Chapter 25 Micro

Retroviridae (HIV is in this class of viruses) +ssRNA viruse

- Genomes contain two identical molecules of positive ssRNA

- Retroviruses don't conform to the "central dogma"

- Retroviruses transcribe dsDNA from ssRNA using reverse transcriptase

2 types: viruses can be oncogenic or immunosuppressive

Reverse transcriptase

converts ssRNA to dsRNA-DNA hybrid, then dsDNA- high mutation rate

- Glycoproteins gp120 and gp41 impede

immune clearance of HIV

- Glycoproteins gp120- antigenic variability

- gp41- promotes fusion of envelop to cell

HIV: Gag

p17 (matrix or ma)

p24 (capsid)

p2 (virion assembly,Spacer Protein)

p7 (binds ssRNA, regulated Rev. trans also called nucleocapsid protein NC)

HIV:Pol

reverse transcriptase, protease, integrase, RNase

HIV:VIF

early onset, adds ubiquitin tag to APOBEC, Host protease degrades antiviral proteins

HIV:Vpr

aids in viral nucleic acid transport to nucleus, triggers arrest in G2- activated DNA repair could play a role in allowing integrase to function

HIV:Tat

phosphorylated Host transcription proteins, increases viral transcription

HIV:Rev

helps mRNA exportation from nucleus

HIV: Env

gp160 (gp120 +41) - attachment to CD4 and CCR5

HIV:Vpu

degrades CD4 from inside host cell, chews transmembrane receptor, dislodges CD4

HIV:NERF

down regulates CD4 production and increases T-cell

activation.

RNA Viruses

•Four types of RNA viruses

-Positive single-stranded RNA (+ssRNA) (Coronavirus)

-Retroviruses (+ssRNA viruses that convert their genome to DNA) (HIV)

-Negative single-stranded RNA (-ssRNA) (Influenza)

-Double-stranded RNA (dsRNA) (Rotavirus)

Acquired Immunodeficiency Syndrome:

caused by advanced HIV, rare infections from low CD4

HIV: sticks to CD4 T cells, leading to degradation of Helper T cells, immunodeficiency

Transmission: blood, semen, saliva, vaginal secretions, breast milk contacting tear in skin

Acquired Immunodeficiency Syndrome: Diagnosis

• -Serological diagnosis involves detecting antibodies against HIV

• ELISA- enzyme linked immunosorbent assay- uses wells with gp41 and gp120

• Blood sample washed over proteins, HIV antibodies bind, secondary antibodies for Fc of HIV antibodies conjugated to enzyme- put in substrate, concentration of HIV abs determined by reaction product concentration

• + test: antibodies for gp proteins, immunological memory

Acquired Immunodeficiency Syndrome: Treatment

HAART- combination of antiviral drugs, prevents HIV genome incorporation

Acquired Immunodeficiency Syndrome: Nucleotide reverse transcriptase inhibitors (treatment)

RT uses analogs, prevent formation of DNA

Acquired Immunodeficiency Syndrome: Non-nucleotide reverse transcriptase inhibitors (treatment)

shaped to bind RT active site

Acquired Immunodeficiency Syndrome: Integrase inhibitors (treatment)

bind active site, stops dsDNA binding, no genome incorporation

Acquired Immunodeficiency Syndrome: Fusion inhibitors (treatment)

stops CD4-gp120 binding or stops rearrangement for membrane fusion

Acquired Immunodeficiency Syndrome: T-cell transplant (treatment)

full body radiation + stem cell donor from CCR5 negative person

Acquired Immunodeficiency Syndrome: Prevention

TRUVADA for pre-exposure- nucleotide analogs to affect reverse transcriptase

Vaccine prevention: HIV highly mutable, latent phase, insertion into genome

Naked, Positive +ssRNA Viruses: RHINOVIRUS

Rhinoviruses, causes common cold

-Infections limited to the upper respiratory tract

-A single virus is often sufficient to cause a cold

-Virus transmitted by aerosols, by fomites, or via hand-to-hand contact (most commonly transmitted by hand-contact)

-The number of infections tends to decrease with age

-Hand-washing is the most important preventative measure

Enveloped, Unsegmented Negative -ssRNA Viruses: Measles

- No antiviral treatment is available

- Vaccine has eliminated endemic measles in the United States

Enveloped, Unsegmented Negative -ssRNA Viruses: Rabbies

- Classical zoonotic disease of mammals

- Primary reservoir of rabies in urban areas is the dog

- Bats are the source of most cases of rabies in humans

- Transmission usually occurs via a bite

Enveloped, Unsegmented Negative ssRNA Viruses: Hemorrhagic Fevers

- Marburg virus and Ebola virus are the causative agents

- Natural reservoir and mode of transmission to humans unknown (although fruit bats are now a prime suspect- reservoir evidence)

- Spread person to person by contaminated body fluids and syringes

- Virions attack many cells of the body

- Especially macrophages and liver cells

Filamentous Ebola viruses

Virus appears to be able to inhibit innate interferon response via VP24/VP35.

