HIV Structure, Lifecycle and Replication (1)

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HIV Structure, Lifecycle and Replication
(1) Background Basic Virology and
Pathogenesis Structure Virion structure,
genomic structure, and accessory
molecules Lifecycle Infection and
Expression January 9 January 14
2013 F. Javier Ibarrondo,
Ph.D. fibarrondo_at_mednet.ucla.edu
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Pneumocystis pneumoniaLos Angeles. Gottlieb M S,
Schanker H M, Fan P T, Saxon A, Weisman J D
Polzalski In the period October 1980-May 1981, 5
young men, all active homosexuals, were treated
for biopsy confirmed Pneumocystis carinii
pneumonia at 3 different hospitals in Los
Angeles, California. Two of the patients died.
All 5 patients had laboratoryconfirmed previous
or current cytomegalovirus (CMV) infection and
candidal mucosal infection. Morbid. Mortal,
Weekly Rep. 30250-2. 1981.
(I) Identification of AIDS
Pneumocystis carinii Pneumonia and Mucosal
Candidiasis in Previously Healthy Homosexual Men
Evidence of a New Acquired Cellular
Immunodeficiency Michael S. Gottlieb, M.D.,
Robert Schroff, Ph.D., Howard M. Schanker, M.D.,
Joel D. Weisman, D.O., Peng Thim Fan, M.D.,
Robert A. Wolf, M.D., and Andrew Saxon, M.D. N
Engl J Med 1981 3051425-1431December 10, 1981
Isolation of a T-Lymphotropic Retrovirus from a
Patient at Risk for Acquired Immune Deficiency
Syndrome (AIDS) F. Barré-Sinoussi J. C.
Chermann F. Rey M. T. Nugeyre S. Chamaret J.
Gruest C. Dauguet C. Axler-Blin F.
Vézinet-Brun C. Rouzioux W. Rozenbaum L.
Montagnier. (May 20, 1983) Science, New Series,
Vol. 220, No. 4599., pp. 868-871
(II) Isolation of the virus
Detection, isolation, and continuous production
of cytopathic retroviruses (HTLV-III) from
patients with AIDS and pre-AIDS Frequent
detection and isolation of cytopathic
retroviruses (HTLV-III) from patients with AIDS
and at risk for AIDS Serological analysis of a
subgroup of human T-lymphotropic retroviruses
(HTLV-III) associated with AIDS Antibodies
reactive with human T-lymphotropic retroviruses
(HTLV-III) in the serum of patients with
AIDS Gallo RC. et al. (May 1984) Science 224
(4648) 497508
(III) Link Virus-AIDS
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From GRID to AIDS
Pneumocystis carinii Pneumonia and Mucosal
Candidiasis in Previously Healthy Homosexual Men
Evidence of a New Acquired Cellular
Immunodeficiency Michael S. Gottlieb, M.D.,
Robert Schroff, Ph.D., Howard M. Schanker, M.D.,
Joel D. Weisman, D.O., Peng Thim Fan, M.D.,
Robert A. Wolf, M.D., and Andrew Saxon, M.D. N
Engl J Med 1981 3051425-1431December 10, 1981
An African HIV-1 sequence From 1959 and
implications for the origin of the epidemic Tuofu
Zhu, Bette T. Korber, Andre J. Nahmiask, Edward
Hooper, Paul M. Sharp David D. Ho. February
1998 Nature, Vol 391, 5
The emergence of HIV/AIDS in the Americas and
beyond M. Thomas P. Gilbert, Andrew Rambaut,
Gabriela Wlasiuk, Thomas J. Spira, Arthur E.
Pitchenik, and Michael Worobey PNAS , November
20, 2007, 1856618570
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Human immunodeficiency virus (HIV) is a
retrovirus that causes acquired immunodeficiency
syndrome (AIDS). Since the beginning of the
epidemic in 1981, more than 60 million people
have contracted HIV and nearly 30 million have
died of HIV-related causes. At the end of 2011,
an estimated 34 million people, an estimated 0.8
of adults aged 15-49 years worldwide, are living
with HIV. 2.5 million new infections in 2011
330,000 were children. 7,000 people contract HIV
everyday, nearly 300 every hour. In 2011 alone,
AIDS claimed an estimated 1.7 million lives, of
which 230,000 were children. HIV primarily
infects vital cells in the human immune system
such as helper T cells (CD4 T cells),
macrophages and dendritic cells. HIV infection
leads to low levels of CD4 T cells.
