1. Viruses: Their Structure and
Replication

2. What are Viruses
• Small, Filterable, infectious agents
– Cannot be seen by light microscope
– Electron Microscope
• Obligatory Intracellular Parasites
– Not enough ATP by itself

3. Characteristics Of Viruses
• Genetic Material: DNA or RNA – never both!
– Single stranded (ss) or double stranded (ds)
– Linear or circular
• Capsid
– Protein subunits (shell)
– Protect the genetic material
– May be involved in cell entry
• Envelope (required for entry if present)
– Lipid, protein and carbohydrate
– Protein: viral origin
– Lipid, carbohydrate: host origin
– Involved in cell entry (located outside the capsid)
• Subunit Replication only
– Assembled after parts are made (quick log phase)
• NEVER contain enzymes for protein synthesis or ATP metabolism!!
– Always appropriate the host cell machinery

5. Size of Viruses

6. Virus Classification
• Based on Host Range (determined by specific receptors)
– Bacterial Viruses (Bacteriophages)
– Animal Viruses
– Plant Viruses
– Others – (amoeba, insects)
• Based on genome structure
– DNA or RNA (never both)
• ssDNA viruses
• dsDNA viruses
• ssRNA viruses
– Plus Strand (+RNA viruses)
» Same
– Negative strand (- RNA viruses)
» Complementary
– Retroviruses
» Converted into complementary DNA, then into the cell for replication
• dsRNA viruses
– Linear or circular
– Size
• 2000 to 200,000 nucleotides

7. Virus Classification (cont.d)
• Based on Shape
– Polyhedral viruses (icosahedral -20 faces, 12 vertices)
– Helical Viruses
– Complex viruses
• Based on Envelope
– Naked viruses
– Enveloped viruses
• Based on Disease caused
– Respiratory viruses
– Gastrointestinal viruses
– Sexually transmitted viruses

8. Viral Structure: Capsid
Capsid = protein coat that encloses and protects the nucleic
acid of a virus
• Accounts for most of the viral mass
• Composed of single or multiple proteins
• Each subunit = capsomeres

9. Viral Structure: Envelope
Sometimes, Capsid covered with envelope
•spikes = carbohydrate-protein complexes (glycoproteins)
that project from the envelope
• Can be used to attach to host cell
• Influenza virus causes hemagglutination – clumping
of red blood cells by use of spikes
Non-enveloped viruses/ Naked Viruses = viruses whose
capsids are not covered by an envelope

10. An Enveloped Virus

11. Virus mutations and immunity
When a virus infects a host cell:
•Host immune system produces antibodies
•Antibodies = proteins that inactivate the virus by reacting
with virus surface proteins
 Stops further infection
Why you can get some viruses more than once:
• Genes that code for viral surface proteins are
susceptible to mutation
• Antibodies can’t react with the altered surface
proteins  infection
• Ex) influenza; frequent mutations in its spikes
Non-neutralizing antibodies do not inhibit function
Neutralizing inhibits function

12. Viral Structure:
General Morphology
Capsid Structure determines shape:
Helical Viruses = nucleic acid is inside a hollow cylindrical
capsid with a helical structure
• Rabies, Ebola viruses, Tobacco Mosaic Virus
Polyhedral viruses = many sided; icosahedron is common
with 20 equilateral triangles as sides and 12 vertices
• Poliovirus, Adenovirus, herpes, others??

13. Viral Structure:
General Morphology
Enveloped Viruses = can be helical or polyhedral, but the
capsid is surrounded by an envelope
• Helical: influenza virus
• Polyhedral (icosahedral): Herpes simplex virus
Complex viruses = Complex structures; additional structures
attached to capsids, combos of helical and polyhedral, may
have several coats around nucleic acid
• Bacteriophage, poxviruses

14. Virus Structure

15. Virus Taxonomy
International Committee on Taxonomy of Viruses (ICTV)
groups viruses based on:
• Nucleic acid type
• Mode of replication
• Morphology
Viral species = defined as a group of viruses sharing the
same genetic information and host range
• Viral species are given common names
• Ex) human herpesvirus
• The suffix –virus is used for genus names
• Ex) Simplexvirus
• Family of viruses is given the suffix –viridae
• Ex) herpesviridae

16. Some Viral Families & Genera affecting humans

17. Some Viral Families & Genera affecting humans:
Continued

18. Isolation & cultivation of viruses
Our understanding of viruses comes mostly from
bacteriophages, as they are easily grown on bacterial
cultures
• Liquid suspensions or solid media
Plaque method for detecting & counting viruses:
1) bacteriophages are mixed with host bacteria and melted
agar, poured onto petri plate with existing layer of solid
growth medium
2) Top layer solidifies ~ one cell thick
3) After several rounds of infection, multiplication and lysis,
bacteria surrounding the virus are destroyed  plaque

19. Bacteriophage lambda
on a lawn of E. coli
• Each plaque is from a single virus (theoretically)
• Number of plaques can be used to calculate
plaque forming units (PFU) in initial suspension

20. Bacterial Viruses
• Bacteriophages
• DNA and RNA viruses
– ds and ss
– Linear and circular
• Important tool
– Alternative to antibiotic therapy
• Basis to study viral replication in host cells
– Lytic cycle (lyses cell)
– Lysogenic cycle
http://www.youtube.com/watch?v=gU8XeqI7yts
It is very easy to grow viruses in bacteria, so it another reason it’s an important tool
Never marketed phage therapy because it doesn’t work too well

21. Lytic Cycle of a T-Even Bacteriophage
1
2
3
Figure 13.11
HAS TO BE A DNA VIRUS
Only infects cells with specific receptors
“syringes in”

22. 4
Figure 13.11
Lytic Cycle of a T-Even Bacteriophage
Integrates genome into host genome

23. Steps for Replication
• Adsorption
• Penetration
• Biosynthesis
– Uncoating
– Replication
• Assembly
• Release
Memorize

24. Lysogenic cycle:
bacteriophage lambda
Prophage: DNA incorporated and now it will make bacteriophages
DNA randomly pops off in lysogenic cycle then
goes through lytic

25. Lysogeny: importance
• Lysogenic cells are immune to infection by the same phage
(but not to other phages)
• Phage conversion = tendency of host cell to exhibit new
properties when carrying lysogenic phage
• Ex) Cornyebacterium diptheriae produces toxin only
when carrying lysogenic phage  diptheria
• Same is true for shiga toxin by pathogenic E. coli
• Specialized transduction = since bacterial DNA is
incorporated with phage DNA, adjacent genes on host
DNA may remain attached when phage DNA is excised for
initiation of the lytic cycle
• Introduce foreign genes into a new cell’s genome
Specialized transduction – horizontal gene transfer

26. Multiplication of Animal Viruses
• Entry
– Adsorption (not misspelled)
• Sticks to the surface
– Entry/ Penetration
– Uncoating (if capsid goes in)
• Replication/ Synthesis
• Assembly/Maturation
• Release
– Affect on host cell
DNA matures in the nucleus, RNA matures in the cytoplasm

27. Multiplication of Animal Viruses:
Attachment
• Attachment
– Virus attachment sites
• Spikes or capsid proteins
– Receptor Sites
• Proteins, glycoproteins on host cell membrane

28. Multiplication of Animal Viruses: Entry
• Endocytosis
– Pinocytosis (unseen)
• Plasma membrane folds inward into vesicles
– Receptor mediated Endocytosis (creates own
vesicles)
• Influenza virus
• Fusion (membranes are the same)
– Viral envelope fuses with cell membrane

29. Multiplication of Animal Viruses:
Entry
Above: Togavirus entering a cell through pinocytosis

30. Multiplication of Animal Viruses:
Entry
Above: Herpesvirus entering a cell through fusion

31. Multiplication of Animal Viruses: Uncoating
• Separation of nucleic acid from protein capsid
– Capsid digested by host enzymes
– Viral proteins synthesized to uncoat
• poxviruses

32. Replication/Biosynthesis/Maturation/Release:
DNA viruses
• Gene expression in most viruses
– Stage specific
– Temporal Cascade
• DNA viruses
– DNA shuttled to host nucleus
– EARLY Gene transcription
• Uses host RNA polymerase
• mRNA shuttled to protein translation sites in cytoplasm
• Viral Enzymes (proteins) shuttled back to nucleus
– Viral DNA replication
• Viral DNA polymerase replicates DNA
– LATE gene expression
• Uses host RNA polymerase
• mRNA shuttled to protein translation sites in cytoplasm
• Viral structural proteins Proteins shuttled back to nucleus
– VIRIONS assembled, shuttled back to cytoplasm
– Trafficked via ER, Golgi, to Cell membrane for release
“Too much detail, I just need you to remember
that some genes are expressed before
replication, some are expressed after. It just
depends on when it needs that expression.”

