1. Viruses
Chapter 26

2. The History of Viruses / Virology
Viral diseases such as rabies have affected humans for many centuries.
Perhaps the first written record of a virus infection consists of a heiroglyph from Memphis, the capital of ancient Egypt, drawn in approximately 3700BC, which depicts a temple priest called Ruma showing typical clinical signs of paralytic poliomyelitis.

3. The History of Viruses / Virology
Smallpox was endemic in China by 1000BC. In response, the practice of variolation was developed.
What’s endemic?
Recognized that survivors of smallpox outbreaks were protected from subsequent infection.
variolation involved inhalation of the dried crusts from smallpox lesions, or in later modifications, inoculation of the pus from a lesion into a scratch on the forearm of a child.

4. The History of Viruses / Virology: Smallpox
In 1717 the wife of an English ambassador to the Ottoman Empire, observed local women inoculating their children against Smallpox.
In the late 18th century, Edward Jenner observed and studied Miss Sarah Nelmes, a milkmaid who had previously caught Cowpox and was subsequently found to be immune to Smallpox, a similar, but devastating virus.
On 14th May 1796, Edward Jenner used cowpox-infected material obtained from the hand of Sarah Nemes, a milkmaid from his home village of Berkley in Gloucestershire to successfully vaccinate 8 year old James Phipps.

5. The History of Viruses / Virology: Smallpox
On 1st July 1796, Jenner challenged the boy by deliberately inoculating him with material from a real case of smallpox ! He did not become infected !!!
Jenner developed the first vaccine, based on these findings, and smallpox is currently all but wiped out. (Read the Demon in the Freezer)

6. The History of Viruses / Virology: Smallpox
Although initially controversial, vaccination against smallpox was almost universally adopted worldwide during the 19th century.
Cartoon by James Gillray, 1802.

7. The History of Viruses / Virology
However, it was not until Robert Koch & Louis Pasteur jointly proposed the 'germ theory' of disease in the 1880s that the significance of these organisms became apparent.
Where should you be familiar with Pasteur’s name in your refrigerator?
Robert Koch ( )
Louis Pasteur ( )

8. The History of Viruses / Virology
Koch defined the four famous criteria now known as Koch's postulates which are still generally regarded as the proof that an infectious agent is responsible for a specific disease:
The agent must be present in every case of the disease.
The agent must be isolated from the host & grown in vitro.
The disease must be reproduced when a pure culture of the agent is inoculated into a healthy susceptible host.
The same agent must be recovered once again from the experimentally infected host.

9. The History of Viruses / Virology
In the late 19th century Charles Chamberland developed a porcelain filter. This filter was used to study the first documented virus, tobacco mosaic virus.
Shortly afterwards, Dimitri Ivanovski published experiments showing that crushed leaf extracts of infected tobacco plants were still infectious even after filtering the bacteria from the solution.
At about the same time, several others documented filterable disease-causing agents, with several independent experiments showing that viruses were different from bacteria, yet they could also cause disease in living organisms.
These experiments showed that viruses are orders of magnitudes smaller than bacteria. The term virus was coined by the Dutch microbiologist Martinus Beijerinck.

10. The History of Viruses / Virology
In the early 20th century, Frederick Twort discovered that bacteria could be attacked by viruses.
Felix d'Herelle, working independently, showed that a preparation of viruses caused areas of cellular death on thin cell cultures spread on agar.
Counting the dead areas allowed him to estimate the original number of viruses in the suspension.
The invention of Electron microscopy provided the first look at viruses. In 1935 Wendell Stanley crystallised the tobacco mosaic virus and found it to be mostly protein.
A short time later the virus was separated into protein and nucleic acid parts.

11. Viruses: The Basics
What are the “requirements” for life? Or how do you know if something is alive?
In small groups discuss
Movement, sensitivity, death, complexity, heredity, growth, cellular organization, development, reproduction, regulation
Are viruses alive?
Class opinion
Bruening / Rest of Science opinion

12. Viruses: The Basics
Most virologists consider them non-living, as they do not meet all the criteria of the generally accepted definition of life.
They are similar to obligate intracellular parasites as they lack the means for self-reproduction outside a host cell, but unlike parasites, viruses are generally not considered to be true living organisms.
A definitive answer is still elusive because some organisms considered to be living exhibit characteristics of both living and non-living particles, as viruses do.
For those who consider viruses living, viruses are an exception to the cell theory as viruses are not made up of cells.

