VIROLOGY - ‐ S1

ABBAS ADEL GROUP 4

General
Properties:

• They are obligate intracellular parasites — can grow only in live hosts or in cell cultures
• Size = in nanometers (nm)
• They have a simple structure:
-‐ Genome = RNA or DNA —> infectivity (possibility to replicate)
-‐ Proteic coat:
• Capsid (capsomeres)
• Envelope (peplomeres)
-‐ Lacks ribosomes & mitochondria
• They are NOT susceptible to antibiotics

Examples of common viruses:

• Polio virus = Poliomyelitis (inflammation of the spinal cord grey matter —> paralysis)
-‐ Spinal polio = in the motor neurons —> acute flaccid paralysis
-‐ Bulbar polio = extends into the brainstem —> apnea (requires an “iron lung”)
-‐ Asymptomatic infection in 85-‐90%
-‐ Abortive infection in 2-‐4%
-‐ Polio vaccines:
• Inactivated (SALK 1955)
• Live attenuated vaccine (SABIN 1962)

• Smallpox:
-‐ Incubation —> macula —> papule —> vesicle —> pustule —> crusts (scabs) —> scars
-‐ Variolation (method of prevention)
• Inhalation of the dried crusts from smallpox lesions like snuff
• Inoculation of the pus from a lesion into a scratch on the forearm of a child
-‐ Vaccination = Vaccinia (cowpox virus, cross antigenicity with smallpox virus)
-‐ Smallpox is a potential bioterorist agent

Structure of a virus:
• Viral genome = DNA (ds) or RNA (ss)
-‐ It supports infectivity (possibility to replicate)
• Proteic coat:
-‐ Protects & ensures efficient delivery of the nucleic acid genome to the new cells
-‐ Supports antigenicity
-‐ Capsid = formed of identical subunits called capsomeres
• Helical symmetry = the protein subunits & nucleic acids are arranged in a helix
• Icosahedral symmetry = protein subunits are in a symmetrical shell,
covering the nucleic acid containing core
-‐ Envelope
Viral Life Cycle:
• The genetic material of a virus enters a host cell & directs the production of the
building blocks of new virus particles
• It has 3 stages:
1. Eclipse — conducted by the viral shell
-‐ Attachment (to host cell receptors / susceptible cells)
-‐ Penetration
-‐ Uncoating
2. Logarithmic growth — conducted by the viral genome
-‐ New nucleic acids & viral proteins are produced
-‐ Viruses must generate mRNAs from their genomes to produce
proteins & replicate themselves, but different mechanisms are used to
achieve this in each virus family
3. Plateau = maturation, assembly & release

1. Eclipse: = a?achment, penetration & uncoating

• Viral a:achment:
-‐ Susceptibility = depends on the presence of the receptors on the surface of the cell
-‐ Permissive cells = are cells which have receptors & allow virus entry into the cell
A. Enveloped viruses = viral encoded peplomere spikes (protruding from the
envelope) serve for receptor recognition & binding to
the susceptible cells — forms bridges
B. Naked viruses = viral attachment ligands are inside the deep
depressions in the capsid structures — “canyon ridge
nodes” or pits
• Viral penetration:
-‐ The interaction of a virus with its cell receptor initiates conformational changes
that lead to the penetration and uncoating of the viral RNA

A. Enveloped viruses = penetration via fusion (receptors/GPs; peplomers/

spikes for receptor recognition)
B. Naked viruses = penetration via endocytosis (accumulation of virus
particles inside a cytoplasmic vesicle)
• Uncoating:
-‐ Viruses lose the protective envelope or the capsid upon entry into the cytoplasm
• This is usually done by cellular proteases (which degrade the proteic coat)
-‐ In influenza virus, a viral protein called M2 may allow endosomal protons into
the virion particle, resulting in it partial dissolution & permitting replication

2. Logarithmic Growth:
• Formation of nucleic acids from viral genome:
-‐ Parental genome —> progeny genome
• Formation of proteins from viral genome:
-‐ Parental genome —> mRNA —> proteins
Classification of viruses: Baltimore Classification System
Group I: dsDNA viruses (Adenoviruses, Herpesviruses, Poxviruses)
Group II: ssDNA viruses (+ strand/sense DNA;
Parvoviruses) Group III: dsRNA viruses (Reoviruses)
Group IV: (+)ssRNA viruses (sense RNA; Picornaviruses, Togaviruses)
Group V: (--)ssRNA viruses (antisense RNA; Orthomyxoviruses, Rhabdoviruses)
Group VI: ssRNA--RT viruses (sense RNA with DNA intermediate in life cycle;
Retroviruses) Group VII: dsDNA--RT viruses (Hepadnaviruses)
DNA viruses:
• Intranuclear replication — depends on the host cell’s polymerases; during the cell cycle?

• The virus may induce the cell to forcefully undergo cell division, which may lead to
the transformation of the cell oncogenic viruses (cancer)
• The viral proteins produced can be:
-‐ Early viral proteins = enzymes; forms the viral inclusions
-‐ Late viral proteins = forms the viral coat

RNA viruses:
• Most RNA viruses are single stranded (ss)
• (+) strand RNA genomes:
-‐ Are naked
-‐ Ready to be translated upon entry
• (-‐) strand RNA genomes:
-‐ Are coated with proteins
-‐ Ready to begin mRNA synthesis upon entry

(+)ssRNA viruses: naked

• Viral genome = mRNA
• Starts replication with direct translation (since it is an mRNA) / monocistronic transmission
-‐ It can be directly accessed by host ribosomes to immediately form proteins
• The 5’ methylated cap is replaced by IRES (internal ribosomal entry site)
-‐ IRES is essential for replication & translation
• Oral polio vaccine (OPV) = LAV; mutations in the virus’ IRES alters the stem-‐loop
structures & reduces its ability to translate its RNA template within the host cell —
Attenuated virus

(-‐)ssRNA viruses: coated with proteins

• Must be transcribed by viral polymerases into the readable complementary (+) sense
-‐ This is done via replicase (transcriptase), which leads to formation of mRNA
• RNA is synthesised by using a template
-‐ Directed stepwise incorporation of NTPs, elongated in 5’3’ direction by RdRp
(RNA dependent RNA polymerase)
• Thus, RNA viruses have great variability
-‐ Lack of proofreading activity in RdRp can cause errors, which can produce
defect proteins

3. Plateau maturation, assembly & release

• Maturation
• Assembly:
-‐ Accompanied by host chaperon proteins
• Involved in transmembrane transport, post-‐translation assembly & protein folding
• Release:
A. Enveloped viruses = budding through the cell membrane
B. Naked viruses = cytolysis
ANTIVIRAL IMMUNITY:
• Innate:
-‐ Soluble effectors = Interferons (IFN)
-‐ Cellular effectors = NK cells
• Acquired:
-‐ Soluble effectors = Antibodies (via B cells)
-‐ Cellular effectors = T lymphocytes / APCs

Interferons: Innate
• PAMPs = Pathogen Associated Molecular Patterns
-‐ They are located on viruses
-‐ They are recognised by pa\ern recognition receptors (PRRs):
• Membrane linked = Toll-‐like receptors (TLR)
• Intracellular = RIG-‐I
-‐ The binding of such receptors result in the expression of the IFN genes
• There are 3 types of interferons:
-‐ Interferon alpha (IFN α) = produced by leukocytes
-‐ Interferon beta (IFN β) = produced by fibroblasts
-‐ Interferon gamma (IFN ɣ) = produced by immune activated cells (aka immune IFN)
• Roles:
-‐ Anti-‐viral:
• Prevents infections of non-‐infected cells in species specific manner
• Via direct degradation of viral mRNA & inhibition of protein synthesis
-‐ Immuno-‐modulator:
• Enhancement of the specific immune response by increasing the MHC
class I expression on the surface of infected cells
-‐ Anti-‐proliferative:
• Enhances the ability of macrophages to destroy tumor cells & inhibit cellular
DNA division
• IFN ɣ is a powerful activator of NK cells (has same purpose as macrophages)
• Interferon Receptors:
-‐ JAK (Just another kinase)
-‐ STAT (signal transducer & activator of transcription)
-‐ ISGF3 (IFN stimulated gene factor 3) — contains STAT1, STAT2 & IRF9
(factor of transcription)
NK cells: Innate
• NK cells do not require prior contact with the antigen, they are not MHC restricted
• Action:
A. Self / normal cells:
-‐ MHC Class I molecules are present
-‐ No harm is done to the cell
B. Non-‐self / abnormal cells:
-‐ MHC Class I molecules are absent
-‐ Cell is killed via:
• Perforins & granzymes

