5′- and 3′-noncoding regions in flavivirus RNA

Abstract

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Comparative Analysis of Full-Length Genomic Sequences of 10 Dengue Serotype 1 Viruses Associated with Different Genotypes, Epidemics, and Disease Severity Isolated in Thailand over 22 Years

“…This observation is consistent with a previous report that the last 100 nucleotides in the 3′-NTR are conserved in all four DENV serotypes. 18 Similar to what was seen for the coding region, the more recent isolates of the genotype I strains had more nucleotide substitutions than earlier isolates; the percentage of nucleotide substitutions ranged from 0.22% to 1.95% ( Table 2 ). Genotype III had 3.90% nucleotide substitutions in the 3′-NTR, which was approximately 60% more than the genotype I strain ThD1-0081-82 (2.2%) isolated two years later ( Table 2 ).…”

Dengue virus type 3 vaccine candidates generated by introduction of deletions in the 3′ untranslated region (3′-UTR) or by exchange of the DENV-3 3′-UTR with that of DENV-4

“…The DENV 3'-UTRs range in length from approximately 400-450 nucleotides and contain three defined regions, namely, the variable region which abuts the NS5 gene stop codon, the core region, and an essential 3' terminal stem loop structure which is well-conserved among the flaviviruses [34]. The DENV 3'-UTR is believed to play a key role in the regulation of viral replication by virtue of controlling RNA synthesis [35].…”

“…The DENV 3'-UTR is believed to play a key role in the regulation of viral replication by virtue of controlling RNA synthesis [35]. Both viral and cellular factors are known to bind to the 3'-UTR, and these interactions appear to regulate the efficiency of RNA replication [34]. There is some evidence suggesting that the attenuating effects of deletion mutations in the 3'-UTR are mediated by a disruption in secondary structure that results in a decrease in the efficiency of RNA replication [35].…”

Rapid fixation of a distinctive sequence motif in the 3′ noncoding region of the clade of West Nile virus invading North America

“…A number of authors have described different regions of the 3′NCR of flaviviruses based on such factors as nucleotide content, degree of conservation, occurrence of repeated sequence motifs, and predicted secondary structure (Proutski et al 1997;Markoff 2003;Tajima et al 2006;Gritsun and Gould 2006). In general, the more upstream portion of the 3′ NCR has been found to be more variable than the downstream portions (Markoff 2003;Tajima et al 2006).…”

“…In general, the more upstream portion of the 3′ NCR has been found to be more variable than the downstream portions (Markoff 2003;Tajima et al 2006). In the present paper, we analyzed separately the region designated the AT-enriched region by Gritsun and Gould (2006) on the basis of their alignment of a wide variety of flavivirus 3/NCR sequences.…”