13. Viruses: The Basics
A virus is a microscopic “particle” that can infect the cells of a biological organism.
Viruses can only replicate themselves by infecting a host cell and therefore cannot reproduce on their own.
At the most basic level, viruses consist of genetic material contained within a protective protein coat called a capsid. They infect a wide variety of organisms: both eukaryotes and prokaryotes.
A virus that infects bacteria is known as a bacteriophage, often shortened to phage.
The study of viruses is known as virology, and those who study viruses are known as virologists.
The word virus comes from the Latin, poison (syn. venenum).

14. The Nature of Viruses
Viral structure - core of nucleic acid surrounded by protein
classified by nature of genomes
Either DNA or RNA
RNA-based viruses – retroviruses (more later)
Lack ribosomes and necessary enzymes for protein synthesis
nearly all form a protein sheath or capsid around their nucleic acid core
Many animal viruses form an envelope around the capsid.
Host range - suitable cells for a virus

15. Viral Structure

16. Bacterial Virus - Structure
(a) Electron Micrograph
(b) diagram of a T4 bacteriophage

17. Viral Replication
Viruses can reproduce only when they enter cells and utilize the host’s cellular machinery.
viral genes translated into proteins by the cell’s genetic machinery
Compare to computer virus
Video – How does a virus enter a cell

18. Viral Shape helical - rodlike isometric - spiral Icosahedron
structure with 20 equilateral triangular facets
most efficient symmetrical arrangement that linear subunits can form a shell with maximum internal capacity
basic design of geodesic dome 

19. Viral Genome Structure
Viral genomes types exhibit great diversity
Some use DNA others RNA
Some double stranded, others single stranded
dsDNA, ssDNA, dsRNA, ssRNA
In ssRNA, the genome can contain the same base sequences as the mRNA used to produce viral proteins. RNA strand can serve as mRNA and is called a positive-strand virus
Genome can contain bases complementary to viral mRNA and is called negative-strand virus

20. Types of Viruses DNA Viruses RNA Viruses Adenoviruses Coronaviruses
Iridoviruses Filoviruses
Herpesviruses Orthomyxoviruses
Papovaviruses Paramyxoviruses
Parvoviruses Picornaviruses
Poxviruses Retroviruses
Viral Hepatitis Rhabdoviruses
"Arboviruses" Arenaviruses, Bunyaviruses, Flaviviruses, Togaviruses
Diarrhoea Viruses Astroviruses, Caliciviruses, Reoviruses (inc. Rotaviruses)

21. Important Human Viral Diseases – Table 26.1
Molecular biologists call a DNA single strand or sequence sense (or positive (+) sense) if an RNA version of the same sequence is translated or translatable into protein, and they call its complement antisense (or negative (-) sense)

22. Important Human Viral Diseases – Table 26.1

23. Types of Viruses - Adenoviruses
Adenoviruses are viruses of the family Adenoviridae.
There are 2 genera, Aviadenovirus (avian) and Mastadenovirus (mammalian) where they infect both humans and animals.
Adenoviruses are a frequent cause of acute upper respiratory tract (URT) infections, i.e. "colds". In addition, they also cause a number of other types of infection; 5–10% of upper respiratory infections in children, and many infections in adults as well
Adenoviruses were first isolated in human adenoids (tonsils), from which the name is derived.
Widespread in nature, infecting birds, many mammals and man.

24. Types of Viruses - Adenoviruses
Can undergo latent infection in lymphoid tissues, becoming reactivated some time later.
They're medium-sized (60-90 nm), nonenveloped icosahedral viruses containing double-stranded DNA.
genome is linear, non-segmented double stranded (ds) DNA which is between 26 and 45 Kbp. This allows the virus to theoretically carry 22 to 40 genes
Adenoviruses represent the largest nonenveloped viruses, because they are the maximum size able to be transported through the endosome (i.e. envelope fusion is not necessary).
Endosome? a membrane bound compartment inside eukaryotic cells. It is a compartment of the endocytic membrane transport pathway from the plasma membrane to the lysosome.

