Competency M6 - Microbiology
Apply principles of the biology of microorganisms in normal physiology and disease
to explain the etiology of disease, identify preventive measures, and predict response
to therapies.
Virology
Introduction
The main subjects of discussion in the preclinical virology section include structural
features of viral particles, criteria for classification, mechanisms of virus replication,
virus genetics, mechanisms for emergence of "new viruses", viral aspects of
pathogenesis and host defense mechanisms, antiviral therapy and antiviral vaccines,
principles in diagnosis of a viral disease. Selected viruses and virus groups will be
discussed in more detail as models for viruses causing latent infections (Herpes
viruses), chronic infections (Hepatitis viruses B,C,D), slow infections (HIV), cancer
(RNA and DNA tumor viruses) and epidemics (Influenza epidemiology)
Learning Objectives and Lecture Topics
Learning Objectives 1: Apply the principles of pathogen structure, genomics,
life-cycle, transmission, and host response to microorganism infection, to
understand the pathogenesis of infectious diseases.
A. Viral Structure and classification
a.
Introduction
1. Viral characteristics.
2. Pathological effects of viral infection on cells.
b.
Structure and Morphology
1. Virion morphology.
2. Nucleocapsid: structure, composition and function.
3. Viral proteins.
4. Viral genome: type of nucleic acid, control elements for
replication and transcription.
5. Envelope: structure, components, biological functions.
c. Classification
1. Criteria for classification into families, genera, species.
References A (a-c): Murray et al., Medical Microbiology, Elsevier Mosby, 5th ed.,
pp. 47-53.
Lippincot’s illustrated reviews: Microbiology, Lippincott’s Wiliams and wilkins, 3rd
ed., PP 233-235.
B. Viral genetics and replication
a.
Virus Multiplication
1. Early phase: adsorption, penetration, uncoating.
2. Synthesis phase: genome transcription, translation into
viral proteins.
3. DNA viruses: double-strand genome replication.
4. Replication of the viral genome: double-strand gapped
genome, single strand genome.
5. Replication of viral genome: RNA viruses: single strand
sense or antisense genome, segmented genome,
retroviruses.
6. Late phase: morphogenesis; release from infected cells.
b.
Genetic Aspects of viral replication
1. Genetic alterations: mutation, recombination,
reassortment.
2. Non-genetic alterations: complementation, phenotypic
mixing.
References B (a-b): Murray et al., Medical Microbiology, Elsevier Mosby, 5th ed.,
pp. 53-65.
Lippincot’s illustrated reviews: Microbiology, Lippincott’s Wiliams and wilkins, 3rd
ed., PP 235-244.
C. Viral pathogenesis and host defense mechanisms
a.
Pathogenesis
1. Types of viral infections.
2. Steps in viral spread in the body.
3. Mechanisms of disease production.
4. Molecular determinants of viral virulence.
5. Viral transmission and epidemiology.
b.
Host response to viral infection:
1. Nonspecific host defense mechanisms: Innateimmunity.
2. Immune-specific mechanisms: Humoral immunity.
3. Immune-specific mechanisms: Cell mediated immunity.
4. Interferon
References C (a-b): Murray et al., Medical Microbiology, Elsevier Mosby, 5th ed.,
pp.121-133, 143-149, 491-502.
References C (a-b): Richard A. Harvey et al., Lippincot’s illustrated reviews:
Microbiology, Lippincott’s Wiliams and wilkins, 3rd ed., PP 15-18.
Learning Objectives 2: Apply the principles of microbial structure and biology,
host–pathogen and pathogen–population interactions to the prevention,
diagnosis and treatment of infectious disease
D. Viruses causing latent infections: Herpes viruses
a. Introduction and History
1. Origin of name
2. Discovery
b.
Classification, Evolution
1. Eight recognized human herpes viruses.
2. unique features of herpes viruses.
