3.4 & 3.5 SARS COVID-19

What are some viral gene expression strategies?

-Alternate start codons -Overlapping genes -premature termination -read through stop codons -polypeptide cleavage (long polypeptide gets cut to smaller fragments)

What is SARS-CoV-2 lifecycle?

-Attachment -Penetration and Uncoating -Translation -Assembly of the virus in the ER and Golgi -RdRp synthesizes (+) RNA -Release

SARS-CoV-2 details:

-Enveloped virus -spherical ~120 nm -linear (+) ssRNA genome 27-32kb -5' G-cap & poly-A tail (stabilizes it in the cell) -RNA genome is coated with N protein= nucleocapsid ~26 orfs -RdRp has proofreading ability

What are the different shapes virons can be?

-Helical (rod shaped) -Polyhedral (many sided, Icosahedral) -Binal (pleomorphic, irregular shaped (influenza A))

What are the number of COVID-19 cases/deaths in the US? (know for test)

80, 399,474 cases 985,482 deaths

Viral genomes consist of: •All choices are correct. •single-stranded DNA •single-stranded RNA •double-stranded RNA •double-stranded DNA

All choices are correct.

What is a viron?

An individual complete virus particle

Where do mAbs bind to and what do they cause?

Bind to epitopes on the spike protein -can neutralize the virus -serve as opsonins, tag virus so that macrophages can engulf it

What does Paxlovid do?

Contains 2 antiretroviral drugs; Protease inhibitors -Nirmatrelvir: binds to the Mpro= main protease (also called 3CLpro) -Ritonavir: protease inhibitor, pharmacokinetic enhancer or booster, slows the breakdown of Nirmatrelvir by liver enzymes (often used with other protease inhibitors)

What makes Delta and Omicron different from each other?

Delta: more deadly, Ro= 6-8 Omicron: easily transmittable, infects and multiples 70x faster in human bronchus, more prevalent in the bronchus, Ro= 8-15

N95 mask details:

Designed to remove more than 95% of all particles that are at least 0.3 um in diameter -most are capable of filtering ~99.8% of particles w/ diameter of ~0.1 um -Not recommended for use with beards

What makes SARS-CoV-2 insidious?

Due to the asymptomatic carrier phenomenon -actively making virus but infecting other -has unknown mechanism(s) to delay/evade the immune system -Covid-19 patients transmit the virus before the appearance of symptoms

What is the enzyme that proofreads in Sars-CoV-2?

Exoribonuclease (3' to 5' exonuclease) -reverses and removes errors -not perfect, reason for variants appearing

Identify the Sars-CoV-2 protein responsible for proofreading?

Exoribonuclease (ExoN) protein

True or False. 50% of human common colds are caused by alpha-coronaviruses.

False. ~25% of human common colds are caused by alpha-coronaviruses

Identify the COVID-19 vaccine that employs an adenovirus. -Johnson & Johnson -Pfizer -Moderna -Only two of the choices are correct -All of the choices are correct.

Johnson & Johnson

What are envelopes?

Lipid bilayer that surrounds virus -derived from host cell -contains viral glycoproteins required for infecting cells

What is viral host specificity?

Lock and Key, compatibility must be present! -Complementary receptors on the surface of the susceptible host and its infecting virus -Virion must bind to protein receptor found in the host cell's membrane -Host cell receptor carries out normal functions for cell **Noneveloped viruses attach via arrangement or shape of capsids***

How are mAbs made?

Mice are injected with antigens of Sars-CoV-2 spike protein -B cells of mouse's spleen are fused to myeloma cells (cancerous plasma cells) -Hybridoma cells are cultured and produce antibodies to the antigen -Administered via IV infusion

Viral Mutation Rate details:

Most Viral polymerase lack proof-reading -viral mutation rate ~1 in 10,000 nts -Virus do not have nucleic acid repair systems

True or False. SARS-CoV-2 has a circular genome.

The statement is false. (it has a linear genome)

SARS-CoV-2 is an enveloped virus. (True or False)

True!

True or False. Coronaviruses are extremely common viruses of animals and humans.

True!

True or False. Eukaryotic cells do not have RdRps?

True!

True or False. Most visible droplets fall within 6 feet.

True!

True or False. Droplets can float for several hours & travel 200 feet.

True! 😬

True or False. Not all mAbs are effective against all variants.

