Virus Genomes, Antiviral Drugs, and Viral Replication

Flashcards based on lecture notes about viruses and antiviral drugs.

What does the genome of a (+)ssRNA virus mimic?

Host mRNA

Where do enveloped (+)ssRNA viruses typically make polyproteins?

At the ER

What enzymes chop up long viral polyproteins into individual proteins?

Host and viral proteases

What enzyme is required to transcribe the genome of a (+)ssRNA virus?

RDRP (RNA-dependent RNA polymerase)

What are the two RNA products of RdRp?

(-)ssRNA intermediates and (+)ssRNA genomes

What is the initial genome replication sequence?

+ssRNA -> -ssRNA -> +ssRNA

What type of drug is Ribavirin?

Nucleoside analog

What is Ribavirin's mechanism of action?

It is phosphorylated and activated in cells, then incorporated into viral RNA during genome replication and induces hypermutation

What viruses are targeted by Ribavirin?

Influenza, Hepatitis C, Polio, Measles, Yellow fever, West Nile, and Dengue Viruses

What bases can Ribavirin bind to?

Uracil (U) or Cytosine (C)

What does Ribavirin cause in viruses that depend on RdRp?

Lethal hypermutation

How is Hepatitis C transmitted?

Via blood from host to host

What disease can Hepatitis C cause?

Hepatitis (liver disease), which can sometimes progress to hepatocellular carcinoma (liver cancer)

What is a possible treatment for Hepatitis C and what has made it easier to treat?

Liver transplants are often necessary, but it's challenging to prevent disease in new liver. New anti-HCV drugs can be more than a treatment, there is potential for a cure. Since 2011, Hepatitis C has been treated with direct acting antivirals. They directly target Hep C replication and the cure rate is about 95%

How is Hepatitis C transmitted?

Unprotected sex, blood, bodily fluid exposure, and IV drug use

What is the treatment regimen for Hepatitis C with direct acting antivirals?

A 12-week regimen with treatment through oral tablets

What is the name of the drug used for Hep C?

Sofosbuvir

What is Sofosbuvir's mechanism of action?

It is a pro-drug that is converted into triphosphate form by cellular enzymes, incorporated into growing HCV RNA molecule and inhibits the viral RNA dependent RNA polymerase (RdRp) causing chain termination

What happens when Sofosbuvir blocks the RdRp?

You're preventing copying of the genome into the (-)ssRNA strand intermediates and the copying again to return to (+)ssRNA. This means there will be no viral RNA synthesis meaning replication is stopped.

Where is the (+)ssRNA of coronavirus is directly translated in the host cell?

Cytoplasm

What are the key features of coronavirus RNA that mimic mRNA?

5' cap and 3' poly A tail

Where is the RdRp found on the coronavirus?

Only on the longer polyprotein after cleavage

What does Paxlovid target in COVID-19?

The 3CL protease

What does Paxlovid do?

Prevents the 3CL protease from cleaving RdRp from the polyprotein, preventing RNA synthesis and virus replication

What is a reading frame in translation?

Starts with and AUG codon to encode methionine and continues until stop codon

What is a frameshift?

Ribosomes can get confused and slip off the triplet codon and moves to a different reading frame

What causes ribosomal frameshifting?

An RNA pseudoknot

Why does frameshifting have to occur in coronaviruses?

Because the RdRp for its replication is only found in the extended, frameshifted RNA genome

How does Remdesivir inhibit RdRp?

By causing chain termination which prevents viral RNA synthesis

Where are Coronavirus transmembrane proteins localized?

ER

What are Replication Organelles made from?

Viral proteins and stolen ER membranes

What are the two functions of RdRp inside viral replication organelles?

Copies the genome (+ssRNA genome to -ssRNA intermediate to +ssRNA product) and makes shorter 'sub-genomic' +ssRNAs that encode structural proteins like the spikes

What do crown-shaped pores of replication organelles do?

Allow ribonucleotides in, and lets viral RNAs exit to be translated into cytoplasm or full-length genomes to be packaged into new viral particles

What does HA bind to in Influenza virus?

Sialic acid, which promotes attachment and entry

What is neuraminidase (NA)?

An enzyme that cleaves sialic acid from the cell surface allowing progeny influenzas viruses to escape the cell and spread to new hosts

How are influenza subtypes classified?

Based on antigenically distinct HA and NA glycoproteins

What are the natural reservoir hosts for influenza A virus?

Birds (except H17N10 and H18N11 which circulate in bats)

Which influenza A virus strains currently circulate in human populations?

H1N1 and H3N2

What type of influenza viruses only circulate in humans?

Influenza B viruses

What are the currently circulating influenza B virus strains?

'Victoria' and 'Yamagata' lineages

What are the key differences between antigenic drift and antigenic shift?

Antigenic Drift is rapid mutation and selection of new strains that escape neutralizing antibodies. Antigenic Shift is spillover events from animal hosts into humans, and the segmented genome that allows swapping of genetic material between viruses

What is attached to each (-)ssRNA genome segment in influenza?

Viral RdRp

What is the function of RdRp in influenza?

To decode (-)ssRNA into viral mRNAs with 5' caps and poly(A) tails, (+)ssRNA replication intermediates and (-)ssRNA genomes copies

Why is the influenza RdRp significant for vaccine mismatches?

It is error-prone, which supports rapid evolution resulting in antigenic drift and frequent vaccine mismatches

Who discovered the concept of zoonotic spillover of influenza virus from birds to humans?

Rob Webster

What is antigenic shift?

Abrupt, major change, it can cause entirely new viruses, not recognized by the immune system

How are influenza vaccines created?

Clone selected HA and NA genes into plasmids, combine with 6 remaining 'standard' genome segments \nInsert 8 plasmids into cells, harvest hybrid viruses that have correct HA/NA antigens at the surface and use them to inoculate eggs

Why are eggs used for influenza vaccine production?

They are a rich environment for virus replication and the egg fluid contains the virus

What strains are included in the current influenza vaccine?

Quadrivalent with strains of Flu A, H1N1 and H3N2, and Flu B, Victoria and Yamagata

How are virus capsids typically built?

From sub-assemblies

How do Non-enveloped viruses escape the cell?

By killing the cell (breaking out)

Where do viruses acquire organelle membranes?

By budding into an internal membrane, followed by Exocytosis

How do glycoproteins HA and NA get to the cell surface?

HA and NA proteins bear hydrophobic signal sequences, and are translated/processed in the ER (protein synthesis), and proceed to the Golgi which sends them to be embedded into the plasma membrane

How do Tamiflu and Relenza keep influenza virus tethered to the cell surface?

Drugs that are neuraminidase inhibitors

Where do Herpesviruses go through secondary envelopment?

Golgi

How is the coronavirus genome translated?

Directly by ribosomes into polyprotein, and being made amongst the poly protein is the RdRp that can replicate RNA

Where does assembly happen for coronaviruses?

At the ERGIC, when the full-length genomic + ssRNA, coated with N, binds to viral structure glycoproteins and 'buds' into the ERGIC

What cells does HIV directly infect?

T helper cells

What receptors do HIV use on T helper cells?

CD4 and chemokine coreceptor or CCR5

What is characteristic of reverse transcriptase in HIV?

Very poor proofreading activity which causes random errors

What grabs hold of the double stranded DNA of HIV and carries it through a nuclear pore into the nucleus?

Integrase

What makes HIV a lifelong infection?

Integrase makes a cut in the host DNA and allows the HIV DNA to be inserted into the host chromosome

What digests the polyprotein chain is HIV virion maturity?

Protease enzymes