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Chapter 2a: Virology

Similar recombinant subviral particles (RSPs) The 5’-UTR contains a type 1 cap
of a slightly larger size (approximately 30 nm (m7GpppAmG), followed by a conserved
in diameter) can be produced by cells stem-loop structure. The 3’-UTR is not
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expressing only prM and E proteins. polyadenylated and is characterized by
extensive length and sequence hetero-
The TBEV genome consists of a single- geneity. This region of the viral genome can
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stranded positive sense RNA molecule, be divided into 2 parts: a proximal (localized
approximately 11 kilobases in length. The behind the ‘stop’ codon of the ORF) and a
genome encodes 1 open reading frame (ORF)
distal (‘core’, the 3′ terminus itself). The distal
of over 10,000 bases, which is flanked by
part of this region (approximately 340 nt) is
untranslated (non-coding) regions (UTRs). The
highly conserved, whilst the proximal part is a
ORF encodes 1 large polyprotein of approxi- noticeably variable segment with common
mately 3400 amino acids, which is co- and 34–36
deletions and insertions.
post- translationally cleaved by viral and
cellular proteases into 3 structural proteins (C, RNA structural models demonstrate that
prM, and E) and 7 non-structural proteins flavivirus genomes, including TBFVs, form
(NS1, NS2A, NS2B, NS3, NS4A, NS4B, and dsRNA cyclization stems or ‘panhandles’ at
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NS5) (Figure 4). A second short upstream their 5′- and 3′-termini. The ‘panhandle’ of the
ORF is present in the 5′-UTR of some TBEV TBFV group (5′CYCL) is formed by a perfectly
strains. However, no protein encoded by this conserved continuous 21-nucleotide sequence
ORF has been found in TBEV-infected cells, located in the 5′-UTR. The 5′-UTR and 3′-UTR
indicating that it is not expressed or is present sequences directly involved in cyclization are
at undetectable concentrations, suggesting located downstream from the 5′ Y-shaped
that this additional ORF has either minor or no structure and the 3′ long stable hairpin,
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biological role in the TBEV replication cycle. respectively. The terminal 5′-UTR and 3′-UTR
A common feature of all flavivirus genomes is regions not involved in cyclization also show
their high purine content and low GC and UA homology, suggesting they are evolutionary
doublet frequencies, which may influence remnants of a long cyclization domain that
translation of the genome and/or reflect the probably emerged through duplication of 1 of
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requirement for flaviviruses to grow in the UTR termini.
different hosts and cell types; however, a
specific role for this unique genomic 5’-untranslated region
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characteristic remains unclear. A replication
The 5’-UTR is 132 nucleotides long in most
enhancer element (REE) has been found
TBEV strains and its secondary structure is
within the capsid gene of TBEV. The REE folds
as a long stable stem-loop (designated SL6), highly conserved among different TBEV
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conserved among all TBFVs. Although SL6 REE strains. Common secondary structures in this
is not essential for growth in tissue culture, it region can also be found among different
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acts to up-regulate virus replication. flaviviruses, although the sequence is
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diverse. The function of these conserved
In addition to coding for the polyprotein, the secondary structures is probably related to
genome has RNA structural motifs that play a translation of the genome and in the
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crucial role in the viral life-cycle. In complementary RNA strand serves as a site for
particular, the untranslated regions form initiation of synthesis of positive-stranded
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secondary stem-loop structures that probably RNA molecules.
serve as cis-acting elements for genome
replication, translation, and/or packaging. 33–36

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