True, that is why it is important to know what version of the virus the patient has. -New variants have different epitopes

COVID-19 details:

Upper respiratory infection -spread by respiratory droplets (airborne) -Outbreaks associated with crowded conditions (markets, cruise ships, assisted living facilities, religious services, soccer matches, gyms, bars & restuarants) -Outbreak in Wuhan; Huanan seafood market was the epicenter

The active ingredient of the Pfizer and Moderna COVID-19 vaccines is:

Viral mRNA

What COVID-19 pandemic is?

World wide epidemic

What is the WIV?

Wuhan Institute of Virology -where the coronavirus isolation and culture work was performed -est. before covid-19 pandemic

What is a nucleoside?

any various compounds, like adenosine or guanine, that consist of a sugar (ribose or deoxyribose), linked to a purine or pyrimidine base. -Do NOT have phosphate groups

MERS, SARS, and Sars-Cov-2 are?

beta-coronaviruses, have a bat origin

What does the Spike (S) protein do?

binds to ACE2 host cell receptor and mediates viral entry within the host cell

What is a capsomere?

protein subunits, large number of proteins that build capsids (the shell) -can be 100s of same or different capsomeres

What are Non-structural proteins (NSP1-NSP16)?

proteins that have multi-purpose roles via viral replication, transcription, morphogenesis, and evasion of host response -Dont need to memorize list!

What does SARS-CoV-2 stand for?

severe acute respiratory syndrome coronavirus 2 (original SARS emerged in 2002)

What is a naked virus?

virus without an envelope

What is the estimated time of entry of the Sars-Cov-2 virus into a cell?

~10 min

What is the eclipse phase?

~10hr time between infection and virus production

What does Remdesivir triphosphate do? (RDV-TP)

competes with ATP -has a low pairing efficiency with UTP -Slows or stops viral RNA synthesis

What is an interferon?

cytokine that interferes with viral replication

What does the Membrane (M) protein do in Sars-CoV-2?

maintains spherical membrane curvature of the virus, stabilizes nucleocaspid and facilitates viral assembly, antagonizes interferon response

What does the Envelope (E) protein do in Sars-CoV-2?

maturation of virion (development of virus)

What is the basis of the Pfizer/BioNTech and Moderna vaccines?

messenger RNA within a nano-size lipid bubble -mRNA is translated to a viral spike protein Pfizer: 30 ug of mRNA, 21 days Moderna: 100 ug of mRNA, 28 days -Stored at -80℃ (mRNA is fragile)

What causes antigenic drift?

mutations

What is the difference between (+) and (-) RNA?

(+) RNA is the equivalent of mRNA and can be translated (SARS-Cov-2 is +RNA virus) (-) RNA CANNOT be translated (Influenza is (-) RNA virus)

Identify the type of nucleic acid that makes up the Sars-CoV-2 genome. (+) single stranded RNA (-) single stranded RNa ds DNA ds DNA with an RNA intermediate ds RNA

(+) single stranded RNA

What results in the formation of new strains and variants of Sars-Cov-2?

mutations in the spike proteins

What are the different virus nucleic acids?

-ds (+/-) DNA -ss (+) DNA -ss (-) DNa -ds (+/-) RNA -ss (+) RNA -ss (-) RNA

What is the burst size that causes cells to burst from the amount of virions it has?

10^3 (1,000 virions)

What does Remdesivir do? (brand name Veklury)

Adenosine nucleoside analog -it is converted into a nucleotide in cells -administered through IV -causes RNA-dependent RNA polymerase to pause -possibly interferes with ExoN proof reading -Delayed chain terminator

What are the number of COVID-19 cases/deaths Worldwide? (know for test)

497,952,004 cases 6,176,053 deaths

What are does the cases & deaths of female vs. male say for COVID-19?

50.5% female, 49.5% male cases -More female cases than male cases BUT there are more male deaths than female deaths

What are the number of COVID-19 cases/deaths in Clark County, Nevada? (know for test)

707,980 cases 10,136 deaths

What is the basis of the Johnson & Johnson and Oxford-AstraZeneca vaccines?

Adenoviruses vector (cold disarmed virus with Sars-CoV-2 spike protein gene) -stored at 2-8℃ -Only 1 immunization

Nucleoside analog therapy exists for what other viruses?