http//www.unaids.org/en/
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Region (lower- and middle-income countries) Region (lower- and middle-income countries) Antiretroviral therapy coverage Estimated number of people receiving antiretroviral therapy Estimated number of people needing antiretroviral therapy
Sub-Saharan Africa Sub-Saharan Africa 37 3,911,000 10,600,000
  Eastern and Southern Africa 41 3,203,000 7,700,000
  Western and Central Africa 25 709,000 2,900,000
Latin America and the Caribbean Latin America and the Caribbean 50 478,000 950,000
  Latin America 51 425,000 840,000
  The Caribbean 48 52,400 110,000
East, South and South-East Asia East, South and South-East Asia 31 739,000 2,400,000
Europe and Central Asia Europe and Central Asia 19 114,000 610,000
North Africa and the Middle East North Africa and the Middle East 11 12,000 100,000
Total Total 36 5,254,000 14,600,000
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Viruses Microscopic infectious agents that can
infect the cells of a biological
organism. Viruses can only replicate themselves
by infecting a host cell and are incapable to
reproduce on their own. A complete viral
particle, known as a virion consists of nucleic
acid surrounded by a protective coat of protein
called a capsid.
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Types of Viruses (Baltimore Classification) I
Double-stranded DNA (Adenoviruses Herpesviruses
Poxviruses, etc) Herpesviridae (Herpes, CMV,
EBV), Poxviridae (Smallpox, Chickenpox,
Vaccinia), Papilloma virus, Adenovirus II
Single-stranded () sense DNA (Parvoviruses) Eryt
hema infectiosum, Phages III Double-stranded
RNA (Reoviruses Birnaviruses) Rotavirus,
Reovirus IV Single-stranded () sense RNA
(Picornaviruses Togaviruses, etc) Polio, SARS,
Hep A, Hep C, Rubella, Yellow fever V
Single-stranded (-) sense RNA (Orthomyxoviruses,
Rhabdoviruses, etc) Rubella, Influenza, Rabies,
Measles, Mumps, Ebola VI Single-stranded ()
sense RNA with DNA intermediate
(Retroviruses) HTLV, HIV VII Double-stranded
DNA with RNA intermediate (Hepadnaviruses) Hep B
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HIV Classification Group Group VI
(ssRNA-RT) Family Retroviridae Genus
Lentivirus (Enveloped) Species Human
immunodeficiency virus 1 Species Human
immunodeficiency virus 2
Species Virulence Infectivity Prevalence
Inferred origin HIV-1 High High Global
Chimpanzee HIV-2 Lower Low West Africa
Sooty Mangabey
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HIV phylogeny
CRF14_BG
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HIV-1 Tropism
www.hivmedicine.com/textbook/pathogen.htm
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HIV-1 Transmission Sexual route. Blood or
blood product route. Mother-to-child
transmission (MTCT).
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Infection
Fusion Entry
Binding
Nuclear localization entry
Integration
CD4
CXCR4
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Cellular Activation
Assembly
Post-translational processing
Budding
Translation
Expression
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HIV Structure Virion Genomic Proteomic
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HIV Structure
SIV
HIV
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HIV Structure Virion Genomic Proteomic
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Infection
Fusion Entry
Binding
Nuclear localization entry
Integration
CD4
CXCR4
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HIV Genome
HIV RNA
Reverse transcription Integration
HIV DNA
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HIV-1 RNA
Nature 460, 711-716 (6 August 2009)
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HIV-1 Integrated DNA
Source The AmFAR AIDS Handbook, D Ward, pp. 348
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RNA Splicing
Translational Frameshift
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Source The Molecular Biology of HIV/AIDS, D
Ward, pp. 19
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Source Atlas of Infectious Diseases, Mandell
Mildvan (ed.), pp. 3.13
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Dr. Isabelle BOUALLAGA Institut Pasteur.
http//www.123bio.net/
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Source Atlas of Infectious Diseases, Mandell
Mildvan (ed.), pp. 3.13
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HIV Structure Virion Genomic Proteomic
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HIV Proteins Structural Proteins Gag Matrix,
Capsid, NC, p6 Pol Protease, Reverse
Transcriptase, Integrase Env gp120,
gp41 Regulatory Proteins Tat Rev Nef Accessory
proteins Vif Vpr Vpu
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Source The Molecular Biology of HIV/AIDS, D
Ward, pp. 19
33
Source BioAfrica Bioinformatics for HIV
Research. http//bioafrica.mrc.ac.za/
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Gene/Protein
Mass,
KDa
Function
gag
(Pr) 55gag
p55
Gag precursor protein
MA - Matrix
p17
Aids nuclear import and viral assembly
CA - Capsid
p24
HIV central core contains HIV genome and enzymes
NC - Nucleocapsid
p15 (p6,p9)
p6 Precise location in virion unknown, not
generally present in
other retroviruses, may direct proteins to
secretory path of cell.
p9 Assoc. with HIV RNA, involved in packaging
of HIV
RNA into virions
RNA binding RNA packing
Association with membrane
Formation of Gag multimers
myristate
Matrix p17
Capsid p24
NC p9
p6
p1
p2
Envelope Incorporation
Viral Budding
Viral Entry
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Source BioAfrica Bioinformatics for HIV
Research. http//bioafrica.mrc.ac.za/
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Gene/Protein
Mass,
KDa
Function
pol
(Pr) 160gag-pol
p160
Gag-
Pol precursor protein
PR - protease
p10
Cleaves Gag and Gag-Pol
IN -
integrase
p32
Integrates viral genome into host DNA
RT reverse
p66/p51
p66 copies RNA genome. RNAse H
transcriptase
p51 regulatory?
