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