Viruses in history I

1
Viruses in history - I

• Virology as a science is approx. 100 years old -
  but virus diseases have been known for millennia
• In Ancient Greece ios a poisonous substance
• In Latin virus a poisonous malodorous substance
• Mesopotamian laws concerning rabid dogs date from
  before 1,000 B.C.E
• Smallpox was endemic in the Ganges river basin by
  the 5th century B.C.E
• Hippocrates first attempted to rationalize
  plagues - concluded they were caused by small
  animals in the air too small for human vision

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Viruses in history II

• In 1494 Frascatero advanced the theory that
  disease was caused by seminaria, which
  spontaneously arose from dead material
• Unknowingly, viruses were well characterized by
  the 16th century due to striping patterns on
  tulips
• A case of economic advantage (a broken tulip
  was worth 3x more than a Rembrandt masterpiece)
• The birth of microbiology occurred by the
  invention of the microscope - notably van
  Leuwenhoek wee animalcules first seen in the
  17th century. But how did these microorganisms
  arise?
• Jacob Henle (1840) was the first to have the idea
  of a microorganism too small to be seen by a
  microscope
• Spontaneous generation of life was finally
  refuted by Louis Pasteur in the mid 19th century
  - disease was not caused by poisonous air
  (miasma) by by specific microorganisms. Pasteurs
  famous successes were anthrax (a bacterium) and
  rabies (a virus)

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Kochs postulates

• In 1890 Robert Koch explained the following
• The parasite can be encountered in all cases
  under those conditions which correspond to the
  pathological changes and the clinical course of
  the disease - the microbe is always there when
  there is disease
• The pathogen may not occur incidentally as a
  non-pathogenic parasite in any other disease the
  microbe is never anywhere else - it is specific
• The parasite must be isolated and bred in
  adequate numbers in pure culture and must be
  able. the microbe can be cultured
• To cause the disease anew. the culture must
  cause disease in a new host
• - for bacterial disease

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The germ theory

• Pasteur, Koch and Joseph Lister were the founded
  of the germ theory of disease in the 19th century
  - but at this point all identified pathogens were
  bacteria (and fungi)
• The germ theory placed a study of infectious
  disease on secure scientific footing
• However a failure of the existing paradigms led
  to the identification of submicroscopic pathogens
  --- viruses

Semmelweis 1840s Vienna. Childbirth mortality
dropped from 29 to 1 on introduction of hand
washing and chlorine disinfection
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The birth of Virology

• Adolf Mayer (1876) took the sap from infected
  tobacco plants and transmitted it to healthy
  plants - note isolation of the germ was not
  achieved and Mayer considered his experiment
  unsuccessful
• A case of (great) economic disadvantage
• Failed Kochs postulates
• Dimitri Ivanovski (1892) first noted that the
  infection was not retained by a filter
  (Chamberland filter) - again Ivanovski thought he
  was unsuccessful and blamed a cracked filter on
  his failure
• Martinus Beijerinck (1897) achieved the same
  result, but was less able to accept defeat and
  concluded that his Contagium vividum fluidium
  in order to reproduced itself, must be
  incorporated into the living protoplasm of the
  cell, into whose reproduction it is, so to speak,
  passively drawn
• Friedrich Loeffler and Paul Frosch (1897)
  observed that Foot and Mouth Disease was also
  filterable - the first animal virus

Tobacco mosaic virus
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Kochs postulates as modified for viruses by
Rivers (1937)

• Isolation of the virus from diseased host
• Cultivation in host cells
• Proof of filterability
• Production of a comparable disease in the
  original animal host, or a related one
• Re-isolation of the virus
• Detection of a specific immune response to the
  virus

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What is a virus? I

• Serial transmission of TMV and FMDV by diluted
  extracts proved that the virus was not a toxin.
• Failure of the agents to propagate in solution,
  and dependence of host cells, showed they were
  distinct from bacteria.
• Were they liquids or particles? Biological or
  chemical?
• Early work on showed that TMV behaved like a
  protein (electrophoresis and raising of
  antibodies) and
• Eventually TMV was crystallized in 1935 by
  Wendell Stanley -- rods of constant diameter in
  hexagonal arrays - viruses can be analyzed
  according the the laws of chemistry, as well as
  biology
• and was seen by electron microscopy

