Chapter+5,+25,+37 (microbiology) 8th edition

1. Viruses
Chapter 5, 25 & 37

2. Viruses
Major cause of disease
– also importance as a new source of
therapy
– new viruses are emerging
Important members of aquatic world
– move organic matter from particulate
to dissolved
Important in evolution
– transfer genes between bacteria,
others
Important model systems in
molecular biology

3. Viral replication
 Video

4. General Properties of Viruses
Virus: genetic element that cannot
replicate independently of a living
(host) cell
Virus particle (virion): extracellular
form of a virus, complete virus particle.
– Exists outside host and facilitates
transmission from one host cell to
another
– Contains nucleic acid genome
surrounded by a protein coat and,
in some cases, other layers of
material

5. Viral Hosts and Taxonomy
– Viruses can be classified on the basis of
the hosts they infect
Bacterial viruses (bacteriophages)
Archaeal viruses
Animal viruses
Plant viruses
Viruses come in many shapes and sizes
– Most viruses are smaller than prokaryotic cells;
range from 0.02 to 0.3 µm
Most viral genomes are smaller than those of
cells

6. Nature of the Virion
 Virion size range is ~10–400 nm in diameter and most
viruses must be viewed with an electron microscope
– Capsid: the protein shell that surrounds the
genome of a virus particle.Composed of a number
of protein molecules arranged in a precise and
highly repetitive pattern around the nucleic acid
– Nucleocapsid: complete complex of nucleic acid
and protein packaged in the virion.
– Capsid can be more or less complex and
composed of only one or more than one type of
proteins.
– Capsomere: subunit of the capsid
Smallest morphological unit visible with an
electron microscope

7. Helical Capsid
 Helical capsid are shaped like hollow tubes with
protein walls (Tobacco Mosaic Virus is the best
studied example)

8. Icosahedral Capsids
 An icosahedron is a regular polyhedron with 20
equilateral faces and 12 vertices
 Capsomers
– ring or knob-shaped units made of 5 or 6 protomers
– pentamers (pentons) – 5 subunit capsomers
– hexamers (hexons) – 6 subunit capsomers

9. Capsids of Complex Symmetry
 Some viruses do not fit into the category of
having helical or icosahedral capsids
– poxviruses – largest animal virus
– large bacteriophages – binal symmetry
 head resembles icosahedral, tail is helical

10. Bacteriophage
Bacteriophage are viruses that infect
bacteria.

11. Nature of the Virion
– Enveloped virus: virus that contains additional layers
around the nucleocapsid
– Animal virus envelopes (lipids and carbohydrates) usually
arise from host cell plasma or nuclear membranes

12. Nature of virion
Some virions contain enzymes critical to
infection
– Lysozyme
Makes hole in cell wall
Lyses bacterial cell
– Nucleic acid polymerases
– Neuraminidases
Enzymes that cleave glycosidic
bonds
Allows liberation of viruses from cell

13. Morphology of different viruses

14. Viral genome
 Diverse nature of genomes
 A virus may have single or double stranded
DNA or RNA
 The length of the nucleic acid also varies
from virus to virus
 Genomes can be segmented or circular

15. Viral replication

16. Viral Attachment and Penetration
Bacteriophage T4: virus of E. coli; one of
the most complex penetration mechanisms
– Virions attach to cells via tail fibers that
interact with polysaccharides on E. coli
cell envelope
– Tail fibers retract and tail core makes
contact with E. coli cell wall
– Lysozyme-like enzyme forms small pore
in peptidoglycan
– Tail sheath contracts and viral DNA
passes into cytoplasm

17. Attachment of bacteriophage T4 to the cell wall of
Escherichia coli and injection of DNA

18. Viral Entry and Uncoating

19. Assembly

20. Virion Release

21. Isolation, cultivation, identification
Bacteriophages can be grown
1- In suspension of bacteria in liquid
media
2- In bacterial cultures on solid media.
On solid media the phage infection
produces plaques that can be counted
and theoretically correspond to one
virus per plaque. The count is given as
pfu (plaque forming units).

22. Quantification of bacterial virus by plaque assay using the agar
overlay technique

23. Isolation, cultivation, identification
Animal viruses can be grown in
– Living animals (mice, rabbits, and
guinea pigs)
– Embryonated eggs
– Cell cultures
Identification can be difficult. Most
common are serological methods.
Molecular methods such as PCR are
becoming routine for the identification
of some viruses.

