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HIV
&
GENETICS
Rohan W. Jayasekara
HIV Classification
Family: Retroviridae
Species: Human immunodeficiency virus 1
Human immunodeficiency virus 2
Virologically, HIV is a highly variable
virus that lacks proof reading
mechanisms accompanied by high
error rate (0.2-2 mutations per
genome per cycle), high replication
rate, an apparent high tolerance and
selection for change.
Group M - Global epidemic
Group O - Outlier
Group N – Neither M nor O
HIV
Three distinctive groups
These groups have genetic sequence differences of
>40% in some coding regions
Globally >90 per cent of HIV-1 infections belong
to HIV-1 group M
Nine genetic subtypes (A,B,C,D,F,G,H,J,K)
circulate in an epidemic
Two recombinant forms (CRF01_AE and
CRF02_AG) are also of major importance
HIVThree distinctive groups
NATURAL HISTORY OF HIV INFECTION
HIV is a virus that infects and destroys cells of the
immune system (CD4+ cells).
Initial infection Asymptomatic period
(clinical latency) Aquired Immune Deficiency Syndrome
Opportunistic infections and cancer
AIDS is the late-stage HIV disease. This occurs when
immune system becomes so damaged that it cannot fight
off diseases and certain types of cancer.
Often (not always) accompanied by severe flu like symptoms
Approximately 8-10 years
NATURAL HISTORY OF HIV INFECTION
DISEASE PROGRESSION
Rapid Progressors (RPs) who cannot control
viraemia and develop AIDS within three years of
infection
DISEASE PROGRESSION
Long-Term Non-Progressors (LTNP) maintain
stable CD4 levels and low virus load (VL) for
ten or more years
DISEASE PROGRESSION
Elite Controllers (EC) who represent just
1% of HIV-infected persons, control HIV
replication to <50 copies/ml
DISEASE PROGRESSION
Long-Term Non-Progressors (LTNP) maintain stable CD4
levels and low virus load (VL) for ten or more years
Elite Controllers (EC) who represent just 1% of HIV-infected
persons, control HIV replication to <50 copies/ml
DISEASE PROGRESSION
Exposed uninfected (EU) individuals show resistance
to HIV acquisition even after multiple exposures and
high risk behaviour.
CCR5-Δ32 genotype seems to confer near complete
protection from HIV infection.
DISEASE PROGRESSION
HIV GENOMIC STRUCTURE
9 Genesgag, pol, vif, vpr, tat, rev, vpu, env, nef.
15 Proteinsmatrix, capsid, p6; NC (p7)
protease, reverse transcriptase, integrase, vif, vpr, tat, rev, vpu,
gp120, gp41, nef
Regulatory Proteins
Accessory Proteins
TAT :Trans-Activator of Transcription
REV: Regulator of Virion protein expression
NEF: Negative Regulatory Factor
VIF: Virion Infectivity Factor
VPU: Viral Protein U
VPR: Viral Protein R
gag [group specific antigen]
p24 / p7 / p6 & matrix p17
Makes the cone shaped viral capsid
-----------------------------------------
pol [polymerase]
Codes for Viral Enzymes / Reverse Transcriptase
Integrase / Viral Protease
env [envelope]
Makes surface protein gp120 and transmembrane gp 41
enabling HIV to fuse to CD4 cells
----------------------------------------
Retroviral Genes
HIV VIRUS
env [envelope]
Makes surface protein gp120 and transmembrane gp 41
enabling HIV to fuse to CD4 cells
Retroviral Genes
gag [group specific antigen]
Makes the cone shaped viral capsid
Retroviral Genes
pol [polymerase]
Codes for Viral Enzymes / Reverse Transcriptase
Integrase / Viral Protease
Retroviral Genes
HIV GENOMIC STRUCTURE
9 Genesgag, pol, vif, vpr, tat, rev, vpu, env, nef.
15 Proteinsmatrix, capsid, p6; NC (p7)
protease, reverse transcriptase, integrase, vif, vpr, tat, rev, vpu,
gp120, gp41, nef
HIV REPLICATION
ATTACHMENT
PENETRATION
UNCOATING
REVERSE TRANSCRIPTION
INTEGRATION
REPLICATION
ASSEMBLY
RELEASE
HIV REPLICATION
ATTACHMENT & PENETRATION
HIV REPLICATION
ATTACHMENT
&
PENETRATION
Env produces the only exposed viral protein in the
virion (neutralization resistant)
Binding/fusion with the host cell is mediated by gp120
& gp41 (CD4 & CCR5 or CXCR4 co-receptors)
CCR5-Δ32 - a 32 base pair deletion frameshift
mutation that truncates C-C chemokine receptor 5
(CCR5) - the HIV entry receptor on lymphoid cells.