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Bacteriophages

• Bacterial viruses first identified in 1915 by
  Frederick Twort and in 1917 by Felix dHerrelle -
  given the name bacteriophage (phage greek for
  eating)
• The modern era began with Max Delbrück, (a
  physicist) who promoted the genetic nature of
  phage
• In 1939 Ellis and Delbrück designed the one-step
  growth curve and defined the latent period of
  infection
• In 1941 they were joined by Salvador Luria (a
  geneticist) to form the Cold Spring Harbor phage
  group (WWII-1975) - pioneers of modern molecular
  biology

T-even phage
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2 classic experiments

• Hershey and Chase - T2 bacteriophage - 1952 - the
  Waring blender experiment
• Fraenkel-Conrat and Singer - Tobacco Mosaic Virus
  (TMV) - 1957
• These experiments (along with many others) laid
  the foundation of our understanding of nucleic
  acid as the genetic material of life

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Hershey/Chase experiment
T2 phage grown in E. coli and labeled with either
- 35S (as sulphate) - to label protein or -
32P (as phosphorous) - to label DNA Phage were
allowed to attach and infect, and then put into
the Waring blender The shear force of the
blender stripped away the phage components
attached to the surface, but did not affect
components that had penetrated the E. coli When
E. coli was centrifuged, 75 of the 35S was
removed from the cells, whereas only 15 of the
32P was removed i.e the DNA (and not the
protein) is carried into the cell and it the
carrier of viral heredity
From Introduction to Modern Virology, 5th ed
Dimmock et al. Blackwell
11
Fraenkel-Conrat/Singer experiment
Already known that TMV particles can be
dissociated, and reassembled into infectious
particles Also known that TMV (as with other
viruses) can exist as different strains (i.e
different symptoms in the host) Different
strains were dissociated and protein and RNA
isolated. The RNA of one strain was then
reassociated with the protein of another ( and
vice versa) The hybrid particles were then
inoculated into plants, and the disease outcome
matched the RNA and not the protein i.e RNA (and
not protein) is the genetic material Later
proven by the finding that purified RNA is
capable of initiating infection (under special
circumstances)
From Introduction to Modern Virology, 5th ed
Dimmock et al. Blackwell
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The development of animal virology

• The first human virus was identified in 1901
  (yellow fever) by Walter Reed and colleagues
• But a study of animal and human viruses was very
  slow due to the lack of an experimental system -
  need for single cells
• Use of embryonated eggs by the 1930s were of
  great value
• In the period 1948-55 animal virology finally
  became a laboratory science by the development of
  cell or tissue culture by Renato Dulbecco -
  plaque assay (1953)
• Other notable highlights of animal virology in
  the late 20th century include
• the breakdown of the central dogma of molecular
  biology by the finding of reverse transcriptase
  in retroviruses (Howard Temin and David
  Baltimore)
• the discovery of oncogenes, fundamental knowledge
  of gene regulation, transcription/translation,
  restriction mapping (Nathans expt.), DNA cloning

Poliovirus
SV40
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What is a virus ? II

• The fundamental characteristic is their absolute
  dependence on a living host organism for
  reproduction - they are obligate (intracellular)
  parasites
• They are small -- usually in the nanometer range
  - hence they are filterable and visible only by
  the electron microscope

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Diphtheria

• Corynebacterium diphtheriae (a bacteria) was
  originally identified as the causative agent of
  diphtheria, according to Kochs postulates
• Now known that disease per se caused by a
  bacterial toxin
• However, all virulent strains are lysogenic with
  a phage (b)
• The lysogenic phage is responsible for toxin
  production
• i.e the virus causes the disease
• A fundamental breakdown of Kochs postulates

