retroviruses:HIV (Lect 14)

enveloped icosahedral, 2 copies +ssRNA

retroviridae shape, capsid, genome

long terminal repeats (LTRs)

simple retroviruses have unique regions that encode genes flanked by these, one on each side

gag, pol, env

three simple retrovirus genes

gag

simple retrovirus gene: makes up capsid, nucleocapsid, and matrix

pol

simple retrovirus gene: polymerase

env

simple retrovirus gene: surface glycoproteins

gp120, gp41

HIV-1 env surface glycoprotein is made of two subunits

gp120

HIV-1 surface (SU) subunit, VAP

gp41

HIV-1 transmembrane (TM) subunit, fusion protein

plasma membrane, endocytic vesicle

retrovirus fusion can occur at these two sites

CD4

HIV-1 entry dependent on binding this receptor along with two other co receptors (CCR5, CXCR4) to target specific cell types

CCR5, CXCR4

HIV entry is dependent on CD4 receptor, and can target specific cell tyes with these two co receptors

reverse transcriptase (RT)

packaged with virus particle, makes DNA from RNA or DNA template

integrase

packaged in viral particle along with RT, mediates integration into host cell chromosome

requires cell division, non-dividing cells

cell type required for simple RV integration? Complex RVs?

provirus

integrated RV genome

transcription

follows RV integration

Gag Gag-Pol

located in cytosol after synthesis

Gag

drives assembly of virus particle and associates with the genome

Env

goes through secretory apparatus after synthesis (ER→golgi→plasma membrane)

surface(SU), transmembrane(TM)

Env is cleaved into two subunits by the cell during RV assembly

after budding

Gag is cleaved by viral proteas for maturation, when does this occur?

matrix (MA), capsid(CA), nucleocapsid(NC)

Gag cleaved by viral protease into these three separate proteins after budding: protein underlies lipid envelope, forms protein shell, tightly associates with genome

human immunodeficiency virus HIV-1

first identified at the Pasteur institute in Paris in 1983, in early 80s young healthy males were seen getting rare diseases like Kaposis Sarcoma and Pneumocystis

M(major), O(outlier), N(non M, non O)

three major lineages of HIV-1

clades/subtypes

many of these within HIV-1 group M, mostly B in the US

SIV chimpanzee

HIV evolutionarily related to this non human primate virus

chimpanzees, monkey

SIV is acquired by … from asymptomatic .. host

macaque SIV

HIV-2 has gotten into the human population 9x , originated from:

HIV-2

originated from macaque SIV, gotten into human population 9 separate times

CD4+ T cells

local epithelium are not infected by HIV-1, instead, these immune cells are

dendritic cells

can bring HIV to CD4+ T cells in a lymph node without being infected

GALT gut associated lymphoid tissue

depleted of CD4+ T cells and usually does not recover as HIV replicates locally and is released into the blood

peripheral circulation

due to the immune response, HIV is cleared from … but continues to replicate in lymph nodes and GALT

lymph nodes and GALT

due to the immune response, HIV is cleared from peripheral circulation but continues to replicate in

thymus

its function is compromised, meaning CD4+ T cells cannot be replaced when destroyed by HIV

>95%

mortality from untreated HIV-1

opportunistic infection

loss of immune function leads to HIV patients often succumbing to:

primary infection

HIV phase lasts 4-8 weeks, highest levels of infectious virus, symptoms include fever, swollen lymph nodes, other flu like symptoms

asymptomatic phase

HIV phase lasts 2-12 years, no disease

symptomatic/AIDS

HIV phase lasts 0-1 years, immunosuppression leads to opportunistic infection then death

set point

level of viral load in blood during asymptomatic phase, dictates disease progression

viral genotype, immune response

set point of HIV is determined both by:

200 uL

what level of CD4 T cells/uL is clinically defined as AIDS

fast progressors

~10-20% of HIV-1 infected people, 2-3 years to AIDS, loose >100 CD4 T cells/yr

slow progressors

~65-75% of HIV-1 infected people, average 8-10 years to AIDS loose CD4 T cells at moderate rate (30/yr)

long term non progressors

~5% detectable HIV but no noticeable decrease in CD4+ T cell counts, very low percent revert to late term fast progressors

elite controllers

~0.5%, they are infected with HIV but have undetectable virus in plasma and do not progress

highly exposed, persistently seronegative

in high risk groups but fail to be infected with HIV

Kaposi’s Sarcoma, CMV

common killers for those that develop AIDS, all of us tend to have these but can normally fight off with strong immune response