25. Types of Viruses - Adenoviruses
Several types have oncogenic potential.
What does this mean?
In recent years, there has been considerable interest in developing Adenoviruses as vectors to carry and express foreign genes for therapeutic purposes.
One reason for this is that the Adenovirus genome is relatively easily manipulated in vitro

26. Types of Viruses - Adenoviruses
Structure of Adenovirus

27. Types of Viruses - Retroviruses
Most of the retroviruses infect vertebrates, but as a group, they have been identified in virtually all organisms including invertebrates - evolutionarily successful design!
They are enveloped viruses possessing a RNA genome, and replicate via a DNA intermediate.
The virus itself stores its nucleic acid in the form of a +mRNA genome and serves as a means of delivery of that genome into cells it targets as an obligate parasite
rely on the enzyme reverse transcriptase to perform the reverse transcription of its genome from RNA into DNA, which can then be integrated into the host's genome with an integrase enzyme.

28. Types of Viruses - Retroviruses
Once in the host's cell, the RNA strands undergo reverse transcription in the cytosol and are integrated into the host's genome, at which point the retroviral DNA is referred to as a provirus.
It is difficult to detect the virus until it has infected the host.
Simply, the retrovirus enters a host cell and provokes the RNA strands inside of the normally-functioning cell to undergo reverse transcription, which is violating the 'central dogma of biology.' DNARNAProtein
When a retrovirus is inside of a cell, the first two steps of that process would be switched. (Rather than DNA --> RNA --> Protein, it would be RNA --> DNA) The host cell would become a provirus as this has occurred.
Video How retroviruses work & Simpler Video & Book Video

29. Types of Viruses - Retroviruses
When retroviruses have integrated their genome into the germ line, their genome is passed on to a following generation.
These endogenous retroviruses, contrasted with exogenous ones, now make up surprisingly large portion of the human genome. Most insertions have no known function and are often referred to as "junk DNA".
However, many endogenous retroviruses play important roles in host biology, such as control of gene transcription, cell fusion during placental development in the course of the germination of an embryo, and resistance to exogenous retroviral infection.

30. Types of Viruses - Herpesviruses
Name comes from the Greek 'Herpein' - 'to creep' = chronic/latent/recurrent infections. Epidemiology of the common Herpesvirus infections puzzled clinicians for many years.
all herpesviruses are composed of relatively large double-stranded, linear DNA genomes encoding genes encased within an icosahedral protein cage.
~100 Herpesviruses have been isolated, at least one for most animal species which has been looked at. To date, there are 8 known human Herpesviruses.

31. Types of Viruses - Herpesviruses
Herpes simplex virus 1 and 2 (HSV-1 and HSV-2), also known as Human herpes virus 1 and 2 (HHV-1 and -2), are two members of the herpes virus family, Herpesviridae, that infect humans.
ubiquitous and contagious. They can be spread when an infected person is producing and shedding the virus.
Symptoms of herpes simplex virus infection include watery blisters in the skin or mucous membranes of the mouth, lips or genitals. Lesions heal with a scab characteristic of herpetic disease.
However, as neurotropic and neuroinvasive viruses, HSV-1 and -2 persist in the body for the life of the carrier by becoming latent and hiding from the immune system in the cell bodies of nerves.
After the initial or primary infection, some infected people experience sporadic episodes of viral reactivation or outbreaks. In an outbreak, the virus in a nerve cell becomes active and is transported via the nerve's axon to the skin, where virus replication and shedding occur and cause new sores.
There is no known cure for HSV infection, but treatments can reduce the likelihood of viral shedding and spread.

32. Bacteriophages
Bacteriophages - viruses that infect bacteria
Bacteriophages are among the most common biological entities on Earth.
The term is commonly used in its shortened form, phage.
some named as members of a “T” series

33. Bacteriophages
One of the densest natural sources for phages and other viruses is sea water, where up to 9×108 virions per milliliter have been found in microbial mats at the surface, and up to 70% of marine bacteria may be infected by phages.
They have been used for over 60 years as an alternative to antibiotics in the former Soviet Union and Eastern Europe.
They are seen as a possible therapy against multi drug resistant strains of many bacteria.
How would this work?

