Assignment Overview

ASSESSMENT TASK: INDIVIDUAL ASSIGNMENT

Outlining:
Instructions: Read each paragraph on the reference book, Chapter 20 & 24 of Stevens, C. D.
(2016). Clinical Immunology and Serology A Laboratory Perspective Fourth Edition. F.A. Davis
Company. Then fill in the blanks in the outlines that follow. Just include a short summary of the
main points of the topic of interest and some additional information about it.
*(This will also be recorded under lecture performance task)

Human–Microbe Relationships
Main Idea: connection or relationship between human as the host and microbe. There three types
of relationship that exist between human and microbe; (1) communalistic, (2) mutualistic, (3)
parasitic

Support details: human and bacteria have a symbiotic relationship starting when a human is born.
We have normal flora or indigenous microbiota that live and reside in our body. In a
communalistic relationship, there is no harm nor benefit the human or microorganism get, an
example is the Staphylococcus epidermis that reside in our skin which gave neither benefit or
harm to us. In mutualistic relationship, there is a benefit that the human acting as a host and the
microbe get in this relationship, an example is the Lactobacillus spp. Which the human host
provide the optimal condition for growth and proliferate for the microbe and in return, the
microbe help prevent the growth of other microorganism causing disease. Meanwhile in parasitic
relationship, the microbe cause harm to the host while benefiting from it, an example of this is
viruses.

Immune Defenses Against Bacterial Infections and Mechanisms of Evasion

Main Idea:
Immune defense - both innate and adaptive responses may occur after
a coming across with foreign antigens. It is the immune response of the body against foreign or
invading antigen.

Bacterial Evasion Mechanisms – ability of bacteria or microorganism to evade or bypass the

activation or/and action of immune response. Three main mechanisms for evasion are avoiding
antibody, blocking phagocytosis, and inactivating the complement cascade
Support details:
Immune defense – first line of defense is intact skin and mucosal surface. There are a specific
and non-specific antimicrobial defense, an example is Lysosome enzyme is a specific
antimicrobial defense that destroy the peptidoglycan of bacterial cell wall. A defensin is a
soluble peptide that is produce constitutively by the cells in the body. There are 3 main
classifications of defensin (1) alpha – is believe to disrupt microbial membrane, (2) beta –
believe to increase resistance of epithelial cell to colonization; and (3) theta -is not found in
human. And many antimicrobial proteins contribute to the innate immune response such as
complement protein, interleukins, prostaglandin, and etc. Complement protein promotes
chemotaxis, interleukin help in regulating immune and inflammatory response. Adaptive
immune responses include the production of antibodies directed against bacterial antigens or
extracellular products produced by bacteria such as exotoxin. Antibody formation is the main
defense against extracellular bacteria.
Bacterial Evasion Mechanisms – in a process called antigenic variation, bacteria alter their
bacterial antigen thus evading the antibody by coating themselves with host proteins; through
hiding their surface molecule through antigenic disguise; or through downregulating of MHC
molecule and degrade IgA by producing protease.
Most evasion target several stages of phagocytic process. Some bacteria inhibit the release of
chemotactic factors or by producing protein M which will interfere with adhesion to phagocytic
cell. furthermore, if there is a polysaccharide present I the capsule of a organism it will inhibit
binding that is needed for initiating phagocytosis. In evading digestion, some bacteria block the
fusion of lysosomal granules with phagosome.
In blocking the complement action, microorganism produce a capsule that do not bind with C3b
making said organism hard to phagocytized. Some disrupt complement pathway such as the
cascade pathway.

Characteristics of HIV
Main Idea:
Composition of the Virus- it belongs to the genus Lentivirinae of the virus family Retroviridae, it
contains RNA as its nucleic acid and reverse transcriptase
Structural Genes - The genome of HIV includes three main structural genes—gag, env, and pol
—and a number of regulatory genes
Viral Replication – reproductive cycle of HIV is first is the virus attach itself to the host cell by
binding to the CD4 molecules with Th-cell being the main target as it contains many CD4
molecules. Upon entry to the host cell, the virus promotes fusion of HIV envelope to the plasma
membrane. After fusion occur the virus is taken into the cell and uncoated exposing the viral
genome and with action of the reverse transcriptase enzyme that produce complementary DNA
from viral RNA which is then synthesize and become integrated into host cell as a provirus.
Viral replication happens to the extreme amount in antigen-activated Th cells. Since viral
replication happens very quickly and the reverse transcriptase enzyme lacks proofreading
activity, genetic mutations happen at a great degree, making distinct isolates that exhibit an
extraordinary level of antigenic variation,

Supporting details:
Composition of the Virus – reverse transcriptase is a essential step in the virus’s life cycle as its
transcribes the viral RNA into DNA. It is a spherical particle with a diameter of 100-120 nm and
comprises an inner core with two copies of single-stranded RNA enclosed by a protein coat or
capsid and an outer envelope of glycoproteins (knoblike structure) fixed in a lipid bilayer
Structural Genes – gag gene code for p55 which have four core structural protein p6, p9, p17,
and p24 which are all found in nucleocapsid of the virus. P24, p6, and p9 can be found in the
capsid that surround the internal nucleus acid while p17 can be found in the matric which is the
layer between the protein core and envelope. Env gene code for gp160, gp120, and gp41 which
are located in the viral envelope. Gp160 is a precursor protein. Gp120 form the knob or spike
from the outside protein, and gp41 ia transmembrane and is attached to gp120. For fusion and
attachment of HIV, both gp120 and gp41 are involve. The pol genes code for enzyme that is
essential for replication including reverse transcriptase (p51) , RNase (p66), integrase (p31),
protease (p10) and etc. which are found in the core of the virus that is associated with HIV RNA.
There are several other genes that are not integral part of viral structure but have regulatory or
accessory functions in controlling replication and infectivity which include tat (transactivator),
rev (regulator of expression of virion proteins), nef (negative effector), Vpu (viral protein “U”),
Vpr (viral protein “R”), and Vif (viral infectivity factor). The gene sequence is surrounded by 5’
and 3’ LTR regions which help in regulating the expression of the gene. The homology between
HIV-1 and HIV-2 genome is roughly 50% with being the gag and pol region having the most
similarity and the env region having the most difference thus it make it easy to distinguish base
on the basis of antigenic difference in the env protein.
Viral Replication – the first step is when the virus attaches to a susceptible host cell which is
mediated through the host CD4 and serves as a receptor for the virus by binding the gp120
glycoprotein on the outer envelope of HIV. Th-cell is the main target for infection as they have a
high number of CD4 on their surface and bind the virus with high affinity. Other cells that have
surface CD4 will also be infected with the virus. HIV viruses that specially infect T cells are
known as T-tropic or X4 strains, while those that can infect both macrophages and T cells are
called M-tropic or R5 strain. Upon entry to the host cell it required an additional binding step
involving co-receptors which are known as chemokine receptors, whose main function is to
direct white blood cells (WBCs) to sites of inflammation. CXXR4 is essential for the virus to
enter T lymphocytes, while CCR5 is essential for entry into macrophages. People who have
genetic mutation in the CCR5 gene have been discover to be resistant to HIV infection. After
fusion occur the virus is taken into the cell and uncoated exposing the viral genome and with
action of the reverse transcriptase enzyme that produce complementary DNA from viral RNA
which is then synthesize and become integrated into host cell as a provirus which then remain
dormant for a long time and viral replication does not occur. The virus is only activated when
infected cell binds to an antigen or expose to cytokines which is then transcribe into genomic
RNA and mRNA that are then transported to the cytoplasm. The intact virions sprout out from
the host cell membrane and during the process obtain their envelope. The precursor proteins are
cleaved by the viral protease enzyme in the mature virus particles which then can progress to
infect another healthy cell.

Immunologic Manifestations of HIV

Main Idea:
Immune Responses to HIV – the body’s immune response against HIV.
Effects of HIV Infection on the Immune System – decrease CD4 T cell number, abnormal
function and impaired memory. Gastrointestinal immune system (GALT) being the most affected
as it is the largest immune organ in the body. It also affected the B cell maturation and function
causing defects. Cell-mediated immunity is also affected resulting in a decline in CTL activity
and delayed hypersensitivity responses. Different production of cytokines and chemokines has
also been observe, including increases in the levels of some cytokines during early stages,
followed by declining levels of IL-2 and interferon-γ and a shift in the cytokine profile from Th1
to Th2 as the infection progresses toward development of AIDS. In late infection, widespread
damage to the lymphoid tissues with absence of germinal centers and follicular dendritic cells
resulting in an inability to activate T and B lymphocytes is obvious. Other immunologic
abnormalities, such as defective antigen presentation and oxidative burst, decreased natural killer
(NK) cell activity, have also been observed in AIDS patients

Supporting details:
Immune Responses to HIV - The initial replication can be detected when there is an increase
level of p24 antigen and viral RNA in blood and as the virus replicates some viral proteins yield
complexes with class I MHC antigens and are transported to the cell surface wherein they
stimulate lymphocyte responses which then generate HIV-specific CD4 Th cell that assist in both
humoral and cell mediated immune response against the virus but these responses are unable to
eliminate HIV in the body. B lymphocytes are stimulated to produce antibodies to HIV, which
can usually be detected in the serum by 6 weeks after primary infection with being the gp41
transmembrane glycoprotein being the first to be detected, follow by gag proteins and lastly the
production of antibodies to the env, pol, and regulatory proteins. After 2-3 months after infection
most immunogenic proteins are found in the viral envelope and prompt the production of
neutralizing antibodies which then stop the virus from infecting near cells. Antibodies toward the
envelope proteins have been revealed to bind to Fc receptors on NK cells and partake in ADCC-
mediated killing of HIV-infected cells but these antibodies may also join in the pathogenesis of
HIV infection by helping Fc-receptor mediated endocytosis of opsonized virus by uninfected
cells. CD8 appear within weeks of HIV infection and are associated with a decrease in the
quantity of HIV in the blood during acute infection. Antibodies can attach only to virions
circulating freely outside of host cells while CTLs can attack host cells harboring viruses
internally which involves the binding of CTLs containing HIV-specific antigen receptors to HIV
proteins associated with class I MHC molecules on the surface of infected cells. HIV-specific
CTLs are stimulated to develop into mature and activated clones through the effects of cytokines
released by activated CD4 Th cells, a process that is common to immune responses against other.
CTLs can also inhibit replication and spreading of HIV by producing cytokines such as
interferon-γ, which have antiviral activity. During acute HIV infection, NK cells become
activated and mediate cytolysis of cells infected with the virus. Furthermore, dendritic cells
recognize viral components through pattern recognition receptors, resulting in release of
proinflammatory cytokines that have antiviral effects and can activate other cells of the immune
system.
Effects of HIV Infection on the Immune System - The capability of HIV to evade the immune
response results in a persistent infection that can destroy the immune system with CD4 Th cells
being the virus’s prime targets. In the early infection of HIV, it causes a fast lessening of CCR5+
CD4+ memory T cells in the GALT. Th17 helper cells and the secretion of antimicrobial
defensins which play an important role in the homeostasis of the epithelial cells lining the
intestinal mucosa are also specially affected. Which results in damage to the intestinal epithelial
barrier. As CD4 is the main target of the virus, it is thought to be killed or reduce to
nonfunctional through a variety of mechanism. In the early infection, there is only a partial
recovery of the T cells as infected T cells turn over much more quickly than they can be
replaced, having a half-life of 12 to 36 hours, this is followed by a progressive decrease in CD4
T cells during untreated infections, the virus also causes abnormalities in function and damage of
memory CD4 T cell responses which in turn also affected both T and B cells as the destruction of
CD4 T cell result in decreased effectiveness of both antibody- and cell-mediated immune
responses not only against HIV but from other antigens as well. HIV proteins also stimulate
polyclonal activation of B cells, resulting in maturational and functional defects with increased
circulating immunoglobulin levels, immune complexes, and autoantibodies. Because of decrease
of T-cell in HIV infected persons, the B cells have a reduced ability to mount antibody responses
after exposure to specific antigens.

Laboratory Testing for HIV Infection

Main Idea: HIV antibody detection, HIV antigen detection, viral nucleic acid testing (NAT), and
CD4 T-cell enumeration are example of laboratory tests used to diagnose and monitor HIV
infection. For initial diagnosing of HIV, serological test is used such as ELISA as the standard
method, and also rapid test. For confirmatory test the used of western blot test is the standard

Supporting details:
ELISA - The first generation of ELISAs were based on a solid-phase, indirect-assay system that
detect only HIV-1 antibodies. The second-generation ELISAs, is base on indirect binding assays
that used highly purified recombinant or synthetic antigens from both HIV-1 and HIV-2, which
improve it sensitivity and specificity. Third-generation assays use the sandwich technique, based
on the ability of antibody to bind with more than one antigen. The fourth-generation assays can
detect at the same time HIV-1 antibodies, HIV-2 antibodies, and p24 antigen. Fifth-generation
assays that provide more diagnostic information have been developed. One of these assays is a
bead-based immunoassay which is similar to the fourth-generation assays, but in addition can
differentiate between HIV-1 and HIV-2 infection. False-negative results for HIV antibody
happen might be caused by the collection of the test serum before the patient develops HIV
antibodies, administration of immunosuppressive therapy or replacement transfusion, conditions
of defective antibody synthesis such as hypogammaglobulinemia, or technical errors attributed to
improper handling of kit reagents. False-positive results may also occur in these assays. These
can result from several factors, including heat inactivation of serum before testing, repeated
freezing and thawing of specimens, the presence of autoreactive antibodies, history of multiple
pregnancies, severe hepatic disease, passive immunoglobulin administration, recent exposure to
certain vaccines, and certain malignancies
Rapid Tests – can detect antibodies to HIV-1 alone or to both HIV-1 and HIV-2; they can be
used on serum, plasma, whole blood samples obtained by venipuncture or fingerstick, or, for
some kits, oral fluid. Base on lateral flow or flow-through immunoassays that produce a
colorimetric reaction if positive.
Western Blot - for a more specific confirmatory method. The testing laboratory then applies
patient serum to the test strip. During the incubation period, any HIV antibodies present in the
sample will bind to their corresponding antigens on the test membrane. Unbound antibody is
then removed by washing. Next, an anti-human immunoglobulin with an enzyme label is added
directly to the test strip and binds to specific HIV antibodies from the patient sample. Unbound
conjugate is removed by washing, whereas bound conjugate is detected after adding the
appropriate substrate, which produces a chromogenic reaction. Colored bands appear in the
positions where antigen-specific HIV antibodies are present