BIOL 2421 Microbiology Lecture Notes: Viruses, Retrovirus HIV and AIDS Dr. Weis
Retrovirus
Linear, 2 ss + RNA, linked by Hydrogen bonds
Also contains a 3rd type of nucleic acid: a specific type of tRNA (trp, pro, or lys)
Spherical, slightly pleomorphic
Phospholipid Envelope with spikes
Contains enzyme, Reverse transcriptase that transcribes vRNA to vDNA to be incorporated into host cell.
7 Genera of Retroviridae:
Gammaretrovirus: mouse mammary tumor (MMT)
Episilonretrovirus: reptile virus (MLV)
Alpharetrovirus: Avian leucosis (ALV)
Betaretrovirus: Monkey virus (MPMV)
Deltaretrovirus: Bovine leukemia (BLV); HTLV
Spumavirus: chimpanzee, human spumavirus (Foamy cell leukemia)
Lentivirus:
Subgenus
Bovine Lentivirus group: Bovine immunodeficiency virus (BIV)
Equine Lentivirus group: Equine Infectious Anemia (EIA)
Feline Lentivirus group: Feline immunodeficiency virus (FIV)
Ovine/Caprine Lentivirus group: Arthritis (CAEV)
Primate Lentivirus group: HIV-1, HIV-2
Human HIV possibly evolved from viruses that affected
African monkeys. Transition probably around 1930’s.
Earliest
known infection 1959 in
In U.S, 1981.
HIV-1 has 11 clades [branches or subtypes; examples A-H, O]
HIV-1
B is in the
HIV-1 C is in Africa
HIV-1 E is in Asia
Lentivirus diseases
* Immunodeficiency
* Slow, progressive wasting disorders
* Allow for opportunistic infections
* Neurodegeneration
* Death
HIV core = RNA genome + Nucleocapsid protein + RT + IN
The core appears conical / helical inside the capsid
RNA genes for HIV
3 genes for replication: env, gag, pol
3 regulatory genes: tat, rev, nef
3 auxiliary genes: vif, vpr, vpu
All retroviruses have 5’-gag – pol – env – 3’
Gag and pol genes are translated into a single protein molecule which is cleaved by viral proteases into
* capsid proteins
* protease
* RT
* integrase
Env genes are translated into an envelope protein, gp 160 which is then cleaved by host proteases into
* Surface glycoprotein
* Transmembrane glycoprotein
HIV retrovirus has: 5’ – cap –R-U5-PBS-leader -gag-pol-env -ppt- U3- R - 3’
Generalized structure of retrovirus
|
Name |
Protein |
Gene |
Function |
|
MA |
Matrix [p17] |
Gag gene |
Creates a continuous inside membrane protein that lines the envelope |
|
CA |
Capsid [p24] |
Gag gene |
Capsid protein that protects the core |
|
NC |
Nucleocapsid [p 9, 6] |
Gag gene |
Forms the core, helical in appearance |
|
PR |
Protease [p11], [p9] |
Gag gene |
Cleaves protein during maturation |
|
RT |
Reverse transcriptase [p51 and p 66] |
Pol gene |
Transcribes vRNA genome to make vDNA |
|
IN |
Integrase, [p32] |
Pol gene |
Integration of provirus |
|
SU |
Surface glycoprotein [gp 120] |
env gene |
Major antigen in outer envelope, receptor binding to CD4 cells, linked to TM. Avoids immune cells by changing shape. Also, most of protein is hidden |
|
TM |
Transmembrane protein [gp 41] |
env gene |
Holds SU in envelope, responsible for membrane fusion after initial receptor binding with gp 120 |
Outer shell = Viral Envelope that is derived from a host Plasma Membrane which is acquired when the virus buds through the cell membrane composed of host cell constituents with viral proteins as spikes.
Contains env = cap + stem
Glycoproteins (gp)
Cap = gp 120 is attached to the stem
Stem = gp 41 that transverses the envelope
Within the viral envelope is a matrix protein (p): p17
Matrix protein is icosahedral
Functions to
^ Anchor Transmembrane envelope protein
^ Assist in viral penetration
^Transport proviral integration complex across nuclear envelope
^Localizes assembly of virion to the cell receptor
Within the matrix is a viral core (capsid) is a core antigen protein, p24
Within the capsid is
RNA + proteins
Integrase, p 32
Reverse transcriptase, p51 and p66
tRNA lys 3, which acts as an RT primer by binding to its complementary
site on the viral RNA and initiating reverse transcription
Vpu: Viral protein U that enhances virus particle release from infected cells and induces the degradation of CD4.
Vpr: Viral protein R that changes ion channel activity and promotes nuclear entry of viral RNA. Also causes G2 cell cycle arrest that leads to cell death
Protease: Hydrolytic enzyme associated with RNA, critical for viral replication. Important in early step of replication to assemble immature form of virus. Also helps to form mature virus as it is used to cut the long protein pieces into their proper size peptides to make functional protein products that are essential for viral assembly.
Nef: negative factor
* Interacts with host cell signal transduction proteins to allow long term survival of virus in infected T cells by binding to cellular protein kinases
* Causes the destruction of non-infected cells by inducing apoptosis
* Advances endocytosis of surface receptors (downgrades CD4 proteins & MHC)
to impair T-cytoxic cells to evade host immune system response
* Renders resting T lymphocytes highly permissive to HIV-1 infection by
interacting with the CD40L receptor signaling pathway
* Contributes to the progression
of AIDS
Integrase: helps cut host DNA regions in order to allow integration of vDNA into host cell genome.