33. It’s acidity is what causes the endosome to fuse with the envelope
and release the capsid
budding

34. biosynthesis of DNA viruses example
Back into nucleus

35. RNA viruses
• Multiplication is same as that of DNA viruses except
mechanisms of how mRNA is generated
• Four nucleic acid types of RNA viruses
• Single (+) strand of RNA
• Ex) picornaviridae, togaviridae
• Single (–) strand of RNA
• Ex) rhaboviridae
• Double stranded RNA
• Ex) reoviridae
• “Reverse transcriptase” RNA (retroviruses)
• Ex) retroviridae
+  transcription  - translation  +
- strand makes message, so
- stays -
- Strand will make one part (like capsid)
+ will make other part (like the RNA)
Prophage – bacteriophage DNA incorporated???
Provirus – any other virus DNA incorporated???
RNA polymerase is more
likely to make errors than
DNA polymerase

36. Avian Influenza
Clinical Focus, p. 371
Antigenic drift – mutations in how it looks
Antigenic shift – so many mutations, very virulent, no antibodies to fight it

37. Biosynthesis of DNA vs RNA viruses

38. Multiplication of Animal Viruses:
Release
Non-enveloped viruses = released from host through ruptures
in plasma membrane  host cell death
Enveloped viruses = the envelope develops around the capsid
by budding: virus takes portion of plasma membrane as it
pushes through it to extracellular space
• Doesn’t immediately kill host cell

39. Budding: formation of the envelope

40. Viruses and Cancer
Oncogenic viruses (cancer generating) = viruses capable of
inducing tumors in animals (aka oncoviruses)
• ~10% of cancers induced by viruses
Oncogenes = parts of the genome that cause cancer when
mutated; expressed at high levels in tumor cells
Transformation = viral genetic material integrates into host
DNA and replicates with it (like bacterial lysogeny)
• Used by all oncogenic viruses
Oncolytic – viruses that grow in and lyse cancer cells

41. DNA oncogenic viruses
Herpesviridae
•Epstein Barr virus causes infectious mononucleosis
- remains latent in some throat and blood cells
throughout life
 various lymphomas (Hodgkin’s, Burkitt’s)
Papovaviridae
•all uterine (cervical) cancers are caused by human
papillomavirus
Hepadnaviridae (Hep B) & Flaviviridae (Hep C)
•hepatitis B and C can cause liver cancer

42. RNA oncogenic viruses
• ONLY the retroviridae family of RNA viruses cause
cancer
Human T-cell leukemia viruses 1 & 2 = cause adult T-cell
(white blood cell) leukemia and lymphoma
Mechanism of tumor generation:
Viral reverse transcriptase generates the double
stranded viral DNA (provirus) that integrates into the
host chromosome
• Changes in genetic material always put the cell at
risk for tumor formation
Know oncogenic viruses and diseases with them

43. Latent viral infections
Viruses may infect host cells but cause disease only after a
long period of time = latent infections
All human herpesviruses can remain in host cells for a
person’s lifespan, until reactivation:
• Immune suppression (ex: AIDS)
• Fever, sunburn (cold sores from herpes simplex)
•Reactivation may never occur  no symptoms
Chronic can be latent or persistant

44. Persistent viral infections
Persistent (chronic) viral infections occur gradually over a
long period of time
• Infectious virus builds up over time, rather than
appearing suddenly (like latent infections)
• Typically fatal
Example:
Subacute sclerosing panencephalitis (SSPE) = a
progressive, debilitating, and deadly brain disorder
• Caused by immune resistant measles
• No cure; may be managed with medication
Remember this one

45. Figure 13.21
Latent and Persistent Viral
Infections
Peaks, looks like it will go away, then spikes (can be lethal)

46. Prions
Prions = proteinaceous infectious particles
• No nucleic acid, just purely protein
• Cause infections diseases - neurological
• Bovine spongiform encephalophathy (mad cow)
• Creutzfeldt-Jakob disease (CJD)
• Gerstmann-Straussler-Sheinker syndrome
Run in families, indicating genetic component
 not purely genetic:
 Eating infected meat transmits mad cow
 CJD transmitted via transplanted nerve tissue
Only killed by formaldehyde, very resistant
KNOW ALL PRIONS

47. Prion Diseases
• Crutzfedt-Jakob
• Kuru
• Bovine Spongiform
encephalopathy (mad
cow)
• vCJD
http://www.beatricebiologist.com/2010/08/watch-out-for-
prions.html

48. Plant viruses and viroids
Plant viruses = similar in morphology and nucleic acid types to
animal viruses
Common crop viruses:
- Bean mosaic virus
- Wound tumor virus
 corn and sugarcane
- Potato yellow dwarf virus
Must penetrate cell wall by:
- Wounds
- Parasites
 Ex) aphids that eat sap
Result = color change, deformed/stunted growth, wilting
Only destructive

49. Plant viruses and viroids
Infected plant spreads virus via pollen and seeds
viroids = short pieces of RNA with no protein coat
• Known to cause some plant diseases
• Pathogens of plants only
• Potato spindle tuber viroid
Prions are only protein
Viroids are only RNA

