Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

MICB 202 > Orthmyxoviruses - 7,8,9 : Influenza > Flashcards

Orthmyxoviruses - 7,8,9 : Influenza Flashcards

1
Q

Orthomyxoviruses

A

Enveloped viruses
RNA genome
Pleomorphic -many shapes

There are several types of influenza viruses that infect human : A, B , C

Influenza A has a broad host range

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Influenza A Structure:

A

(-) Sense RNA virus with segmented Genome:

Enveloped virus
- Enveloped derived from the plasma membrane of previously infected cell

Under the enveloped is the matrix protein which links the virus genome segments to the envelope

Each segment of the RNA is separately encapsidated with several copies of NP (nucleoprotein)

  • And is associated with its own 8 polymerase complex

Three viral proteins are embedded in the envelope

  1. Hemagglutinin H
    - for attachment to host cell
  2. Neuraminidase N
    - release from host cell
  3. Matrix proteins
    - Allows protons to enter
    - important for un-coating once the particles has entered host cell cytoplasm
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Influenza A genome

A
  • Has 8 segments
  • Some can bind to RDRP
  • Some encode more than one protein in one genomes

Each segment of the influenza genome is organized as a ribonucleoprotein (RNP)

The RNA is coated with NP and packaged with its own RDRP

PB1 = basic pol 1
PB2 = basic polymerase 2
PA = acidic pol
These are bound to each other

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Naming Influenza:

A 
Antigenic type (A/B/C/D)
→ host of origin (swine)→ geographical origin (bangkok) → strain number → year collection

eg A/Sydney/ 05/ 97 (H3N2)

  • if host of origin is human, no need to show
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Why these strains:

A

Many countries have influenza surveillance programs
- Some patients suspected of having the flu are collected and analyzed

  • The influenza viruses in the seasonal flu vaccine are selected each year based on surveillance data - which type is circulating the most

Challenge has reduced availability of fertilized egg to make the vaccine

Sometimes predictions are wrong, takes around 6 months or a yr to get a vaccine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Influenza A virus receptor and Anti-receptors:

A

The host’s virus receptor for influenza is sialic acid,
- found on membrane of glycoproteins (on host)

Many mammals and birds have slightly different versions of SA on their membrane glycoproteins: determines what influenza A can bind to

Influenza anti receptor is hemagglutinin (H) (binds to SA)
- There are many variants of H and this determines virus host range

Need right fit between H and SA for influenza A to infect

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Influenza A Host Range: I

A

Natural host of influenza A are ducks
- resulting in benign diseases

It’s very adaptable virus and has been able to infect a wide range of hosts

Humans and other mammals are accidental hosts

All influenza A virus strains infect mammalian species originate from wild birds/ducks

Some influenza strains have adapted so well they prefer to infect humans

  • Their antireceptor fit better with SA
  • they still could infect other species under certain circumstances

Some influenza strains prefer to infect birds
-Their anti-receptors fit better with bird SA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Influenza A Host Range:

II

A

Pigs can often be infected with influenza A strains that preferentially infect humans and strains that preferentially infect birds

  • They have 2 forms of SA on their cells - those that are found on both humans and birds
  • Because of this they are referred to as mixing vessels - make new strains of influenza
  • Most new influenza strains emerge from pigs

Genetic and biological observations suggest that pig maybe serve as mixing vessels for the generation of human avian influenza A virus and re-assortments with pandemic potential

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Influenza A host range - III

A

The disease associated with the infection in these accidental hosts show a broad range of symptoms - from mild to very severe and death

The differences are due to both the genetic properties of the virus and the species of host infected

In humans influenza A primarily infects the respiratory tract

  • Result in respiratory diseases and spread through inhaling virus particles in the airs - mucours, coughing saliva
  • Through virus particle in the air

In birds it is initially a GI infection which is transmitted by fecal-oral route
- It can then spread to respiratory, reproduction and nervous system

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Influenza A host range - III

A

The host range of influenza A virus with the natural reservoir of influenca A virus, accidental hosts, and the subtypes have been identifies in groups

Influenza A viruses are divided into subtypes based on H and N envelope proteins

There are 18 known H subtypes and 11 known N subtypes

  • many different possible combinations
  • different combinations hvae different host range because different SA on host cel surface

Some types are considered an endemic - appear all the time

Most illness in humans due to Influenza A are H1/2/3 types

Other subtypes that affect species
Eg H5N1 in birds
- Can’t affect us but can mutate
- Also the disease can spear really fast in the farm and kill all the birds (eg chicken ) bad financially

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Should we be concerned that H5N1 causes illness in domesticated birds?