34. Bacteriophages
Structure
Picture on left is a real SEM image

35. Lytic Cycle
tail fiber contacts lipoproteins of host bacterial cell wall
tail contracts and tail tube passes through opening in base plate, piercing bacterial cell wall
contents injected into host cytoplasm
will kill infected cell by lysis
virulent viruses
Picture of phages on outside of cell 

37. Lysogenic cycle
Does not immediately kill the cell
integrate their nucleic acid into the genome of the infected host cell (prophage).
prophage - phage genome inserted as part of the linear structure of the DNA chromosome of a bacterium
The integration of a virus into a cellular genome is termed lysogeny.

38. Lysogenic cycle
prophage may exit genome and initiate virus replication
lysogenic cycle
lysogenic (or temperate) viruses
Lytic and Lysogenic Cycle

39. Cell Transformation and Phage Conversion
Transformation - genetic alteration of a cell’s genome by the introduction of foreign DNA
phage conversion - foreign DNA contributed by bacterial virus
disease-causing bacteria Vibrio cholerae usually exists in harmless form
bacteriophage that infects V. cholerae introduces into the host bacterial cell a gene that codes for the cholera toxin

40. AIDS
Acquired Immunodeficiency Syndrome (AIDS) was first reported in the US in 1981.
estimated over 33 million people worldwide are infected with Human Immunodeficiency Virus (HIV)
Infection cycle
In normal individuals, white blood cells patrol the bloodstream and attack invading bacteria or viruses.

41. AIDS
In AIDS patients, the virus hones in on CD4+ T cells, infecting and killing them.
Without T cells, the body cannot defend against invading bacteria or viruses.
Each HIV particle possesses glycoprotein (gp120) on its surface that precisely fits a cell-surface marker protein (CD4) on surfaces of macrophages and T cells.

42. AIDS
After docking onto the macrophage CD4 receptor, HIV requires a second macrophage receptor (CCR5) to cross the cell membrane.
Once inside the macrophage, the HIV particle sheds its protective coat.
RNA and reverse transcriptase left floating in cytoplasm
double strand of DNA, complementary to RNA, produced
viruses released via exocytosis

44. The Future of HIV Treatment
Combination drug therapy
AZT and protease inhibitors
keeps disease in check
Vaccine therapy
may reduce reproductive capability of HIV
Blocking replication
chemokines bind to and block receptors
CAF prevents viral replication
Disabling receptors

46. Disease Viruses
Many human diseases are caused by viruses:
influenza, smallpox , chicken pox, herpes
Viruses may also play a role in autoimmune diseases such as multiple sclerosis and diabetes.
Influenza
Flu viruses are animal retroviruses distinguished by their capsid.
types A, B, and C
subtypes differ in protein spikes

47. Disease Viruses
Recombination
Viral genes are readily re-assorted by genetic recombination.
novel combinations of H and N spikes unrecognizable by human antibodies
inability to make perfect vaccines
flu pandemics
How? And Why?

48. Disease Viruses Emerging viruses
viruses that originate in one organism and then pass to another and cause disease
Ebola –one strain has 90% lethality
Severe Acute Respiratory Syndrome (SARS) –
coronovirus in 2003
Unrelated to any previous coronovirus
most likely came from civets (weasel-like animals) in China eaten as delicacies

49. Association between hepatitis B infections and liver cancer
Viruses and Cancer
Viruses are capable of altering growth properties of human cells they infect by triggering oncogene expression.
Association between hepatitis B infections and liver cancer
Cervical cancer linked to certain strains of HPV (human papilomaviruses)
Why are some groups against vaccine?
15% of all cancers worldwide

50. Prions
Prions – proteianceous infectious particle
Nobel Prize in 1997
infectious proteins that some believe may be responsible for transmissible spongiform encephalopathies (TSE’s)
scrapie in sheep
mad cow disease in cattle
Humans
Kuru in Fore people of New Guinea
Creutzfeldt-Jakob disease

51. How Prions Arise
Shortcut to how_prions_arise.lnk

52. TSE’s

54. Viroids
tiny, naked molecules of RNA that are an important infectious disease agent in plants
recent outbreak killed 10 million coconut palms in Phillipines
Not clear how they cause disease
Viroid nucleotide sequences resemble sequences of introns within ribosomal RNA genes
capable of catalyzing destruction of chromosome integrity??

55. The Ebola Virus