Alphavirus (taxid:11019)
VIRION
Enveloped, spherical, icosahedral, 65-70nm in diameter, capsid with a T=4 icosahedral symmetry made of 240 monomers. The envelope contains 80 spikes, each spike are trimer of E1/E2 proteins.
GENOME
Monopartite, linear, ssRNA(+) genome of 11-12 kb. The genome is capped and polyadenylated.
GENE EXPRESSION
The virion RNA is infectious and serves as both genome and viral messenger RNA. The whole genome is translated into a non-structural polyprotein which is processed by host and viral proteases. RdRp is expressed by suppression of termination at the end of 10% of nsP polyproteins.
In late phase of infection, structural polyprotein is expressed through a subgenomic mRNA. The mRNA contains a Downstream Hairpin Loop (DLP)to avoid the translation shutoff induced by the host PKR in the late phase of infection. A truncated version of the structural polyprotein is produced by ribosomal frameshifting in the 6K region, the frameshift induces the translation of the TF protein 
.
ENZYMES
- Alpha-type capping [N7MTase + GTase nsp1, 2'OMTase nsp2/3]
- RNA-dependent RNA polymerase [nsp4]
- Polyprotein major protease (Peptidase C9) [nsp2]
- Capsid protease (Peptidase S3) [capsid]
- ADP-Ribosylhydrolase [nsp3]
REPLICATION
CYTOPLASMIC
- Attachement of the viral E glycoprotein to host receptors mediates clathrin-mediated endocytosis of virus into the host cell.
- Fusion of virus membrane with host endosomal membrane. RNA genome is released into the cytoplasm.
- The positive-sense genomic ssRNA is translated into a polyprotein, which is cleaved into non-structural proteins necessary for RNA synthesis (replication and transcription).
- Replication takes place in cytoplasmic viral factories at the surface of endosomes. A dsRNA genome is synthesized from the genomic ssRNA(+).
- The dsRNA genome is transcribed/replicated thereby providing viral mRNAs/new ssRNA(+) genomes.
- Expression of the subgenomic RNA (sgRNA) gives rise to the structural proteins.
- Capsid assembly occurs in cytoplasm.
- The capsid is envelopped by budding at the plasma membrane where the virion exits the cell .
Host-virus interaction
Chikungunya probably activates an autophagic process which promotes viral replication
.
Host gene expression shutoff by virus
Togaviruses mediate host translation shutoff.
Alphaviruses induce strong PKR activation leading to
leading to the almost complete phosphorylation of eIF2alpha and host translation arrest
.
Alphaviruses perform host transcription shutoff by inhibiting host RNA polymerase II. Host RNA-pol II catalytic subunit is targeted for degradation as early as 4-6h p.i.
.
Andrew E. Firth, Betty Yw Chung, Marina N. Fleeton, John F. Atkins
Virol. J. 2008; 5: 108
Joyce Jose, Jonathan E. Snyder, Richard J. Kuhn
Future Microbiol September 2009; 4: 837?856
Kurkela S, Manni T, Vaheri A, Vapalahti O.
Emerg Infect Dis. 2004 May;10(5):889-94.
Matching UniProtKB/Swiss-Prot entries
(all links/actions below point to uniprot.org website)60 entries grouped by protein
25 entries
Polyprotein P1234 (P1234) (Non-structural polyprotein)
32 entries
Structural polyprotein (p130)
3 entries
Frameshifted structural polyprotein (p130)
Chikungunya virus (strain S27-African prototype) taxid:371094
| Protein | ModelArchive |
| Structural polyprotein (p130) | ma-jd-viral-30956 |
Eilat virus taxid:1231903
| Protein | ModelArchive |
| Structural polyprotein (p130) | ma-jd-viral-30954 |
Middelburg virus taxid:11023
| Protein | ModelArchive |
| Structural polyprotein (p130) | ma-jd-viral-30953 |
Sagiyama virus taxid:59303
| Protein | ModelArchive |
| Structural polyprotein (p130) | ma-jd-viral-30952 |
Sindbis virus taxid:11034
| Protein | ModelArchive |
| Frameshifted structural polyprotein (p130) | ma-jd-viral-35113 |
Tai Forest alphavirus taxid:1930825
| Protein | ModelArchive |
| Structural polyprotein (p130) | ma-jd-viral-30951 |