1. Viral pathogenesis and genetics

2. Viral Pathogenesis
Viral pathogenesis is the process by which a viral infection leads to disease.
Viral pathogenesis is an abnormal situation of no value to the virus.
The majority of viral infections are subclinical. It is not in the interest of the virus to severely harm or kill the host.
The consequences of viral infections depend on the interplay between a number of viral and host factors.

3. Outcome of Viral Infection
Acute Infection
Recovery with no residue effects
Recovery with residue effects e.g. acute viral encephalitis leading to neurological sequelae.
Death
Proceed to chronic infection
Chronic Infection
Silent subclinical infection for life e.g. CMV, EBV
A long silent period before disease e.g. HIV, SSPE (Subacute sclerosing panencephalitis), PML (progressive multifocal leukoencephalopathy) Reactivation to cause acute disease e.g. herpes and shingles.
Chronic disease with relapses and exacerbations e.g. HBV, HCV.
Cancers e.g. EBV, HTLV-1, HPV, HBV, HCV, HHV-8

4. Factors in Viral Pathogenesis
Effects of viral infection on cells (Cellular Pathogenesis)
Entry into the Host
Course of Infection (Primary Replication, Systemic Spread, Secondary Replication)
Cell/Tissue Tropism
Cell/Tissue Damage
Host Immune Response
Virus Clearance or Persistence

5. Cellular Pathogenesis
Cells can respond to viral infections in 3 ways: (1) No apparent change, (2) Death, and (3) Transformation
Direct cell damage and death from viral infection may result from
diversion of the cell's energy
shutoff of cell macromolecular synthesis
competition of viral mRNA for cellular ribosomes
competition of viral promoters and transcriptional enhancers for cellular transcriptional factors such as RNA polymerases, and inhibition of the interferon defense mechanisms.
Indirect cell damage can result from
integration of the viral genome
induction of mutations in the host genome
inflammation
host immune response.

6. Viral Entry
Skin - Most viruses which infect via the skin require a breach in the physical integrity of this effective barrier, e.g. cuts or abrasions. Many viruses employ vectors, e.g. ticks, mosquitos or vampire bats to breach the barrier.
Conjunctiva and other mucous membranes - rather exposed site and relatively unprotected
Respiratory tract - In contrast to skin, the respiratory tract and all other mucosal surfaces possess sophisticated immune defense mechanisms, as well as non-specific inhibitory mechanisms (cilliated epithelium, mucus secretion, lower temperature) which viruses must overcome.
Gastrointestinal tract - a hostile environment; gastric acid, bile salts, etc. Viruses that spread by the GI tract must be adapted to this hostile environment.
Genitourinary tract - relatively less hostile than the above, but less frequently exposed to extraneous viruses (?)

7. Course of Viral Infection
Primary Replication
The place of primary replication is where the virus replicates after gaining initial entry into the host.
This frequently determines whether the infection will be localized at the site of entry or spread to become a systemic infection.
Systemic Spread
Apart from direct cell-to-cell contact, the virus may spread via the blood stream and the CNS.
Secondary Replication
Secondary replication takes place at susceptible organs/tissues following systemic spread.

8. Cell Tropism
Viral affinity for specific body tissues (tropism) is determined by
Cell receptors for virus.
Cell transcription factors that recognize viral promoters and enhancer sequences.
Ability of the cell to support virus replication.
Physical barriers.
Local temperature, pH, and oxygen tension enzymes and non-specific factors in body secretions.
Digestive enzymes and bile in the gastrointestinal tract that may inactivate some viruses.

9. Cell Damage
Viruses may replicate widely throughout the body without any disease symptoms if they do not cause significant cell damage or death.
Retroviruses do not generally cause cell death, being released from the cell by budding rather than by cell lysis, and cause persistent infections.
Conversely, Picorna viruses cause lysis and death of the cells in which they replicate, leading to fever and increased mucus secretion in the case of Rhinoviruses, paralysis or death (usually due to respiratory failure) for Poliovirus.

10. Immune Response
The immune response to the virus probably has the greatest impact on the outcome of infection.
In the most cases, the virus is cleared completely from the body and results in complete recovery.
In other infections, the immune response is unable to clear the virus completely and the virus persists.
In a number of infections, the immune response plays a major pathological role in the disease.
In general, cellular immunity plays the major role in clearing virus infection whereas humoral immunity protects against reinfection.

11. Immune Pathological Response
Enhanced viral injury could be due to one or a mixture of the following mechanisms;-
Increased secondary response to Tc cells (Cytotoxic T cells) e.g. HBV
Specific Antibody-dependentcell-mediated-cytotoxicity  ADCC or complement mediated cell lysis
Binding of un-neutralized virus-Ab complexes to cell surface Fc receptors, and thus increasing the number of cells infected e.g. Dengue haemorrhagic fever, HIV. An Fc receptor is a protein found on the surface of certain cells - including natural killer cells, macrophages, neutrophils, and mast cells - that contribute to the protective functions of the immune system. 
Immune complex deposition in organs such as the skin, brain or kidney e.g. rash of rubella and measles.

12. Viral Clearance or Persistence
The majority of viral infections are cleared but certain viruses may cause persistent infections. There are 2 types of chronic persistent infections.
True Latency - the virus remains completely latent following primary infection e.g. HSV, VZV (Varicella zoster virus). Its genome may be integrated into the cellular genome or exists as episomes. Episomes are the eukaryotic equivalent of bacterial plasmids. In general, in eukaryotes, episomes are closed circular DNA molecules that are replicated in the nucleus. Viruses are the most common examples of this, such as herpesviruses, adenoviruses, and polyomaviruses.
Persistence - the virus replicates continuously in the body at a very low level e.g. HIV, HBV, CMV, EBV.

13. Mechanisms of Viral Persistence
antigenic variation
immune tolerance, causing a reduced response to an antigen, may be due to genetic factors, pre-natal infection, molecular mimicry
restricted gene expression
down-regulation of MHC class I expression, resulting in lack of recognition of infected cells e.g. Adenoviruses
down-regulation of accessory molecules involved in immune recognition e.g. LFA-3 and ICAM-1 by EBV.
infection of immuno privileged sites within the body e.g. HSV in sensory ganglia in the CNS
direct infection of the cells of the immune system itself e.g. Herpes viruses, Retroviruses (HIV) - often resulting in immunosuppression.

14. Pathogenesis: Cycle of infection
Primary site replication
Spread (not all viruses)
Secondary site replication (not all viruses)
Shedding, transmission

15. Viral pathogenesis
From Medical Microbiology, 5th ed., Murray, Rosenthal & Pfaller, Mosby Inc., 2005, Fig. 49-1

16. Routes of entry and shedding
Portals of entry of viruses into the host, and sites of shedding from the host. (From Fields Virology, 4th ed, Knipe & Howley, eds, Lippincott Williams & Wilkins, 2001, Figure 9-2)

17. Mousepox pathogenesis
The pathogenesis of mouse-pox (ectromelia). (From Fields Virology, 4th ed, Knipe & Howley, eds, Lippincott Williams & Wilkins, 2001, Figure 9-6)

18. Modes of infection
From Medical Microbiology, 5th ed., Murray, Rosenthal & Pfaller, Mosby Inc., 2005, Fig. 49-3

19. Plaque assay (the real thing) vaccinia
Fields Virology, 4th ed, Knipe & Howley, eds, Lippincott Williams & Wilkins, 2001, Fig. 2-5

20. Vaccinia temperature sensitive, drug resistant mutant
Fields Virology, 4th ed, Knipe & Howley, eds, Lippincott Williams & Wilkins, 2001, Fig. 2-5

21. Examples of Viral Pathogenesis

22. Rubella
Transmitted by the respiratory route and replicates upper/lower respiratory tract and then local lymphoid tissues.
Following an incubation period of 2 weeks, a viremia occurs and the virus spreads throughout the body.
Clinical Features:-
maculopapular rash due to immune complex deposition
lymphadenopathy
fever
arthropathy (up to 60% of cases)

23. Rubella infection during pregnancy
Rubella virus enters the fetus during the maternal viremic phase through the placenta.
The damage to the fetus seems to involve all germ layers and results from rapid death of some cells and persistent viral infection in others.
Preconception Risks
0-12 weeks 100% risk of fetus being congenitally infected
  resulting in major congenital  abnormalities.
Spontaneous abortion occurs in 20% of cases.
13-16 weeks deafness and retinopathy 15%
after 16 weeks normal  development, slight risk of  deafness and retinopathy

24. Herpes Simplex Virus
HSV is spread by contact, as the virus is shed in saliva, tears, genital and other secretions.
Primary infection is usually trivial or subclinical in most individuals. It is a disease mainly of very young children i.e. those below 5 years.
About 10% of the population acquires HSV infection through the genital route and the risk is concentrated in young adulthood.
Following primary infection, 45% of orally infected individuals and 60% of patients with genital herpes will experience recurrences.
The actual frequency of recurrences varies widely between individuals. The mean number of episodes per year is about 1.6.

25. Pathogenesis
During the primary infection, HSV spreads locally and a short-lived viraemia occurs, whereby the virus is disseminated in the body. Spread to the to craniospinal ganglia occurs.
The virus then establishes latency in the craniospinal ganglia.
The exact mechanism of latency is not known, it may be true latency where there is no viral replication or viral persistence where there is a low level of viral replication.
Reactivation - It is well known that many triggers can provoke a recurrence. These include physical or psychological stress, infection; especially pneumococcal and meningococcal, fever, irradiation; including sunlight, and menstruation.

26. Clinical Manifestations
HSV is involved in a variety of clinical manifestations which includes ;-
1. Acute gingivostomatitis
2. Herpes Labialis (cold sore)
3. Ocular Herpes
4. Herpes Genitalis
5. Other forms of cutaneous herpes
7. Meningitis
8. Encephalitis
9. Neonatal herpes

27. Dengue (1)
Dengue  is the biggest arbovirus problem in the world today  with over 2 million cases per year. Dengue is found in SE Asia, Africa and the Caribbean and S America.
Flavivirus, 4 serotypes, transmitted by Aedes mosquitoes which reside in water-filled containers.
Human infections arise from a human-mosquitoe-human cycle
Classically, dengue presents with a high fever, lymphadenopathy, myalgia, bone and joint pains, headache, and a maculopapular rash.

28. Distribution of Dengue

29. Man-Arthropod-Man Cycle

30. Dengue (2)
Severe cases may present with haemorrhagic fever and shock with a mortality of 5-10%. (Dengue haemorrhagic fever or Dengue shock syndrome.)
Dengue haemorrhagic fever and shock syndrome appear most often (90%) in patients previously infected by a different serotype of dengue, thus suggesting an immuno-pathological mechanism.
Antibody-dependent enhancement - Binding of heterotypic antibodies to the virus, and subsequent infection of macrophages with Fc receptors.

31. Hepatitis B Virus 28

32. Hepatitis B - Clinical Features
Incubation period: Average days
Range days
Clinical illness (jaundice): <5 yrs, <10% yrs, 30%-50%
Acute case-fatality rate: 0.5%-1%
Chronic infection: <5 yrs, 30%-90% yrs, 2%-10%
Premature mortality from chronic liver disease: 15%-25% 29

33. Outcome of Hepatitis B Virus Infection
by Age at Infection
100
100 80
Chronic Infection (%) 80 60 60
Chronic Infection
Symptomatic Infection (%) 40
Chronic Infection (%) 40 20 20
Symptomatic Infection
Birth
1-6 months
7-12 months
1-4 years
Older Children
and Adults
Age at Infection 34

34. Spectrum of Chronic Hepatitis B Diseases
1. Chronic Persistent Hepatitis - asymptomatic
2. Chronic Active Hepatitis -symptomatic exacerbations of hepatitis
3. Cirrhosis of Liver
4. Hepatocellular Carcinoma

35. HIV Pathogenesis
The profound immunosuppression seen in AIDS is due to the depletion of T4 helper lymphocytes.
In the immediate period following exposure, HIV is present at a high level in the blood (as detected by HIV Antigen and HIV- RNA assays).
It then settles down to a certain low level (set-point) during the incubation period. During the incubation period, there is a massive turnover of CD4 cells, whereby CD4 cells killed by HIV are replaced efficiently.
Eventually, the immune system succumbs and AIDS develop when killed CD4 cells can no longer be replaced (witnessed by high HIV-RNA, HIV-antigen, and low CD4 counts).

37. HIV half-lives
Activated cells that become infected with HIV produce virus immediately and die within one to two days.
Production of virus by short-lived, activated cells accounts for the vast majority of virus present in the plasma.
The time required to complete a single HIV life-cycle is approximately 1.5 days.
Resting cells that become infected produce virus only after immune stimulation; these cells have a half-life of at least 5-6 months.
Some cells are infected with defective virus that cannot complete the virus life-cycle. Such cells are very long lived, and have an estimated half-life of approximately three to six months.
Such long-lived cell populations present a major challenge for anti-retroviral therapy.

39. Summary
Viral Pathogenesis depends on the complex interplay of a large number of viral and host factors.
Viral factors include cell tropism and cellular pathogenesis.
The immune response is the most important host factor, as it determines whether the virus is cleared or not.
Sometimes, the immune response itself is responsible for the damage (Auto immune responses).
Cycle of infection
Effects on cells (Abortive, lytic, persistent, latent, transforming infections
Effects on the organism
Genetics (Mutation, genotype, phenotype, reversion, recombination, selection