CCR-5, CD4

HIV receptors present on activated and memory T cells, and macrophages

CXCR-4, CD4

HIV receptors present on naive T cells

X4 virus (T tropic)

HIV-1 tropism, uses CXCR4 as co receptor, appears late in infection/pathogenesis, infect naive T cells

R5 tropic (M tropic)

HIV-1 tropism, uses CCR5 as co-receptor, transmitted virus, mostcommon, can infect macrophages and activated/memory T cells

sexual contact, genital secretion

HIV transmission

receptive anal sex

highest rate of sexual contactHIV transmission (1 in 70)

air/water, saliva/sweat/closed mouth kissing, insects/pets, sharing toilets/food/drinks

big scare early in 1980s, thought to be methods of HIV transmission leading to lot of sigma around gay men, but HIV is NOT transmitted via these routes

high viral load

associated with higher risk of HIV transmission

acute infection

HIV transmission has highest viral load during this period, highest risk of transmission

post natal, intrapartum, intrauterine

around 1/3 infants born to HIV+ mothers become infected, pre or perinatal transmission leads to accelerated disease progression, ranks highest to lowest transmission rates mother → child

eclipse period

HIV diagnosis is combination between testing for virus and immune response, al tests have a time between infection and detectable result ranging from 10 days to 5 weeks

be confirmed

while there are home/rapid HIV tests available, results must:

RT-PCR for viral load, CD4+ T cell count, assay to test for drug resistance

HIV tests to guide therapy

ELISA

detects and counts certain antibodies, antigens, proteins and hormones in bodily fluid samples, used to detect HIV-1 antigen (p24) and antibodies against HIV-1 or 2

acute HIV-1 infection

if you test HIV- for both 1 and 2, and further HIV-1 nucleic acid test comes back positive, what does this mean?

chronic

HIV infection is persistent, constant producing infectious particles, what kind of infection is this?

quasi-species

one error is incorporated into HIV genome every 30,000 bases replicated (1 per every 2-3 genomes replicated), high mutation rate creates:

monotherapy

use of one antiviral

cART

combination of antiretroviral therapy

nucleoside RT inhibitors, non-nucleoside RT inhibitors

two classes of HIV ART reverse transcriptase inhibitors including:

nucleoside RT inhibitors

HIV antiviral, mechanism: mimic natural nucleosides, incorporated into DNA leading to chain termination, all these drugs have side effects, still used in cART due to their effectiveness

HIV antiviral, mechanism: inhibit RT by changing the shape of the enzyme, inexpensive, effective, and generally safe althought some side effects

integrase strands transfer inhibitors

class of ART, mechanism: prevent integration of the provirus, potent, well tolerated, newer drugs that have really changed HIV therapy

integrase strands transfer inhibitors

newer class of ART drugs that have really changed HIV therapy

protease inhibitors

class of ART prevent maturation, prevent cleavage of GAG, expensive and can cause GI problems and lipid dysregulation

attachment, fusion

ART entry inhibitors can target two main mechanisms:

entry inhibitors

classes of ART, mechanism: block binding CCR5 or block fusion, not useful if patient has virus that uses CXCR4, must be injected twice daily

entry inhibitors

you have a patient with a virus that uses CXCR4 receptor, what is not an appropriate antiviral to give them?

can accumulate over lifetime of use

while ~25 unique drugs have been approved spanning the 5 major classes, there are still side effects for HIV ART, why is this an issue?

reservoir of long lived cells with integrated genomes

why is cART not curative, and can only manage disease?

condom use

cornerstone of HIV prevention

men who have sex with men, IV drug users, people in prisons, sex workers, transgender individuals

high risk individuals for HIV

pre exposure prophylaxis

use of cART before HIV exposure, can reduce infection rates by 75%, U=U (undetectable=untransmittable)

post exposure prophylaxis

PEPs given within 24-72 hours of infection

NAbs (neutralizing antibodies), cell mediated immunity, both

vaccine for HIV-1 remains elusive, what are the three major ideas circulating?

latent reservoir

infected cells harboring full length transcriptionally inactive, replication competent HIV-1 provirus in cART+ patients, major barrier to HIV-1 cure

memory CD4+ T cells

where is latent HIV-1 reservoir established?

shock and kill

strategies to activate latent HIV-1 reservoir in CD4+ T cells and target these cells for killing