T cells: Acquired
• A T cell receptor recognises the antigen in the form of a complex of a foreign
peptide (epitope) bound to a MHC molecule
• This results in either the activation of CD4+ cells (T helper) or CD8+ cells (T cytotoxic)
• TCR (T cell receptor) = does not recognise & bind the antigen directly
-‐ Are short peptide fragments of pathogen protein antigens (epitopes), bound to
MHC molecules on the surface of APCs
• Types of T cells involved:
-‐ T cytotoxic cell (CD8+)
• MHC Class I molecules
• Secretes IFN ɣ
• Acts by:
-‐ Secreting perforins & granzymes
-‐ Fas molecule binding on target cell by using their Fas ligand
• Leads to the activation of caspase enzymes —> cell apoptosis
-‐ T helper cell (CD4+)
• MHC Class II molecules
• Has 2 types:
-‐ Th1 = activates macrophages & T cytotoxic cells (secretes IL-‐2 & IFN ɣ)
-‐ Th2 = activates B cells (secretes IL-‐4, IL-‐5, IL-‐6)

B cells: Acquired
• BCR (B cell receptor) = membrane bound immunoglobulin of 1 isotype + a signal transducer
• B cell activation:

-‐ Via clonal proliferation Primary immune response =

-‐ Can be: IgM Secondary immune
• Direct = binds to antigen directly response = IgG Local immune
• Indirect = by the help of Th2 cells response = IgA
• Antibodies:
-‐ Have direct anti-‐viral activity

-‐ Antibody dependent cytotoxic cells (ADCC) — involved with NK cells?

-‐ They block virus-‐host cell interaction
-‐ They recognise viral antigens on virus infected cells
• This leads to ADCC or complement mediated lysis
Macrophages: Acquired
• Secretes IL-‐1, TNF α, IFNs

APCs: Dendritic cells

• Immature dendritic cells accumulate antigens
• Mature dendritic cells are APCs
-‐ They connect the innate & acquired immune response
VACCINES:
Vaccination = immunologic memory
• The principle is to induce a primed state in the person so that, when the person is
exposed to a pathogen, a rapid secondary immune response is generated — leads
to accelerated elimination of the organism & provide protection from the clinical
disease
-‐ Success depends on the generation of memory T and B cells & the
presence of antibodies in the serum
• Types of viral vaccines:
-‐ Inactivated vaccines
-‐ Live Attenuated vaccines (LATs)
-‐ Recombinant DNA vaccines / DNA technology

Inactivated vaccines:
• Killed (inactivated) viruses — can’t replicate, so can’t cause infections
• These vaccines are not infectious so they are relatively safe
• Have lower immunogenicity — needs multiple doses
• Examples = anti-‐influenza, injectable polio vaccine (IPV; anti polio Salk)

Live A\enuated vaccines (LAT):

• “A\enuation” = the process of weakening a virus to the point where it can still provoke
an immune response, but does not cause illness in a human host
-‐ Cross reactivity between an animal virus (non-‐pathogenic for humans) & a
human virus = vaccinia-‐smallpox)
-‐ Naturally attenuated strains (Max Theiler — yellow fever)
-‐ In vitro-‐attenuation = “cold strains” (influenza, oral polio (OPV; anti-‐polio Sabin),
MMR, VZV, rotaviruses)
• Have sub-‐optimal temperatures
• Essential mutations in IRES 5’ NT —> RNA secondary structure is altered
• These vaccines contain viruses which have had their virulence artificially reduced
-‐ The alterations can be done by reducing temperature
-‐ So the virus can still replicate and infect the host, but the severity is much lower
• Advantages:
-‐ Administration through natural routes (high acceptability, low price)
-‐ Global immune response (cellular, humoral, local)
-‐ Increased immunogenicity auer first administration, durable immunity
-‐ Immune response against all native antigenes (inactivation may alter the antigenicity)
-‐ Dissemination to contacts
• Disadvantages:
-‐ Vaccine virus can revert to a form capable of causing disease -‐ especially OPV
(VAPP)
• Mutations that can occur when the vaccine virus replicates in the body may
result in a more virulent strain
-‐ Severe reactions in immunosuppressed persons
-‐ Maintenance of the cold chain is difficult (during transport or storage)
-‐ Possible interference with viruses that share the same habitat /
potential contamination with animal viruses infecting the isolation
substrate
Recombinant DNA Vaccines DNA technology:
• These vaccines also use live viruses
• They are altered via genetic engineering to produce recombinant genes (foreign genes)
• The foreign genes will replicate in the host, producing recombinant proteins, which
in turn will initiate an immune response
• Examples = VLP (viral like particles); anti-‐hepatitis B, anti-‐HPV

Poliomyelitis — Poliovirus:
• Asymptomatic infection in 95% of the cases
• Abortive infection in 2-‐4% of the cases:
-‐ Fever, fatigue, headache, stiffness in the neck, pain in the limbs
• Bulbar polio = mortality rate 2-‐5% children; 15-‐30% adults
• Spinal polio = destroys the anterior horn cells in the spinal cord
• Poliovirus has 3 antigenic distinct serotypes
-‐ PicoRNAviridae = (+)ssRNA, naked
-‐ Enterovirus = high environmental stability
• Transmission = Fecal or oral route
-‐ Contaminated hands, water or food
-‐ Virus shed in oral secretions for several weeks; in faeces for several months
• Paralytic polio = Acute flaccid paralysis (AFP)
-‐ Reduced muscle tone, limp, sudden onset, asymmetric
-‐ Ouen permanent neuronal damage
• Post-‐polio syndrome:
-‐ A prior episode of paralytic poliomyelitis with residual motor neuron loss
• Can be confirmed through a typical patient history, a neurologic examination,
and if needed, an electrodiagnostic examination)
-‐ A period of neurologic recovery followed by an interval (usually > 15 years)
of neurologic & functional stability
-‐ A gradual or abrupt onset of new weakness or abnormal muscle fatigue
(decreased endurance), muscle atrophy, or generalised fatigue

Vaccine Associated Paralytic Polio (VAPP):

• OPV strains can mutate during their replication in the human intestine & some
mutations may result in recovery of neurovirulence -‐ VDVD (vaccine derived polio
virus)
• An excreted vaccine = the virus can continue to circulate for an extended period of time
in the case of a low population immunity
-‐ The longer it is allowed to survive, the more genetic changes it undergoes
• Surveillance cVDPV:
-‐ Polio type 2 accounts for about 40% of VAPP ?
-‐ type 2 cVDPVs account for 97% of cVDPVs ?
MMR vaccine:
• A trivalent live a\enuated vaccine against measles, mumps & rubella
• Measles virus: Measles
-‐ (-‐)ssRNA, enveloped
-‐ An airborne virus, highly contagious
-‐ Symptoms:
• Mild to severe fever, for several days
• Cold-‐like symptoms: cough + sneezing, coryza (runny nose), conjunctivitis
(watery eyes) & swollen eyelids
• Exanthem — red-‐brown spotty rash
• Enanthem — tiny grey-‐white spots (Koplik’s spots) in the mouth, throat
tiredness, irritability & general lack of energy, aches & pains, poor appetite, dry
cough
-‐ Complications = otitis, pneumonia, encephalitis / SSPE (Subacute
sclerosing panencephalitis)

