Microbio -4- introduction to virology
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| what is a virus and its sole functions | nucleic acid (RNA or DNA) that encodes proteins for 3 functions
1-control an infected cell
2-replicate more viruses
3-infect more cells
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| In regards to viruses what functions of viruses do we try to stop | stop them from gaining control of a cell and stop them from replicating more viruses
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| All viruses can be grouped into two types what are they | enveloped and naked viruses
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| what is a virion | infectious particle of virus
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| what is a capsid | coat of protein that surrounds the nucleic acid genome of the virus
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| what is a nucleocapsid | protein core that comes into direct contact with the nucleic acid (some viruses don't have this)
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| What is a viral envelope | lipid bilayer carrying viral glycoproteins surrounding the capsid or nucleocapsid
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| what are the components of virions in enveloped viruses | envelope, glycoprotein receptor, capsid/nucleocapsid, genome
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| what are the components of the virion in naked viruses | capsid/nucelocapsid, genome
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| what is the function of the glycoproteins in virus envelopes | usually involved in binding to receptors on surface of target cell and are used to induce cell entry
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| What determines the host range of the virus | the viral receptors on the virus that allow it to bind and target a specific host cell
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| when speaking of structural proteins with regards to viruses what are we talking about | capsid(nucleocapsid) proteinsand envelope glycoproteins
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| What are the non-structural proteins of virus | any protein not in capsid, or glycoproteins in the envelope
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| why do viruses package non-structural proteins into the virion | these are proteins that are needed immediately after infection to allow the virus to infect the host. Most of the proteins are not readily available in the host or saves precious time for the virus
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| What are some non-structural proteins commonly packaged in the virion | polymerases, reverse transcriptase, transcription factors, host defense attack proteins
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| How are viruses classified | Genome strucutre: DNA or RNA, single stranded or double stranded, segmented or single nucleic acid molecule
Presence or absence of a viral envelope
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| Will you find a virus with both DNA and RNA genome | NO
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| HOw can genomes be arranged | linear or circular arrangements
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| What is the term for a virus with multiple pieces of nucleic acid that form their complete genome and give an example | segmented, influenza
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| What virus has a diploid genome where it carries two copies of its genome | HIV, retroviruses
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| The genome of most DNA viruses is generally what structure and what is the exception to this rule | double stranded, except parvoviruses
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| RNA viruses genomes are usually what structure except which exception to this rule | Single stranded except reoviruses
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| Viruses can be classified based on which which strand of their nucleic acid is the coding strand what are the two terms for this | + and -
Normal Coding= +
Non-coding= -
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| What is the method of classification that clinicians use for viruses and give the names of classification | classification based on route of entry
enteric
respiratory
zoonotic
sexually transmitted
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| A virus cultured from an individual that is unique and distinct from other related viruses would be known as what | isolate
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| a virus or group of viruses that are distinguished based on the ability of an antibody to recognize the capsid or envelope glycoproteins are known as what | serotypes
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| dsRNA genome of 10-12 bases naked | reoviruses
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| +ssRNA virus, naked | caliciviridae or picornaviridae
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| +ssRNA virus, enveloped | Flaviviridae, Togaviridae, retroviridae, coronaviridae,
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| -ssRNA viruses, enveloped | Bunyaviridae (3 circular segments), orthomyxoviridae (8 seg), Paramyxoviridae, arenviridae (2 seg)
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| +or- ssDNA virus, naked | parvoviridae
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| dsDNA viruse, naked | Papovaviridae (circular genome), Adenoviridae,
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| dsDNA virueses, enveloped | Hepadnaviridae (gapped genome), Herpesviridae,
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| dsDNA virus, double enveloped, irregular capsid | Poxviridae
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| this virus has a unique gapped genome | Hepadnaviridae
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| what are the six parts of the virus life cycle | 1- attachment
2- penetration/entry
3- transcription and translation of early proteins
4- replication & synthesis of late proteins
5- assembly
6- exit
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| What must a cell express in order to be infected by a virus | specific proteins that the virus can bind
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| Why can a virus be species specific | even though we have proteins that are functional the same they are structurally different which means a virus may not be able to bind them
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| What is the term for the specific group either species or cells that a virus can PRODUCTIVELY REPLICATE in | Host Range
Species- pig, human
Cell type- neuron, myocytes, enterocytes
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| What factors can determine a viruses host range | ability to bind the target cells
ability to interact with needed host replication machinery
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| Why can't adenovirus infect rat cells even though they can enter them | they can't interact with the transcription factors in the rat like they can in the human and therefore can't cause infection
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| After step 1 (attachment) of the viral life cycle is complete what must a virus now do | 2 penetrate or enter the cell
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| What are the normal routes for nutrients and objects to get into the cell | diffusion
transport through channels
endocytosis pinocytosis
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| How can a virus use diffusion to penetrate or enter the cell | Virus binds and then fuses the viral envelope directly with the cell membrane and then the viral envelope become part of the cell membrane and the virion gets dumped into the cell
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| How do viruses uses transport channels to penetrate or enter the cell | some create their own channels other physically pierce the membrane creating a channel
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| Viruses that have the cell endocytose them have to make sure what doesn't happen to them and what are the two main ways they avoid this | that they get transported in the endosome to the lysosome to be degraded.
1 Some have a pH trigger that as the pH in the endosome increases it triggers the envelope to bind to the endosome membrane and fuse
2 some lyse the endosome as the pH changes
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| where do most DNA viruses complete replication and transcription | nucleus except Pox virus
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| Where do most RNA viruses complete replication and transcription | cytoplasm except orthomyxoviruses, and (retroviruses?)
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| Are RNA polymerase I, II and III RNA or DNA dependent polymerases and which one carries out most mRNA synthesis | DNA-dependent, RNA Polymerase II
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| what type of RNA polymerase do RNA viruses need for replication, & transcription | RNA-Dependent RNA polymerase
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| some viruses regulate gene expression in groups and are identified by the timing of expression what are the groups | early genes, immediate early genes, late genes
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| Most DNA viruses use ________ __________ factors to regulate expression of their genes | Most DNA viruses use CELLULAR TRANSCRIPTION factors factors to regulate expression of their genes
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| Do most RNA viruses use introns and/or alternate splicing | no only retroviruses have introns and alot of the DNA viruses have introns as well
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| What must happen to allow mRNA to leave the nucleus why is this a problem for viruses | it must be fully spliced, poly a'd and capped viral mRNA is not any of those things when it needs to leave the nucleus
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| What is one viral adaptions that allows HIV to get its unspliced mRNA to get out of the nucleus | HIV has one fully spliced mRNA that encodes for a protein called REV. REV then enters nucleus and shuttles out ANY HIV mRNA/genomic RNA out of the nucleus
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| what are some of the unique features of viral genomes | small genomes for optimizing space, use alternate splicing, overlapping genes, transcription from both strands (DNA viruses only) and other mechanisms
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| Do any viruses make their own ribosomes | no they ALL use cellular ribosomes
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| With RNA viruses that replicate in the cytoplasm does this occur just free floating | no, requires an aggregate surface or substrate such as mitochondria or autophagosomes
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| All RNA viruses except retrovirus must encode what to replicate their genomes and/or create mRNAs | RNA-dependent RNA polymerase
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| dsRNA viruses must carry what in their virion | RNA-dependent RNA polymerase
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| how is replication different for RNA viruses than DNA viruses | RNA viruses use a unique and varied priming system to initiate replication DNA viruses use origins of replication similar to cellular types
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| What is the target of most anti viral therapy against DNA viruses | target their DNA polymerases to inhibit replication
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| A state where the virus is not actively replicating- minimal or no viral protein synthesis, only maintenance of viral genome | latency
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| What two viruses are the main viruses to enter into latency | herpesviruses and Retroviruses
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| What is assembly for viruses | organized production of new virions, capsids most be assembled with genome inside
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| How do viruses exit the cell | lysis
budding
exocytosis
syncitia formation
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| what is the most common form of exit for naked viruses | lysis
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| what is the most common form of exit for enveloped viruses | budding
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| How do viruses that bud end up killing the host cell since they don't cause lysis | they shut down other functions in the cell like protein synthesis and DNA synthesis which eventually kills the cell
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| what is the main mode of entry into the cell for viruses | receptor mediated enodcytosis
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| Heritable changes in the nucleotide sequence of a segment of DNA or RNA | mutation
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| exchange of segments between similar nucleic acid molecules | recombination
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| exchange of entire nucleic acid molecules | reassortment
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| Why do viruses tend to accumulate mutations more rapidly and evolve into new strains and serotypes that can evade the immune system | their polymerases are not as accurate as cellular polymerases and have poorer proofreading capabilities
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| what is common in in picornaviruses with recombination | template switching
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| Infection by two strains of the same virus can lead to what when parts from each strain end up packaged in the virion | reassortment
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| what type of immunity allow most cells in the body to detect when they are infected by a virus and produce interferons that activate the immune system, change the infected cell to inhibit viral replication, and alert neighbors to prepare for infection | Innate immunity
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| What cell has antigen non-specific methods to detect virus infected cell and kill them | natural killer cells
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| branch of the immune system that uses internally derived peptides presented on MHC-1 receptors to present viral proteins being made inside to the T lymphocytes | cell mediated immunity
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| branch of the immune system where neutralizing antibodies are produced to surface of the virion (either capsid, naked viruses, or envelop proeins) this can clear away the viruses from the body | humoral immunity
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| What do some viruses do to avoid cell mediated immunity | they block presentation of proteins to MHC 1 molecules, other secret cytokines to screw up the immune response,
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| What are emerging pathogens | viruses that evolve to infect new hosts or mutating into new viral species
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| From what species have most of the recent emerging viruses seem to have come from | bats
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| what type of virus has most of the emerging viruses been | RNA viruses
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| What are the three basic approaches to clinical viral testing | 1. viral culturing
2. direct detection of virus in clinical samples
3. serological testing to detect viral antibodies
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| why is viral culturing limited in its ability to detect viral infections | virus has to be able to reproduce ex vivo, needs to be performed during onset or acute phase of infection, requires correct specimen source (i.e. throat swab, stool sample)
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| What are the methods for direct detection of viruses | microscopy, enzyme immunoassays, nucleic acid based tests
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| Since viruses are even to small to be seen by most microscopes what are you looking for in microscopy | changes the virus has induced in the host cells
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| What does elisa stand for | enzyme linked immunosorbent assay
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| how does elisa work | use antibody specific for target of interest (viral protein), link the antibody to a reporter enzyme (color, light) if the target is present you will see the change
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| what are some applications of the elisa test | rapid strep test, HBsAg detection,
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| what is the test for nucleic acid of virus | PCR (polymerase chain reaction) test also RT- PCR (reverse transcriptase- polymerase chain reaction)
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| What is the substrate for RT-PCR | single stranded mRNA
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| how would you diagnose infection with non cultivable agents, determine an immune response, determine the status of the infection | serological testing to detect viral antibodies
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| If you have had class switching from IgM to IgG with viral antibodies what does this indicate | acute/recent infection to chronic/past infection
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