3. properties distinguishing human herpes viruses.
c. Transmission and Epidemiology
d. Structural characteristics
1. Viral Morphology.
2. Genome organization.
e. Life cycle
3. Replication
4. Regulation of transcription-translation.
f. Molecular mechanisms of pathogenesis
5. Latency and reactivation.
6. Immune response.
g. Diagnostics
7. Symptoms
8. Laboratory diagnosis.
h. Treatment
1. Prevention
2. Antivirals
3. Vaccines
References D (a-f): Murray et al., Medical Microbiology, Elsevier Mosby, 5th ed.,
pp.541-564
Lippincot’s illustrated reviews: Microbiology, Lippincott’s Wiliams and wilkins, 3rd
ed., PP 255-272.
E. Viruses causing chronic infections: Hepatitis viruses B, C, D
a. Introduction and History
4. Origin of name
5. Introduction - Liver functions
6. Discovery
b. Classification, Evolution
1. General aspects of viral hepatitis caused by 5 types of
recognized hepatitis viruses (A-E).
c. Transmission and Epidemiology
d. Structural characteristics
1. Viral Morphology.
2. Genome organization.
e. Life cycle
1. Replication
2. Regulation of transcription-translation.
f. Molecular mechanisms of pathogenesis
1. Detailed discussion of each of the 5 types of
hepatitis viruses causing chronic infection.
2. Immune response
3. Hepatitis viruses increase the risk of hepatocellular
carcinoma.
g. Diagnostics
1. Symptoms
2. laboratory diagnosis
h. “New” hepatitis viruses (E, G)
i. Treatment
1. Prevention
2. Antivirals
3. Vaccines
References E (a-i): Murray et al., Medical Microbiology, Elsevier Mosby, 5th ed.,
pp. 675-689.
References E (a-i): Lippincot’s illustrated reviews: Microbiology, Lippincott’s
Wiliams and wilkins, 3rd ed., PP 273-282, 286-287, 289-291.
F. Virus with rapid evolution Influenza viruses
a. Introduction and History
1. Origin of name
2. Discovery
b. Classification, Evolution
c. Transmission and Epidemiology
d. Structural characteristics
1. Viral Morphology.
2. Genome organization.
e. Life cycle
1. Replication
2. Regulation of transcription-translation.
f. Molecular mechanisms of pathogenesis
g. Diagnostics
1. Symptoms
2. Laboratory diagnosis.
h. Treatment
1. Prevention
2. Antivirals
3. Vaccines
References F (a-h): Murray et al., Medical Microbiology, Elsevier Mosby, 5th ed.,
pp. 609-617
Lippincot’s illustrated reviews: Microbiology, Lippincott’s Wiliams and wilkins, 3rd
ed., PP 315-321.
i. Other Respiratory viruses – Adenovirus, RSV, Parainfluenza.
Corona and Rhinovirus
References F (i): Murray et al., Medical Microbiology, Elsevier Mosby, 5th ed.,
pp. 597, 603-604, 606-608, 591-594, 697-699.
684Lippincot’s illustrated reviews: Microbiology, Lippincott’s Wiliams and wilkins,
3rd ed., PP 250-252, 314-315, 362, 291, 286.
G. Oncogenic Retroviruses
a. Introduction and History
1. Oncogenes and Tumor Suppressor genes.
2. Origin of name.
3. Discovery
b. Classification, Evolution
1. General aspects of acute and slow transforming
viruses.
c. Transmission and Epidemiology
1. Exogenous and Endogenous viruses.
d. Structural characteristics
1. Viral Morphology.
2. Genome organization.
e. Life cycle
1. Replication
2. Regulation of transcription-translation.
f. Molecular mechanisms of pathogenesis
1. Mechanisms of viral oncogenicity.
2. Acute oncogenic viruses- oncogene transduction.
3. Slow oncogenic viruses – insertional mutagenesis.
g. Diagnostics
1. Symptoms
2. Laboratory diagnosis.
h. Treatment
1. Prevention
2. Antivirals
3. Vaccines
References G (a-h): Murray et al., Medical Microbiology, Elsevier Mosby, 5th ed.,
pp. 671-673
Lippincot’s illustrated reviews: Microbiology, Lippincott’s Wiliams and wilkins, 3rd
ed., PP 306-30.
H. Virus inducing slow infection – Human immunodeficiency virus
(HIV)
a. Introduction and History
1. Origin of name
2. Discovery
b. Transmission and Epidemiology
c. Structural characteristics
1. Viral Morphology.
2. HIV receptors and co-receptors.
3. Genome organization and viral gene function.
d. Life cycle
1. Replication
2. HIV infection of CD4+ lymphocytes and
macrophages.
3. Cell destruction and immunosuppressive
interactions.
4. Genetic variations.
5. Viral latency and activation.
e. Molecular mechanisms of pathogenesis
f. Clinical Features
1. Chronology of HIV induced disease.
2. Asymptomatic and symptomatic HIV infection
3. Symptoms
g. Diagnostics
1. Clinical Diagnosis.
2. Laboratory diagnosis.
h. Treatment
1. Prevention
2. Antivirals
3. Vaccines: Obstacles in the development of vaccines
References H (a-h): Murray et al., Medical Microbiology, Elsevier Mosby, 5th ed.,
pp 657-670.
References H (a-h): Richard A. Harvey et al., Lippincot’s illustrated reviews:
Microbiology, Lippincott’s Wiliams and wilkins, 3rd ed., PP 293-306.
I. DNA Oncogenic Viruses
a. Introduction
1. Tumor suppressor genes.
2. Mechanisms of tumor progression.
3. General features of oncogenesis by DNA tumor
viruses with emphasis on viruses causing cancer in
humans.
b. Human papillomaviruses
1. Types and clinical syndromes.
2. High and low risk HPV types.
3. Genome structure.
4. Viral oncogenes and mechanisms of oncogenesis.
References I(b): Murray et al., Medical Microbiology, Elsevier Mosby, 5th ed., pp.
523-528.
References I (b): Richard A. Harvey et al., Lippincot’s illustrated reviews:
Microbiology, Lippincott’s Wiliams and wilkins, 3rd ed., PP 245-250.
c. Oncogenic human herpesviruses
1. Classification and oncogenic potential.
2. Epstein-Barr virus (EBV) - role in African Burkitt's
lymphoma and nasopharyngeal carcinoma.
3. Human hepesvirus 8 (HHV8) - role in Kaposi’s
Sarcoma.
References I (c): Murray et al., Medical Microbiology, Elsevier Mosby, 5th ed., pp
553-558; 562-563.
References I (c): Richard A. Harvey et al., Lippincot’s illustrated reviews:
Microbiology, Lippincott’s Wiliams and wilkins, 3rd ed., PP 267-269.
d. Human Hepatitis B
4. Classification and oncogenic potential.
References I(d): Murray et al., Medical Microbiology, Elsevier Mosby, 5th ed., pp
684
References I (d): Richard A. Harvey et al., Lippincot’s illustrated reviews:
Microbiology, Lippincott’s Wiliams and wilkins, 3rd ed., PP 278-279.
J. Protein Infectious Agents - Prions
a. Introduction and History
1. Nature of the infectious agent – the Prion Only
theory.
2. Origin of name.
3. Discovery
b. Classification, Evolution
c. Transmission and Epidemiology
d. Structural characteristics
1. Prion Structure.
2. Genome organization.
e. Life cycle
1. Replication
2. Regulation of transcription-translation.
f. Molecular mechanisms of pathogenesis
1. Creutzfeld Jacob Disease (CJD).
2. Gerstmann-Straussler-Scheimker disease (GSS).
3. Fatal familial insomnia (FFI).
4. New variant CJD.
5. Mad Cow Disease.
g. Diagnostics
1. Symptoms
2. Laboratory diagnosis.
h. Treatment
1. Prevention
2. Antivirals
References J (a-h): Murray et al., Medical Microbiology, Elsevier Mosby, 5th ed.,
pp. 691-995
Lippincot’s illustrated reviews: Microbiology, Lippincott’s Wiliams and wilkins, 3rd
ed., PP 327-330.
Learning Objectives 3: Apply the knowledge of microbial genetics and biology,
and principles of epidemiology to understand the causes underlying the
emergence of new microorganisms and microbial diseases, and the outbreak of
epidemics and pandemics.
K. Zoonotic viruses-Dengue, West Nile, Chikungunia, Yellow Fever
References K: Murray et al., Medical Microbiology, Mosby Science Company, 5th
ed., pp. 442-444+ relevant manuscripts will be given during class
L. Mechanisms for emergence of "new viruses" (emerging viruses)
a. Introduction
1. Molecular mechanisms for virus evolution.
b. General interactions of hosts and viruses
1. Infiltration and spread of viruses.
2. Factors that influence virus infiltration and spread.
References L(a-b): Principles of Virology, Flint et al., Eds. ASM Press 2000,
Chapter 20 (optional)
c. Modern evolution of viruses- SARS as an example:
References L(c): relevant manuscripts will be given during class
M. Immunization against viral infection
a. Introduction
b. Inactivated Vaccines: types, modes of inactivation,
advantages/disadvantages
c. Live attenuated vaccines: types, modes of attenuation,
advantages/disadvantages
d. New Approaches:
1. Subunit vaccines, synthetic peptides, production of
recombinant antigens in bacteria, yeast or eukaryotic
cells. Anti-idiotype antibodies as vaccine.
2. New approaches for attenuated vaccines: genetic
reassortment - infulenza, directed mutagenesis;
genetic immunization (naked DNA).
e. Methods of vaccine production
f. Towards an anti-HIV Vaccine
References M (a-f): Murray et al., Medical Microbiology, Elsevier Mosby, 5th ed .,
pp 159-167
Lippincot’s illustrated reviews: Microbiology, Lippincott’s Wiliams and wilkins, 3rd
ed., PP 33, 36, 39-40, 285
N. Anti-viral agents
a. Introduction
1. Why do we need antiviral agents ? aren’t vaccines
enough?
2. Concerns
b. Anti-HIV compounds
1. RT inhibitors - DNA synthesis.
2. RT inhibitors- Nucleoside RT inhibitors (NRTIs).
3. Tenofovir A nucleotide RT inhibitor (NtRTI).
4. Non-nucleoside RT inhibitors (NNRTIs).
5. Protein processing inhibitors.
6. Comparison of HIV protease substrate with protease
inhibitors.
7. Novel Anti-HIV compounds.
8. HIV envelope spike, HIV–Inhibition of viral
attachment, HIV co-receptor antagonists, HIV
fusion inhibitor, Anti-HIV compounds, DNA
integration inhibitor.
9. Highly active anti-retroviral therapies (HAART).
Lippincot’s illustrated reviews: Microbiology, Lippincott’s Wiliams and wilkins, 3rd
ed., PP 303-305.
c. Anti-Herpes compounds
1. HSV-TK
2. Clinical application of acyclovir.
3. Other anti-HSV drugs.
d. Anti-influenza drugs
1. Uncoating-Influenza.
2. M2 inhibitors.
3. Neuraminidase inhibitors.
e. Anti-hepatitis B drugs
1. A summary of the resistance rates for lamivudine,
adefovir dipivoxil, and entecavir.
f. General Action of interferons
1. Recombinant interferon α.
2. Clinical indications.
References N (a –f): Murray et al., Medical Microbiology, Elsevier Mosby, 5th ed .,
pp 503-511
Lippincot’s illustrated reviews: Microbiology, Lippincott’s Wiliams and wilkins, 3rd
ed., PP 45-47
O. Principles of lab diagnosis of viral infection
a. Methods for virus isolation and detection
1. Specimen collection and tansport to the lab.
2. Biological methods for viral isolation and
identification: cell cultures, cytopathogenic effect
(CPE),hemagglutination (HA),
Hemadsobtion (Had ).
3. Transformation
4. Direct detection of viral Ag in a specimen: ELISA,
Immunofluorescence test.
5. Direct detection of viral genome in a specimen:
PCR.
b. Serological methods for detection of viral infection
a. Detection of specific IgM antibodies : IgM capture test
b.
Detection of seroconversion:
Methods for detection of seroconversion: ELISA,
neutralization test (NT , hemagglutination inhibition test (HI),
WB assay- Confirmation test for HIV infection.
References O (a –b): Murray et al., Medical Microbiology, Elsevier Mosby, 5th ed .,
513-519