Viral initiation of translation

Many viruses have evolved alternative ways to initiate viral mRNA translation, either because the virus shuts off classic host translation, or because the viral RNAs are not classical, i.e. lack a cap or polyadenylation.

Internal Ribosome Entry Site (IRES) are RNA structures that allow cap-independent initiation of translation and are capable of initiating translation in the middle of a messenger RNA. Cripavirus IRES also allow translation initiation at an alanine or glutamine tRNA.

Downstream Hairpin Loop (DLP) are RNA structures that allow initiation of cap-dependent translation in the absence of the initiation factor eIF2, where the initiating methionine tRNA is placed on the ribosome by the DLP structure.

CUG initiation involves initiation with a leucine and is more likely to occur under stress with eIF2 inhibition. .

In VpG initiation, a direct interaction with the 5'-covalently bound protein VPG occurs with EIF4E. This has been described in plants. EIF4E mutations consequently make certain plant varieties resistant to virus infections.


Family Genus Type Species GROUP Initiation codon Host References
Dicistroviridae Cripavirus Cricket paralysis virus CrPV IRES Group I Alanine
Flaviviridae Hepacivirus Pestivirus Hepatitis C virus
Bovine diarrhea virus
Classical swine fever virus
IRES Group II Methionine Vertebrate
Nimaviridae Whispovirus White spot syndrome virus IRES Methionine Invertebrate
Picornaviridae Cardiovirus Aphthovirus Encephalomyocarditis virus
Foot and mouth disease virus
IRES Group III Methionine Vertebrate
Picornaviridae Enterovirus Hepatovirus Poliovirus
Hepatitis A virus
IRES Group IV Methionine Vertebrate
Polyomaviridae Polyomavirus SV40 IRES Methionine Vertebrate
Retroviridae Alpharetrovirus Rous sarcoma virus IRES Methionine Vertebrate
Betaretrovirus Mouse mammary tumor virus IRES Methionine Vertebrate
Gammaretrovirus Murine leukemia virus IRES Methionine Vertebrate
CUG Leucine Vertebrate
Deltaretrovirus Human T-lymphotropic virus IRES Methionine Vertebrate
Lentivirus Human immunodeficiency virus IRES Methionine Vertebrate
Togaviridae Alphavirus Sindbis virus DLP Methionine Vertebrate
Rubivirus Rubella virus DLP Methionine Vertebrate
Tombusviridae Carmovirus Pelargonium flower break virus IRES Methionine Plant
Totiviridae Giardiavirus Giardia lamblia virus IRES Methionine Protozoa
Potyviridae Potyvirus Lettuce mosaic virus VpG Methionine Plant