HIV, Hep B virus (HBV), Hep C virus (HCV), Cytomegalovirus (CMV), Herpes simplex virus (HSV), and varicella-zoster (VZV) infection

Spike protein details:

Has 2 domains: S2 and S1 -S1 contains the receptor binding domain (RBD) responsible for binding to the ACE2 receptor -S2 required for virion fusion •S protein releases the S1 region and undergoes a structural change to its post-fusional form in order for the virus to enter the host cells

What causes a conformational change in the S protein?

Host cell protease decapitates the spike (S1 domain) which is necessary to permit the virion to fuse with the lung cell -S2 protein unfolding permits the spike protein to insert into the membrane and pulls virion closer to cell membrane

What are the 3 categories of ORFS in Sars-CoV-2?

Non-structural proteins Accessory proteins Structural proteins

What are monoclonal antibodies (mAbs)?

Produced in commercial laboratory mono= one antigen clonal=clone -Block virus attachment and entry into human cells (neutralization)

What is a capsid?

Protein shell enclosing the nucleic acid can contain: -DNA or RNA -viral enzymes

What type of viruses are SARS-Cov-2 and Influenza?

RNA viruses

What are examples of viral host specificity?

Rabies virus infects neurons Hepatitis B infects liver cells

What causes antigenic shift?

Reassortment -exchange nucleic acid segments with different strains of the same virus -produces new antigens, assists virus in evading the immune system

Characteristic of Viruses

nm (10^-9) to um range (10^6) -obligate intracellular molecular parasites -infectious -highly specific host range -acellular -DNA or RNA -Lack metabolic pathways -Lack ribosomes -Accumulate mutations -Respond to natural selection -Acquire new alleles/genes -Exceptionally diverse

What is a nucleocapsid?

nucleic acid + capsid

What is the Novavax COVID-19 vaccine? (unique: contains saponins)

Recombinant nanoparticle vaccine -spike proteins attached to cholesterol and phospholipid base to form virus-like particle -27.2 nm nanoparticle -has 2 proline substitutions (prevent conformational change) -5 ug of nanoparticle spike protein + 50 ug of adjuvant; saponins (plant glycosides, from soapwort plant) -2 immunization: 21 days apart

What is the R naught of Sars-CoV-2?

Ro of 2.5 (1.8 to 3.1)

What virus has the longest known corona genome?

Sars-CoV-2

Which corona strain become adapted to humans and fully humanized? -MERS -SARS -Sars-CoV-2

Sars-CoV-2 -humans have no prior exposure and no adaptive immunity to it

What virus has proofreading capability?

Sars-Cov-2

What is an Open Reading Frame (orf)?

Sequence between a start and stop codon, used to describe hypothetical or suspected genes

What are the 4 predominant structural proteins for Sars-CoV-2?

Spike (S) Membrane (M) Envelope (E) Nucleocapsid (N)

What are viral gene expression strategies?

Strategies that viruses employ to maximize the number of proteins made from a compact genome

DNA viruses:

depend upon host cell DNA polymerase to synthesize viral DNA -Host cell DNA polymerase are accurate and proofread= less chance of viral mutations

What are saponins?

derived from soapbark tree (plant sugar) -highly antigenic and attracts immune cells to the site of infection -Macrophages and dendritic cells phagocytize the nanoparticles

What does the Nucleocapsid (N) protein do in Sars-CoV-2?

encapsulates viral nucleic acid

The Sars-CoV-2 genome resembles....

eukaryotic messenger RNA

RNA viruses:

have RNA depended RNA polymerase (RdRp) -viral RdRp tend to be inaccurate and generate mutations viral enzymes can synthesize (+) RNA from (-) RNA, and (-) RNA from (+) RNA

What is coprophagy and how does it play a role in viral and bacterial pathogen transmission?

it is the ingestion of feces. -some mammals, sniff, lick, chew or eat the feces of other animals -Play a role bc humans acquire pathogens from dogs and cats by kissing their pets on the mouth

what does R naught mean?

the number of people (on avg) that a single infected person can be expected to transmit that pathogen to.

What is Molnupiravir (treatment for COVID-19)?

therapeutic drug that contains: Nucleoside analog (includes both purine analogues and pyrimidine analogues) -Makes the virus nonfunctional -Host and viral polymerases cannot distinguish between real and fake analog -results in lethal mutagenesis -causes G-to-A and C-to-U transition mutations