Gag
PR p10
RT
IN p32
p6
p51
p66
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Anti-HIV drugs Nucleoside/Nucleotide Reverse
Transcriptase Inhibitors lamivudine (3TC),
zalcitabine (ddC), zidovudine (AZT),
didanosine (ddI), stavudine (d4T),
tenofovir  Non-Nucleoside Reverse Transcriptase
Inhibitors Delavirdine, efavirenz,
nevirapine Protease Inhibitors Amprenavir ,
indinavir, saquinavir, saquinavir,
lopinavir/ritonavir, ritonavir,
nelfinavir  Integrase Inhibitors Isentress
(Raltegravir or MK-0518) , JTK303/GS-9137 Fusion
or Entry Inhibitors Enfurvitide (Fuzeon or T20),
Maraviroc (Selzentry -CCR5 antagonist-) HAART
(Highly Active Antiretroviral Therapy) three or
more anti-HIV drugs (antiretrovirals) from
different classes in combination allows them to
work together to keep HIV levels down
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Gene/Protein
Mass,
KDa
Function
env
(Pr) 160 env
gp160
Env precursor protein
SU Envelope
gp120
Surface glycoprotein that binds CD4
TM - Transmembrane
gp41
Transmembrane protein that anchors gp120 to virus,
responsible for fusion between virus and host
cell membrane.
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Gene/Protein
Mass,
KDa
Function
gag
(Pr) 55gag
p55
Gag precursor protein
MA - Matrix
p17
Aids nuclear import and viral assembly
CA - Capsid
p24
HIV central core contains HIV genome and enzymes
NC - Nucleocapsid
p15 (p6,p9)
p6 Precise location in virion unknown, not
generally present in
other retroviruses, may direct proteins to
secretory path of cell.
p9 Assoc. with HIV RNA, involved in packaging
of HIV
RNA into virions
pol
(Pr) 160gag-pol
p160
Gag-
Pol precursor protein
PR - protease
p10
Cleaves Gag and Gag-
Pol precursor proteins
IN -
integrase
p31
Integrates viral genome into host DNA
RT reverse
p66/p51
p66 copies RNA genome. RNAse H
transcriptase
p51 regulatory?
env
(Pr) 160 env
gp160
Env precursor protein
SU Envelope
gp120
Surface glycoprotein that binds CD4
TM - Transmembrane
gp41
Transmembrane protein that anchors gp120 to virus,
responsible for fusion between virus and host
cell membrane.
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Source The Molecular Biology of HIV/AIDS, D
Ward, pp. 19
41
Regulatory Proteins TAT Trans-Activator of
Transcription REV Regulator of Virion protein
expression NEF Negative Regulatory
Factor Accessory Proteins VIF Virion
Infectivity Factor VPU Viral Protein U VPR
Viral Protein R
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TAT Trans-Activator of Transcription
Recruitment of CDK9
Poor transcription
Enhanced transcription
Release to extracellular medium Apoptosis
bystander T-cells CXCR4 negative interaction
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REV Regulator of Virion protein expression
RRE rev-response element
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NEF Negative Regulatory Factor
Downmodulation the expression of several
surface molecules important in host immune
function MHC I, MHC II, CD4 Activation from
latency? Extracellular Nef might activate NF kB.
T-cell activation (activates the production of
MIP-1alpha and MIP-1beta in macrophages)
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VIF Virion Infectivity Factor
www.hivmedicine.com/textbook/pathogen.htm
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VPU Viral Protein U
Involved in viral budding, enhancing virion
release from the cell Downregulation of CD4
VPR Viral Protein R
Regulation of nuclear import of the HIV-1
pre-integration complex Required for virus
replication in non-dividing cells such as
macrophages. Induces cell cycle arrest and
apoptosis in proliferating cells
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• Take-home points
• Structure
• env is only exposed viral protein
  (neutralization resistant)
• infectivity mediated by gp120 gp41 (CD4
  CCR5 or CXCR4)
• RNA genome -- requires HIV reverse
  transcription to DNA
• integration requires HIV integrase
• LTR/promoter requires cellular transcription
  factors
• productive viral gene expression requires HIV
  protease activity
• accessory genes modulate
• 1) cellular function (e.g., nef, vpr)
• 2) viral gene expression (e.g., tat, rev)
• gag (p24) represents the primary structural
  component of virion
• small molecule inhibitors of these structures
  functional activity
• represent the primary current antiviral
  therapeutic strategy