Epidemiological studies show that individuals
homozygous for CCR5-Δ32 had a 100-fold
reduction in HIV infection incidence.
CCR5-Δ32 genotype seems to confer near complete
protection from HIV infection.
ATTACHMENT & PENETRATION
Exposed uninfected (EU) individuals show resistance
to HIV acquisition even after multiple exposures and
high risk behaviour.
CCR5-Δ32 genotype seems to confer near complete
protection from HIV infection.
DISEASE PROGRESSION
HIV REPLICATION
UNCOATING
HIV REPLICATION
REVERSE TRANSCRIPTION
HIV REPLICATION
REVERSE TRANSCRIPTION
The Pol gene encodes for enzymes involved
in viral replication including the reverse
transcriptase
that converts viral RNA into DNA
INTEGRATION &
REPLICATIONINTEGRATION &
HIV REPLICATION
REPLICATION
Integrase that facilitates incorporation of the viral
DNA into host chromosomal DNA (the provirus)
The accessory or regulatory genes of HIV (tat, rev, vif, vpr,
nef etc.) modulate virus replication.
INTEGRATION &
Cellular function (e.g., nef, vpr)
Viral gene expression (e.g., tat, rev)
HIV REPLICATION
Protease that cleaves large
gag and pol protein precursors into their components
ASSEMBLY
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
Precise location in virion unknown, not generally present in
other retroviruses, may aid in incorporation of Vpr into virion
pol
(Pr) 160gag-pol p160 Gag- Pol precursor protein
p6 p6
ASSEMBLY
RELEASE
HIV Life cycle
CD4 with HIV Infection (EM)
LABORATORY DIAGNOSIS OF
HIV INFECTION
Screening (serological) test
Enzyme Linked Immunosorbent Assay (ELISA)
Confirmatory test - Western Blot (identifies
the specific HIV virus proteins)
LABORATORY DIAGNOSIS OF
HIV INFECTION
Reverse Transcription PCR (RT-PCR)
Most helpful in diagnosis of HIV before seroconversion
(i.e. during the 3-6 months window period - no antibodies inserum even though infected with HIV)
Helps to detect HIV infection in newborns of HIV positivemothers
Real time PCR (qPCR)
Useful in determining viral load to assess treatment - fordiagnosis and monitoring the level of viraemia
Correlates with response to antiretroviral drugs
NEWER TESTS FOR
HIV INFECTION
HIV RNA Genome Sequencing
Detects virus mutations associated with
drug resistance
Enfurvitide (Fuzeon or T20)
Maraviroc (Selzentry - CCR5
co-receptor antagonist)
Delavirdine
Efavirenz
Nevirapine
Lamivudine, zalcitabine,
zidovudine, didanosine,
stavudine, tenofovir
Amprenavir, indinavir,
saquinavir, lopinavir /
ritonavir, ritonavir,
nelfinavir
Integrase
Inhibitors
Isentress (Raltegravir orMK-0518), JTK303/GS-9137
HIV ANTIRETROVIRAL THERAPY
HAART
(Highly Active Antiretroviral Therapy)
Three or more anti-HIV drugs
(antiretrovirals) from at least 2 different
classes in combination allows potent
inhibition of HIV replication.
RECOMBINANT VACCINES - made up of
genetically engineered component combinations of the
HIV pathogen.
DNA VACCINES - made up of copies of single or
multiple genes from the HIV pathogen.
VECTOR VACCINES - same strategy as DNA
vaccines, addition of a “vector” for better delivery e.g.
adenovirus.
HIV VACCINES – ANY HOPE?
TYPES OF HIV VACCINES
DEVELOPING AN HIV VACCINE IS
“DIFFICULT”
Numerous modes of transmission
HIV kills the very immune cells used in defending the
body against HIV
HIV has a high replication & mutation rate, making
itself unrecognizable to the immune system
Mutation leads to different subtypes of the virus
worldwide
HIV VACCINES – CHALLENGES
DEVELOPING AN HIV VACCINE IS
“DIFFICULT”
Numerous modes of transmission
HIV has a high replication & mutation rate, making
itself unrecognizable to the immune system
Mutation leads to different subtypes of the virus
worldwide
HIV kills the very immune cells used in defending the
body against HIV
HIV VACCINES – CHALLENGES