Virology Flashcards
infectious progeny particles, formed by de novo self- assembly, vehicle for transmission of the viral genome
virion
obtained crystals of TMV in 1935
Wendell Stanley
direct visualization of virus particles for the first time in 1930a was done using the
electron microscope
giant viruses infecting amoeba
mimivirus
like other organisms virsuses;
possess genes
evolve by natural selection
reproduce by creating multiple copies
unlike any other life forms viruses;
do not have cellular structure
do not have their own metabolism
cannot naturally reproduce outside a host cell
observed that the causative agent of tobacco mosaic disease was not retained by filters 1892
Dmitri Ivanovsky
discovered that TMD is caused by a distinctive agent which is a infectious liquid; contagium vivum fluidum= soluble living germ; confirmed and extended Ivanovsky’s results 1898
Martinus Beijerinck
discovered that the causative agent of foot and mouth disease can pass through filters; infectious filterable agents- small particles (could be retained by a finer filter); virus as a particulate matter
Friedrich Loeffler
Paul Frosch
origin of viruses; genetic elements that gained the ability to move between cells
progressive/ escape hypothesis
origin of viruses; previously free-living organisms that became parasites
regressive/reduction hypothesis
origin of viruses; precursors of life
virus first hypothesis
cell components that are potential candidates as precursors of viruses
eukaryotic mRNA
plasmid
transposon
contains relatively large repertoire of putative genes associated with translation which may be remnants of a previously complete translation system; depend less on their host cell for replication; does not differ significantly from parasitic bacteria (Rickettsia prowazekii)
Giant mimivirus (microbe-mimicking virus)
an isolate whose genome sequence differs from that of a reference virus (may contain on or more mutations)
virus variants
variant that possesses a unique and stable phenotypic characteristics
virus strain
a group of closely related viruses with a common ancestor
lineage
hypermutable viruses; there is no fixed sequence of basis for their genome; genome exist as a large # of variants “quasispecies”
RNA viruses
a population structure of viruses with a large number of variant genomes
viral quasispecies
results from high mutation rates as mutants arise continually and change in relative frequency as viral replication and selection proceeds
quasispecies
process that results in the production of new genome derived from 2 parental genomes
recombination
a category of recombination that may occur with segmented genome viruses having all the segments packaged in one virion (reovirus, bunyavirus, influenza viruses)
reassortment
progeny virions containing mixtures of genome segments from two parental strains
reassortants
a change in the phenotype because of the accumulation of point mutations over time
antigenic drift
change in the surface glycoproteins (ie influenza) because of genetic reassortment
antigenic shift
ultimate species jumper
influenza virus
evolutionary relationships between viruses are determined through
sequence comparisons
to determine/identify evolutionary relationships between closely related viruses you try to identify the
virus hallmark (vh) genes
functions of the virion:
protects the genome
delivers the genome
delivers protein contained in the virion
interactions with the host
functions of capsid:
protects the viral genome
recognition & interaction with hose cell
facilitate transfer of the viral NA
determines the antigenic characteristic of the virus
basic protein building block of the capsid
protomer
morphological unit on the surface of the virus, mau have pentamer or hexamer protomers
capsomere
virion symmetry; 20 faces each an equilateral triangle, 12 vertices each formed where the vertices of the five triangles meet, 30 edges at each of which sides of the two triangles meet
icosahedral (cubic, icosahedron)
why icosahedral shape is very common in viruses
allows tight packing of subunits
size of subunits can be smaller (economizing on genetic info)
most efficient arrangement for subunits in a closed shell (uses the smallest # of units to build a shell)
virion symmetry; NA is coiled in the form of a helix, protein subunits arranged helically like hollow cylinders around the coil (may either be rigid (plant viruses), or long and flexible (animal viruses)).
Helical
virion symmetry; influenced by both NA and capsomeres
size of helical capsid
virion symmetry; determined by size, shape, and protein interaction
diameter/width
virion symmetry; determined by the length of NA
length
virion symmetry; atypical viruses; ie poxvirus, bacteriophage T4
complex
genomes of most plant viruses
ssRNA
genomes of most fungal viruses
dsRNA
genomes of most prokaryotic viruses
dsDNA genomes
genomes of large viruses
dsDNA
example of viruses with the largest RNA genomes
some coronaviruses (33kb)
largest virus genome
pandoravirus 2.8mb larger than the smallest genomes of cellular organisms
segmented genomes with segments that are in the same capsid not contained; each genome segment is packaged into a separate virus particle; occurs in both DNA and RNA plant viruses; solves the problem of breakages but all virus particles must be taken up by a single host cell to establish productive infection
multipartite genomes
much more common amongst RNA viruses than DNA viruses
segmented genomes
genome type common among plant viruses
multipartite genomes
predilection of viruses to infect particular cell types
tropism
acquired by ingestion (fecal-oral transmission) and replicate primarily in the intestinal tract
enteric viruses
acquired by inhalation or by fomites and replicate primarily in the respiratory tract
respiratory viruses
replicate in their hematophagous arthropod vectors, transmitted to bite to vertebrate hosts (virus replication via viremia
arboviruses
acquired by close contact, injection, fomites and by unknown means ( infects only specific cells in particular target organs, become persistent and may evoke transformation of the host cells (malignancy))
oncogenic viruses
method to determine the number of virus particles
titration
period between apparent disappearance of the infecting virus and the release of newly synthesized progeny; extracellular virus cannot be detected
latent period: eclipse and maturation phase
event during eclipse phase
early viral genes are transcribed into RNA
translation of early gene products
three main types of early gene products
proteins that shut down cellular NA and protein synthesis
proteins that regulate the expression of the viral genome
enzymes required for the replication of the viral NA
nucleus as the site of transcription and DNA replication
utilize cellular RNAP II and other cellular enzymes
most DNA viruses
replicate in the cytoplasm
lack enzymes to copy RNA from an RNA template
viral genome itself must function as an mRNA or the virus must encode and carry its own RNA polymerase to transcribe RNA from the RNA genome
most RNA viruses
interval in which progeny virions accumulate in the cell or in the surrounding medium at exponential rates
lytic viruses; infected cells cease metabolic activity and lose structural integrity (viral production ceases, titers slowly drop)
non-lytic viruses: cells may continue to synthesize virions indefinetely
maturation phase
virus replication cycle; initiation phase
- attachment
- penetration
- uncoating
virus replication cycle; replication phase
- transcription of early mRNA
- translation of early proteins
- replication of viral NA
- transcription of late mRNA
- translation of late proteins
virus replication cycle; release phase
- assembly of virions
- release
HIV gp120 receptor
CD4
HIV gp41 receptor; coreceptor of CD4
CCR5, CXCR4
two main mechanisms virions can enter cells during penetration/ uptake
receptor-mediated endocytosis (viropexis)
membrane fusion
viropexis vesicles is coated with
clathrin
viropexis; after clathrin coat is removed, it is followed by
endosome fusion then release of the viral nucleocapsid into the cytoplasm
entry by direct fusion of envelope and plasma membrane
merging of two different membranes occur as a result of the activity of specific viral fusion proteins that mediate the process
herpesviruses, paramyxoviruses, HIV
membrane fusion
intracellular transport ( transport from the cytoplasm to a location close to the nucleus ) is via
microtubules with motor proteins
necessary for the viral genes to become available for transcription
removal of capsid, freeing the nucleic acid, exposing the viral genome to the host cell machinery
genetic material of the virus is introduced into the cell, often accompanied by essential viral protein cofactors
uncoating
production of virion components including the genomic NA
sometimes, cellular enzymes replicate the viral genome, assisted by viral proteins
in most cases, viral proteins are responsible for genome replication although they utilize cellular proteins to aid this
replication phaseq
viruses arranged based on the different form of NA that is incorporated into virions; widely differ in their abundance, diversity of the constituent viruses and other MGE, and spread among the cellular life forms
Baltimore classes of viruses
two most abundant and diverse classes of viruses
dsDNA which dominates the prokaryotic virome
(+) RNA viruses which is most common in eukaryotes
mimic the replication expression strategy of cellular life forms
class I
typically replicate via RCM
Class II
genome same polarity as the mRNAs for virus proteins
class IV
genome is an ssRNA complementart to the mRNa (or in some groups of viruses, an ambisense RNA)
class V
+RNA genome replicated via a DNA intermediate, produced by reverse transcriptase of the genome
class VI
replicate via reverse transcription, package dsDNA form or an RNA-DNA hybrid into virions
class VII
viral DNA genomes
host genetic system is based on DNA
many DNA viruses emulate the host
almost all viral DNA genomes are not like cell chromosomes
viral RNA genomes
cells have no RdRp
encode RdRp
RdRp produce RNA genomes and mRNA from RNA templates
retrovirus; virus integrated into the host chromosome; can remain latent; target T cells (HIV)
provirus
release phase; assembly
packaging of the genome into the capsid to from the nucleocapsid
many viruses are assembled all at the same time
release phase; assembly; can condense in the absence of NA
icosahedral capsid
release phase; assembly; cannot form without the viral NA
nucleocapsid of viruses with helical symmetry
release phase; maturation
further modification which happens after assembly such as addition of the envelope
happens at membrane sites with added viral proteins
release phase; exit from the cell
final step of the rep cycle
rise period; rapid rise in the extracellular virus titer until a constant titer is reached at the end of the replication cycle
unique occurrence during the final stage of maturation of viruses like HIV and paramyxoviruses
does not occur until virus particle is released from the host cell
HIV; viral glycoprotein has to be cleaved by a virus-coded protease after virus release
Paramyxoviruses; cleavage of surface glycoprotein spikes to become infectious upon virus release
outcomes of virus infection; results to production of progeny virion; often lysis
productive infection
outcomes of virus infection; persistence of viral genomes but not infectious viral particles in transiently permissive cells without the destruction of the infected cell; sequence integrated into cell genome or as multiple copies of cccDNA; may be activated to become productive; can be episomal
latent infection
outcomes of virus infection; infection of a susceptible cell, which may be non-permissive, allowing only a few viral genes to be expressed
infection of either permissive or non-permissive cells with defective viruses, which lack a full complement of viral genes
abortive infection
outcomes of virus infection; infected cells may be only transiently permissive. and that the virus persists in the cell until the cell becomes permissive; only a few of the cells in a population produce viral progeny at any time; may have serious consequences- cell transformation and cancer
restrictive/ restringent infection
outcomes of virus infection; death of cell prior to the production of progeny virions; apoptosis- suicide mechanisms among cells
PCD
cell culture; prepared form animal tissues, limited life span (5-20 cell div); derived from monkey, kidney, human foreskin
primary cell culture
cell culture; homogenous population of a single type, can divide up to 100 times, can retain diploid number (human embryonic lung WI-38 strain)
diploid cell strains
cell culture; single cell type, can be propagated indefinitely, aneuploid (HeLa cells)
continuous cell line
characteristic morphologic changes in the host cells or tissue;
necrosis - poliovirus
syncytia- measles, hsv
inclusion bodies- rabies
transformation
lysis
cytopathic effects
assays of infectivity, infectious unit count
ie plaque, end-point titration method
biological assays
assays to measure non-infectious virus; ie electron microscopy, immunological methods
physical assays
conc of a virus in a sample
virus titer
useful for determining the tires of retroviruses that do not form plaques
transformation assay
most common indirect method of measuring number of virus particles; gives relative estimates of titers
hemagglutination assay
uses antibody to detect viral proteins; use viral proteins to detect immune response
serological assays
dsDNA; largest genome; complex
poxvirus
dsDNA; associated with latent infections; some oncogenic
herpesvirus
dsDNA; respiratory, enteric infections; “gland”, excellent models for molecular studies of eukaryotic cell processes; conjunctivitis, gastroenteritis
adenovirus
dsDNA; restricted host range; epitheliotrophic
papillomavirodae
dsDNA; poxvirus; orthopoxvirus; extensive fatalities; eradicated
variola virus- smallpox
dsDNA; poxvirus; cause milker’s nodes (pseudocowpox) and orf (sore mouth or contagious ecthyma, scabby mouth of sheep and goats, papulovesicular eruption in the lips, in humans lesion on the hand or forearm); occupational viral disease
parapoxvirus
dsDNA; poxvirus; multiple discrete nodules 2-5mm in diameter; limited to the epidermis except on soles and palms; pink/white wart-like tumors having a central dimple
molluscipoxvirus infection; Molluscum contagiosum
dsDNA; herpesvirus; realm
duplodnavaria
dsDNA; herpesvirus; subfamily; short GC and cytolytic; genus simplex (HHSV 1,2), varicella (VZV), latent in neurons
alphaherpesvirus
