chapter+5,+25,+37 (microbiology) 8th edition
TRANSCRIPT
Viruses Chapter 5, 25 & 37
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
Viral replication
Video
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
Viral Hosts and Taxonomy
– Viruses can be classified on the basis of the hosts they infect
Bacterial viruses (bacteriophages)Archaeal virusesAnimal virusesPlant 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
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 capsidSmallest morphological unit visible with an
electron microscope
Helical Capsid Helical capsid are shaped like hollow tubes with
protein walls (Tobacco Mosaic Virus is the best studied example)
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
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
Bacteriophage
Bacteriophage are viruses that infect bacteria.
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
Nature of virion
Some virions contain enzymes critical to infection
– Lysozyme Makes hole in cell wallLyses bacterial cell
– Nucleic acid polymerases– Neuraminidases
Enzymes that cleave glycosidic bonds
Allows liberation of viruses from cell
Morphology of different viruses
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
Viral replication
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
Attachment of bacteriophage T4 to the cell wall of Escherichia coli and injection of DNA
Viral Entry and Uncoating
Assembly
Virion Release
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).
Quantification of bacterial virus by plaque assay using the agar overlay technique
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.
Cell cultures in monolayers grown on a Petri plate
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)
Mechanisms to diminish viral infectionsEukaryotes possess mechanisms to diminish viral
immune defense mechanismsProkaryotes 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 DNAViral mechanisms to evade bacterial restriction systems
– Chemical modification of viral DNA (glycosylation or methylation)
– Production of proteins that inhibit host cell restriction system
Classification of virusesClass Type of
nucleic acidBacterial 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
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
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.
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 proteinsSynthesized later Include proteins of virus coatTypically structural componentsSynthesized in larger amounts
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
Schematic representations of the main types of bacterial viruses
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
Temperate Bacteriophages, Lambda, and P1
Temperate viruses: can undergo a stable genetic relationship within the host
– But can also kill cells through lytic cycleLysogeny: state where most virus genes are
not expressed and virus genome (prophage) is replicated in synchrony with host chromosome
Lysogen: a bacterium containing a prophageUnder certain conditions lysogenic viruses
may revert to the lytic pathway and begin to produce virions
Lytic and lysogenic cycles
Lytic and lysogenic
Temperate Please click on the link to watch this video
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)
Overview of Animal Viruses
Consequences of Virus Infection in Animal Cells
– Persistent infections: release of virions from host cell does not result in cell lysisInfected 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
Possible effects that animal viruses may have on cells they infect
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.
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.
Retroviruses
Retroviruses have a unique genome
– Contain specific genesgag: encode structural proteinspol: encode reverse transcriptase
and integraseenv: encode envelope proteins
Retrovirus structure and function
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
HIV life cycle
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
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
Diseases associated with AIDS
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.
Poliovirus
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
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
Coronavirus
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.
Replication of a negative-strand RNA virus
Influenza virus
Replication cycle of Influenza A virus
Antigenic shift
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).
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
Antigenic drift
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
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.
Herpesvirus
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
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
dsDNA virus - Herpesvirus
Chickenpox
Varicella zoster virus
Chickenpox (Varicella) and Shingles (Herpes Zoster)
Shingles (herpes zoster; postherpetic neuralgia)– reactivated form of
chickenpoxvirus resides in
cranial and sensory neurons
reactivation - virus migrates down neuron
Treatment – supportive; acyclovir
and others
Chickenpox (Varicella) and Shingles (Herpes Zoster)
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)
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
Burkitt's Lymphoma
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.
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
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)
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
Hepatitis
– inflammation of liver, caused by 11 different viruses2 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
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
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
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
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.
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)
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.
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.
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
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
Prion overview
video
Prion characteristics
video