50. Some major plant viruses

51. DNA virus families
Adenoviridae = cause acute respiratory disease (common
cold)
Poxviridae = cause skin lesion diseases
• Pox = pus-filled lesions
• Smallpox
• Cowpox
Herpesviridae = named after herpetic (spreading)
appearance of cold sores
• Genus simplexvirus (cold sores)
• Genus varicellovirus (chickenpox)
• Genus lymphocryptovirus (mononucleosis)

52. Figure 13.5b
Poxviridae
• Double-stranded DNA, enveloped
viruses
– Orthopoxvirus (vaccinia
and smallpox viruses)
– Molluscipoxvirus
– Smallpox
– Molluscum
contagiosum
– Cowpox

53. Mastadenovirus
(adenoviridae)
Herpes simplex virus
(herpesviridae)
DNA virus families

54. DNA virus families
Papovaviridae = named for the papillomas (warts)
polyomas (tumors) and vacuolation (development of
cytoplasmic vacuoles)
• Genus papillomavirus causes warts
- HPV: cervical cancer and cauliflower-like growths
in cervix
- Vaccine: Gardasil
• Polyomavirus diseases primarily affect the
immunocompromised  tumors

55. DNA virus families
Hepadnaviridae = named for their role in causing hepatitis
and containing DNA
• Only one genus  causes hepatitis B
• The other hepatitis viruses (A,C,D,E,F,G) are RNA
viruses
Hepatitis = inflammation of liver
• Hep B is similar to Hep C (an RNA virus)
• Both transmitted through blood
- Associated with intravenous drug use
• Cirrhosis, liver failure, liver cancer
• Vaccine for Hep B, no vaccine for Hep C!

56. RNA viruses
Picornaviridae = small (-pico) and contain RNA
• Single stranded RNA viruses
Important genera:
Rhinovirus = responsible for >50% of common colds
Enterovirus = fecal oral transmission
poliovirus, coxsackie virus (aseptic meningitis)
Hepatovirus = only species in the genus causes Hep A
• Fecal-oral transmission
• Contaminated food or water
• Primarily affects less developed countries
• Replication: mucosa  intestine  liver
• Symptoms: fever, nausea, diarrhea, jaundice
• Prevention: vaccine

57. Togaviridae are enveloped (toga = covering)
• Like picornaviruses, have a single strand of RNA
Important genera:
Rubivirus = only member is rubella virus
• Part of MMR vaccination series
• Rubella = (latin: little red) aka german measles
- Itchy red rash
- Swollen glands, fever
• Transmission: respiratory droplets
• Treatment: none, usually subsides in days
- Less severe than measles (rubeola virus)
RNA viruses

58. RNA viruses
Paramyxoviridae = enveloped viruses with spikes
• single stranded RNA viruses
Important genera:
Rubulavirus = contains the species Mumps virus
• Transmitted by respiratory droplets
• Was common before MMR vaccine (1960s)
• Symptoms: fever, headache, muscle aches, tiredness
- swelling of parotid (salivary) glands!
- Orchitis = swelling of testicles (~30% of males)

59. RNA viruses
Rhabdoviridae = bullet-shaped viruses with a single strand
of RNA
• ~150 viruses of vertebrates,
invertebrates and plants
Lyssavirus = genus that contains the
species rabies virus
• Transmission: animal bite
• Salivary glands highly concentrated with virus
• Spreads from muscle cells into CNS
• Fatal if not treated prior to severe symptoms

60. RNA viruses
Orthomyxoviridae = enveloped helical viruses with a
single strand of RNA
Influenza virus = three genera (A,B,C) that cause influenza,
a contagious respiratory illness
Symptoms: cough, sore throat, aches, fatigue
and serious complications:
- Pneumonia
- Bronchitis
- Worsening of chronic health problems
TEM of H1N1 Influenza

61. Avian Influenza
Clinical Focus, p. 371

62. RNA viruses
Reoviridae = respiratory, enteric, orphan
• Affect gastrointestinal system, respiratory tract
• Double-stranded RNA viruses
Rotavirus = genus in family reoviridae
• Most common cause of severe diarrhea
among infants and children
 Fecal-oral transmission
• 2009: included into U.S. recommended
vaccination program by W.H.O.
Stylized SEM: rotavirus

63. RNA viruses
Retroviridae = reverse transcriptase viruses
• Reverse transcriptase = uses viral RNA as template to
produce double-stranded DNA
• integrated into host chromosome  provirus
- protected from host immune system & antivirals
- Replicates with host DNA
- Can be expressed to produce new virions and infect
adjacent cells
Human Immunodeficiency virus (HIV)
• Infects immune cells, progresses to AIDS
• No cure: hard to target latent infected cells

64. Retroviruses