A

Yes, it could cause a farmer to have to cull the entire flock (can be thousands of birds)

This causes financial hardship to the farmer. It can also result in the reduced production of food (poultry meat, eggs) and the eggs needed for vaccine production

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Should we be concerned about influenza in the management of livestock?

A

Yes! we should manage livestock such that the virus doesn’t spread to the entire flock

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Could an H5N1 strain cause illness in humans?

A

Yes -it had done so several times. Usually a person is exposed to a large number of virus particles (perhaps someone working in an aviary)and enough virus particles are able to bind to the person’ cells to initiate an infection

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

SPACER - Chapter 8

A

Influenza A is an RNA virus that replicates its genome in the nucleus, the cell lacks a polymerase that can read RNA as a template and synthesize RNA and mRNA

solution: It encodes several genes for the synthesis of an RDRP complex

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Challenges in replication - 2

A

The viral genome is - sense RNA → cannot be translated by ribosomes

Solution:
The virus synthesizes + sense RNA that functions as mRNA using the RNA polymerase complex (RDRP) that is packaged with the genome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Challenges in replication - 3 & 4

A

3 - Viral RNA dependent RDRP requires a primer for making mRNA

4 - cells ribosome interact with cells mRNA that contains a 5’cap and 3’ poly A tail, and the virus mRNA must compete with the cells mRNA for access to ribosomes

Solution

  • The virus constructs its mRNA by stealing cap of cellular mRNA and using that as a primer to provide the 3’OH group
  • (the 3’OH needed to attach a nucleotide, phosphate, 3’)
  • 5’ cap used at primer by RDRP
  • The viral genome has a signal to construct a poly A tail on the mRNA
  • Cellular mRNA is destroyed when the virus steals the cap to synthesize its own mRNA
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Challenges in replication - 5

A

Viral genome must have at the very least, a RDRP, structural protein and envelope protein

Eukaryotic cell ribosomes can only translate monocistronic mRNA

Solution

  • genome is segmented
  • most fragments contain only one gene
  • fragments with 2 genes use the cells splicing enzyme to modify the RNA

End result: mRNA that has 5’ cap poly A tail and one open reading frame with multiple genes(operons)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Replication cycle: Attachment

A

Virus enters into respiratory tract

Tryptase clara in the secretions cleave the H → H1 and H2
- Tryptase clara is an arginne specific protease localized exclusively in and secreted from clara cells of bronchial epithelium

The influenza virus H binds to SA residues on the cell glycoprotein → trigger endocytosis of the virus particle into the cell

The H also plays an important role in release of viral RNA into the cell by causing fusion of viral cellular membranes

H must be cleaved by cellular protease outside of the cell

  • It is cleaved by trypsin-like protease localized exclusively in the bronchial epithelium
  • It is secreted from clara cells - protease is a part of you anatomical/physiological defense

influenza viruses are restricted to the respiratory tract, because that is the only location where the protease that cleaves H is produced

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

FYI: Where else in the cell and when in replication cycle would a virus glycoprotein be modified (if not by clara)

A

Possibly by an enzyme in golgi

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Replication cycle: Attachment

A

If H0 is not cleave into H1 and H2, fusion cannot occur
- Therefore viruses with intact H are not infectious

H must undergo a pH dependent conformation change to reveal the fusion peptide
- Cuz endosomes have lower pH

Cleavage of H occurs after newly synthesized virus particles are released from the cells (maturation?)
- they are still in the host bronchial tract

After the fusion peptide of H is revealed, it inserts into the endosomal membrane causing the fusion between the endosome membrane and viral envelope

Protons would also enter into the cavity of the virus particle through the matrix proteins in the envelope (M2)
- Triggers release of viral genome

The viral genome (RNA) are then released into the cytoplasm

The RDRP complex and associated proteins move into the nucleus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Replication cycle: Entry and release of the genome

A

2 modifications to H are needed for virus to gets its own genome into the cytoplasm

  1. Tryptase Clara cleaves H to reveal the fusion peptide (external)
    - happens before binding to SA but is not required for binding of SA
    - H2 is fusion peptide
  2. pH-dependent change in endosome
    - allows H to unfold so fusion peptide (H2) inserts into the endosome membrane
    - the 2 lipid layers fuse
  • protons enter - cells normal process of acidifying endosomes
  • proton enter cavity of virus via matrix proteins - separates RNPs from matrix protein
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Attachment summary