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The size of viruses
From Principles of Virology Flint et al ASM Press
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What is a virus ? III

• A virus is a very small, infectious, obligate
  intracellular (molecular) parasite
• The virus genome comprises either DNA or RNA
• Within an appropriate host cell the viral genome
  is replicated and directs the synthesis, by
  cellular systems, of other viral components
• Progeny virions are formed by de novo assembly
  from newly synthesized components within the host
  cell
• A progeny virion assembled during the infectious
  cycle is the vehicle for transmission of the
  viral genome to the next host cell or organism,
  where its disassembly leads to the beginning of
  the next infectious cycle

But viruses dont actually do anything (see Box
1.5 in Flint)
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What is a virus ? IV

• A virus is an elementary biosystem that possesses
  some of the properties of living systems such a s
  having a genome and being able to adapt to
  changing environments
• However, viruses cannot capture or store free
  energy and they are not functionally active
  outside their host cells.
• A virus has both intrinsic properties (e.g. its
  size) and extrinsic properties (e.g. its host)
• Viruses are not living organisms however they
  can be considered to lead a borrowed life

It is important to discriminate between the
entity called a virus and the single, discrete
virus particle or virion
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Virus Classification I- the Baltimore
classification

• All viruses must produce mRNA, or () sense RNA
• A complementary strand of nucleic acid is ()
  sense
• The Baltimore classification has RNA as its
  central point
• Its principles are fundamental to an
  understanding of virus classification and genome
  replication, but it is rarely used as a
  classification system in its own right

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From Principles of Virology Flint et al ASM Press
20
Virus classification II -the Classical system

• This is a based on three principles -
• 1) that we are classifying the virus itself, not
  the host
• 2) the nucleic acid genome
• 3) the shared physical properties of the
  infectious agent (e.g capsid symmetry,
  dimensions, lipid envelope)

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Virus classification III -the genomic system

• More recently a precise ordering of viruses
  within and between families is possible based on
  DNA/RNA sequence
• By the year 2000 there were over 4000 viruses of
  plants, animals and bacteria - in 71 families, 9
  subfamilies and 164 genera

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RNA viruses
From Principles of Virology Flint et al ASM Press
23
DNA viruses
From Principles of Virology Flint et al ASM Press
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Virus taxonomy
Order virales e.g Mononegavirales Family virid
ae e.g. Orthomyxoviridae Herpesviridae Subfamily
virinae e.g. Alphaherpesvirinae Genus e.g.
influenzavirusA Simplexvirus Species e.g.
influenza A virus human herpesvirus1 Informally T
ype e.g. herpes simplex virus 1 Strain
e.g. influenza A/PR/8/34 SC16
In biology, binomial names are used. e.g Rattus
rattus, Saccharomyces cerevisiae In virology,
this does not happen Tobacco etch potyvirus
sounds OK Influenza A influenzavirus A does not!
Bacteriophage have their own rules
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The species concept in virus taxonomy

• How different is different enough to be something
  else?
• Species is the universally accepted term for
  the lowest taxonomic clustering of living
  organisms
• Taxonomy now ratified by the International
  Committee on Taxomony of Viruses (ICTV)
• Plant viruses are especially problematic
  (taxonomically-speaking)
• The Potyviridae - filamentous particles, 650-900
  nm, ve sense RNA, polyprotein
• 6 genera with initially very confusing biological
  properties, can now be classified based on
  sequence
• The animal Picornaviridae can be equally
  challenging

RNA viruses especially are not a single molecular
species, but must be viewed as a dynamic
population consisting of thousands of viral
mutants that are always present in a viral
clone This population is often referred to as a
viral quasi-species
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What is a virus species?

