Virus structure + diagnosis methods Flashcards
Virus definition and main features
OBLIGATE INTRACELLULAR PARASITES: they are unable to replicate outside of a host because they have no metabolism, so cannot transduce energy to make proteins
-very small
-survive for little time
-require host’s transcription and translation machinery, but contain certain enzymes for replication cycle (polymerase, proteases)
Classification of viruses (ways)
- TAXONOMICAL:
Order
Family
Subfamily
Genus
Species - STRUCTURE: can be classified on characteristics that only SOME viruses possess (envelopes, essential enzymes, accessory proteins)
Describe the structure of a viral particle
IN ALL VIRUSES:
CORE: nucleic acids + molecules for stability
CAPSID: self assembly capsomere units (either in helical or icosahedral symmetry, encloses the core -
!!! (nucleocapsid = core + capsid)
IN SOME VIRUSES:
ENVELOPE: external layer of phospholipids
PEPLOMER: viral glycoprotein present on envelope
+ the enzymes and proteins that are specific to each virus
what is a virion
def: complete viral particle released outside the cell
!! inside hosts, the viruses are NOT found in complete form, only when they are released (budding phase) - inside host you can find viral genetic material and partially assembled viral proteins
different types of viral symmetry + what it arises from(2)
SYMMETRY: arises from the genom-protein interactions and the self assembly of the capsomere units
- HELICAL: have the envelope for a FULL protection of their genome
- ICOSAHEDRAL: can be either naked OR enveloped (allows the formation of a closed shell)
- COMPLEX: structure not classified by the classical capsomere shape - eg bacteriophages and poxviruses
what is the function of the viral capsid
- PROTECT NUCLEIC ACIDS FROM:
Mechanical stress, UV radiation (which could cause mutations) and enzymatic degradation (by nucleases secreted as cellular defense) - Viral genome packaging
!!!! IN NAKED VIRUSES: capside contains the major antigens of the virus, so this part mediates the binding and penetration of the virus inside host (+ is responsible for the host’s immune response)
Pericapsid function
-only present in certain viral families
-made up by phospholipids + contains glycoproteins (acting as viral receptors and can stimulate immune responses)
-presence of pericapsid accounts for sensitivity to certain disinfectents (eg alcohols) bcos they can dissolve lipids
What are the different types of nucleic acids that can be present in the viral genome?
single or double stranded DNA or RNA
some atypical viruses can also go against the central dogma of biology bcos they have the enzymes to turn RNA into DNA - retroviruses and hepadnaviruses (like hepatisisB)
Describe the replication cycle of dsRNA viruses
-start and end their replication in the cytoplasm
-dsRNA enters cell, synthesis of new +RNA using RNA dependent RNA polymerase (RDRP)
-this is similar to mRNA so it is translated using host machinery for viral proteins
-amongst these proteins, the virus makes Rpol to replicate the +RNA strand and replicate viral genome
Describe the replication cycle of +ssRNA viruses
since these viruses have +RNA (very similar to mRNA) they can translate and replicate VERY FAST upon entry
they follow the standard sequence of steps after +RNA synthesis, but they are RAPID - important from a clinical perspective
Describe the replication cycle of retroviruses
-upon entry into the CYTOPLASM, RNA is converted into DNA using reverse transcription enzyme
-the retrotranscribed DNA forms a complex with the integration complex (protein complex)
-this moves into the nucleus of the cell where the DNA can integrate inside the host’s genome using INTEGRASE enzyme
Describe the replication cycle of DNA viruses
2 diff ways of replication depending on whether they have THEIR OWN DNA polymerase:
MOST CASES: they do not have DNApol, hence they use their host’s (bcos they have adapted well in order to use it)
!! the host cells need to be in active replication (so that the virus genome can also be replicated)
What are the OVERALL stages of the viral replication cycle (6)``
- Adsorption
- Penetration
- Uncoating
- Replication
- Maturation
- Release
!! PERIOD OF ECLIPSE: the period between the viral penetration and maturation of viral progeny
Describe adsorption (1st stage rep cycle)
-induction of the virus inside the host cell
-in order for this to occur the host cell needs to be:
1. succeptible (have the right receptors for the virus, eg. HIV = CD4, SARS- COV2 = ACE2 receptors)
- permissive (have the machinery for the virus to reproduce)
what are the 3 possible situations upon viral infection of a host cell
- productive infection - if the cell is permissive
- abortive infection - if the cell is resistant
- restrictive infection - if the cell is permissive or resistant depending on the phase of its life
Describe penetration (2nd stage rep cycle)
3 WAYS TO DO SO:
- endocytosis: receptor mediated, engulfed in vehicle made by host membrane (both for naked and enveloped)
- fusion: of capsid/ envelope with host membrane (only for enveloped)
- pore mediated: eg for poliovirus that presents PV1 receptors (only for naked)
Describe uncoating (3rd stage rep cycle)
disruption of capside to release genome into the cell –> usually spontaneous disaggregation of proteins
IN CERTAIN CASES: eg influenza virus, there are ion channels that cause acidification of endocytotic vesicle with the virus + this favours release of nucleocapside
Describe replication (4th stage rep cycle)
describe the baltimore classification system
7 groups of viruses depending on their genomic material, mechanism for mRNA production, and hence their replication mechanism
GROUP 1: dsDNA
GROUP 2: ssDNA
GROUP 3: dsRNA
GROUP 4: ssRNA (+)
GROUP 5: ssRNA (-)
GROUP 6: ssRNA with DNA intermediate
GROUP 7: incomplete dsDNA (partially dsDNA)
GROUP 1 VIRUSES:
dsDNA uses host machinery in nucleus for mRNA production which is then translated into proteins by ribosomes
HERPESVIRUSES, ADENOVIRUSES, PAPOVIRUSES
GROUP 2 VIRUSES
ssDNA converted to dsDNA
PARVOVIRUS
GROUP 3 VIRUSES
dsRNA -> means that one strand is -ve and other is +ve.
- copying the + and -ve strand gives copies of the dsRNA for viral genome
- Transcription of the -ve RNA strand ONLY (using RNA polymerase) forms +viral mRNA to form viral proteins
REOVIRUSES
GROUP 4 VIRUSES
ssRNA (+) closesly resembles mRNA, binds to ribosome to form polyprotein and split into 2 single proteins
!! diff viruses can have certain +RNA secondary structures for ribosome interaction
One of the two proteins ats as -ve RNA template, hence being used to form final +mRNA via RNA polymerase
PICORNAVIRUS, NOROVIRUS, TOGAVIRUS, FLAVIVIRUS, CORONAVIRUS
GROUP 5 VIRUSES
ssRNA (-) is transcribed into mRNA (by RNA dependent RNA polymerase), and a full length RNA+ template
RNA+ template is used to make RNA- genomic progeny
RHABDOVIRUS, PARAMYXOVIRUS, ORTHOMYXOVIRUS
GROUP 6 VIRUSES
GROUP 7 VIRUSES