dsDNA; herpesvirus; subfamily; long GC, cytomegalic (genus cytomegalo) latent in gland, kidneys; CMV / long GV lymphoproliferative (genus roseola), HHSV6,7 latent in lymphoid tissue
betaherpesvirus
dsDNA; herpesvirus; subfamily; variable GC, lymphoproliferative; lymphoid (genus lymphocrypto), Epstein-Barr virus, (genus Rhadino), Kaposi sarcoma-associated herpesvirus, latent in lymphoid tissue
gammaherpesvirus
dsDNA; herpesvirus; alphaHV; oral-facial lesions; transmitted through DC with virus containing secretions (saliva), or with lesions on mucosal surface, herpetic whitlow
HSV 1
dsDNA; herpesvirus; alphaHV; genital lesions; sexual contact, infection of a newborn during birth ; primary infection via mucoepithelia (genital herpes); latency in sacral or lumbar ganglia causing recurrent genital herpes
HSV 2
dsDNA; herpesvirus; alphaHV; highly contagious; transmission via contact or respiratory route; febrile infection; primary and secondary infections (latency after PI in neuron); acyclovir can shorten duration and severity
VZV
PI-varicella or chicken pox
SI- zoster or shingles
dsDNA; herpesvirus; betaHV; target T lymphocyte; transmission via direct contract/ respiratory; latency in T lymphocyte; cause roseola/exanthem subitum, febrile convulsions, encephalitis
HHV-6
dsDNA; herpesvirus; gammaHV; KSHV; target endothelial cells; latency in leukocytes; transmission via exchange of body fluids
HHV-8
dsDNA; herpesvirus; gammaHV; targets B lympho and epithelial cells; latency in B lympho; transmission via saliva known as kissing disease; cause infectious mononucleosis
EBV
dsDNA; closely related to papilloma, smaller
polyomaviridae
dsDNA; polyomaviruses; cause a fatal illness known as progressive multifocal leukoencephalopathy (PML)
JC virus
dsDNA; polyomaviruses; affects kidneys of immunosurpressed transplant patients and produces a mild respiratory infection
Polyomavirus hominis 1 or BK virus
dsDNA; polyomaviruses; respiratory infections
KI and WU viruses
dsDNA; polyomaviruses; form of skin cancer
Merkell cell polyomavirus
ssDNA; small; one human pathogen, B19; has tropism for red blood cell progenitors, one genus contains replication-defective viruses
parvovirus
dsDNA; parvovirus; erythema infectiosum/ fifth disease/ slapped cheek rash; transmission via direct contact, droplet infection; cause aplastic anemia with chronic hemolytic anemia, hydrops fetalis, acute arthritis
HPV-B19
dsRNA; respiratory enteric orphans; double capsid shell allows them to resist vey low pH in gut thus assoc with enteric infections; linear, segmented 10-12; genetic reassortment (rotavirus- major cause of infantile diarrhea); realm riboviria
reoviridae
dsDNA; reovirus; transmitted by wood ticks (Dermocentor andersoni); dengue like disease with frequent rash, headache, chills, muscle pain, occasional encephalitis, hemorrhagic symptoms esp in children; deaths are rare
colorado tick fever
+ssRNA; large genome; S proteins; HFr
coronaviridae
+ssRNA; small RNA virus; among the oldest and most diverse virus; host range at least 5 of the 7 vertebrae classes; cytoplasmic rep; realm ribovaria
picornaviridae
+ssRNA; picornaviridae; major global animal health problem (infectious); genus Aphthovirus; 7 serotypes O,A,C SAT 1, SAT 2 SAT 3 , ASIA 1; vaccination via blocking symptoms not virus transmission
foot and mouth disease by FMDV
+ssRNA; picornaviridae; one of the 1st disease ever recorded; genus Enterovirus - inflammation of grey matter, spinal cord; transmission fecal-oral, respiratory; vaccine available
poliomyelitis
+ssRNA; picornaviridae; inflammation of the liver; infectious/ epidemic; transmitted via fecal-roal,sexual anal-oral, and blood transfusion; symptoms include yellow eyes (jaundice), loss of apetite, nause, diarrhea, fatigue, abdominal pain
Hepatitis A
+ssRNA; picornaviridae; common colds; replication restricted in URT; ~10 serotypes hence repeated infections; spread via aerosol/ hand contact 2-3 days IP; no vaccine due to antigenic diversity
Rhinoviruses
+ssRNA; yellow; 13/70 cause disease in humans; prev classified under group B arboviruses and togaviruses; spread through arthropod vectors mainly ticks and mosquitoes; host range mammals of all genera
flavivirus
+ssRNA;flavivirus; most important human -arthropod borne viral disease in the world; break-bone fever/ bonecrusher disease; 1-4 viruses; A. aegypti,albopticus, scutellaris; high fever, frontal headace, retro-orbital pain, myaligias, arthralgias, nausea, vomiting, and often maculopapular rash
Dengue fever
+ssRNA;flavivirus; vector Aedes; sexual transmission; cause of microcephaly; symptoms include mild fever, skin rash, conjunctivitis, muscle and joint pain, malaise or headache
zika virus
+ssRNA;flavivirus; blood-borne, sexual (low risk); major target cells is hepatocytes; no vaccine; cirrhosis, hepatocarcinoma
Hepatitis C virus
+ssRNA; non segmented; enveloped alphaviruses; replication in cytoplasm; mosquito/arthropod borne; realm ribovaria;
togaviruses
+ssRNA; new family of rubella; not arthropod borne; only one recognized species (Rubivirus- Rubella virus)
matonaviridae
rubella (german measles) is caused by; measles (tigdas) is caused by
rubella virus ( matonaviridae); paramyxovirus
