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Chapter 2a: Virology

The folding of 333 nt as a reverse complement mission cycle of TBEV. 44,45 A short poly(A) tract
of the 5′-end (3′-end of the negative-stranded is genetically more stable compared with the
RNA) of TBEV revealed a stem-loop pattern virus having a long poly(A) tract. 46
different from the 3′-UTR of positive-stranded Previous studies reported that the variable
RNA. However, 2 nucleotide regions in these region plays no role in viral replication and
3′-ends are identical and conserved among all 43
virulence for laboratory mice. However,
TBFVs. One of these, an 11-nt region, forms a
recent studies revealed that partial deletions
loop within the folding pattern at the 3′-end of and poly(A) insertion in the variable region
the negative strand and a stem at the 3′-UTR
34 increases TBEV virulence in the mouse
of the positive strand. These structural 45,47
model. These data suggested that the
motifs at the 5′ and 3′-UTR termini could be variable region of 3′-UTR might impact neuro-
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recognition sites for viral RNA polymerase.
virulence and function as a critical virulence
The alignment of the 5′-UTRs of different factor. 45,46
TBFVs demonstrated an internal hypervariable All TBFVs share a common folding pattern of
domain in which Powassan virus has a secondary structures at the C3′-UTR position.
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deletion of 27 bases. The predicted folding
RNA in this region is predicted to fold into a 3’
of the 5′-UTR sequence produces a stem-loop
stem-loop and it contains conserved sequence
structure similar for all TBFV, and the 27 nt elements. However, these structures are
deletion in the Powassan virus has no effect different from those observed in mosquito-
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on the typical 5′-UTR folding. This indicates 34
borne flaviviruses. Indeed, some RNA
that the length of stem-loop structure 3 is not sequences within the 3’-UTR clearly
critical for virus infectivity. 34 37,38
distinguish mosquito-borne from TBFVs.

Modifications within the 3’-UTR of TBEV that
3’-untranslated region affect the conserved structural motifs are
known to attenuate the virus without altering
The alignment of 3′-UTRs of all TBFVs revealed
their antigenic specificity. Modification of this
2 nucleotide regions, 1 about 340 bases in region might form the basis for live-
length, of conserved sequence at the extreme attenuated vaccines and/or for antiviral
3′-end (designated C3′- UTR) and another therapeutics.
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hypervariable region placed between the stop
codon and the C3′-UTR where even strains Short direct repeat sequences (20-70
from a single species showed deletions of nucleotides long) in the 3′-UTR were found to
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different lengths, whereas some TBEV strains be conserved for each flavivirus group or
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have a 30-250 nt long poly(A) sequence in this subgroup. Four R1 repeats, two R2 repeats,
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region. Deletions or a poly(A) sequence and two R3 repeats, approximately 23, 26, and
insertion in the variable region were found in 70 nucleotides long, respectively, apparently
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strains passaged in mammalian cell culture, arranged randomly, have been described in
37,48
and deletions of different lengths were also the 3′-UTR of the TBFVs. These short
observed in TBEV strains isolated from human repeats apparently originated from at least 6
patients. 41–43 It was suggested that the hyper- long repeat sequences (LRS) approximately
variable region could act as a spacer separat- 200 nucleotides in length, arranged in tandem.
ing the folded 3′-UTR structure from the rest Four of these LRS are present in the 3′-UTR
of the genome that might be necessary for and 2 in the 3′ region of the ORF. Thus, it
efficient binding of viral RNA polymerase and seems that evolution of the 3′-UTR and
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cellular factors involved in transcription probably the ORF occurred through multiple
and may play a role in the natural trans- duplications of LRS that form the basis for the

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