Retrovirus Replication
Attachment: SU envelope protein [gp 120] binds to host target cell receptor, CD4
HIV also infects macrophages to inhibit phagocytosis of IgG and
Complement opsonized pathogens
Second binding to co-receptors
surface chemokine, CCR5 on macrophages in the early stages
surface chemokine, CXCR4 on T helper cells, in the late stages
Co-receptor binding
is necessary to cause the change in the fusion protein
Penetration: TM protein fusion
domain revealed, virus fuses
Partial uncoating of nucleocapsid
in cytoplasm
Genome Replication:
Reverse Transcriptase inside nucleocapsid core
tRNA carried by the virus serves as a primer
RT copies the ss+RNA to form a RNA–DNA hybrid
Ribonuclease H (a component of RT) degrades +RNA strand to leave –DNA
RT then copies this
strand to produce a dsDNA called proviral DNA
Integration
Catalyzed by Integrase
Linear ds DNA is used and ends brought together
Proviral DNA takes on a circular form and is incorporated into host genome
Provirus is present
for lifetime of cell
Translation
Proviral DNA then serves to create mRNA and new ss+ RNA strands
Fresh RNA reenters the cytosol where some are translated by ribosomes
HIV may remain as latent virions in vacuoles within the cell
Lack of proof reading
corrections creates a higher mutation rate
Viral Protease
Cleaving of viral
proteins to create functional peptides for virus
Assembly and Budding
Capsid assembly at the plasma membrane
Host plasma membrane used to create part of viral envelope
Transmission: aided by Langerhans cells in mucosal epithelial cells and STDs.
Horizontal: Blood, organ transplants, coitus, blood transfusion, needles, AI
Vertical: Infected mother to child > breast milk, placenta
Direct: Infected cell to other cells via fusion
Rate of HIV infection to clinical AIDS is about 10 years
NOTE: HIV is present in other fluids (urine, feces, sweat, saliva, tears) but
No known transmission.........yet!
Prodromal
Early Phase
Primary: flu-like symptoms: fever, sweat, sore throat, diarrhea
Middle phase
Sero-conversion in 2-4 weeks post infection
May be asymptomatic
Continuous infection
Decreases life span of CD4 cells as well as destruction
Replacement efforts decrease
Late Phase
Symptoms proceed and progress towards AIDS
* constitutional: fever, lymphadenopathy, diarrhea, weight loss
* neurological: dementia, myelopathy
* immunodeficiency: allows for secondary, opportunistic infections
destruction: lysis of infected cells [CD4+]
syncytium formation
* rare malignancies: Kapsoi’s sarcoma, lymphoma
Stages of HIV
Category A: asymptomatic, lymphadenopathy, more severe = increase load
Category B: beginning of opportunistic infections, rare cancers, diarrhea, fever
Category C: clinical AIDS, T-h count below 200/cubic mm
Persistant Opportunistic infections
a) Viruses: HSV-1, VZV, EBV
b) Bacteria: TB
c) Fungus: candidia, pneumocystis
d) Protozoans: Microsporidia
Dx:
IgG: indicates infection, except in infants exposed from mother, must wait for seroconversion
ELISA of p24 antigen
PCR to detect vRNA
Tx:
Supportive
HAART => Highly Active AntiRetroviaral Therapy
(1) Drugs to decrease viral replication
~ Nucleoside analogues
Interfers with RT
AZT: Thymidine analog drug lacks 3’ Oxygen, creating DNA chain termination
Dideoxyinosine, Dideoxycytidine
Lamivudine
~ Nonnucleoside inhibitors of RT
APA : binds to pocket between the p66 protein of RT, near the polymerase activation sites.
Delavirdine
Nevirapine
~ Protease inhibitors (must be used with AZT)
blocks viral protease so that the proteins needed for assembly cannot
be cleaved from the large protein precursors
Lamivudine
Stavudine
Saquinavir
Ritonavir
Indinavir
Viracept
Amprenavir
(2) Entry Inhibitors
Competative inhibitor that interferes with fusion process of gp41 penetration of host plasma membrane.
Enfuvirtide
NOTE: No vaccine due to rapid mutation rate during reverse transcription of vRNA to DNA
Opportunistic Infections
Pneumocystis carinii
Most frequent opportunistic infection seen with AIDS
Produces pneumonia with perihilar infiltrates
Other symptoms: fever, non-productive cough, dyspnea
Dx: lavage or biopsy to find P carinii cysts
Cytomegalovirus
Herpes virus; Can cause: pneumonia,
retinitis
Mycobacteria
M. tuberculosis : granulomatous pulmonary disease
M. avian complex
: affects mononuclear phagocyte system(LN, spleen, Liver, BM)
Fungal Infections
Candidia: invasive infections in esophagus, URTI, and lung
Systemic infections: Cryptococcus, Histoplasmosis, Coccidioides.
Protozoan
Toxoplasmosis : T. gondii à brain to create abscesses
Crytposporidium, Microsporidium, Isospora à watery diarrhea
Viral
Herpes
HSV-1 can involve the GI tract at esophagus and perianal region
VZV can involve
the skin
Malignant Neoplasms
Kaposi’s Sarcoma (KS)
Reddish, purple patches, plaques or nodules over the skin
Malignant lymphoma à brain
Miscellaneous
Lymphoid interstitial pneumonitis (LIP)
Lung condition involving children
Interstitial pulmonary infiltrates