VP40 virus assembly and budding.

VP30 involved in regulation of Ebola gene transcription.

GP is a glycoprotein involved in viral attachment and membrane fusion. The sGP form is soluble and unknown function.

L is an RNA polymerase.

Enveloped, Segmented Negative -ssRNA Viruses: Influenza

Influenza, orthomyxovirus type A and B, 8 genes Infection from inhalation of airborne virus, eliminates lung epithelial lining

Fever, malaise, headache, myalgia; induces by cytokines of immune system

Influenza

Influenza A: avian, porcine, humans- antigenic shift: merge of species viral strains- NEW virus

Influenza B: humans, seals- common antigenic drift: small changes due to RNA mutations

Error Prone ---> RNA dependent RNA polymerase: converts -ssRNA to +ssRNA to -ssRNA, making copies

HA (hemagglutinin)

binds sialic acid modified proteins in lungs for attachment

NA (neuramidase)

cleaves sialic acid membrane to allow for virus exocytosis with envelope

NP (nucleoprotein)

capsid, covers -ssRNA

M1

stabilized membrane, coats inside of envelope

M2

forms pore for ion passage, H+ enters, drops pH, triggers viral release

NS1

forms dimer with polyA RNA, inhibits host mRNA export from nucleus, ^ viral translation

NS2

blocks interferon response, no antiviral protein production

PB1 and PB2

These form the RNA dependent RNA polymerase complex.

Influenza Treatment

prevent viral un-coating (amatadine- block M2 ion channels),

-Drugs that prevent viral release from infected cells (Neuramidase Inhibitors such as Relenza and Tamiflu

Prevent neuramidase from cleaving sialic acid on nose, throat and lung cells so virus is not released when trying to bud off). -----> (no RNA use prevent viral release from infected cell )

-Must be administered within first 48 h of infection

Vaccination preparation

Combine two strains of the flu in a single host (fertilized egg in this case). Strain 1 will have surface spikes that are common in human population and strain two is more adept at growing in avian species. Gene combinations result that provide the immune system with exposure to the outer proteins (HA and NA) but attenuated ability to reproduce in a human host (inhaled vaccine). Additionally, the virus can be treated with radiation to inactivate the any potential for replication (injected vaccine).

Trivalent vaccine are usually provided

Measles attachment/pathogenicity

Hemagglutinin can attach to human cells as shown below. F or Fusion protein, (also on measles membrane) then triggers fusion to human cells.

The viral genome also codes two non-structural proteins C and V.

Immune Evasion

The V protein acts as a potent inhibitor of the host interferon response by interacting with molecules involved in induction and signaling,

Rabbies Treatment

- Treatment

- Treatment of the site of infection

- Injection of human rabies immune globulin

- Vaccination with human diploid cell vaccine (HDCV)

Prevention

- Vaccination of domestic dogs and cats can help control rabies

Coronavirus +ssRNA virus (non-segmented).

S protein: Spike protein- binds ACE-2 and TMPRSS2 (Omicron only needs ACE-2)

Composed of S2 (the stalk part is pretty conserved and as a result is a good drug/vaccine target stock, transmembrane, conserves)

S1 (so not a good drug target, extracellular, variable)

Replicase produced 1st, converts +ssRNA to -ssRNA to +ssRNA- translated in ER (HIDES)

Coronavirus E protein

envelope protein inhibits interferon release- no antiviral proteins (AVPs)

Coronavirus M protein

membrane glycoprotein

Coronavirus N protein

nucleocapsid, binds and protects +ssRNA

Coronavirus Immune avoidance

-viral RNA capped and poly-adenylated, hides in ER, avoids degradation

-Some of the NSP (non-structural proteins) appear to bind and interfere with alpha and beta interferon release. This circumvents the production of anti-viral proteins in non-infected cells.

-The proteins that are produced "hide" in the ER and thus are not seen as PAMPS (pathogen associated molecular patterns), that would normally help trigger our immune response.

mRNA vaccines

uses host cells to generate viral proteins, mRNA for spike protein injected Spike protein integrated into membrane, cell dies, macrophage engulfs, displays particles MHC I/II presentation- B and cytotoxic T cell response

mRNA vaccine safer, quicker, and cheaper to produce at high volume, easy to alter

PAXLOVID

3 CL protease inhibitor for SARS-2COV proteins, prevents polycistronic breakdown

Share COVID antibodies: admin of neutralizing abs in serum, for immunocompromised

AED

antibody enhanced disease: abs bind wbc, close association passes COVID to wbc

Biosafety level classification (BSL) Level 1

organisms are safe and no separate facility required (Lactobacillus)

Biosafety level classification (BSL) Level 2

supervision, hood required

(via centrifugation for example) then hood use required.

(Many foodborne pathogens)

Biosafety level classification (BSL) Level 3

biosafety cabinet, neg flow vent

(Influenza)

Biosafety level classification (BSL) Level 4

separated area, hood and suit, decontamination chambers, neg flow ventilation

(Influenza).