Consequences of viral infection Flashcards
Virus replication - ssRNA (-ve sense) viruses
a) Group V
b) Differences in influenza
a) eg measles, rabies. (see image) First, they undergo transcription (-ve sense to +ve sense mRNA). They then either undergo transcription again to replicate more -ve sense nucleic acid; or they undergo translation to produce viral proteins (including RNA-dependent RNA polymerase and capsid proteins). New viral particles are then assembled. All occurs in the cytoplasm.
b) Most ssRNA (-ve sense) viruses replicate in the cytoplasm, but influenza virus replicated in the nucelus. It requires both host DNA-dependent RNA polymerase II and viral RNA-dependent RNA polymerase. Additionally, influenza virus has a segmented genome, which presents difficulty as virion assembly, but it gives opportunity for gene re-assortment between different influenza viruses
Viral replication - ssRNA (+ve sense) viruses (Group IV)
eg poliovirus, FMDV (see image). First they undergo entry and uncoating. The ssRNA can be directly translated to form new viral proteins (including RNA-dependent RNA polymerase and capsid proteins). The genome can also be replicated, first being convered to ssRNA -ve sense, and then transcripted to form many new viral genomes. The virus is then assembled. This occurs in the cytoplasm.
Viral replication - ssRNA (+ve sense) retroviruses (Group VI)
eg HIV, FeLV (see image). First, they undergo reverse transcription (from ssRNA +ve to dsDNA) and uncoating in the cytoplasm. They are then transported to the nucleus where they are integrated into the host DNA (the provirus). There is then transcription to produce more viral genome (still in the nucleus), and then some of the transcripted mRNA is used for translation of new viral proteins (including reverse transcriptase and capsid proteins), which occurs in the cytoplasm. The new virion is then assembled in the nucleus in the cytoplasm.
Viral replication - dsDNA viruses
a) Group I
b) Differences in poxviruses
a) eg herpes, adeno. (see image) First they enter the cell cytoplasm, then undergo uncoating when they entr the nucleus. Here, they either undergo transcription in the nucelus, and then translation in the cytoplasm to produce new viral proteins (including viral capsid proteins and viral DNA polymerase); or they can undergo DNA replication to create further viral genomes. The virus is then assembled in the nucleus.
b) These replicate in the cytoplasm, rather than the nucelus. They encode transcriptional enzymes and package these in the virion (DNA-dependent RNA polymerase, capping enzymes, and polyadenylating enzymes). The DNA genome itself is non-infectious
Virus gene expression
a) Temporal control
b) Quantitative control
a) Proteins with a replicative or regulatory function (such as nucleic acid polymerases or immune mudulators) are made early. Virus capsid protiens are made late for the assembly of new virions. Large DNA viruses (eg herpes viruses and poxviruses), have several distinct gene classes - which are expressed in a strictly regulated cascade
b) Virus enzymes for replication (being catalytic) are needed in low amounts. Viral structural proteins are needed in high amounts to build new viral particles
a) how do ssRNA (+ve sense) express their proteins from one RNA
b) gene expression by polyprotein processing and splicing
c) gene expression by ribosomal frameshifting
a) Eukaryotic mRNAs are monocistronic, so how is it possible to make many proteins from only one mRNA? The solution is to translate the genome into a giant polyprotein. The giant polyprotein then undergoes proteolytic cleavage into mature proteins - polyprotein processing (eg poliovirus)
b) eg HIV also use polyprotein processing (see image). Additionally, retroviruses also use splicing to place the coding region for some of their proteins at the mRNA 5’ (see image)
c) Usually, translation stops after ‘gag’, but the ribosome may pause (around 5% of the time) before the stop codon, then slip one nucleotide and restart translation in a -1 reading frame to form a gag-pol polyprotein (see image)
a) Viral assembly
b) Viral release and spread
a) The assembly of viral protein and nucleic acid marks the end of the eclipse phase. This can be spontaneous (eg tobacco mosaic virus, TMV), or a complex process with multiple stages (eg assembly of the capsid, insertion of genome into the capsid, and release, with or without an envelope). Assembly can occur at the cell surface or internally, and it may require cleavage of a capsid protein.
b) Can involve budding from the cell surface (in enveloped viruses like HIV and influenza) - with some viruese this can occur for prolonged periods without cell death, hence a feature of persistent infection. There may be cell to cell spread by cell fusion (eg measles virus using syncytium). Can involve cell lysis (eg in picornaviruses, adenovirus, bacteriophage T4, mimiviruses)
Latent infection - retroviruses
a) The ssRNA (+ve sense) genome is first converted to dsDNA by viral reverse transcriptase, and then integrated into the host’s chromosome (forming the provirus). This may be transcribed by host RNA pol II to express the virus genome and proteins, and new viral particles, or the provirus may remain latent. There is potential for vertical transmission. Endogenous retrovirus sequences take up 8% of the human genome (and 2% of the genome encodes protein). Human endogenous retrovirus (HERVs) - proviral remnants of ancestral germ-line infections by active retroviruses have meant more than 30,000 copies in our genome, although they are mostly non-functional. The syncytins (retrovirus envelope genes) captured 25-40 Mya, and now expressed by all placental mammals and is needed for placenta formation
b) The virus DNA enters the nucleus, becomes circular (an episome), but usually does not integrate. Often, there is little or no transcription, so no virus proteins are expressed, and no replication (latency), and they may remain latent for decades. They are able to switch from the latent to the lytic cycle (reactivation). In herpes simplex virus (HSV) the primary and reactivated (recurrent) infection causes cold sores. In varicella zoster virus (VZV) the primary infection causes chicken pox, and a recurrent infection causes shingles.