• Rubella virus: Rubella

-‐ (+)ssRNA, enveloped
-‐ Airborne, contagious (7 days before/auer a rash)
-‐ Complications: arthralgia, arthritis , encephalitis
-‐ Mother-‐to-‐fetus transmission:
• During the first trimester of pregnancy
• Leads to congenital malformations (Congenital rubella syndrome)
1. Sensorineural deafness
2. Eye abnormalities = retinopathy, cataract, micro-‐ophtalmia
3. Congenital heart disease = pulmonary artery stenosis, patent
ductus arteriosus

• Mumps virus: Mumps

-‐ (-‐)ssRNA
-‐ Complications: meningitis, encephalitis, orchitis, pancreatitis
HERPESVIRUSES:

Structure:
• Herpesviruses have a unique 4-‐layered structure:
-‐ A core containing the large double stranded DNA genome
-‐ An icosapentahedral capsid —> encloses the viral genome; composed of capsomeres
-‐ An amorphous protein coat = tegument ; surrounds the capsid
-‐ A glycoprotein-‐bearing lipid bilayer envelope

Pathway of a Herpes Infection:

1. Primary infection:
-‐ The herpesvirus enters the body through the skin or mucous membranes
-‐ All genes are expressed —> viral shedding = productive infection

2. Latency:
-‐ Auer the initial infection, the herpesvirus settles in the nerves near the spine
-‐ The virus goes into a dormant state in which no clinical features are apparent
-‐ Immune evasion

3. Reactivation:
-‐ Herpesvirus travels along the nerves, back to the skin to form new blisters
-‐ Can be subsequent, periodic recurrences or “outbreaks”
• They may be asymptomatic or symptomatic
-‐ All genes are expressed —> viral shedding = productive infection

Viral Replication:
• Tegument = contains pre-‐formed viral proteins; they initialise viral replication
-‐ VHS (virion host shut-‐off protein)
-‐ VP16 ( alpha TIF (alpha trans-‐inducing factor)) — a viral transcription factor
• Replication involves a cascade of herpes virus genes expression:

alpha genes (IE) beta genes gamma genes (L)

(E)

Viral DNA —> host RNA polymerase —> sequential mRNA transcription

-- Alpha genes (IE): immediate early

• Are trans-‐activators of all genes associated with lytic infections
• Consensus sequences that bind viral (alpha TIF) & cellular transcription
factors (HCF1 and oct1)
-- Beta genes (E): early
• Are enzymes & DNA binding proteins involved in the viral genome replication
• Timidin kinase, DNA polymerase
-- Gamma genes (L): late
• Are structural proteins

• DNA replication: rolling circle

-‐ Concatemer = long continuous DNA molecule that contains multiple copies
of the same DNA sequence linked in series
• Are separated by cleavage via a viral enzyme & are placed into pre-‐formed capsids
Latency:
• Direct or inverted repeats code for LATs (Latency Associated Transcripts)
• So depending on how the direct or inverted genes are located, the virus can have
several isoforms
• mRNA molecules are expressed only during latency, no protein translation occurs —

inhibits the transcription of IE/E genes

Alpha-‐herpesviruses = latency in neurons in the sensory ganglia

I. Herpes Simplex 1 virus (HSV1)
II. Herpes Simplex 2 virus (HSV2)
III. Varicella-‐Zoster virus (VZV)
-‐ Have a short replicative cycle
-‐ Induces cytopathic effects (CPEs) in monolayer cell cultures — high cytopathogenicity
-‐ Have a broad host range
-‐ Frequent reactivations
-‐ Neurotropism & neuroinvasion — can cause meningitis, encephalitis

Beta-‐herpesviruses = latency in T lymphocytes; monocytes, solid organs (lungs, kidneys)

I. Cytomegalovirus (CMV)
II. Human Herpesvirus 6 (HHV6)
III. Human Herpesvirus 7 (HHV7)
-‐ Have a long replicative cycle
-‐ Have a restricted host range

Gamma-‐herpesviruses = latency in B lymphocytes; capillary endothelium

I. Epstein Barr virus (EBV)
II. Human Herpesvirus 8 (HHV8) = Kaposi associated
-‐ Have a very restricted host range
Herpes Simplex 1 (HSV1) & Herpes Simplex 2 (HSV2):
• Both the primary infections with HSV & the endogenous recurrences may be
asymptomatic & produce immune responses without overt clinical signs
-‐ HSV1 = mainly associated with upper body infections
-‐ HSV2 = mainly associated with lower body infections

HSV1:
• Primary infection = gingivostomatitis
-‐ It spreads easily among household members, or through kissing
-‐ Fever, sore mouth, pain, bleeding gums, 1-‐8mm ulcers with necrotic bases
-‐ Neck lymph nodes are commonly enlarged
• Reactivation = cold sore (herpes labialis)
-‐ Stimulus: sunlight, fever, menstruation, stress, trauma, immunosuppression
-‐ A prodrome of tingling, warmth or itching is felt
• 12h later, there is redness followed by papules & then vesicles
• Herpes gladiatorum, Herpes in immunosuppressed patients, encephalitis

HSV2:
• Genital herpes STD; has various manifestations
-‐ Typical symptoms: prodrome, vesicular lesions on external genitalia
• HSV2 can be transmi:ed from mother to fetus
-‐ The newborn has disseminated herpes & encephalitis
• Meningitis, herpes whitlow, etc.
Varicella-‐Zoster virus (VZV):
• Primary infection = varicella (chickenpox)
-‐ Transmission = respiratory
-‐ Incubation period = 14-‐21 days
-‐ Symptoms = fever, lymphadenopathy, widespread vesicular rash
-‐ Prevention = live attenuated vaccine (LAT)
nd
• Given to children aged 19-‐35 months; the 2 dose is 5 years later
• Varicella vaccine (Varivax) = effective inf administered 72h auer infection
• MMR-‐V vaccine (proquad)
• Herpes-‐Zoster Vaccine (Zostavax)

• Reactivation = Herpes zoster = shingles

-‐ It manifests as a vesicular rash with a dermatomal distribution & acute neuritis
-‐ The latent virus may spread from 1 or more ganglia along the nerves of an
affected segment & infect the corresponding dermatome
• Results in a painful rash
-‐ Zostavax = A shingles LAT
• For adults over 50 years old who have had childhood chickenpox or
who previously had shingles

Treatment for alpha-‐herpesviruses’ infections:

• Acyclovir = is a guanosine analogue
-‐ It is selectively converted into acyclomonophosphate by viral timid kinase
-‐ Subsequently, the monophosphate is further phosphorylated by cellular
kinases into the active form = the triphosphate form
-‐ The active form is incorporated into the viral DNA, which results in premature
chain termination

Diagnosis:
• Relies on the isolation of the virus through culturing (cell cultures)
-‐ It produces the typical cytopathic effect (CPE) of multinuclear giant cells with
intra-‐ nuclear inclusions
• Detection of viral genes can be done thought PCR
• Detection of antigens can be done through immunofluorescence

Cytomegalic Virus (CMV): “owl eye” inclusions in cell cultures!

