Lecture 3: viral genome and classification Flashcards
what do all viral genomes need to make in order to be recognized by host ribosomes
mRNA
describe the baltimore classification system
designed by david baltimore
all viruses must produce mRNA
source of RNA polymerase from host cell or virus
(+) sense RNA viruses (5’-3’)
-direct translation
(-) sense RNA virus (3’-5’)
-antisense strand, lacks coding regions
large viruses are encodes for by virus
small viruses hijack from host cell or virus
how can (+) sense RNA virus be directly translated
5’ cap and 3’ poly A tail tricks cell to allow it in; recognized mRNA by ribosomes
mRNA is always on the ( ) strand
+
DNA of equal polarity is on ( ) strand
+
RNA and DNA complements of ( ) strands are ( ) strands
+
-
ribosome ready and can be translated into protein
mRNA
7 viral genome types
dsDNA gapped dsDNA ssDNA dsRNA ss (+) RNA ss (-) RNA ss (+) RNA with DNA
what info is encoded by the viral genome
gene products and regulatory signals for:
- replication of genome
- assembly/packaging of genome
- regulation of replication cycle
- controlling host defenses
- transmission to other cells and hosts
info not encoded in viral genome
- no complete protein synthesis machinery (elF’s and tRNA)
- not involved in energy production/ membrane synthesis
- lack essential centromeres or telomeres found in host chromosome
- dsDNA
- cellular (or viral) DNA-dependent RNA polymerase
- adenovirus, herpesvirus, polyomavirus, poxviruses
baltimore class 1
- ssDNA
- cellular DNA-dependent RNA polymerase (ssDNA to dsDNA)
- circoviruses, parvovirus
baltimore class 2
describe RNA genomes
- cells lack RNA-dependent RNA polymerase (RdRp) activity capable of replicating viral RNA
- RNA virus genomes encode an RdRp
- RdRp produce RNA genomes and mRNA from RNA templates
- dsRNA
- virion packaged RdRp
- mRNA synthesized from (-) sense strand
- rotavirus, reovirus
baltimore class 3
- ssRNA
- (+) sense RNA translated
- picornaviruses, flaviviruses, coronaviruses, togaviruses
baltimore class 4
examples of ssRNA (+) sense
- poliovirus, rhinovirus
- gastroenteritis
- SARS
- yellow fever virus, west nile, hep C virus
- rubella virus, equine encephalitis virus
- ssRNA
- (-) sense RNA not translated
- virion packaged RdRp
- synthesize (+) sense viral mRNA
- filoviruses, orthomyxoviruses, paramyxovirus, rhabdovirus
baltimore class 5
examples of ssRNA (-) sense
- measles, mumps
- rabies
- ebola, marburg virus
- influenza
- lassa virus
consequence of segmented genome
reassortment
coding strategy used by arenaviruses and some members of the bunyavirus family, in which an RNA genome segment contains both positive- and negative- sense genes
Therefore, some viral proteins are made from messenger RNAs copied from the genome RNA, while other proteins are made from messenger RNAs
copied from the antigenome RNA.
ambisense RNA genomes
-ssRNA
-(+) sense
-virion associated reverse transcriptase (ssRNA to dsDNA)
carries its own reverse transcriptase
-retroviruses (HIV)
baltimore class 6
- ssDNA/dsDNA
- virion associated reverse transcriptase
- hepdnaviruses (Hep B)
baltimore class 7
example of gapped dsDNA genome
hep B
how are viruses classified
virion properties
host interactions
molecular properties
how are viruses classified through virion properties
filterable agents
disease symptoms
physical properties
-biomechanics, virion morphology, and serology
how are viruses classified through host interactions
transmission (vectors)
entry (envelope fusion, receptors)
how are viruses classified through molecular properties
genome (topology- ss or ds; strandedness) sequence data (genome and capsid protein) replication mechanisms
sequence homology
similar hosts
target cells/ tissue
species
virion size/shape
replication strategy
genome organization
genus
virion structure
replication mechanisms
family
genome composition
genome topology
order