Viral modifications to the host cell
i) There is subversion of cellular biochemistry to only make viral macromolecules, and a stimulation of host metabolism. ii) There is an expression of virus enzymes to increase dNTP pools and enhance virus nucleic acid synthesis. iii) There is alterations to host membranes and other morphological changes (cytopathic effect, cpe). iv) There is suppression of the innate immune response, and there can be a persistent (non-lytic) infection. v) There may also be cell transformation, which can cause cancer
Subversion of host cellular biochemistry - shut off of host proteins
a) Poliovirus
b) Other viruses
a) 1 hour after infection with poliovirus, host protein synthesis is shut down, but virus proteins continue to be made. In eukaryotic mRNA translation, there is a ribosome cap-binding complex, followed by the start codon, an open reading frame where mRNA will be translated, and then a stop codon (see image). A poliovirus protease cleaves a component of the cap-binding complex, so translation of capped host mRNAs stops. The virus mRNA has an internal ribosome entry site (IRES) upstream of its start codon, and the ribosome recognises this IRES, so there is translation of uncapped poliovirus mRNA. This is cap-independent translation
b) i) destuction of DNA template, so no host mRNA synthesis ii) increased turnover of host mRNAs iii) Influenza virus RNA-dependent RNA polymerase can recognise and cleave capped mRNAs a few nucleotides downstream of the 5’ cap iv) poxviruses encode de-capping enzymes that cleave 5’ cap from mRNAs (both host and viral). Viral mRNAs are more abundant, so are predominant. The mRNA turnover aids transition from early to late virus protein expression
a) Stimulation of the host cell
b) Stimulation via VGF encoded by vaccinia virus
a) Virus replication needs high levels of NTPs or dNTPs. Resting cells have low levels of these, hence the cell needs to be stimulated. Herpesviruses, adenoviruses, papovaviruses and poxviruses encode proteins for cell stimulation: i) simian virus 40 (SV40) T antigen ii) HPV E6/E7 iii) Adenovirus E1A. Some viruses express a growth factor: i) Epstein-Barr virus vIL-10 ii) vaccinia virus epidermal growth factor (VGF)
b) VGF is made early and released from the cell. VGF binds to cells and stimulates growth. The virus spreads to cells with high metabolic activity
a) Virus-encoded enzymes from HSV and vaccinia virus
b) Modifications to the cell surface
a) (see image)
b) i) insertion of virus proteins into host membranes (especially for enveloped viruses) ii) promotion of fusion between cells (eg measles virus enables cell to cell spread without virions being neutralised by antibodies) iii) alteration to host proteins/carbohydrates (down regulation of virus receptors, eg HIV down regulates CD4; influenza virus removed sialic acid to prevent re-infection and aids virus dissemination. Also down regulation of MHC class I to evade CD8+ T cells)
a) Virus-induced cytopathic effect (cpe)
b) Changes in specific cells by different viruses (3)
a) i) There are rounded, more refractile, motile, alterations to the cytoskeleton actin and tubulin ii) viruses use cell sytoskeleton (actin and microtubule) to around and between cells
b) i) Rabies - infection of Purkinje cells of the cerebellum, causes Negri bodies ii) Human cytomegalovirus (HCMV) - large nuclei where chromatin is detached from the nuclear membrane, forming ‘owl eye’ inclusions iii) Poxviruses - cytoplasmic eosinophilic inclusion bodies form, and mitotic bodies
a) Different outcomes of infection (4)
b) Cell transformation by viruses
c) Transformation by DNA viruses
a) i) Cell lysis (productive infection by DNA viruses is lytic; Non-enveloped RNA viruses are lytic; Viruses inducing host cell shut-off are lytic) ii) Latent infection (herpes viruses and retroviruses) iii) Persistent infection eg retroviruses (cell not killed and continues to divide; Viruses released over long periods) iv) Transformation (virus-induced cancers, around 20% of human cancers are virus related)
b) Some viruses can transform cells, leading to cancer (uncontrolled cell growth, loss of contact inhibition, growth in soft agar)
c) eg papilloma viruses: Infection promotes cell division and virus DNA synthesis, capsid formation, virus release and cell death (cell division before virus replication causes a wart - HPV 6 and HPV 11). But sometimes the virus replication cycle fails, yet stimulation endures and the cell continues to divide - HPV 16 and HPV 18 are associated with cervical carcinoma, they produce proteins E6 which degrades p53, and E7 which interacts with Rb
Cell transformation by retroviruses
Provirus integration may cause transformation in 2 ways:
1) Retrovirus may acquire a host gene during replication. If the host gene controls cell growth, the retrovirus can transform cells and may induce cancer. eg Rous sarcoma virus causes sarcomas in chickens, where it acquires a host src gene, which is a tyrosine kinase (an oncogene)
2) Provirus integration into, or adjacent to, a cellular gene that regulates cell division may lead to inactivation or dysregulation of that gene (see image). Uncontrolled cell growth can result, but this type of transformation is rare