• Primary infection = in immunocompetent persons;
asymptomatic
• Reactivation = in immunosuppressed persons; symptomatic
-‐ Post-‐tranfusions —> mononucleosis-‐like
-‐ HIV/AIDS = retinitis / encephalopathies
-‐ Post-‐transplant:
• Pneumonia = fatality rate >85% T: Toxoplasma
O: Others (VZV, HBV, HIV, etc.)
• Hepatitis, encephalitis
R:
Rubella
C: CMV H: HSV2
• Materno-‐fetal transmission of CMV:
-‐ Prenatal (first trimester of pregnancy) -‐ teratogen
• Premature delivery, intrauterine growth, retardation, severe congenital
malformations, microcephaly, intra-‐cerebral calcifications, intellectual
impairment
-‐ Perinatal (third trimester):
• Hepato-‐splenomegaly, jaundice, petechiae, thrombocytopenia, hemolytic anemia
-‐ Postnatal:
• Asymptomatic or mononucleosis-‐like
-‐ Intrauterine infection occurs in 40% of the primary maternal infections
-‐ There is a 10-‐15% delivery of symptomatic newborns
-‐ Late neurologic sequels in 10% of those asymptomatic at birth — 60%
have sensorineural hearing deficits

-‐ Congenital rubella syndrome (CRS): [related to it?]

• It can occur in a developing fetus of a pregnant woman who has
contracted rubella during her first trimester
• Sensorineuronal deafness, eye abnormalities, congenital heart disease

Treatment of CMV infections:

• Gancyclovir
• Cidofovir — for retinitis caused by CMV
• Foscarnet

Human Herpesvirus 6 (HHV6) & Human Herpesvirus 7 (HHV7):

• Primary infection:
-‐ HHV6 = Roseola infantum (sixth disease)
-‐ HHV7 = Exanthem subitum

• Reactivation:
-‐ HHV6 = it is common in transplant recipients
• It can cause encephalitis, bone marrow suppression & pneumonia

Epstein Barr Virus (EBV):

• Primary infection = infectious mononucleosis (kissing disease) “atypical mononuclear cell”
-‐ Symptoms: fever, sore throat, fatigue, lymphadenopathy, splenomegaly

• Reactivation:
-‐ Burki\’s Lymphoma — endemic in Africa, in children
-‐ Carcinoma of the nasopharynx
-‐ Post-‐transplant lymphoproliferative disease
-‐ Hairy leukoplakia & CNS lymphomas — HIV infection

Human Herpesvirus 8 (HHV8):

• Kaposi Sarcoma = Classic or AIDS defining illnesses
RESPIRATORY VIRAL INFECTIONS /
INFLUENZA
People at risk for serious complications:
Transmission: • Persons of >65 years
• Respiratory droplets from human to • Persons with chronic diseases
human • Infants
• Coughing and sneezing • Pregnant women
• Touching a contaminated surface • Nursing home residents

Symptoms:
• Fever, chills
• Headache, body aches
• Fatigue, weakness
• Sore throat, non-‐productive cough
• Non-‐specific GI symptoms

Complications:
• Primary viral pneumonia
• Secondary bacterial pneumonia
• Bacterial sinusitis
• Myositis
• Myocarditis / pericarditis

• Exacerbation of underlying chronic disease (congestive cardiac failure, asthma)

• Encephalitis, seizures
• Guillan-‐Barre syndrome
• Reye’s syndrome

General characteristics of Influenza virus:

• Orthomyxoviridae family
• Types = A, B, C (according to NP, M)
• Genome = (-‐)ssRNA segmented
• Subtypes = HA & NA
-‐ Neuraminidase (NA) — 9 types
-‐ Hemagglutinine (HA) — 16 types

Life cycle:
• Cellular proteases —> HA cleavage —> activates infectivity
• Transcription = (-‐)ssRNA + transcriptase
• Uncoating = through the M Protein (ionic channel)
-‐ Protein M inhibitors = adamantanes (amantadine, rimantadine) —>
interferes with viral uncoating inside the cell
• Eclipse phase = receptor-‐mediated endocytosis
• Plateau phase = NA cleaves the receptor on host cell—> release of new virions
-‐ Neuraminidase inhibitors = interferes with the release of progeny virions
from the infected host cells; influenza A & B
• Oseltamivir (Tamiflu) — 75mg x2/day = treatment & prevention
• Zanamivir (Relenza) — 10mg (2 inhalations x 5mg /day)
Variability of influenza viruses:
• Antigenic driU:
-‐ Error-‐prone transcriptase —> point mutations —> epidemics
-‐ A new vaccine is required every year because the influenza virus has the
ability to undergo antigenic driu
• Antigenic shiU = new subtypes
1. Reassortment — exchange of minigenes
2. Direct interspecies transfer (adaptation)
3. Re-‐emergence of an ancient viral strain
• Pandemics = epidemic spreads over several countries or continents
1. New virus — distinct antigenicity (antigenic shiu)
2. Immunologic — naive human population
3. Readily transmissible virus — easily spread from human to human
(wide geographical spread)

Influenza Type A: has major variability

• Antigenic shis:
1. Reassortment:
-‐ The genes for structural proteins are acquired from other animal hosts
resulting in a sudden dramatic change in the viral genome
• Human strains = SA-‐2-‐6-‐beta Gal
• Avian strains = SA-‐2-‐3-‐beta Gal
-‐ Natural reservoir; wild aquatic birds (Avian influenza)
-‐ Virus replicates in the GI epithelium & is shed in the faeces
• Swine strains = SA-‐2-‐3-‐ Gal & SA-‐2-‐6-‐beta Gal
-‐ There is a continuous replication of avian influenza virus in
the swine strains that will preferentially bind to human
receptors
-‐ Reassortants between swine & avian strains can infect
humans & determine severe infections
2. Adaptation = direct transfer of avian strains to humans
-‐ Low pathogenicity (LPAI) = mild respiratory disease, decreased egg
production
-‐ High pathogenicity (HPAI) = H5,H7 = lethal
• Insertions in the basic aminoacids at the HA cleavage site
• Conformational changes in HA — interspecies transfer
• Supplementary basic amino acid —> multiple cleavage sites —
> different proteases can cleave HA & activate infectivity —>
altered tropism —> increased virulence

Influenza vaccines:
• Inactivated vaccine = whole virus or subunit vaccine (HA/NA)
• Live-‐a\enuated vaccine: cold strains
-‐ Stable mutations in the polymerase complex genes (PA, PB1. PB2)
-‐ Serial subcultures at 25°C in cell cultures
• Trivalent inactivated vaccine:
-‐ Subunit vaccines (HA, NA)
-‐ One injection lasts ~6months
-‐ Side effects = local soreness, fever within 24h, flu-‐like illness
• Different types of vaccines:
-‐ DNA-‐based vaccines
-‐ Recombinant subunit vaccines
-‐ Viral vector vaccines
-‐ Synthetic peptide vaccines

Vaccine development:
• Each year it takes about 6 months form the time the strains have been selected until
the vaccine is available
• The flu virus is grown in chicken eggs:
-‐ The process requires a large supply of fertile chicken + eggs
-‐ It is entirely dependent on how well the virus grows in the eggs — accelerating
the vaccine production in a time of influenza pandemic is very difficult
• The vaccine is produced by using a vaccine strain & the new antigenic strain
-‐ The vaccine strain is a?enuated, non-‐pathogenic, with no replication in humans
-‐ Reassortant = 6 genes from the vaccine strain; HA & NA from the new antigenic strain

Priority groups for Influenza vaccination:

• Children 6-‐23 months of age
• Adults >65 years
• Persons of 2-‐64 years of age with underlying chronic medical conditions:
-‐ Pulmonary diseases (emphysema, asthma)
-‐ Cardiovascular diseases (congestive heart failure)
-‐ Metabolic diseases (diabetes)
-‐ Renal diseases (chronic renal failure, nephropathy)
-‐ Hemoglobinopathies (sickle cell disease)
-‐ Immunosuppression (HIV)
• Pregnant women
• Obese persons (BMI >30-‐40)
• Healthcare workers with direct, face-‐to-‐face patient contact
• Residents of nursing homes & long-‐term care facilities
HEPATITIS VIRUSES
General information:
• Viral hepatitis = a necroinflammatory liver disease of variable severity
• Common symptoms:
-‐ Jaundice
-‐ Dark urine
-‐ Extreme fatigue
-‐ Nausea, vomiting
-‐ Abdominal pain

Hepatitis A virus (HAV): HepaRNAviridae (+ssRNA virus; non-‐segmented)

• Transmission: infectious
-‐ Contaminated food & water (raw shellfish, infected food handler)
-‐ Close personal contact (household contact, child daycare centres)
-‐ Feces
-‐ Blood exposure = very rare
• Inactivation of HAV:
-‐ Boiling at >85°C for at least 3 minutes
• Incubation period = 15-‐50 days
• Clinical symptoms:
-‐ Acute Hepatitis A:
• Jaundice
• Complications (rare) = fulminant hepatitis, cholestatic hepatitis
-‐ NO chronic infection!
• Diagnosis:
-‐ HAV in feces (1st month)
-‐ Symptoms = jaundice, dark urine, etc.
-‐ Acute hepatitis A = IgM anti-‐HAV antibodies
-‐ Recovered hepatitis A / Immunisation = IgG anti-‐HAV antibodies
• Prophylaxis:
-‐ Inactivated vaccine (HAV vaccine)
-‐ HAV immune Globulin = IM administration within 2 weeks auer HAV exposure
-‐ Hygiene (washing hands)
-‐ Sanitation (clean water sources)

Hepatitis E virus (HEV): Hepeviridae (+ssRNA virus; non-‐segmented)

• It is similar to HAV
• Transmission:
-‐ Most outbreaks are associated with drinking fecally contaminated water
-‐ Enteric transmission (fecal-‐oral)
-‐ Minimal person-‐to-‐person transmission
-‐ Hepatitis E zoonosis = travel to endemic areas; eating undercooked pork meat/liver
• High mortality in pregnant women (3rd trimester)
Hepatitis B virus (HBV): HepaDNAviridae (enveloped, dsDNA)
• Structure:
-‐ Genome = DNA; partially double--stranded & partially circular
-‐ Has 4 overlapping open reading frames
-‐ Reverse transcriptase / DNA polymerase domain overlaps with the surface gene
-‐ Antigens:
• HBsAg = surface Ag
• HBeAg = envelope Ag
• HBcAg = core Ag

• HBV life cycle:

-- The virus replicates through an RNA intermediate form via reverse transcription
-- Steps:
1. Infectious HBV enters host cell via endocytosis
2. The contents (DNA & core proteins) are released into the host’s cytoplasm
3. The partially ds DNA transforms into cccDNA
4. cccDNA (covalently closed circular DNA) is used as a template to produce mRNA
5. mRNA is used to make new copies of the viral genome, using DNA polymerase
6. mRNA is recycled to produce more cccDNA via reverse transcription
7. The synthesised viral DNA is used to produce viral proteins

• Transmission:
-- Parenteral = blood / serum; percutaneous/permucosal
-- Sexual contact
-- Close/direct contact
-- Mother to fetus (perinatal)

• Acute infection:
-‐ Acute Hepatitis B —> recovery
-- Subclinical hepatitis (5-‐20%) —> recovery
-- Fulminant (sudden onset) hepatitis (<1%) —> death (rare) or recovery
-- Can lead to a chronic infection
• Chronic Hepatitis B:
-- HBsAg persists for >6months
-- Viral replication persists = HBeAg + high viral load (HBV DNA)
• Active chronic hepatitis (cirrhosis, hepatocellular carcinoma)
--Transaminases (ALT) = persistent or increased intermittently
-- Progressive necro-‐inflammatory activity (+/-‐ fibrosis)
• Treatment:
-- For patients with an active disease:
• HBeAg+ chronic hepatitis B
• HBeAg-‐ chronic hepatitis B (core/precore mutants)
-- Monotherapy with nucleosidic/nucleotidic analogs RT inhibitors
-- PEG-‐IFN
-- Vaccination = recombinant vaccines (rHBsAg)
-- Hepatitis B immunoglobulin (HBIG) = effective auer 48h of exposure to HBV
• Also given to neonates with Hepatitis B positive mothers (HBsAg+ & HBeAg+)

• Diagnosis:
-‐ HBsAg = present in the incubation period (1-‐6 months)
-‐ anti-‐HBs Ab = present in recovery/immunisation
-‐ IgM anti-‐HBc Ab = present in acute hepatitis B
-‐ IgG anti-‐HBc Ab = present in past infection; chronic hepatitis B
-‐ HBeAg = active viral replication (high viral load)
-‐ anti-‐HBe Ab = present when there is no viral replication

Hepatitis D virus (HDV):Defective virus (RNA)

• HDV can only cause a disease if there already is a HBV infection
• Co--infection B--D:
-‐ Severe acute disease
-‐ Has a very low risk of becoming chronic
• Superinfection B--D:
-‐ Has an increased risk of becoming chronic & cirrhosis
-‐ Pathogeny = immune-‐mediated lysis (cytotoxic T cells)
• Diagnosis:
-‐ Co-‐infection B-‐D:
• HBsAg+
• IgM anti-‐HBc+
• IgM anti-‐HD+
-‐ Superinfection B-‐D:
• HBsAg+
• IgG anti-‐HBc+
• IgG anti-‐HD+
• Treatment:
-‐ Vaccination = HBV vaccine; it prevents HDV infections as well
Hepatitis C virus (HCV): Hepacivirus (+ssRNA = mRNA, enveloped)
• Transmission:
-‐ Parenteral = percutaneous / permucosal
• Transfusions/transplants = immunological window
• Accidental lesions, Hemodialysis, IDU
-‐ Perinatal = from HCV--RNA+ mothers to child
• Asymptomatic infection in newborns, slow evolution of chronic infection
• Higher risk if co-‐infected with HIV
-‐ Sexual
• Immunological window / Incubation = 100 days (6-‐7 weeks)
-‐ HCV has hydrophobic proteins (plasma beta lipoproteins) —> shields the antigenicity
• HCV replication:
1. Entry (endocytosis) = via LDL receptors, scavenger receptor BI, CD81
2. Translation of +ssRNA (mRNA) into a large polypeptide
3. The large polypeptide is cleaved into mature proteins via HCV protease (NS3-‐NS4a)
4. NS5B (RNA-‐dependent RNA polymerase; RdRp) catalyses the replication of HCV RNA
5. NS5A is involved in the formation of the replication complex & in the viral assembly

• Viral variability:
-‐ NS5B is an error-‐prone enzyme
• It has a high mutation rate
-‐ Quasuspecies = 2-‐10% differences
• Selection for “escape mutants” = chronicization
-‐ 6 major genotypes = 20-‐48% differences
• Reinfections with distance genotypes = chronicization

• Treatment:
-‐ Aim = sustained viral response (SVR)
• Undetectable HCV RNA auer 6 months of treatment
-‐ Chronic Hepatitis C genotype 2, 3, 4 = double therapy
• PEG--IFN + Ribavirin (RBV)
-‐ Chronic Hepatitis C genotype 1 = triple therapy
• PEG--IFN + RBV + a protease inhibitor (telaprevir or boceprevir)
-‐ NO vaccine!
HIV / AIDS

Structure of HIV:
• Belongs to the lentiviridae genus of the retroviridae family
• Enveloped virus
-‐ Enters the host cell by fusion with the host’s cell membrane
-‐ GP41 (transmembrane protein)
• Genome = +ssRNA-‐RT
-‐ Structural genes:
• ENV = envelope
-‐ gp41 (glycoprotein 41)
• GAG= group antigenic
-‐ p24 (capsid)
-‐ p17 (matrix)
-‐ p7/9 (nucleocapsid; nucleopeptide)
• POL = polymerase
-‐ enzymes present in the viral cell (protease, RT, integrase)
-‐ Regulatory genes:
• REV
• NEF = inhibitory
• TAT = transactivator
-‐ Accessory genes: they decrease the mechanism of the cell to favourite viral replication
• VPR
• VIF
• VPU
-‐ Long-‐terminal repeats (LTR):
• Are the sticky ends which stick to the genome from the infected cell

Transmission pathways:
• Parenteral = blood (horizontal)
• Sexual = semen, vaginal secretions
• Materno-‐fetal = amniotic fluid, breast milk (vertical)

Target cells for HIV:

• CD4+ cells
-‐ T helper cells
-‐ Monocytes / macrophages
-‐ Dendritic cells (Follicular)
TROPIS
M
HIV Viral Life Cycle:
1. Eclipse
-‐ Attachment:
• Main receptor = CD4 (it is bound by gp120 on the envelope)
• Co-‐receptors:
-‐ CCR5 = β-‐chemokine co-‐receptor on macrophages
• HIV isolated during the early stages are macrophage-‐tropic (M-‐tropic)
-‐ Are non-‐syncytium inducing
-‐ Have a low RT rate
• So HIV will mainly bind to the CCR5 co-‐receptors in the early stages
-‐ There will be a higher number of infected macrophages & APCs
-‐ The T lymphocytes will be normal
-‐ CXCR4 = α-‐chemokine co-‐receptor on lymphocytes
• HIV isolated during the late stages are lymphotropic (L-‐tropic)
-‐ Are syncytium inducing
-‐ Have a high RT rate
• So HIV will mainly bind to the CXCR4 co-‐receptors in the late stages
-‐ The T lymphocytes will be infected
-‐ Entry = Through a fusion factor = gp41
-‐ Uncoating
2. Logarithmic Growth
Parental viral genome = +ssRNA
↓ Reversetranscriptase (RTase)
Proviral DNA
↓ Integrase
Integration into the cellular DNA
↓ Host cell RNA Polymerase II
mRNA
↓
Progeny genomes (ssRNA) + Proteins
-‐ Cellular factors promoting viral replication:
• Tat & Rev = are regulatory viral proteins which try to stimulate viral replication
-‐ Cellular factors opposing viral replication:
• TRIM5α = stops replication in the early stages
• APOBEC3G = interferes with reverse transcription
• These 2 can be inhibited by:
-‐ Vif = blocks APOBEC 3G
-‐ Vpr = increases the nuclear import of proviral DNA
3. Plateu
-‐ Maturation, assembly & release (by budding)
-‐ Cellular factors opposing this phase:
• Tetherin = prevents diffusion & stops budding of virus from the infected cells
• VPU = enhances virion release from the plasma membrane of infected cells
• NEF = increases viral infectivity
Viral variability:
• Extraordinary high level of sustained replication & turnover in vivo
• Functional tolerance of amino acid substitutions
• Viral variability occurs because:
-‐ There is a high rate of mutations in the reverse transcriptase (RT) enzyme
• This results in an error-‐prone RT enzyme
-‐ There are also mutations in the host cell RNA polymerase II
• Therefore, every new virus can have at least 1 mutation; leads to variability
• HIV1 = are derived from SIVcpz (chimpanzees) — pathogenic in natural host
-‐ Has 8 subtypes (A-‐J) & 3 groups:
• Group M (major)
• Group N (non-‐major)
• Group O
• HIV2 = are derived from SIVmc — non-‐pathogenic in natural host

Anti-‐Retroviral Treatment:
• Monotherapy = causes virus resistance to the individual drug; not preferred/used
• Combination therapy (cART) = can reduce individual drug toxicity (decreased dosage of drug)
• Main types of cART used:
-‐ 2 NRTI + 1 PI

-‐ 2 NRTI + 1 HAART = highly active anti-‐retroviral therapy

NNRTI HEART = highly expensive anti-‐retroviral therapy
-‐ 2 NRTI + 1
INSTI

• Goals:

- To prolong life & improve the quality of life

- To suppress HIV to below the limits of detection (or as low as possible) for as
long as possible
- To preserve or restore the immune function
• Advantages /Benefits:
- Earlier suppression of viral replication
- Preservation of immune function
- Lower risk of resistance with complete viral suppression
- Decreased risk of HIV transmission
• Disadvantages /Risks:
- Drug-‐related toxicities
- Earlier development of drug resistance, if viral suppression is suboptimal
- Limitation of future treatment options
- Unknown durability of current therapies
• PMTC = prevention of mother to child transmission
-‐ AZT in monotherapy
• Pre-‐exposure Prophylaxis: PrEP
-‐ A new HIV prevention method where HIV negative people take a daily pill to
reduce their risk of getting infected
3

Targets for anti-‐retrovirals:

1. Fusion/entry inhibitors:
-‐ CCR5 inhibitors = Maraviroc
-‐ Fusion inhibitors (gp41) = Fuzeon (enfivurtide)
2. Reverse transcriptase inhibitors:
-‐ Nucleotide RT inhibitors (NRTI) = zidovudine
-‐ Non-‐nucleosidic RT inhibitors (NNRTI) = reutapire?
• It directly inhibits the active site
3. Integrase inhibitors: Raltegravir
-‐ Integrase Strand Transfer inhibitors (INSTI)
-‐ Integrase Binding Inhibitors (INBI)
4. Protease inhibitors: (PI)
- Indinavir = binds to the active site of the enzymes
Natural Evolution of HIV Infection: = without treatment
1. Primary infection: Acute Retroviral Syndrome
-‐ High viral replication (>10 million HIV RNA copies/mL)
-‐ Transient fall of CD4+ cells
-‐ Macrophages & dendritic cells are infected
• Macrophages can be directly infected by CD4+ cells
-‐ No symptoms or non-‐specific clinical signs = mononucleosis-‐like (flu-‐like)
-‐ Infected person can infect others
-‐ Immunological window = 50-‐60 days (4-‐6 weeks)

2. Asymptomatic infection: Strong immune response

-‐ Recently infected CD4+ cells are activated = viremia
-‐ Efficient cytotoxic (CD8) response to kill the infected CD4 cells
• The killing of infected CD4+ cells is compensated by de novo production
-‐ HIV persists in reservoirs, lymph nodes, CNS, genital tract
-‐ Some CD4 cells revert to memory cells (long-‐lived)
-‐ “Set point” = if there is a weak CTL response, there will be a high viral load & a
rapid progression to the last stages of infection (6 months for the viral load to be
??
efficient )

3. AIDS-‐Related complex (ARC):

-‐ Massive viral replication in lymph nodes
• Viral variability due to errors in RT & host cell polymerase II —> selection
of L-‐ tropic strains
-‐ CD4+ cells are depleted
• Leads to the emergence of opportunistic infections & cancers
-‐ Systemic immune activation
-‐ Massive loss of CD4+ cells:
• CD4+ cells are the targets of the virus
• Cells which proliferate to respond to the virus are killed by it = clonal deletion
• Dendritic cells present antigen & virus to the CD4 cells just as they are activated
• Epitope variation allows more virions to escape from the immune response

4. AIDS: CD4+ cells = <200 cells/mL

-‐ The virus titre rises rapidly due to a fall in CD4+ cells = the immune response collapses
• Leads to severe opportunistic infection — death in ~2 years without intervention
-‐ CD4+ cells are activated:
• anti-‐HIV specific humoral & cellular responses
• pro-‐inflammatory cytokines & chemokine synthesis
-‐ HIV replication —> massive production of specific HIV proteins (tat, ref, gp120)
-‐ Massive depletion of CD4+ cells especially in the lymph nodes & GALT
• Reactivation of latent viruses & bacterial translocation
-‐ They all lead to the systemic immune activation:
• Exhaustion of immune response
• Decline in the cells’ regenerative capacity
• Immunosenescence
• “old people” diseases = CV diseases, hypertension, fractures, diabetes
Complications / related diseases / opportunistic infections:
• Pneumocystis carinii
• Kaposi sarcoma
• Herpes zoster

VIRAL
• Disseminated herpes simplex
• Hairy leukoplasia (EBV infection)
• Molluscum contagiosum
• Disseminated papilomatosis
• Chronic parotiditis (unilateral/bilateral)
• Scabies
• Candida albicans infection
• Encephalopathy (neurocognitive syndormes)
• Wasting syndrome

Monitoring:
• Clinical parameters = symptoms
• Immunological parameters = CD4+ cell count
-‐ CD4+/CD8+ ratio = 0.9 -‐ 6 (must be minimum 1)
-‐ CD4+ = 500-‐1200 cells/mm3
• Virological parameters = viral load (HIV RNA)

PRIMARY INFECTION — ASYMPTOMATIC INFECTION — ARC — AIDS

VIRUSES & CANCERS:
• Cancer originates due to the disturbances in the genetic material of cells
- It is induced by chemical or physical agents, infectious agents (viruses &
bacteria) or by hormonal stimulation
• In most cases, a single disturbance is not sufficient, but instead an accumulation of
several critical injuries is required
- This is the reason why cancers usually develop later in life
• Abnormal functioning cellular genes have now been demonstrated in many types of
tumour in humans
- Disruptions in the functioning of these genes can cause 1 cell to slip out of
the network of growth control
• Carcinogenesis = losing control of the normal cell cycle due to inactivation of anti-‐oncogenes
- PROTO-‐ONCOGENES = genes that control the normal growth & division of cells
- ANTI-‐ONCOGENES = P53 & RB genes; genes that provide genetic & cellular stability
1. Cell cycle arrest —> DNA repair —> cell cycle restarts
2. Apoptosis —> death & elimination of damaged cells
-‐ Cyclins = proteins that control the progression in the cell cycle

Oncogenic Retroviruses (oncovirinae):

• They are transforming oncovirusus in vitro / rapid oncogenic in vivo
• Oncogene = genes coding for a protein that induces
transformation in vitro/in vivo (v-‐onc)
- Insertion of viral oncogene (v-‐onc) causes aberrant cell division
Non-‐transforming oncoviruses / Slow oncogenic:
• A retrovirus without oncogenes always inserts near a proto-‐oncogene (c-‐onc)
• Insertion activation:
- Aberrant activation of the proto-‐oncogene by increasing its expression
30-‐100 fold
- The LTRs of the retroviruses contain powerful promoters &
enhancer sequences that are presumably responsible for the
increased expression

Retroviridae:
• HTLV = non--transforming in vitro / slow oncogenic
- Human T-‐cell Lymphotropic Virus 1 (HTLV1) = adult T cell
leukaemia, Sezary T cell leukemia (Africa, Caribbean, Some
Japanese islands)
- Human T-‐cell lymphotropic virus 2 (HTLV2) = Hairy cell leukaemia
• Transactivation of cellular promoters for genes coding for cytokines or co-‐
stimulatory molecules
• HTLV regulatory gene (tax) — LTR transcriptional factor

Oncogenic retroviruses:
• Transforming in vitro & rapidly oncogenic in vivo = oncogenes, usually defective replication
- Most transforming retroviruses have oncogenes that replace a structural gene
• Non-‐transforming in vitro & slow oncogenic in vivo = insertional activation
of proto-‐ oncogenes
• Endogenous retroviruses (ERV) = inserted retroviral genome as an integral part of
the host’s own genome
Epstein Barr Virus (EBV):
• Latency = in B lymphocytes
- EBV transforms human B lymphocytes in vitro
• Reactivation of latent EBV infection:
- Burki\’s Lymphoma — associated antigen = EBNA (Epstein Barr nuclear antigens)
• Chromosomal translocation (8:14) —> the break & exchange of parts of
the chromosomes brings the c-‐onc under the control of a very active
cell promotor & c-‐myc under the control of Ig heavy chain promoter of
IgG
- Carcinoma of the nasopharynx — associated antigen = LTA(latency tumbrel antigens)
- Post-‐transplant lymphoproliferative disease — associated antigen =
LMP (latent membrane proteins)
• Early viral proteins:
- Autocrine growth factors for B cells
- Growth factor receptors
- Activators of cellular oncogenes

Human Herpes Virus 8 (HHV8):

• Kaposi Sarcoma:
- 25-‐30% = HIV and men
- 4-‐5% = HIV and women
• HHV8 = the viral genes are homologous to the cyclins
- Cyclins = proteins that control the
progression in the cell cycle
- CDK = involved in regulating
transcription, mRNA processing

Hepatitis B virus (HBV):

• Hepatocellular carcinoma (HCC):
- Regulatory proteins encoded by the
HBV X gene
• Proto-‐oncogene transactivation
• Aberrant expression
• Chromosomal translocations
• Over-‐expression of apoptosis inhibitors
• Integration is done in the cccDNA —> deletions in the hepatocyte DNA
occurs for genes involved in signal transducing
- Causes of HCC:
• Aphlatoxin B1 = contamination of grain harvests by metabolites of Aspergillus
- Causes cleavage of DNA helix —> mutagenesis
• 90% (in Europe) = aser advanced cirrhosis (co-‐infection with HCV or HIV,
obesity, diabetes, alcohol)
Human Papilloma Virus (HPV):
• Structure of HPV:
- Genome = dsDNA
- Non-‐enveloped
- Has tropism for the skin & mucosa
- Has ~100 genotypes
A. Transient infection = lytic infection
- Productive infections only in permissive cells (keratinocytes of the skin or
mucous membranes; basal layer of the epithelium)
• L1 & L2 = expressed only in the differentiated keratinocytes in the external layers
• E1 = helicase; initiates viral replication
• E2 = transcriptional regulator
• E4 = viral release; disruption of the cytoskeleton
• E5 = destabilising membrane proteins
- The viral particles are released as a result of degeneration of desquamating cells
- E1/E2 genes expression is necessary for the maintenance of the viral
DNA in episomal form
- HPV low-‐risk types = 6, 11, 40, 42, 43, 44, 54, 61, 70, 72, 81
- Clinical manifestation = papillomas (warts), condiloma accuminata, LSIL, recurrent
respiratory papillomatosis
- Symptoms = asymptomatic, subclinical —> cleared by the immune system
• No clinical consequences in immunocompetent individuals
- Incubation period = unclear, probably weeks to months (genital warts) or
several months to years (cervical cellular abnormalities)

B. Persistent infection = not cleared by the immune system; DNA detectable; abortive;
- Non-‐permissive cells —> viral genome integration —> transformation
- LCR = control of viral genes expression; are enhancers that can be activated by
host or viral associated co-‐factors
- Over-‐expression of E6 & E7 genes
- E6 & E7 proteins inactivate 2 tumour suppressor proteins (P53 & RB); they
play a major role in immortality & malignant transformation of infected cells
• E6 binds to P53 —> proteolytic degradation = losing control of
cyclins —> uncontrolled progression in the cell cycle
• E7 binds to Rb —> Rb phosphorylation = inactivation —> uncontrolled
activation of the genes involved in the DNA synthesis
- HPV high-‐risk types = 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 68, 73, 82
- Clinical manifestation = HPV associated cancers (cervical cancer)
• LSIL = low-‐grade squamous intraepithelial cells; CIN I (cervical
intraepithelial neoplasia)
• HSIL = high-‐grade squamous intraepithelial cells; CIN II/III; in situ carcinoma
- Cytological screening will allow early detection & effective intervention
• Cervical cancer can’t develop without a persistent HPV infection
LSI HSI
-‐ Co-‐factors necessary for progression from cervical HPV infection to cancer:
• Established co-‐factors:
-‐ Long-‐term use of hormonal contraceptives
-‐ High parity
-‐ Tobacco smoking
-‐ Co-‐infection with HIV
• Probable co-‐factors:
-‐ Co-‐infection with Chlamydia trachomatis (CT) & HSV2
-‐ Immunosuppression
• Other co-‐factors:
-‐ Genetic & immunological host factors
-‐ Viral factors (variants of type, viral load & viral integration) – not
clearly identified

• Diagnosis of Cervical Cancer: cytological & virological screening

- Cervical cytology:
• A sample of cells is taken from the transformation zone of the cervix,
smeared onto a glass slide & immediately fixed with a fixative (drops or
spray)
• Cytological specimen = using the Papanicolaou stain
- LSIL = cells with perinuclear halos (HPV cytopathic effect). The
nuclei are enlarged & hyperchromatic, with irregular nuclear
outlines.
- HSIL = an abnormally isolated cell with a high nucleus-‐to-‐
cytoplasm ratio, irregular chromatin distribution & an irregular
nuclear envelope.
- HPV DNA testing = with PCR or genotyping
• HPV vaccine:
- Recombinant DNA — using “virus-‐like particles” (VLP)
• L1 protein — type specific neutralising Ab
- Most effective time for vaccination is before exposure to HPV
- Vaccination does NOT replace periodic cytological/virological screening &
must NOT affect prevention against STDs

Viruses involved in oncogenesis:

- Aberrant activation of cellular proto-‐oncogenes
- Insertion of genetic material similar to the porto-‐oncogenes
- Mutations “loss of function” = inactivation of anti-‐oncogenes (tumor suppressor genes)
NEUROVIRUSES:
VIRAL MENINGITIS: check LP
• Meningitis = inflammation of the protective membranes covering the brain & spinal cord
• Diagnostic signs:
- Nuchal rigidity (stiffness of the neck)
- Sudden high fever
- Headache / altered mental status
• Etiology: Enteroviruses
- Poliovirus 1, 2, 3
- Coxsackie A1-‐24 / B1-‐6
- ECHO 33 (Enteric cytopathogenic human orphans)
- Enteroviruses 68-‐71
Poliomyelitis:
• Major illness (1-‐2%)
• Paralytic poliomyelitis = involvement of the anterior horn cells
• Bulbar polio = involvement of the medulla may lead to respiratory paralysis & death
• Anti-‐polio vaccines:
- Intramuscular poliovirus vaccine (IPV) — attenuated
- Oral attenuated poliovirus vaccine (OPV)
• Risk of vaccination:
- The virus can revert to a form capable of causing the disease (due to mutations)
VIRAL ENCEPHALITIS:
• Encephalitis = an acute inflammation of the brain
• Symptoms = headache, fever, confusion, drowsiness, fatigue
• Advanced & severe symptoms = seizures, convulsions, tremors,
hallucinations & memory problems

SYNDROME POSSIBLE ETIOLOGY

Arboviruses
- Flavivirus = West Nile virus
Meningo- - Togavirus = Eastern equine encephalitis virus
encephalitis - Bunyavirus
Herpesviruses
- HSV1, HSV2
- VZV, EBV, CMV
Acute encephalitis
Post-infectious:
Measles, VZV, mumps, influenza

Encephalo-myelitis Rabies

Arboviruses: arthropod-‐borne viruses

• Flaviviridae:
- Yellow fever, Dengue fever, Zika virus
- St. Louis Encephalitis, Japanese Encephalitis; West Nile virus
• Togaviridae:
- Eastern Equine Encephalitis
- Chikungunya virus
• Bunyaviridae = California group Encephalitis
West Nile virus: Flaviviridae
• Member of the antigenic complex of Japanese encephalitis
• Transmission cycle:
- A vertebrate host reservoir (bird)
- A vector (mosquito) —> transmitted by blood-‐sucking insects
- Virusamplification
• Clinical manifestation:
1. Asymptomatic infection
2. West Nile fever = headache, back pain, myalgias, maculopapular rash
-‐ Recovery is rapid & complete
3. West Nile meningoencephalitis — uncommon
-‐ Advanced age & compromised immunity
-‐ Neurological & cognitive dysfunction
-‐ Neurological complications — acute flaccid paralysis syndromes (AFP);
similar to poliomyelitis
-‐ Chorioretinitis, pancreatitis, fulminant hepatitis & myocarditis — extremely rare
• Diagnosis:
1. Viral isolation in cell cultures and/or suckling mice
-‐ Samples = serum, cerebrospinal fluid or necropsy samples
2. PCR for WN virus genome:
-‐ Samples = serum, cerebrospinal fluid
-‐ Primers directed against a conserved flaviviral envelope sequence
-‐ PCR products were identified by hybridisation with a probe specific for WN virus
3. Antigen detection:
-‐ Samples = CSF
-‐ Neutralisation test (plaque assay)
-‐ Monoclonal antibodies
4. Indirect ELISA:
-‐ Samples = serum & CSF
-‐ Tested for IgM & IgG antibodies against WN virus
• Prevention:
-‐ Reduce exposure (drain water from mosquito breeding sites)
-‐ Use mosquito larvicides or maturation inhibitors
-‐ Spray insecticides (organophosphate or pyrethroid)
-‐ Use insect repellents (10–50% N,N -‐diethyl-‐3-‐ methylbenzamide)

Zika virus: flaviviridae

• Symptoms = rash, mild fever, conjunctivitis & muscle pain
-‐ Begins 3-‐5 days auer the bite of an infected mosquito
-‐ Symptoms are similar to those of Dengue & Chikungunya
-‐ Neurological & autoimmune complications are infrequent
• Transmission:
-‐ Via the bite of an infected mosquito (Aedes mosquito)
-‐ Via sexual transmission
-‐ Mother to child —> microencephaly & other CNS malformations
• An increase in Guillain-‐Barre syndrome (GBS) has been observed in epidemic areas
-‐ GBS occurs when the immune system attacks part of the peripheral NS
-‐ Main symptoms = muscular weakness & tingling (paresthesia) in the arms &
legs, severe complications can occur if the respiratory muscles are affected
Measles: Morbilivirus
• Symptoms = red-‐brown spo\y rash, cold-‐like symptoms (runny nose, red
watery eyes), sensitivity to light, high fever (may peak over 40.6°C for
several days)
-‐ Rash appears 3-‐5 days aqer the symptoms begin
• Tiny greyish-‐white spots (Koplik's spots) in the mouth & throat
tiredness, irritability & general lack of energy, aches & pains, poor
appetite, dry cough
• Complications = otitis, pneumonia, encephalitis/PESS
• Diagnosis = Cytopathic effect (syncytium) or plaque assay
• Active prophylaxis = vaccination
-‐ Measles mumps rubella vaccine (MMR) = live-‐attenuated vaccine
-‐ Pediatric dosing is 0.5 ml subcutaneously (ouen between 12–18 months)

Rabies: Rabdoviridae
• Incubation period = from 2-‐12 weeks
• Clinical manifestation:
1. Prodromal stage (2-‐10days) = flu-‐like symptoms
2. Acute neurological symptoms (6-‐12days):
-‐ Symptoms = anxiety, delirium, convulsions, exaggerated sensation at
the bite site, excitability or combativeness, hallucinations, loss of feeling
in an area of the body, loss of muscle function, low-‐grade fever, muscle
spasms, numbness & tingling, pain at the site of the bite, restlessness,
insomnia, swallowing difficulty
3. Coma (2-‐7 days) & abrupt death
• Transmission & pathway:
1. Virus enters via animal bite
2. Virus replicates at the site of entry (muscle)
3. Virus infects nerve in the peripheral NS & moves by retrograde transport
4. Virus replicates in the dorsal root ganglion & travels up the spinal cord into the brain
5. Brain is infected
6. Virus travels from the brain via nerves to other tissues (eye, kidneys, salivary glands)
• Diagnosis = Negri bodies
• Vaccination:
-‐ Inactivated vaccine = grown in human diploid cells or rhesus monkey lungs
-‐ Rabies antibodies = 2 kinds may be used (HRIG or ERIG)
-‐ Vaccination for animals = mandatory for domestic animals
EMERGING DISEASES: