VIROLOGY

THE NATURE OF VIRUSES

I. BIOLOGICAL PROPERTIES
A. NUCLEIC ACID--RNA OR DNA
B. PROTEIN SHELL-CAPSID
C. + OR - ENVELOPE
D. MULTIPLY ONLY IN LIVING CELLS--THE HOST
1. ALL VIRUSES REQUIRE ENERGY
2. MAY REQUIRE REPLICATION, TRANSCRIPTION FUNCTIONS
3. ALL REQUIRE TRANSLATION FUNCTIONS
4. SELF ASSEMBLE
E. PARASITES AT THE MOLECULAR LEVEL
F. CAUSE A VARIETY OF INFECTIOUS DISEASES
G. MORTALITY--SMALLPOX, AIDS & MORBIDITY--HERPES, MUMPS
H. MODEL SYSTEMS FOR MOLECULAR BIOLOGY (EUKARYOTIC CELL)
II. PHYSICAL PROPERTIES
A. THE VIRION--MATURE VIRUS
1. NUCLEIC ACID--RNA OR DNA
2. PROTEIN SHELL-CAPSID
3. + OR - ENVELOPE
B. SOME IN PARACRYSTALLINE FORM--TMV, POLIO
C. SUBVIRAL PARTICLES
III. VIRUS VS. VIRION
IV. ORIGIN OF VIRUSES
A. PROBABLY DERIVED FROM HOST GENETIC MATERIAL
[EG., PLASMIDS, BACTERIOCINS, ETC.]
B. RNA VIRUSES MAY BE VERY OLD
[APPEAR TO BE LARGE SUPERFAMILIES]
C. POXVIRUSES MAY BE DERIVED FROM NUCLEI
V. HISTORY
1798--JENNER
1890S--IWANOWSKI, BEIJERINCK, LOFFLER & FROSCH
1900--REED; 1911--ROUS
1915--TWORT & d’HERELLE
1933--SHOPE
1935--STANLEY
1952--HERSEY & CHASE
1970S--GAJDUSEK, PRUSINER & DIENER
1976--FIERS
1977--SANGER
1970S--TEMIN, BALTIMORE, STEPHLEN, ERIKSON, OTHERS
1983--MONTAGNIER & GALLO
1980S--SEQUENCING OF MANY VIRAL GENOMES
FILTRATION--1890
BACTERIA-FREE FILTRATES
ELECTRON MICROSCOPE--ca. 1940
RADIOACTIVITY--1940S
ULTRACENTRIFUGE--1940S
CHROMATOGRAPHY & ELECTROPHORESIS --1950S
CELL CULTURE--1950S
RESTRICTION ENDONUCLEASES & DNA SEQUENCING--1970S
PCR & CLONING – 1970-90S
VI. METHODS OF STUDY
A. ASSAYS
1. PHYSICAL (EM) COUNTING
HIGHER COUNTS DUE TO COUNTING
DEFECTIVE PARTICLES
2. BIOLOGICAL ASSAYS
a. PLAQUE FORMATION
b. FOCI FORMATION
c. COMPLEMENT FIXATION
d. HEMAGGLUTINATION & HEMAGGLUTINATION
INHIBITION
B. ONE-STEP GROWTH CURVE
1. TERMS
a. MOI--MULTIPLICITY OF INFECTION---10
b. LATENT PERIOD-----6 HOURS
c. ECLIPSE PERIOD----4 HOURS
d. BURST SIZE-----1000
2. PLOT

1000 |
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100 |
|
moi 10 |
|
1 |
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0.1 |
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0.01 |_____________________________________________

0 1 2 3 4 5 6 7 8 9
TIME (hours)

C. TISSUE & CELL CULTURE

D. MONOLAYERS & CELL SUSPENSIONS (SPINNER CULTURES)
E. VIRAL PURIFICATION
1. DIFFERENTIAL CENTRIFUGATION
2. ZONAL CENTRIFUGATION
3. ULTRAFILTRATION
4. DIFFERENTIAL PRECIPITATION
F. ANALYSIS OF COMPONENTS
1. SDS TREATMENT & ELECTROPHORESIS FOR PROTEINS
2. PHENOL EXTRACTION & ELECTROPHORESIS FOR
NUCLEIC ACIDS
3. RESTRICTION MAPPING
4. USE OF RADIOISOTOPES
a. PROTEINS--14C, 3H, AND 35S
b. NUCLEIC ACID--14C, 3H, AND 32P
5. AUTORADIOGRAPHY USING X-RAY FILM
G. CLONING GENES & GENOMES (BOTH DNA & RNA VIRUSES)
H. DNA SEQUENCING (BOTH DNA & RNA VIRUSES)
I. PCR AND RT-PCR (SPECIFIC PRIMERS)
VII. STRUCTURE AND COMPONENTS
A. THE GENOME--PACKED IN NUCLEOCAPSID
1. DNA
a. STRANDEDNESS
b. FORM
CIRCULAR--PAPOVAVIRUSES
LINEAR--MOST ANIMAL VIRUSES
TERMINAL REPETITION
TERMINAL PROTEIN--ADENOVIRUS
TERMINAL CROSSLINKING—POXVIRUS
c. SEGMENTATION (PLANT VIRUSES)
2. RNA
a. STRANDEDNESS
b. POLARITY
1) + OR - OR AMBISENSE
2) mRNA IS ALWAYS +
c. SEGMENTATION
INFLUENZA VIRUS--8 STRANDS
REOVIRUS--10 OR 11
ARENAVIRUS--2; BUNYAVIRUS--3
d. TERMINAL CAPS AND POLY A
e. TERMINAL PROTEIN--POLIOVIRUS
f. TERMINAL REPETITION
B. CAPSID--ENTIRE PROTEIN SHELL SURROUNDING NA
1. STRUCTURE
2. CAPSOMERS--SUBUNITS OF CAPSID
3. PENTONS AT VERTICES (ALWAYS 12)
4. HEXONS ON FACES AND EDGES
5. STRUCTURAL UNITS
6. SUBUNITS OF CAPSOMERS--POLYPEPTIDES
7. FUNCTIONS
a. TRANSPORT OF NA
b. PROTECTION OF NA
c. CONDENSATION OF NA
d. SPECIFICITY OF ATTACHMENT
8. SYMMETRY
a. SPHERICAL OR ICOSAHEDRAL
20 SIDED, 12 VERTICES AND 30 EDGES
5-3-2 FOLD AXES OF SYMMETRY
T--TRIANGULATION NUMBER & COMPLEXITY
C=10T + 2; cu=60T; [C = # of
CAPSOMERS; cu = # of CHEMICAL UNITS]
b. HELICAL
USUALLY IDENTICAL SMALL SUBUNITS
COIL SS RNA (USUALLY) IN HELIX
C. ENVELOPE--MEMBRANE FROM HOST CELL
a. LIPID BILAYER
b. SENSITIVE TO ETHER AND OTHER ORGANICS
c. IN GENERAL-SENSITIVE TO THE ENVIRONMENT
d. MORE COMPLEX
e. COMPONENTS
ENZYMES, tRNAs, RIBOSOMES
GLYCOPROTEIN SPIKES--PEPLOMERS
f. SYMMETRY OF NUCLEOCAPSID
VIII. CLASSIFICATION (SEE HANDOUTS FOR HUMAN VIRUSES)
A. HOST
1. ANIMAL (VERTEBRATES, INVERTEBRATES, FUNGI)
2. PLANT
3. BACTERIA--BACTERIOPHAGE
B. COMPONENTS AND MORPHOLOGY
1. NUCLEIC ACID
a. DNA OR RNA
b. STRANDEDNESS AND POLARITY
2. SYMMETRY OF CAPSID
3. SIZE
4. PRESENCE OF ENVELOPE
C. METHOD OR PRODUCING mRNA--BALTIMORE’S SCHEME
1. ds DNA
2. ss DNA
3. ds RNA
4. ss + RNA
5. ss - RNA
6. ss + RNA---> ds DNA ---> + RNA(mRNA)
7. ds DNA---> + RNA(mRNA)---> ds DNA
D. RESOURCES
1. WEBSITE: http://www.ncbi.nlm.nih.gov/ICTV
2. THE INTERNATIONAL COMMITTEE ON TAXONOMY OF
VIRUSES
3. COMMITTEE MEETS ANNUALLY (SEVERAL TIMES)
a. PROPOSALS ARE PUBLISHED
b. BOOK PUBLISHED EVERY FEW YEARS
"VIRUS TAXONOMY"
8TH EDITION IN 2005
4. GENOME SEQUENCES:
http://www.ncbi.nlm.nih.gov
CLICK ON "TAXONOMY"
GIVES YOU THE TAXONOMY BROWSER
CLICK ON VIRUSES AT LEFT
GIVES A LONG LIST OF SEQUENCED VIRAL
GENOMES
CLICK ON VIRUS NAME
GIVES A GENBANK ENTRY WITH THE
NUCLEOTIDE SEQUENCE