Variability in the 3′ untranslated regions of the genomes of the different tick-borne encephalitis virus subtypes

Near-Complete Genome Sequence of a Swine Norovirus GII.11 Strain Detected in Japan in 2018

“…PCR of the 5= end was unsuccessful and, although we observed clearly the electropherogram ending that connected with the adapter for the 3= end, 447 and 14 nt from the 5= and 3= ends, respectively, were missing when the genome was aligned with the SW/NV/swine43/JP genome. Consistent with our result, some studies reported variability in the 3= untranslated regions in some RNA viruses (10,11). The near-complete genome sequence of the SwNoV/Sw1/2018/JP strain, consisting of 7,090 nt, with a GϩC content of 52.6%, was obtained.…”

Y‐shaped RNA secondary structure of a noncoding region in the genomic RNA of tick‐borne encephalitis virus affects pathogenicity

“…The 5′ and 3′ UTRs are necessary for viral RNA stability, replication, and translation 6 . The 3′ UTR consists of two domains: the 5′‐terminal variable region and the 3′‐terminal conserved region 7 . The conserved region of the 3′ UTR remains unchanged among TBEV strains 5 and the 3′ long stable hairpin structure in this conserved region has a crucial role in virus infection 7,8 .…”

“…The 3′ UTR consists of two domains: the 5′‐terminal variable region and the 3′‐terminal conserved region 7 . The conserved region of the 3′ UTR remains unchanged among TBEV strains 5 and the 3′ long stable hairpin structure in this conserved region has a crucial role in virus infection 7,8 . On the other hand, it was shown that the length and sequence of the variable region vary among TBEV strains 5,8 .…”

“…7 The conserved region of the 3′ UTR remains unchanged among TBEV strains 5 and the 3′ long stable hairpin structure in this conserved region has a crucial role in virus infection. 7,8 On the other hand, it was shown that the length and sequence of the variable region vary among TBEV strains. 5,8 Notably, large deletions were often found in TBEV strains isolated from mammals including human patients, [9][10][11] but not from ticks, 12,13 indicating that the variable region might have an important role in TBEV infection of mammals.…”

“…In these Y-shaped structures, one structure in the variable region (Y-3) and one structure in the conserved region were predicted to produce a subgenomic flavivirus RNA (sfRNA), which is non-coding RNA derived from the viral genome. 7,[14][15][16] Deletion of the Y-3 structure was observed in the isolates from human patients and by experimental passages in mammalian cell lines and mouse brains. 17,18 Furthermore, the deletion of the other variable region was reported to be involved in the pathogenesis of TBEV.…”