Classification and Nomenclature of Viruses Flashcards
how do we classify viruses? (5)
basis of disease
basis of host organism
basis of virus particle morphology
basis of viral nucleic acid
basis of taxonomy
simple way to classify viruses, but very anthropomorphic because they affect humans or our domestic livestock or crops
basis of disease
why classifying based on disease is not suitable?
most viruses either do not cause disease or cause a disease that we do not
recognize because of a lack of understanding of the host.
way of classifying that emphasizes the parasitic nature of the virus–host interaction
basis of host organism
classifying viruses that mplies a fixed, unchanging link between the virus and host in question.
basis of host organism
issue of classfying viruses based on host organism
others may infect a small range of hosts, such as poliovirus which can infect
various primates rather than fixed.
way of classifying viruses whether or not the virus particle has a lipid
envelope - enveloped and non- enveloped
viruses
virus particle morphology
three morphological categories of enveloped viruses
isometric
filamentous
complex
Shape: These viruses have a roughly spherical shape.
Structure: Their protein coat (capsid) is composed of identical subunits arranged in a symmetrical, geometric pattern. Often, this pattern is icosahedral, meaning it has 20 triangular faces.
isometric nonenveloped viruses
Shape: These viruses are elongated and thread-like.
Structure: The capsid is a helical structure that winds around the nucleic acid to form a long, rod-like appearance.
filametous nonenveloped viruses
Shape: These viruses have a more intricate structure that doesn’t fit into the simple isometric or filamentous categories.
Structure: They can have additional components, such as tail fibers or base plates, which are not present in simpler viruses. Despite their complexity, they lack a lipid envelope.
complex nonenveloped viruses
- If enveloped, a further level of classification is
possible by describing the morphology of the
___ found within the membrane.
nucleocapsid
is a viral structure that consists of a capsid and the nucleic acid it contains.
nucleocapsid
d is a protein shell that surrounds the genetic material of a virus.
capsid
issue of clasifying virus based on virus particle morphology
: knowing shape does not allow us to
predict anything about the biology, pathology or
molecular biology of similarly-shaped viruses.
classifying viruses that considers the nature of the virus genome in
terms of the mechanisms used to replicate the
nucleic acid and transcribe mRNA encoding
proteins
basis of nuclei acids
four possible kind of viral nucleic acid
- single- stranded DNA,
- single-stranded RNA,
- double- stranded DNA,
- and double-stranded RNA.
ICTV means
INTERNATIONAL
COMMITTEE ON
TAXONOMY OF
VIRUSES
task is developing, refining, and maintaining a
universal virus taxonomy
ICTV
ICTV is a committee of the Virology Division of the
International Union of Microbiological Studies (IUMS(
ICTV goal is to categorize multitude of known viruses into a single
classification scheme that reflects their ___
relationships, i.e. their individual phylogenies.
evolutionary
process of naming viruses and placing them into a
taxonomic system.
virus classification
why cannot virus be classified with the usual method?
- Due to the pseudo-living nature of viruses,
which is to say they are non-living particles with some
chemical characteristics similar to those of life
result is that a ___exists as a member of a population
where each member has a genome sequence which may
be different to the others but which belongs to a
collection of sequences which will combine to form a
consensus for that virus – type member
virus
virus is said to be a ___, and there is no
defined ‘correct’ genome sequence.
quasispecies
universal virus classification system - employ hierarchical levels o
realm,
subrealm, kingdom, subkingdom,
phylum, subphylum, class, subclass,
order, suborder, family, subfamily,
genus, subgenus and species.
___ that define higher-level
taxa are shared with all lower-level
taxa under the same
properties
is it obligatory to use all levels of taxonomic hierarchy in viruses?
no
are all
non-enveloped, icosahedral particles
containing one or two segments of positivesense RNA
order picornavirales
e is one of
several families belonging to the
order Picornavirales.
family picorviridae
contain a single
monocistronic genome with conserved
genome organization (arrangement of
encoded polypeptides).
family Picornaviridae
share more than 42% amino acid
identity across the length of their
polyprotein.
genus enterovirus
share a limited
range of hosts and host receptors, have
similar polyprotein processing
programs, and share more than 70%
amino acid identity in the polyprotein.
enterovirus C
is a monophyletic group of viruses
whose properties can be distinguished from
those of other species by multiple criteria.
species
species name is written in ___ with the
first word beginning with a capital letter
italics
only begins with a ___ if they are proper
nouns (including host genus names but not
virus genus names**) or alphabetical
identifiers.
capital
- A species name should ___ be abbreviated.
not
observe proper capitalization in species (slide 11)
+1
principles of nomenclature
aim for stability
avoid or reject the use of names which might cause error or confusion
avoid unnecessary creation of names
nomenclature of viruses is independent of other biological nomenclature. Virus taxnon nomenclature is recognized as an exception in the proposed ___
International Code of Bionomenclature (BioCode)
range of characteristics considered by ICTV
- host range
- morphological features of the virion
and nature of the genome nucleic acid
host range includes
eukaryote or prokaryote, animal,
plant, etc
morphological features of virion include
enveloped, shape of capsid or nucleocapsid,
etc.)
nature of genomic nucleic acid include
DNA or
RNA, single stranded or double stranded,
positive or negative sense, etc
additional features of characteristic includes
phylogeny - based on degree of
conservation of specific gene sequences
ICTV Executive Committee (EC) has
established over
___ international Study Groups (SGs)
covering all virus taxa.
100
Artificially created viruses and
laboratory hybrid viruses will ___ be
given taxonomic consideration. T
not
ICTV is not responsible for classification and
nomenclature of virus taxa below the rank of
species
classification and naming of serotypes,
genotypes, strains, variants and isolates of virus
species is the responsibility of
acknowledged international specialist groups
what is the realm of SARS-CoV-2
Ribovaria
which is responsible
for developing the
classification of viruses and
taxon nomenclature of the
family Coronaviridae, has
assessed the placement of the
human pathogen, tentatively
named 2019-nCoV, within
the Coronaviridae
Coronaviridae Study Group (CSG)
CSG decided to follow a ____-based line of reasoning to name SARS-CoV-2
phylogeny
CSG proposes to use the following naming convention for individual isolates of the COVID-19 virus
SARS-CoV-2/host/location/isolate/date
A variety of ___groupings may be
identified within the members of a single virus
species. These may be described as viruses
with alternative names
subspecific
virus that are both classified in the Bean common mosaic virus
blackeye cowpea mosaic virus
peanut stripe virus
subspecies can be
serotypes
genotypes
clades
strains
variants
isolates
over time, virus start to differ slightly in terms of its genetic
sequence
Result in changes to the viral genetic sequence during this process
of mutation and recombinations.
variants
Viral species different from parent virus
it can differ by one or multiple mutations
variants
SARS-CoV-2 variants
Alpha variant
Beta variant
Gamma variant
Delta variant
formerly called the UK Variant and
officially referred to as B.1.1.7)- first found in
London and Kent
Alpha variant
SARS-Cov-2 alpha variant is first found in
London and Kent
SARS-CoV-2 variant is formerly called the ___ and officially referred to as
UK variant/B.1.1.7
(formerly called the South Africa
Variant and officially referred to as B.1.351)
Beta Variant
Beta Variant is called the
South Africa Variant (B.1.351)
formerly called the Brazil Variant
and officially referred to as P.1),
Gamma variant
Gamma variant is officially referred to as
P.1
(formerly called the India Variant
and officially referred to as B.1.617.2)
Delta Variant
Delta Variant is officially referred to as
B.1.617.2
VBM means
Variant Being Monitored
VOI meaning
Variant of Interest
VOC means
Variant of Concern
VOHC means
Variant of High Consequence
SARS-CoV-2 is often discussed in the context of
lineages (and sublineages) – commonly used
Phylogenetic Assignment of Named Global Outbreak (PANGO)
group of closely related viruses with a common
ancestor.
lineage
___ lineage system is hierarchical—like a family
tree.
Pango
evolutionarily descendants of a “parent”
lineage;
lineages
in relation to its parent
lineage.
sublineage
Lineages are named using an ____ ___ such as B or BA and numerical suffic (such as .1 or 1.1.5)
alphabetical lineage
Pangosystem assigns an additional number to the
name of its parent lineage (e.g., BA.2.75 is a sublineage of
BA.2
Composed of an ancestor and its
descendants, as illustrated by the
phylogenetic tree below.
clade
SARS-CoV-2 isolates and HIV-1
isolates are placed in ___ based
on phylogenetic trees constructed
from their genome sequences
clade
a group of organisms believed to have evolved from a common ancestor, according to the principles of cladistics.
clade
The two types of influenza viruses that cause most human illness and that are
responsible for the flu season each year.
influenza A
influenza B
influenza virus that are further classified into
subtypes
infuenza A
influenza virus are further classified into two lineages
influenza B
two lineages of influenza B
B/Yamagata
B/Victoria
. Describe viruses of the
same species that are antigenically different.
serotypes
serotypes is also known as
serovar
there are ___ serotypes of poliovirus, ___ of dengue virus, and ___of rhinovirus
3
4
100
if you are infected with
type 1, immunity generated from it will/will not
protect against other serotypes
will not
___ sequence of the virus is used to infer
whether isolates are serologically different
genome
“propose to include the ancestral
virus and main variants (Alpha,
Beta, Gamma and Delta) in a serotype what number
serotype 1
omicron BA.1, BA.2, and Ba.3 are classified as serotype ___
2
s used to describe the genetic makeup of a
virus.
genotype
is a way to put the hepatitis C
virus (HCV) into categories based on similar genes.
genotype
HCV has ___ genotypes, labeled 1 through 6
6
how many genotypes of ASFV
24
name for a virus isolated from an infected
host and propagated in culture.
isolates
first isolates of SARS-CoV-2 were obtained
from patients with pneumonia in ___ in
late 2019.
Wuhan
An isolate comes from a ___host.
sinlge
are given names so that their origin is known.
isolates
isolate name consist of the
genus
city of origin
isolate number
year
give an isolate name of SARS-CoV-2
BetaCoV/Wuhan/WIV04/2019
When a new variant has
different functional
properties to the original
virus and becomes
established in a population,
it is referred to as a
___ the virus.
strain
are all strains variants?
yes
are all variants strains?
no
*Genetic variant
strain
are a set of criteria used to determine if a microorganism causes a disease.
henle-koch postulates
HKP
___ and ___of viruses is essential in the analysis of
viral diseases.
naming and classification
It becomes well-understood after classifying viruses and eventually
establishing causal relationships between a virus and a disease.
virus classification
One of the great landmarks in the scientific study of infectious
diseases was the development of what have come to be called the
Henle-Koch Postulates of causation
reworked again in 1996 by David Relman and David Fredricks as more and
more genomic sequencing criteria came to dominate the subjec
Henle-Koch Postulates
Henle Koch Postulate 1
The agent should be present in every case of the disease under appropriate condition
Henle Koch Postulate 2
The agent should not be present in any other diesase as a fortuitous and Non-pathogenic agent
Henle Koch Postulate 3
The agent must be isolated from the body of the individual in pure culture
Henle Koch Postulate 4
it should induce disease in a new susceptible experimental animal
Friedricks and Relman’s Guidelines
Strength of the association
Specificity of assocation
Response to treatment
Temporality
Plausibility
Biological gradient
Consistency
Since viruses lack ribosomes (and thus rRNA), they
cannot be classified within the
three domain classification
derived a viral
classification scheme, one that focuses on the
relationship between a viral genome to how it
produces its mRNA.
Dr. David Baltimore
= the cell can process this like its own mRNA in the cytoplasm and translate the mRNA into the proteins
+ssRNA
complementary to the viral mRNA
-SSRNA
should copy this to create an mRNA
-SSRNA
key points in Baltimore Classsificaiton (5)
viral genome’s nucleic acid
strandedness
sense
method of replication determine its class
other classification (morphology)
viral genome’s nucleic acid can be
DNA or RNA
strandedness can be
single-stranded/double stranded
viral mRNA that can be
directly translated into proteins
positive sense RNA
- viral RNA that is complementary to the
viral mRNA
negative sense RNA virus
baltimore classification A
dsDNA
baltimore classification 2
+ssDNA
in Baltimore classification 2, what should it do to create a +ssRNA
copy the +ssDNA to create a -ssRNA to then use as a template
Baltimore Classification 3
dsRNA
Baltimore Classification 4
+SSRNA
in Baltimore Classification 4, what is done to the +ssRNA
copied to create a -ssRNA to create another +ssRNA
in Baltimore Classification 5, what is present to create +ssRNA
-ssRNA
in Baltimore Classification 6, what is done to its existing genome’s nucleic acid
+ssRNA-RT creates a dsRNA to be reverse transcripted to dsDNA
in Baltimore Classification 6, the copied dsDNA can be used to
integrate this copy into their host own
genome
Baltimore Classification 7
dsDNA-RT
in Baltimore Classification 7, the dsDNA-RT’s process to create +ssRNA is
dsDNA-RT > +ssRNA > dsRNA > dsDNA > +ssRNA
Nucleotide Type Classification for DNA Viruses (3)
dsDNA
+ssDNA
dsDNA-RT
Nucleotide Type Classification for RNA viruses
dsRNA
+ssRNA
-ssRNA
+ssRNA-RT
Host Domain Classification (3)
Eukaryotic viruses
Bacterial viruses
Archaeal viruses
adenoviruses, herpesviruses, and poxviruses are what baltimore classification
Baltimore 1 (dsDNA viruses)
Parvoviruses are what kind of Baltimore Classification
+ssDNA (Baltimore2)
Reoviruses are what kind of BC
BC3 (dSRNA)
Picornaviruses, Togaviruses are what BC
BC4 (+ssRNA)
Orthomyxoviruses, Rhabdoviruses are what BC
BC5 (-ssRNA viruses)
retroviruses are what BC
BC6 (ssRNA-RT)
hapadnaviruses are what BC
dsDNA-RT viruses
are the viruses that posses DNA as their genetic material
DNA viruses
viruses that possess RNA as their genetic material
RNA viruses
most common type of DNA Viruses
dsDNA
replication of DNA viruses occurs in the
nucleus
DNA viruses are smaller/larger than RNA viruses
larger
most common type of RNA viruses
ssRNA
RNA viruses replication occurs in the
cytoplasm
which has a higher mutation rate
DNA viruses/RNA viruses
RNA viruses
which has a show and accurate replication and which has a show and error prone replication
DNA viruses
RNA viruses
DNA - accurate
RNA - error prone
mRNA is transcribed directly from DNA template
what BC
dsDNA
what BC
DNA is converted to double-stranded from before RNA is transcribe
ssDNA
what BC
mRNA is transcribed from the RNA genome
dsRNA
what BC
genome functions as mRNA
single stranded RNA (+)
what BC
mRNA is transcribed from the RNA genome
single stranded RNA (-)
what BC
Reverse transcriptase makes DNA from RNA genome; DNA is then incorporated in the host genome; mRNA is transcribed from incorporated DNA
ssRNA viruses with reverse transcriptase
what BC
the viral genome is double stranded DNA but viral DNA is replicated through an RNA intermediate, the RNA may serve directly as mRNA or as a template to make mRNA
dsDNA-RT
replicate DNA and make Viral mRNA in cytoplasm for some
Class I and II
Transcription in cytoplasm.
Class III-V
Reverse transcription inside the virus; DNA copy is
transported to cell nucleus for integration.
Class VI
like bacteriophages, T4 and lambda have
genome exactly the same as the host cell
that they are infecting.
what BC
dsDNA
For this reason, many host enzymes can be
utilized for replication and/or protein
production.
what BC
dsDNA
The flow of information follows a
conventional pathway: dsDNA → mRNA →
protein, with a DNA-dependent RNA
polymerase producing the mRNA and the
host ribosome producing the protein.
what BC
dsDNA (Class I)
what enzyme is needed for Class I (dSDNA) genome replication from either the virus or the host
cell.
DNA-dependent DNA-polmyerase
The flow of information for ssDNA viruses,
such as the parvoviruses, will still follow the
conventional pathway, to a certain extent: DNA
→ mRNA → protein.
ssDNA (class II)
But the viral genome can either have the
same base sequence as the mRNA (plus-strand
DNA) or be complementary to the mRNA
(minus-strand DNA).
ssDNA (Class I)
BCII (+ssDNA) In the former case, a DNA strand that is
complementary to the viral genome must be
manufactured first, forming a
double-stranded replicative form (RF)
This can be used to both manufacture viral
proteins and as a template for viral genome
copies. For the minus-strand DNA viruses, the
genome can be used directly to produce mRNA
but a complementary copy will still need to be
made, to serve as a template for viral genome
copies.
ssDNA
Infect bacteria, fungi, plants, and
animals, such as the rotavirus that
causes diarrheal illness in humans.
dsRNA
in BCIII, But cells do not utilize ___ in any
of their processes and have systems in
place to destroy any dsRNA found in the
cell.
dsRNA
Thus the viral genome, in its dsRNA
form, must be hidden or protected from
the cell enzymes. Cells also lack _____ , necessary
for replication of the viral genome so the
virus must provide this enzyme itself.
RNA-dependent RNA-polymerases
The viral RNA-dependent RNA
polymerase acts as both a ____
to transcribe mRNA, as well as a
____to replicate the RNA genome
transcriptase
replicase
- Viruses with ____ such as
poliovirus, can use their genome directly
as mRNA with translation by the host
ribosome occurring as soon as the
unsegmented viral genome gains entry
into the cell.
+ssRNA
+SSRNA - One of the viral genes expressed yields an
______ (or
RNA replicase), which creates minus
strand RNA from the plus-strand genome.
RNA-dependent RNA polymerase
The minus-strand RNA can be used as a
template for more plus-strand RNA,
which can be used as mRNA or as
genomes for the newly forming viruses.
+ssRNA
*___-strand RNA viruses
include many members notable
for humans
minus
Since the genome of minus
strand RNA viruses cannot be
used directly as mRNA, the virus
must carry an RNA-dependent
RNA-polymerase within its
-___.
capsid
Upon entrance into the host
cell, the plus-strand RNAs
generated by the +____ are
used as mRNA for protein
production.
RNA dependent RNA polymerase
*When viral genomes are
needed the plus-strand RNAs are
used as templates to make
minus-strand RNA.
-SSRNA
the retroviral genome is composed
of +ssRNA, it is not used as ___.
mRNA
Instead, the virus uses its reverse
transcriptase to synthesize a piece
of ssDNA complementary to the
viral genome.
+ssRNA
The reverse transcriptase also
possesses ____activity,
which is used to degrade the RNA
strand of the RNA-DNA hybrid.
ribonuclease
used as a DNA polymerase to make
a complementary copy to the
ssDNA, yielding a dsDNA molecule.
reverse transcriptase
This allows the virus to insert its
genome, in a dsDNA form, into the
host chromosome, forming a
provirus
use reverse transcriptase, example include hepadnaviruses
DNA viruses with RT
contain a DNA genome that
is partially double-stranded, but contains a
single-stranded region.
hepadnaviruses
After gaining entrance into the cell’s
nucleus, host cell enzymes are used to fill in
the gap with complementary bases to form a
dsDNA closed loop.
DNA-RT
Gene transcription yields a plus-strand RNA
known as the
pre-genome
Gene transcription yields a plus-strand RNA
known as the pre-genome, as well as the viral
enzyme
reverse transcriptase
reverse transcriptase is a
RNA-dependent DNA-polymerase
is used as a template for
the reverse transcriptase to produced minus
strand DNA genomes, with a small piece of
pregenome used as a primer to produce the
double-stranded region of the genomes.
pre-genome
