English: Genome organization and gene expression of Japanese encephalitis virus (JEV). (A) Genome organization. The genetically well-characterized JEV strain, CNU/LP2, contains a single-stranded positive-sense RNA genome of 10,968 nucleotides in length, consisting of a methylated cap at the 5′ end, followed by a 95-nucleotide 5′ non-coding region (5′NCR), a 10,299-nucleotide open reading frame (ORF), and a 574-nucleotide 3′NCR [164,165]. (B) Gene expression. The single ORF encoded in the viral genome produces two precursor polyproteins, a full-length 3432-amino acid polyprotein (ppC-NS5) and its C-terminally truncated 1198-amino acid polyprotein (ppC-NS1′), the latter of which is expressed by a −1 ribosomal frameshift (FS) event that occurs between the codons 8 and 9 of NS2A, adding 52 extra amino acids to the C-terminus of NS1 (designated NS1′). Each of the two polyproteins is cleaved by host- and virus-encoded proteases to yield three structural (green) and at least seven nonstructural (orange) proteins. The flavivirus-conserved cleavage sites and the length of cleavage products are indicated. NS3 consists of an N-terminal serine protease (PRO) domain and a C-terminal RNA helicase (HEL) domain, and NS5 consists of an N-terminal methyltransferase (MET) domain and a C-terminal RNA-dependent RNA polymerase (RDRP) domain. Asterisks indicate four N-linked glycosylation sites (NXT/S) found in the pr portion of prM (Asn15), E (Asn154), and NS1/NS1′ (Asn130 and Asn207). (C) Polyprotein membrane topology. The membrane orientation of the 10 major JEV proteins is predicted on the endoplasmic reticulum (ER) membrane, based on previous work with other flaviviruses [142,166,167,168,169].