A

Cleavage of H by tryptase Clara into H1 and H2

Binding to SA

Receptor-mediated endocytosis –> conformational change of H

Acidification of interior of virus –>
uncoating - separation of RNP from matrix protein lining the envelope

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Incomplete and Complete RNA

A

Influenza virus synthesizes 2 types of + RNA during its replication cycle

Incomplete: Needs primer

  • Also known as mRNA - needed for protein synthesis
  • Made early in replication cycle
  • made by stealing the 5’ cap from cellular mRNA

Complete:

  • Also known as + RNA - needed as a template to replicate the genome for the next generation
  • it is made later in the cycle and is not used as mRNA (not transcribe or translated)
  • It is thought that the alternate conformation of RNA polymerase complex does not require a primer

Both are made using the (-) as the template and the viral RDRP complex

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Influenza mRNA synthesis:

A

The RDRP complex has 2 conformations

Default conformation is for mRNA synthesis (transcription)

25
Q

Transcriptionally Active RDRP

A

Composed of 3 polypeptides - each with its own specific function

There are 3 important sites on the complex

  • site that binds to the 5’ cap end of - RNA template and does not release it
  • site that acts as an endonuclease - cuts within the nucleic acid
  • Sites that read the RNA template and catalyzes the synthesis of mRNA
26
Q

Influenza mRNA synthesis - Cap stealing

A

Using Transcriptionally Active RDRP

The polymerase complex binds a host cell mRNA by its cap
– the polymerase also has an endonuclease activity that cuts the mRNA near 5’ cap

The remaining cap –mRNA structure (providing the 3’ OH group) is then used as a primer to make viral mRNA
- the 5’ cap is bound to RDRP (the site that doesn’t let go)

The polymerase reads the - RNA template and adds complementary nucleotides to the end of the cellular mRNA fragments - it binds to the 5’ end but reads from 3’to 5’ and synthesizes 5’ to 3’
- So technically binding on top (5’) but read below (3’)

Uses 5’ cap as primer too

27
Q

Influenza mRNA synthesis - Final product

A

An mRNA hat has a 5’ cap derived from the cellular mRNA and a poly A tail

  • This is exported out to the cytoplasm for translation on a ribosome
  • This process happens for each 8 segment of - RNA
  • Two of the 8 segments would undergo splicing before being exported to the cytoplasm for translation (cuz polycistronic)
28
Q

Not all mRNAs are translated in the same spot:

A

The mRNA for H, N and M2 proteins would be translated on a ribosome associated with the endoplasmic reticulum

  • this ensures that the protein product is inserted into the plasma membrane of the cell
  • Anything that get synthesized on the ER will be inserted into the cell membrane

This mRNA would have a target sequence that guides them to the ribosome associated with the ER

The other mRNAs are translated on cytoplasmic ribosomes

29
Q

How RDRP switches between 2 two form

A

When concentrations of NP protein is sufficiently high enough, (NP protein made with translation from form 1 RDRP)

the RDRP complex dissociates then resembles the alternate conformation for replication of viral genomes

(default form is for making mRNA - for making protens,

the other form is for making virus genome progeny)

Form 1 synthesis of mRNA with cap stealing and stuff

Form 2 is for replicating genome, no 5’ cap, for them to be used for next virus (used which assemble new virus)

30
Q

Influenza genomic RNA synthesis (for next generaation)

A

Mediated by form 2 RDRP

  1. viral RDRP uses the - RNA as template to make mRNA
  2. then viral RDRF uses the z+ RNA as template to make the - sense genomic RNA again (-) –> (+)–> (-)

Negative makes positive
Then used that new positive strand to make more of the negative strand
Happens 8 times because 8 different segments

31
Q

Influenza Virus Particle assembly and release

A

Assembly of the new viral particle takes place at the plasma membrane of the host cell

The RNPs(genome) and M1 proteins associate in nucleus, then are directed towards the plasma membrane of the cell where the envelope proteins that had been inserted (H, N, and M2)

As leaving the cell, the SA is still attached to Neuraminidase

  • N cleaves the SA on the host cell as it is leaving
  • To make sure the the newly infected virus does not infect the same cell because it is dying
  • The host cell eventually dies by programmed cell death (apoptosis, necroptosis and pyroptosis–the latter two are associated with inflammation)
32
Q

How an the virus tell the - RNA from complete + RNA - both are coated with NP

A

unsure but:

  • Tell between the 8 segments
  • size of loop, length
33
Q

Some challenges arise when assembling the progeny virus particles

A

Some challenges arise when assembling the progeny virus particles

  • each virus particle must have 1 of each of the 8 - RNA segments. in order to have a complete genome
  • But we don’t know how it does that
  • random ot not
34
Q

Summary:

A

proteins made in translation

  • H, N by ribosomal ER then gets inserted into membrane for budding off
  • Matrix
  • NP. RDRP

Some of these proteins are also used in transcription thus these probably happen first before making genomic (progeny ) -RNA

35
Q

Summary Attatchment

A
  1. Cleavage of H by trypatse clara
  2. Binding of H to SA
  3. Receptor mediated endocytosis
  4. Acidification of endosome → conformational change in H
  5. Acidification of interior of the virus → uncoating - separation of RNPs from the matrix proteins lining the envelope
36
Q

Summary Release genome

A

Conformational change in H relieving fusion peptide

Fusion peptide inserts into endosome membrane

2 lipid bilayer structures fuse together

Genome released into the cytoplasm → enter into the nucleus

37
Q

Summary of Influenza replication cycle

A
  1. Synthesis of incomplete mRNA - cap stealing
  2. mRNA move to cytoplasm - H, N M2 are translated with the ribosomes associated the ER
    - All others are translated in cytoplasmic ribosomes
  3. NP enters the nucleus - triggers a change in the activity of polymerase complex (change from incomplete to complete)
  4. Synthesis of complete genomic RNA (to assemble)
  5. Assembly of RNPs - RNAs coated with NPs and its own polymerase complex
  6. M1 proteins move into the nucleus and associate with the RNPs and direct RNPs out of the nucleus
38
Q

What is influenza (flu)?

A

Serious respiratory ad highly contagious illness

symptoms can be mild to severe
- depends on immune system and strain, how much infected

Symptoms start about 2 days after

Most symptoms last about a week
-Most symptoms last about a week

Can result in serious complications such as secondary infections
- Eg bacteria infection when your immune system is run down

A lot of symptoms from the flu can be attributed to immune response - cytokines can lead to fever and muscle ache

39
Q

Orthomyxoviruses

A

Virus enters via inhalation of aerosol or transfer to mucosal surfaces

an infected person can release a lot virus particle per sneeze or cough

About ⅓ of infected are asymptomatic

Influenza infection are similar to a cold

40
Q

Cold Vs Flu

A

Check table pic

41
Q

How do new influenza strains arise - antigenic drift/shift

A

Every time the genome is replicated there is a potential for mutation

RNA genomes are replicated by viral RNA polymerase
- RNA pol have high error rate - no proof reading mech.

42
Q

Antigenic Drift

A

Mutation can occur in any piece of genome (a change in single nucleotide of DNA
- These would be point mutations (a change in single nucleotide of DNA eg nucleotide substitution)

Most significant error occurs in H protein (hemmaglutinin)
- Most significant because it is the anti-receptor and needed for attachment to virus receptor on cell surface to infect a host cell

Slightly different versions of H protein

  • antibody may still be able to bind
  • but sometimes changes too much, thus not immune to it anymore
  • this is the cause of seasonal flu

Mutation in N may also be significant
- Does not bind to SA when budding out - can’t detach properly

43
Q

Consequences of drift

- questions to consider

A

Recall that antibodies recognize a 3D epitope
- Is the mutation at the site where the antibody bind?

  • Is the aa that changed chemically similar to original one

Different epitopes in a protein may be bounded by the same antibody, if they have a similar shape and chemistry

The side chains of the aa are important here

The antibodies may bind to the different epitopes with different affinities

So depends on where mutation is happening and which antibodies are involved

44
Q

Consequences of drift

A

The influenza vaccine you received before may have stimulated the production of antibodies that will still fit against the influenza strain with antigenic drift

The fit may not be as precise but adequate to protect you against infection

However change in amino acid may result in an epitope that is to different and the antibodies you have may not offer any protection at all

45
Q

Mutations

A

Mutations are essential for viruses to evolve

  • Either evade host response or adapt to new host
  • Many mutations are neutral, some beneficial some harmful
  • RNA viruses have very fast mutation rate
    eg covid
46
Q

Antigenic Shift

A

Happens when 2 different influenza strains infect the same cell

  • During replication cycle, progeny of the virus assemble containing gene segments from both parent strains
  • reassortment of RNA segments

Pig’s fault

  • pig gets infected by bird influenza and humans influenza at the same tine
  • because pig expresses the same SA as humans and birds
  • pigs are mixing vessel

Occurs less often than drift

Antigenic shift results in new strains that no one has immunity to eg H→ H3
- new strain from antigenic shift has potential pandemic

After virus has shifted, it can continue to replicate in pig, undergoing antigenic drift and becoming a variant that can also infect humans

Antigenic shift results in new strains that no one has immunity to eg H→ H3

Fortunately, this cannot happen with SARS-CoV-2 because it has a single strand of RNA as its genome (i.e.,is an unsegmented genome)

47
Q

Seasonal Flu

A

Usually the same strain as previous year but slight variations due to antigenic drift

Some people have immunity

Vaccines are prepared in advance of “flu season” based on what is circulating elsewhere. No vaccines are available early in the pandemic –it can take at least 6 months to produce the vaccine

48
Q

Pandemic Flu

A
  • happens 2-3 times in a century

Can occur at any time of the year in 2-3 waves several months between

Each wave lasts 2-3 months

Often result of antigenic shift

49
Q

A recent influenza A pandemic

A

H1N1

CDC estimated that 151,700 –575,400 people worldwide died from (H1N1) pdm09 virus infection during the first year the virus circulated.

Globally, 80% of (H1N1)pdm09 virus-related deaths were estimated to have occurred in people younger than 65 years of age

This differs greatly from typical seasonal influenza epidemics, during which 70-90% of deaths are estimated to occur in people 65 years old and older

50
Q

Past pandemics

A

Spanish flu

Asian flu

51
Q

1918 influenza A pandemic

A

1918 influenza A pandemic

Firs wave: typical flu symptoms, few deaths

Second wave: victims died within few hours or days developing the symptoms, their skin turning blue, lungs filled with fluid that cause them to suffocate

1918 flu struck down many people who were previously young healthy people - group normally resistent t this type of infectious illness

More U.S. soldiers died from the 1918 flu than were killed in the battle during the war.

52
Q

Fighting viral infections: Antiviral medication

A

There are very few anti-virus medications compared to antibiotics (anti-bacteria)

  • because viruses replicate inside cells
  • medication must not harm healthy uninfected cells
  • must target a virus specific activity
53
Q

Anti-influenza medication

A

NA (neuriminidase) inhibitors
- Tamiflu: oseltamivir = oral medication in pill form, relatively inactive chemical until metablized in the liver where it is converted into the active form

  • Relenza - Zanamivir = powdered medication that is orally inhaled using a disk inhaler

A mutation in the gene that codes for the N protein could change the structure of the protein such that the drug no longer interacts with the protein’s active site

54
Q

Fighting Viral Infections: Ion Channel inhibitor

A

symmetrel/ amantadine = portal medication in pill form or syrup

  • also used in treatment of parkinsons disease,
  • symmetrel no longer recommended, as virus has shown resistance

Flumadine = rimantadine = oral medication in pill form or syrup

How would Influenza develop drug resistance?

Mutation in the gene that codes for ion channel - M2, could change it such that drug no longer interacts with the protein

M2 is the ion channel allows release of genome

55
Q

Influenza Vaccine Production

A

Each year new vaccines are prepared for seasonal fly

A single dose of vaccine is administered for each patient

  • Most vaccines are designed to generate IgG type antibodies
  • Common trick = release the antigen slowly from the injection site over time

The concept is that the person will make antibodies that neutralize the virus

These antibodies might cause steric hindrance so virus cannot bind
- They may stabilize the structure so that the genome is not released or the envelope does not fuse in the endosomal membrane

Every year, several pharmaceutical companies produce trivalent influenza vaccines that contain 3 strains of influenza most likely to be circulating in the season

These stairs are identified by the WHO based n the data collected by many surveillance programs around the world

However all vaccines are formulated to include a standardized amount of H proteins from the influenza virus

56
Q

Egg based vaccines

A

High production, relatively low cost - production time 6-8 months

Potential adaptation of virus to avian structure (resistant)

57
Q

Cell based vaccines

A

Flexible and scalable but expensive

less likely to see virus adaptation

58
Q

Recombinant DNA vaccines

A

H and/or N gene is cloned into an expression vector

Flexible and scalable but expensive

59
Q

Composition of Inactivated Influenza vaccines

A

The different vaccines formats do have differences in antigen components and immunogenicity

WIV = whole inactivated virus

VIrosome = reconstituted influenza Virus envelopes

Split - disrupted with detergent, contain all virus proteins , virus ssRNA is usually lost

Subunit = purified H and N proteins using after splitting

MICB 202 (19 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions