), nucleocapsid (N), and in some cases, HE (hemagglutinin esterase) protein.
Spike protein, a major surface transmembrane glycoprotein, is responsible for viral entry and tropism, and it generally forms trimers.
Spike proteins bind to a variety of cellular receptors, with different coronaviruses utilizing different receptors for entry.
The replicase gene (gene 1) in coronaviruses is composed of ORF1a and ORF1b, which are translated into polyproteins that are processed by viral proteinases.
RNA helicase and nucleoside triphosphatase activities, as well as RNA exonuclease with proofreading activity, are involved in coronavirus replication.
Membrane association of viral RNA synthesis is common among '+ strand RNA viruses of eukaryotes, and replication complexes are the site of viral RNA synthesis.
Coronavirus-induced membrane alterations involve the rearrangement of subcellular architecture, with replication complexes commonly observed on double membrane vesicles.
Genome replication proceeds via a full-length negative-strand intermediate, used to direct synthesis of full-length '+' strand genomes, and subgenomic mRNAs are transcribed from subgenomic negative-strand mRNA templates.
Subgenomic mRNAs contain overlapping sequences on their 3' end and are transcribed from subgenomic negative-strand mRNA templates made by discontinuous transcription.
Rearrangement of subcellular architecture and membrane association of viral RNA synthesis are observed in coronavirus-infected cells, involving double membrane vesicles and convoluted membranes.
The replicase gene in coronaviruses is composed of ORF1a and ORF1b, which are translated into polyproteins that are processed by viral proteinases.

Coronavirus Structure and Replication Process

Nucleocapsids in coronaviruses are formed from viral N-protein bound to viral RNA in a helical fashion, resembling '-' strand RNA viruses, and some may have a spherical core structure formed via the M-protein.
Corona virions contain multiple envelope proteins: spike (S), membrane (M), envelope (E), nucleocapsid (N), and in some cases, HE (hemagglutinin esterase) protein.
Spike protein, a major surface transmembrane glycoprotein, is responsible for viral entry and tropism, and it generally forms trimers.
Spike proteins bind to a variety of cellular receptors, with different coronaviruses utilizing different receptors for entry.
The replicase gene (gene 1) in coronaviruses is composed of ORF1a and ORF1b, which are translated into polyproteins that are processed by viral proteinases.
RNA helicase and nucleoside triphosphatase activities, as well as RNA exonuclease with proofreading activity, are involved in coronavirus replication.
Membrane association of viral RNA synthesis is common among '+ strand RNA viruses of eukaryotes, and replication complexes are the site of viral RNA synthesis.
Coronavirus-induced membrane alterations involve the rearrangement of subcellular architecture, with replication complexes commonly observed on double membrane vesicles.
Genome replication proceeds via a full-length negative-strand intermediate, used to direct synthesis of full-length '+' strand genomes, and subgenomic mRNAs are transcribed from subgenomic negative-strand mRNA templates.
Subgenomic mRNAs contain overlapping sequences on their 3' end and are transcribed from subgenomic negative-strand mRNA templates made by discontinuous transcription.
Rearrangement of subcellular architecture and membrane association of viral RNA synthesis are observed in coronavirus-infected cells, involving double membrane vesicles and convoluted membranes.
The replicase gene in coronaviruses is composed of ORF1a and ORF1b, which are translated into polyproteins that are processed by viral proteinases.

Viral Translation and Replication Mechanisms

Poly(A) tail is encoded by the genome, but usually added by poly(A) polymerases
5’ NCR contains an internal ribosome entry site (IRES) allowing translation initiation without a 5’ cap
IRES elements contain a pyrimidine rich track near AUG to imitate translation at the correct spot
Virions bind to cellular receptors via ‘canyons’ or loop regions on their surface
Picornavirus infection causes proteolytic cleavage of eIF-4G, abolishing cap-dependent translation
Picornavirus proteins are made as a single precursor polyprotein that is autocatalytically cleaved
Viral RNA is replicated after protein synthesis, involving a multi-protein complex bound to cellular vesicles
Entry of poliovirus RNA into the cytoplasm involves major rearrangement, forming a channel in the cell membrane
Virion assembly involves cleavage of VP0 to VP2 plus VP4, assembling into protomers and provirion
Picornavirus infection inhibits host cell functions, inducing cytoplasmic vesicles and altering intracellular transport pathways
Flavivirus virion contains an envelope and envelope proteins are arranged with icosahedral symmetry
Flavivirus genome organization most resembles that of Picornaviruses, translated into a single, long polyprotein that undergoes proteolytic processing

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Test your knowledge on the genetic makeup and protein synthesis of coronaviruses, specifically focusing on their structure and non-structural proteins (nsp) encoded in the final 1/3rd of the genome. Explore topics such as COVID-19 genome, viral protein synthesis, and genome replication.