• a polythetic class of viruses that constitute a
  replicating lineage and occupy a particular
  ecological niche - as defined by ICTV in 1991

A polythetic class is defined as a class whose
members always have several properties in common,
although no single attribute is present in all of
its members -- allows for some degree of
fuzziness
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Classification based on serology

• A classification based on Diagnostic Virology
• Infectious bronchitis virus (IBV) of chickens
  - a coronavirus
• Three predominant virus types in US
• Massachusetts, Arkansas and Delaware
• No cross-protection (from antibodies) between
  these serotypes
• i.e. significant antigenic differences, but
  perhaps very little genetic or biological
  difference between these viruses

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How are viruses named?

• Based on
• - the disease they cause
• poliovirus, rabies virus
• - the type of disease
• murine leukemia virus
• - geographic locations
• Sendai virus, Coxsackie virus
• - their discovers
• Epstein-Barr virus
• - how they were originally thought to be
  contracted
• dengue virus (evil spirit), influenza virus
  (the influence of bad air)
• - combinations of the above
• Rous Sarcoma virus

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Sub-viral agents

• Satellites
• Contain nucleic acid
• Depend on co-infection with a helper virus
• May be encapsidated (satellite virus)
• Mostly in plants, can be human e.g. hepatitis
  delta virus
• If nucleic acid only virusoid
• Viroids
• Unencapsidated, small circular ssRNA molecules
  that replicate autonomously
• Only in plants, e.g. potato spindle tuber viroid
• Depend on host cell polII for replication, no
  protein or mRNA
• Prions
• No nucleic acid
• Infectious protein e.g. BSE

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Unifying principles

• All viruses package their genomes inside a
  particle that mediates transmission of the viral
  genome from host to host
• The viral genome contains the information for
  initiating and completing an infectious cycle
  within a susceptible, permissive cell. An
  infectious cycle includes attachment, and entry
  of the particle, decoding of genome information,
  translation of viral mRNA by host ribosomes,
  genome replication, and assembly and release of
  particles containing the genome
• All viruses are able to establish themselves in a
  host population so that virus survival is ensured

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Strategies for virus survival

• Finding and getting into a host cell. As viruses
  are obligate parasites they must find the right
  type of cell for their replication, they must
  invade that cell and get their genome to the site
  of replication.
• Making virus protein. All viruses are parasites
  of translation. The virus must make mRNA (unless
  it has a sense RNA genome already). Strategies
  must exist to synthesize mRNA.
• Making viral genomes. Many viral genomes are
  copied by the cells synthetic machinery in
  cooperation with viral proteins.
• Forming progeny virions. The virus genome, capsid
  (and envelope) proteins must be transported
  through the cell to the assembly site, and the
  correct information for assembly must be
  pre-programmed.
• Spread within and between hosts. To ensure
  survival the virus must propagate itself in new
  cells.
• Overcoming host defences.The host defends itself
  against nonself. Viruses have evolved ways to
  fight back.

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Three problems every virus must solve

• 1 How to reproduce during its visit inside
  the cell. How to a) copy its genetic
  information and b) produce mRNA for protein
  production
• 2 How to spread from one individual to another
• 3 How to evade the host defenses. This need
  not be complete.
• Viral diseases are the (usually unintended)
  consequences of the way each virus has chosen to
  solve these three problems.

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Our top 13 virusesanimal plant phage

• 1      Retrovirus (HIV)
• 2      Orthomyxovirus (influenza)
• 3      Picornavirus superfamily (poliovirus,
  potyvirus)
• 4      Adenovirus
• 5      Herpesvirus (HSV1)
• 6      Tobacco mosaic virus
• 7      T-even phage
• 8      Polyomavirus (SV40)
• 9      Rhabdovirus (VSV)
• 10    Reovirus (Rotavirus)
• 11 Poxvirus
• 12 Hepadnavirus (hepatitis B)
• 13 Alphavirus (Semliki Forest, Sindbis)

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Reading assignments

• Chapter 1 of Flint
• Chapter 1 of Fields Virology The Origins of
  Virology (for history)
• The Greatest Benefit to Mankind Porter,
  NortonCo
• An excellent history of medicine
• Lysogeny
• For Thursday Chapter 2 of Flint
• Chapter 3 of Flint 2nd ed, and appendices

On Thursday class is in LH1