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Flashcards in HIV Deck (33)
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-HIV, AIDS, ART, Viral Load, CD4 count


HIV – human immunodeficiency virus

AIDS – acquired immune deficiency syndrome; an advanced stage of HIV disease when opportunistic infections (OI’s) occur

ART – antiretroviral therapy; a combination of at least three drugs that directly act against viral enzymes

Viral Load (VL) – the concentration (number of copies per mL plasma) of HIV RNA detectable in the bloodstream. Goal of ART is viral suppression

CD4 count – the concentration (number per microliter of blood) of circulating CD4+ T-cells - a marker of immune suppression


HIV Epidemiology


Map of HIV-1 (2017)


Untreated HIV Infection Time Course


Plasma HIV-1 RNA titers generally peak 1 week following the onset of symptoms and decline to steady-state levels by 2 months after infection.


HIV Infection Upon Treatment Time Course


A normal range for CD4 cells is about 500-1,500 cells per cubic millimeter of blood.

With treatment can achieve substantial reconstitution of CD4+ T cell counts


Figure of more people living with HIV with the introduction of ART in 1995


High Risk Groups for HIV Infection in US


First cases of HIV

  • Kinshasa, Democratic Republic of Congo
    • Tissue sample from male in 1959
    • Lymph node biopsy from woman in 1960
  • Haiti•Individuals returning from work in DRC 1969 and 1972
  • United States
    • Teenage boy in St. Louis 1969

Mammalian Retroviruses


It turns out that HIV is similar to many other retroviruses that infect other primates and other mammals. In particular, HIV-2 is very similar to a SIV in sooty mangabeys (SIVsmm), and HIV-1 is very similar to a SIV in chimpanzees (SIVcpzPtt = SIV chimpanzee Pan troglodytes troglodytes).


Subgroups of HIV


Shown here is a phylogenetic tree for the main human subtypes of HIV-1 along with gorilla and chimpanzee SIV genomes.

HIV-1 subtype M is the one causing the global pandemic.

Subtypes N, O, and P are rare, restricted to Africa, and arose from different parent SIV strains.


Zoonotic origins of epidemics/pandemics


When viruses jump to a new host there is the potential for severe disease, because the new host has not evolved defenses against the virus. The flip side is that the virus is usually not well-adapted to its new host, which is why we don’t usually catch animal diseases. But as these diseases illustrate, when it does happen it can cause significant illness.

HIV from chimpanzees

Ebola from fruit bats

MERS (Middle East respiratory syndrome) from camels (limited person-to-person spread, so far)

SARS from unknown source (likely bats), efficient person-to-person spread

Avian influenza from poultry (limited person-to-person spread, so far)


HIV-1 vs HIV-2

  • There are actually two HIV viruses that infect humans, HIV-1 and HIV-2
    • And each of those has various sub-types
  • HIV-1 is what most people mean when they say HIV
  • HIV-2 is less common, found mainly in West Africa
  • HIV-2 is somewhat less aggressive in its clinical course, less likely to be transmitted, had a different origin
  • For this class, we discuss HIV-1

HIV - Transmission


HIV - Transmission


Mode (Risk)

  • Sex (0.04 – 1.4%) Mainly blood to blood contact but can also be via bodily fluids. Increased risk: anal sex>vaginal sex>oral sex
  • Intravenous drug use i.e., sharing needles (0.6%). Viral load in index patient matters a lot.
  • Mother-to-child (Up to 35 to 45%). Higher maternal viral load, increased risk for transmission.
  • Blood transfusion (>90%)
  • Needle-stick injuries (0.3%-0.6%)

HIV - Genome Type and General Structure

  • HIV is an RNA virus and it is a retrovirus, meaning it makes DNA from RNA.
    • Harbors two linear copies of (+) ssRNA genome.
    • Reverse transcriptase converts RNA into DNA
    • DNA then integrates into the host genome
  • Spherical
    • Cone-shaped capsid inside an outer envelope
    • Capsid contains the viral genome, enzymes (reverse transcriptase, integrase, and protease), and tRNA primers

HIV Life Cycle

  • 1) Binding: Free virus binds to a CD4 cell via the CD4 receptor and a co-receptor, CCR5 or CXCR4
    • Binds using its viral envelope glycoprotein (gp120)
    • CCR5 is used as the co-receptor in early infection. CCR5 is on cells of the monocyte lineage, including macrophages and dendritic cells.
    • CXCR4 is used as the co-receptor after years of infection (after gp120 mutates). CDCR4 is on T cells. The switch from CCR5-tropic virus to CXCR4-tropic virus is associated with dropping T cell counts and progression of disease.
  • 2) Fusion: Virus fuses with the cell and releases its contents into the cytoplasm
  • 3) Reverse Transcription: Viral reverse transcriptase transcribes the RNA viral genome into DNA. Provides opportunity for mutation.
    • (+) RNA is like mRNA = can be translated into protein
    • Reverse Transcriptase turns viral RNA into cDNA, then makes a complementary DNA strand. Once you have the double stranded DNA it can be integrated into the host. The integrated DNA form of the virus is called the provirus.
  • 4) Integration: The enzyme integrase puts the DNA into the host genome
    • Can integrate anywhere, but a preference is for actively read areas.
  • 5) Replication:
  • 6) Assembly/Packaging:
    • •Viral RNA and proteins made using host machinery
    • New virions packaged and bud off the host cell
    • Proteins are cleaved by protease, which changes immature virions to mature virions
  • 7) Budding: - virus released from the cell.

Natural Immunity to HIV


Some people have a variant form of CCR5, called CCR5-delta32, that makes them resistance to HIV infection. They are relatively immune NOT absolutely immune. A 32 bp deletion in the CCR5 molecule. The deletion on just one allele leads to normal infection, but delayed progression while deletion on both alleles provides resistance to infection.


HIV Cure

Sterilizing cure vs. Functional cure


Sterilizing cure: all virus has been eliminated from the body

The Berlin patient is thought to have achieved a ‘sterilizing cure’ given that no replication competent virus has been found, despite vigorous study several years after the discontinuation of ART. The circumstances which led to this apparent cure were incredibly unique, however, many of the interventions in this unique case have substantial risks associated with them, making this scenario difficult to replicate in a wider population.

  • The Berlin patient
  • Patient had HIV and leukemia
  • Underwent myeloablative bone marrow transplant from a donor who was homozygous for CCR5Δ32 (Twice)
    • Had total body irradiation
  • Viral load undetectable without anti-retroviral treatment

Functional cure: Sustained HIV remission. A couple of examples are:

  • Elite controllers (ECs) who have spontaneous control of HIV and
  • Post-treatment controllers (PTCs) who are placed on treatment and virus doesn’t come back after stopping treatment. So far, this therapy has not been identified yet.

Key Enzymes for HIV

  • Reverse transcriptase
    • Cytoplasmic changing of viral RNA to viral DNA
    • The enzyme is very error-prone: No proofreading mechanism
    • HIV genome is approximately 10,000 base pairs
      • This results in errors during replication
      • End result ~ 1 error per replication cycle
  • Integrase
    • Integrates viral DNA into host chromosome
  • Protease•Essential for viral assembly

The Retrovirus Genome: 3 Main Genes

  • Gag – capsid, matrix, and nucleocapsid (antigens). Core structural proteins.
  • Pol – reverse transcriptase, protease, integrase. Viral enzymes.
  • Env – glycoproteins (for the envelope). Envelope structural proteins.
  • All retroviruses have these three genes
  • HIV has additional genes, called accessory genes, that help it evade and destroy the immune system. They are important in HIV pathogenesis

HIV - Diagnostic Testing

-Current testing algorithm


Two basic methods – antibody-based or PCR-based

  • PCR – measures copies of viral RNA in the blood. Called a direct test
  • ELISA/Western Blot – detects antibodies to HIV. Called an indirect test.

Current Testing Algorithm

  • Test for antibodies and the p24 antigen by ELISA (a combination test). This is the current screening test. If there is suspicion for acute infection, can also do a viral load (PCR) test, but even for that there is a week or so delay so if there is high suspicion then they should be tested again.
    • If you are tested early in infection (only a few weeks in) you may test negative by an antibody test
  • If acute HIV is suspected, viral load (PCR) test can be done
    • Turns positive a few days before the p24 antigen test
    • Positive in 7 to 10 days after infection
    • Viral load testing is used mainly to monitor response to therapy
    • Goal: undetectable viral load

HIV Pathogenesis

  • First infects and depletes CD4+ T-cells, leading to immune system dysfunction
    • Usually uses CCR5 co-receptor in the beginning
    • Kills cells directly
    • Infected cells killed by the immune system
    • Uninfected T-cells kill themselves (apoptosis) due to chronic stimulation
  • As T-cell numbers drop, opportunistic infections occur
    • Late stages switches to CXCR4 co-receptor
    • An early switch from CCR5 to CXCR4 is associated with rapid progression of disease

Stages of HIV

  • Acute HIV – occurs days to 4 weeks after transmission.
    • Often, but doesn’t always occur.
    • Marked by (often looks like mono):
      • fever
      • sore throat
      • rash
      • lymphadenopathy
    • Coincides with a high level of virus in the bloodstream
      • i.e., Very contagious but person doesn’t know they are infect yet
    • Seroconversion (positive antibody test) usually occurs within 4 weeks but can take up to 6 months)
  • Asymptomatic infection – lasts 8-10 years (usually)
    • Viral load relatively stable – “set-point”
    • CD4 count gradually declines
  • Early symptomatic infection
    • General symptoms – weight loss, diarrhea, neuropathy (tingling in hands and feet)
    • Frequent or recurrent infections – thrush (Candida infection of mucosal membranes), shingles (VZV)
  • Advanced HIV (AIDS)
    • T cell drops (CD4 < 200 cells/mm3) or opportunistic infection (OI). T cell count could be slightly above 200 but if the patient also has an OI then they would still be considered to have AIDS. A normal range for CD4 cells is about 500-1,500 cells per cubic millimeter of blood.
    • Symptoms include:
      • wasting
      • dementia
      • pneumonia
      • meningitis
      • diarrhea
      • skin rashes

T-Cell Count and Susceptibility to Disease


HIV - Medicines

  • Nucleoside Reverse Transcriptase Inhibitors (NRTI)
    • First class of antiretrovirals - first clinical trial in 1985
    • AZT was the first example
    • Chain-terminators
  • Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTI)
    • Bind to reverse transcriptase and exert a conformational change that prevents it from working
  • Integrase inhibitors
    • They inhibit HIV integrase, preventing HIV genome integration into the host DNA.
  • Protease inhibitors
    • Prevent HIV protease from processing the translated mega-protein into functional components
    • Mimic peptides and sit in the active site of the enzyme
  • HIV Entry Inhibitors
    • Ibalizumab
      • Humanized monoclonal antibody
      • Binds to CD4 to block entry
      • No cross resistance with other ART
      • Used as a last resort in cases of resistant virus
      • IV infusion every 2 weeks
  • Fusion inhibitors
    • Enfuvirtide
      • Prevents fusion of the viral particle with the cell
      • Injectable and very expensive
      • Used as a last resort in cases of resistant virus
  • CCR5 inhibitors
    • Maraviroc
      • Only works for CCR5 tropic viruses
      • Requires testing for tropism before use, means to test to see if the virus is using the CCR5 co-receptor or the CXCR4 co-receptor
      • Over time the virus typically also uses CXCR4 co-receptor making the virus resistant

HIV Medicines - 3 Main Targets

  • Reverse transcriptase
    • Nucleoside Reverse Transcriptase Inhibitors (NRTIs)
    • Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs)
  • Protease
    • Protease Inhibitors (PIs)
  • Integrase
    • Integrase Strand Transfer Inhibitors (ISTI)

Antiretroviral Therapy (ART)

  • At least three drugs given simultaneously to prevent the emergence of resistance.
    • 2 NRTI + something else (NNRTI, PI, integrase inhibitor) – Regimen currently preferred is 2 NRTI’s plus an integrase inhibitor. (e.g., Emtricitabine, Tenofovir, plus Bictegravir)
  • Early regimens were dozens of pills taken around the clock at specified times.
  • Now we have several one pill (that contains 3 or more medications), once a day regimens.

Problems with Drug Resistance

  • Reverse transcriptase highly error-prone - virus mutates rapidly
    • About 5 mutations per HIV genome every time it replicates. Most of the mutants will be non-functional.
    • Evolves about a million times faster than we do
  • If the virus isn’t kept completely suppressed by therapy, resistance will develop.

Factors Leading to Drug Resistance

  • Virus
    • High replication rate
    • High mutation rate
    • Latent reservoirs of HIV
    • Nearly all drug resistance is due to target modification
  • Patient
    • Poor adherence
    • Toxicity or inconvenience. New drugs are much better tolerated.
  • Drug
    • Inadequate potency
    • Inadequate durability
    • Drug-drug interactions
    • Poor tolerability

Viral Reservoirs

  • Viral Reservoirs are areas in the body where the body can persists
  • ART can generally make the viral load undetectable
    • No virus detected by PCR of the blood
  • But viremia comes back if ART is stopped… so it must be coming from somewhere
  • Latent virus integrated into the genome
  • More likely in cells in tissues the drugs do not reach well
    • E.g., brain, bone, testes, ovaries
    • Resting CD4 T cells. Not very accessible to therapy b/c all of the drugs depend on stopping processes during replication

HIV - Prevention

  • Monogamy, condoms, needle-exchanges, etc.
  • Post-exposure prophylaxis
    • ART given to healthcare workers with needle-sticks from infected patients
    • Victims of sexual assault
  • Pre-exposure prophylaxis (PrEP)
    • Individuals with high risk (e.g., multiple sexual partners, IVDU) take two antiretroviral drugs to prevent acquiring infection
  • Treatment as prevention
    • If a person has an undetectable viral load, s/he is unlikely to spread HIV

HIV - Prevention

  • Monogamy, condoms, needle-exchanges, etc.
  • Post-exposure prophylaxis
    • ART given to healthcare workers with needle-sticks from infected patients
    • Victims of sexual assault
  • Pre-exposure prophylaxis (PrEP)
    • Individuals with high risk (e.g., multiple sexual partners, IVDU) take two antiretroviral drugs to prevent acquiring infection
  • Treatment as prevention
    • If a person has an undetectable viral load, s/he is unlikely to spread HIV

Undetectable = Untransmittable

  • A person living with HIV who has an undetectable viral load does not transmit the virus to their partners

Summary of Key Points

  • What is it? Enveloped retrovirus.
    • Three main genes (gag, pol, env)
    • Three enzymes: Reverse transcriptase, integrase, protease
  • What does it do?
    • Infects and destroys CD4+ T-cells >>> Opportunistic Infections >>> AIDS
  • How do we test for it?
    • Enzyme immunoassay for antibodies and p24 antigen
  • How can we treat it?
    • Anti-retrovirals target reverse transcriptase (mostly), protease, integrase, or entry into the cell
    • Mutates rapidly so must use at least three drugs simultaneously to prevent the emergence of resistance.
  • What is the host range and specificity?
    • Humans. Binds to immune cells via CD4 receptor and the CXCR4 and CCR5 co-receptors
  • What are the symptoms in acute infection?
    • Acute: fever, sore throat, rash, swollen lymph nodes
  • How can it be targeted by drugs?
    • NRTIs, NNRTIs, PIs, INSTIs, entry inhibitors
  • Major problems with treatment?
    • Resistance mutations, reservoirs