The Zika virus genome consists of a single-stranded positive sense RNA molecule with 10794 kb of length with 2 flanking noncoding regions (5' and 3' NCR) and a single long open reading frame encoding a polyprotein: 5'-C-prM-E-NS1-NS2A-NS2B-NS3-NS4A-NS4B-NS5-3'. The polyprotein is cleaved into the structural proteins C, M and E and the nonstructural proteins which carry out functions in replication and assembly. In all likelihood, antagonism of host responses will be mediated by one or several of these non structural proteins.
5' and 3' untranslated regions are important in flavivirus genome cyclisation and replication with conserved sequences (CS1-3) found in related flaviviruses. Kuno and Chang (Kuno and Chang, 2007) identified variation in CS1 and CS3 of Zika virus strain MR 766 (order CS3-CS2-CS1) and this should be further investigated when more sequencing data becomes available, as it may influence replication and possibly virus-host interactions and pathogenicity.
The 3'NCR of the Zika virus genome contains about 428 nucleotides, including 27 folding patterns that may be involved in the recognition by cellular or viral factors, translation, genome stabilization, RNA packaging, or cyclization.
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