24. Cell cultures in monolayers grown on a Petri
plate

25. Quantification of Animal Viruses
 Intact Animal Methods
– Some viruses do not show recognizable changes in cell cultures
yet cause death or disease in whole animals
– Virus is diluted
– Animals are infected with viral dilution
– End point is calculated (LD50 or ID50)

26. Mechanisms to diminish viral infections
Eukaryotes possess mechanisms to diminish viral
immune defense mechanisms
Prokaryotes also possess mechanisms
– Restriction modification system
– DNA destruction system; only effective against
double-stranded DNA viruses
– Restriction enzymes (restriction endonucleases)
cleave DNA at specific sequences
– Modification of host’s own DNA at restriction enzyme
recognition sites prevents cleavage of own DNA
Viral mechanisms to evade bacterial restriction systems
– Chemical modification of viral DNA (glycosylation or
methylation)
– Production of proteins that inhibit host cell restriction
system

27. Classification of viruses
Class Type of
nucleic acid
Bacterial Animal
Class I dsDNA Lambda, T4 Herpes
Class II ssDNA ФX 174 Chicken
anemia
Class III dsRNA Ф6 Reoviruses
Class IV ssRNA (+) MS2 Polio
Class V ssRNA (-) Influenza
Class VI ssRNA. DNA
intermediate
Retroviruses
Class VII dsDNA. RNA
intermediate
Hepatitis B

28. Viral replication
Class I, the DNA has the same
structure as cellular DNA and can be
used to produce mRNA and copies of
the viral genome.
Class II, the ss DNA must be copied
into its complementary strand that can
be used for transcription or as template
for making more copies of the genome.
Class III, viruses require the presence
of a viral enzyme that copies dsRNA
into mRNA and that makes copies of
the genome

29. Viral replication
Class IV viruses can use the RNA
directly as mRNA to synthesize viral
proteins.
Class V viruses require a viral enzyme
to transform the negative strand RNA
into mRNA.
Class VI viruses need reverse
transcriptase to transcribe the RNA into
DNA that is then used to produce
mRNA and copies of the genome.

30. Production of Viral Protein
– Production follows synthesis of viral mRNA
Early proteins
– synthesized soon after infection
– necessary for replication of virus nucleic
acid
– typically act catalytically
– synthesized in smaller amounts
Late proteins
Synthesized later
Include proteins of virus coat
Typically structural components
Synthesized in larger amounts

31. Overview of Bacterial Viruses
 Bacteriophages are very diverse
 Best-studied bacteriophages infect enteric
bacteria
– Examples of hosts: E. coli, Salmonella enterica
 Most phages contain dsDNA genomes
 Most are naked, but some possess lipid
envelopes
 They are structurally complex, containing
heads, tails, and other components

32. Schematic representations of the main types of bacterial
viruses

33. Overview of Bacterial Viruses
Viral Life Cycles
– Virulent mode: viruses lyse host
cells after infection
– Temperate mode: viruses
replicate their genomes in
tandem with host genome and
without killing host
Virus can also be lytic

34. Temperate Bacteriophages, Lambda, and P1
Temperate viruses: can undergo a stable
genetic relationship within the host
– But can also kill cells through lytic cycle
Lysogeny: state where most virus genes are
not expressed and virus genome (prophage)
is replicated in synchrony with host
chromosome
Lysogen: a bacterium containing a prophage
Under certain conditions lysogenic viruses
may revert to the lytic pathway and begin to
produce virions

35. Lytic and lysogenic cycles

36. Lytic and lysogenic
 Temperate
 Please click on the link to watch this video

37. Viral infection
 When bacterial viruses are lysogenic the
virus that is integrated in the bacterial
genome is called a prophage.
 When animal and plant viruses are lysogenic
the integrated virus is called a provirus.
 The viral genome is replicated together with
the host cell genome and is passed on to the
daughter cells. Environmental conditions can
influence the life cycle and stimulate a
lysogenic virus to become lytic (UV
irradiation, X rays)

38. Overview of Animal Viruses
Consequences of Virus Infection in Animal
Cells
– Persistent infections: release of virions
from host cell does not result in cell lysis
Infected cell remains alive and
continues to produce virus
– Latent infections: delay between
infection by the virus and lytic events
– Transformation: conversion of normal
cell into tumor cell
– Cell fusion: two or more cells become
one cell with many nuclei

39. Possible effects that animal viruses may have on cells they
infect

40. Retroviruses
 Genome: ssRNA (two copies in each virion)
 Complex virus: it carries enzymes in the
virion that are essential for replication
(reverse transcriptase)
 Enveloped virus. On the envelope there are
proteins that can bind to the receptor on the
host cell.
 All retroviruses have their genome organized
as follows: gag – pol – env. Gag: structural
proteins, pol: reverse transcriptase and
integrase, env: envelope proteins.

41. Retroviruses
 Retroviruses have a unique genome
– Two identical ssRNA molecules of the
plus (+) orientation
– Complex virus: it carries enzymes in the
virion that are essential for replication
(reverse transcriptase)
– Enveloped virus. On the envelope there
are proteins that can bind to the receptor
on the host cell.

42. Retroviruses
 Retroviruses have a unique genome
– Contain specific genes
gag: encode structural proteins
pol: encode reverse transcriptase
and integrase
env: encode envelope proteins

43. Retrovirus structure and function

44. HIV life cycle
 Virion has viral protein
spike, gp120
– attaches to CD4 cells
(T helper cells and
other cells) and co-
receptors CCR5 and
CXCR-4
 Integrates into host
cell’s DNA as a
provirus
 Can remain latent –
asymptomatic

45. HIV life cycle

46. CDC Classification System for Stages of HIV-Related
Conditions
 Acute
– 2–8 weeks after infection
– most experience brief illness called acute
retroviral syndrome
– rapid multiplication and dissemination of
virus throughout body
– stimulation of immune response
 Asymptomatic (latent)
– may last from 6 months to 10 or more
years
– levels of detectable HIV in blood decrease,
although viral replication continues
– effects on immune functions may occur

47. CDC Classification System for Stages of HIV-Related
Conditions
 Chronic symptomatic
– formerly called AIDS-related complex
– can last for months to years
– viral replication continues
– numbers of CD4+
cells in blood significantly decrease
results in patients developing a variety of illnesses
often caused by opportunistic pathogens and AIDS
related cancers
 AIDS – fourth and last stage
– immune system no longer able to defend against virus
 Definition of AIDS
– all HIV-infected individuals who have fewer than 200
CD4+
T cells/microliter of blood or a CD4+
cell
percentage of lymphocytes of less than 14

48. Diseases associated with AIDS

49. Animal ssRNA (+)
Poliovirus and coronavirus.
Positive strand means that the genome
is also the mRNA and can be used
immediately to make viral proteins.
One very important protein codified by
the mRNA is RNA replicase that
makes negative strand that can be
used as template to make more mRNA
copies.

50. Poliovirus

51. Poliovirus
 Polio is slowly becoming a reemerging disease.
At one point in history polio was almost under
total control because of the presence of an
effective vaccine.
 The virus encodes all the proteins as a single
giant protein (2200 aminoacids) called a
polyprotein that is later cut into about 20
different proteins. The virus also encodes for the
protease that can cleave the polyprotein.
 Replication happens in the cell cytoplasm.
 Nonenveloped

52. Positive-Strand RNA Animal Viruses
 Highly contagious viral disease caused by the
SARS-associated corona virus (SARS-CoV)
– transmitted by droplet spread; can be fatal
– Sudden onset, severe illness in healthy individuals
– dry cough develops in days; most will develop
pneumonia
 No specific treatment is currently approved

53. Coronavirus

54. Animal ssRNA (-)
 The viral genome is negative strand and
needs to be transformed into positive strand
through RNA-dependent RNA polymerase.
 The genome can be transcribed as small
mRNAs or as the whole genome.
 Examples of negative strand RNA viruses
are rabies and influenza virus.
 In the case of influenza the genome is
segmented and is present in the virion as 8
separate pieces. Replication of the genome
happens in the nucleus.

55. Replication of a negative-strand RNA virus

56. Influenza virus

57. Replication cycle of Influenza A virus

58. Antigenic shift

59. Animal ssRNA (-)
 Another mechanism used by these viruses to avoid
the immune system is antigenic drift.
 In antigenic drift the surface proteins of the virus are
altered by mutations that occur in the genome of the
virus.
 Influenza can be prevented with vaccine prophylaxis
that must be repeated every year and that is strongly
suggested for individuals that risk death from
infection with the flu virus.
 Rabies is treated with postexposure prophylaxis
(vaccine and immunoglobulins are injected after
exposure).

60. Influenza (Flu)
An important feature of the influenza
viruses is the frequency with which
changes in antigenicity occur
– Antigenic drift – due to accumulation
of mutations in a strain within a
geographic area
– Antigenic shift – due to reassortment
of genomes when two different strains
of flu viruses (from humans and
animals) infect the same cell and are
incorporated into a single new capsid

61. Antigenic drift

62. Ebola Hemorrhagic Fever
 Ebola-Member of single-stranded, negative
sense RNA family
 Infection is severe and ~80% fatal
 No known carrier state; fruit bat may be
reservoir
 Transmission from direct contact with Ebola
victim, body fluids or clinical samples
 Internal hemorrhaging
 Supportive therapy; no
treatment available
 Experimental vaccines
being evaluated

63. dsDNA virus - Herpesvirus
 HSV (herpes simplex virus, varicella zoster
virus, CMV (cytomegalovirus) Epstein-Barr
virus.
 dsDNA virus can integrate into the genome
of the host and this gives them the ability to
remain latent.
 HSV and Varicella zoster remain latent in the
neurons of the sensory ganglia from which
they can reemerge periodically.
 Viral DNA is uncoated in the nucleus.
 Assembly of the virus is on the nuclear
membrane and envelope is of nuclear origin.

64. Herpesvirus

65. dsDNA virus - Herpesvirus
 HSV-1 belongs to herpesviruses.
– Herpes simplex virus 1 (HSV-1) is
transmitted by oral or respiratory routes and produces
cold sores. It remains latent in the trigeminal nerve
ganglia. Recurrence can be triggered by events such
as stress, UV exposure, emotional upsets, and
hormonal changes.
HSV-1 Cold sores

66. Genital Herpes
 Caused by HSV-2
 Clinical manifestations
– fever, burning sensation, genital soreness, and
blisters in infected area
– blisters heal spontaneously, but virus remains
latent and is periodically reactivated
 Can be treated with antiviral drugs (e.g., acyclovir)
 Congenital (neonatal) herpes
– usually HSV-2
– one of the most life-threatening of all infections
in newborns
– ~1,500–2,200 babies/year in U.S.
– can result in neurologic involvement and
blindness
– Caesarian section recommended

67. dsDNA virus - Herpesvirus
Chickenpox
Varicella zoster virus

68. Chickenpox (Varicella) and Shingles (Herpes Zoster)

69.  Shingles (herpes
zoster; postherpetic
neuralgia)
– reactivated form of
chickenpox
virus resides in
cranial and
sensory neurons
reactivation - virus
migrates down
neuron
 Treatment
– supportive; acyclovir
and others
Chickenpox (Varicella) and
Shingles (Herpes Zoster)

70. dsDNA virus - Herpesvirus
 Herpesviruses can also be tumorigenic.
 EBV can cause Burkitt’s lymphoma that is the most
common cause of childhood cancer in Africa.
 EBV can cause also nasopharyngeal carcinoma
(Southeast Asia).
 EBV is also the cause of a very mild disease called
mononucleosis.
 CMV is also very widely spread and the cause of
mild disease.
 All these viruses can cause serious disease in
immunocompromised patients.
Epstein Barr virus (EBV)

71. Mononucleosis (Infectious)
 Caused by Epstein-Barr virus
(EBV)
– herpes virus, dsDNA,
icosahedral with envelope
– infects B cells
– also associated with Burkitt’s
lymphoma and
nasopharyngeal carcinoma
 Spread by mouth-to-mouth
contact
 Clinical manifestations
– enlarged lymph nodes and
spleen, sore throat, headache,
nausea, general weakness
and tiredness, and mild fever
– self-limited disease, lasting 1
to 6 weeks

72. Burkitt's Lymphoma

73. dsDNA – Pox viruses
 Pox viruses replicate in the cytoplasm.
 Viral DNA synthesis occurs outside the
nucleus.
 They do not have an envelope, but are
covered on the surface with protein tubules
arranged in a membrane-like pattern.
 Smallpox was caused by this virus but the
disease has been officially declared
eradicated after effective vaccination of the
human population.
 During the Middle Ages and estimated 80% of
the Europeans contracted smallpox. Those
who recover had disfiguring scars.

74. Smallpox (Variola)
 Caused by variola virus
– large, brick-shaped complex virus
– linear dsDNA
 Transmitted by aerosol or contact
– humans are the only natural host
Clinical Forms of Smallpox
 Variola major
– most common, severe form
– extensive rash and higher fever
– 33% fatality rate
 Variola minor
– less common form and less severe
– fatality rates of 1% or less
 Both forms usually transmitted by direct and
fairly prolonged face-to-face contact

75. Smallpox (Variola)
Eradication of Smallpox
 1977 – last case from a natural infection
occurred in Somalia
 Why eradication was possible –
– disease has obvious clinical features
– humans are only hosts and reservoirs
– there are no asymptomatic carriers
– short infectivity period (3–4 weeks)

76. dsDNA viruses
 The vaccinia virus is a close relative of pox
viruses and has been very important for the
development of vaccines.
 Adenoviridae cause the common cold.
 Papillomavirus causes warts, but some
strains are capable of causing cancer
 Hepdnaviruse causes Hepatitis B virus all
other forms of hepatitis are caused by RNA
viruses

77. Hepatitis
– inflammation of liver, caused by 11 different viruses
2 herpesviruses—Epstein-Barr virus (EBV) and
cytomegalovirus (CMV)
– cause mild, self-resolving disease
– no permanent hepatic damage
– signs and symptoms include fatigue, nausea, and
malaise

78. Hepatitis A & E viruses (HAV) & (HEV)
 HAV- icosahedral, naked virus,positive strand linear RNA
 Spread by fecal-oral contamination of food, drink, or
shellfish
 Clinical manifestations
– usually mild intestinal infection
anorexia, general malaise, nausea, diarrhea, fever,
and chills
– occasionally viremia occurs leading to liver infection
jaundice
 HEV-implicated in many epidemics in developing
countries
 transmission by fecal contaminated water
 similar to HAV course of disease
 ~15%–25% fatality rates in pregnant women

79. Hepatitis B virus (HBV)
– dsDNA virus
– Dane particle is
infectious virion
– transmitted through
body fluids and intra-
venous equipment
– can pass the placenta
and breast milk
– ~1.25 million chronically
infected in U.S., 200
million worldwide

80. Hepatitis C& D Virus (HCV) & (HDV)
 HCV-RNA virus
 Transmission virus contaminated blood, fecal
oral route, also spread from mother to fetus,
and through organ transplants
 Epidemic with more than 1 million new
cases/yr in U.S.
 HDV -Causes severe acute and chronic
hepatitis in HBV infected
 Treatment, prevention, and control
– serological tests for anti-HDV antibodies
– no satisfactory treatment

81. dsRNA viruses - rotavirus
 Non enveloped and cause of diarrhea in infants.
 Replication takes place in the cytoplasm.
 Genome is segmented.
 The RNA replication is guaranteed by the
presence in the virion of a RNA-dependent RNA
polymerase that can copy RNA from RNA.
 Released by cell lysis.

82. Viruses and Cancer
 Complex, multistep process
 Often involves oncogenes
– cancer causing genes
– may come from the virus OR may be transformed
host proto-oncogenes (involved in normal
regulation of cell growth/differentiation)

83. Viroids and virusoids
Viroids are infectious agents that consist
of only RNA. Cause over 20 different plant
diseases.
 They are covalently closed circular ssRNA
about 250-370 nucleotides long.
 The RNA of viroids does not codify for any
viral product, but it is replicated by the host
RNA polymerase. Probably because of its
structural properties the cell enzyme uses
the viroid as template to make copies.

84. Viroids and virusoids
Virusoids are similar in structure to
viroids, but they codify for one or more
gene products and they need a helper
virus to be able to infect a cell.
The best studied virusoid is the human
hepatitis D virus that uses hepatitis B
as helper virus.
If a host cell contains both hepatitis D
and B viruses, the virusoid RNA and its
gene product (delta antigen) become
able to infect other cells and replicate.

85. Prion
 Prions (Proteinaceous
infectious particles) cause
neurodegenerative disease
(transmissible spongiform
encephalopathies).
 (PrPC
) encodes for the normal
form of prion
 (PrPSc
) encodes for the
abnormal form of a cellular
protein.
 Entrance of PrPSc
induces a
conformational change in the
normal protein and transforms
it into the abnormal form

86. Prions – Proteinaceous Infectious Particle
 Cause a variety of degenerative diseases in
humans and animals
– scrapie in sheep
– bovine spongiform encephalopathy (BSE) or
mad cow disease
– Creutzfeldt-Jakob disease (CJD) and variant
CJD (vCJD) in humans
– kuru in humans
 All prion caused diseases
– have no effective treatment
– result in progressive degeneration of the brain
and eventual death

87. Prion overview
 video

88. Prion characteristics
 video