Impact of virus subtype and host
HCV
RNA secondary structure
RNaseL
UpA dinucleotide
evolution
interferon lambda
Journal
RNA (New York, N.Y.)
ISSN: 1469-9001
Titre abrégé: RNA
Pays: United States
ID NLM: 9509184
Informations de publication
Date de publication:
11 2020
11 2020
Historique:
received:
28
03
2020
accepted:
29
07
2020
pubmed:
5
8
2020
medline:
23
1
2021
entrez:
5
8
2020
Statut:
ppublish
Résumé
Mechanisms underlying the ability of hepatitis C virus (HCV) to establish persistent infections and induce progressive liver disease remain poorly understood. HCV is one of several positive-stranded RNA viruses capable of establishing persistence in their immunocompetent vertebrate hosts, an attribute previously associated with formation of large-scale RNA structure in their genomic RNA. We developed novel methods to analyze and visualize genome-scale ordered RNA structure (GORS) predicted from the increasingly large data sets of complete genome sequences of HCV. Structurally conserved RNA secondary structure in coding regions of HCV localized exclusively to polyprotein ends (core, NS5B). Coding regions elsewhere were also intensely structured based on elevated minimum folding energy difference (MFED) values, but the actual stem-loop elements involved in genome folding were structurally poorly conserved, even between subtypes 1a and 1b. Dynamic remodeling was further evident from comparison of HCV strains in different host genetic backgrounds. Significantly higher MFED values, greater suppression of UpA dinucleotide frequencies, and restricted diversification were found in subjects with the TT genotype of the rs12979860 SNP in the
Identifiants
pubmed: 32747607
pii: rna.075465.120
doi: 10.1261/rna.075465.120
pmc: PMC7566573
doi:
Substances chimiques
IFNL4 protein, human
0
Interleukins
0
RNA, Viral
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1541-1556Subventions
Organisme : Medical Research Council
ID : MR/K01532X/1
Pays : United Kingdom
Organisme : MRF
ID : MRF_C0365
Pays : United Kingdom
Organisme : Department of Health
ID : 14/02/17
Pays : United Kingdom
Organisme : Medical Research Council
ID : MC_UU_12014/1
Pays : United Kingdom
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/K010239/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/P025064/1
Pays : United Kingdom
Organisme : Wellcome Trust
ID : WT103767MA
Pays : United Kingdom
Investigateurs
J Ball
(J)
D Bonsall
(D)
D Brainard
(D)
G Burgess
(G)
J Dillon
(J)
G Foster
(G)
C Gore
(C)
N Guha
(N)
R Halford
(R)
K Whitby
(K)
C Holmes
(C)
A Howe
(A)
E Hudson
(E)
S Hutchinson
(S)
S Khakoo
(S)
P Klenerman
(P)
N Martin
(N)
B Massetto
(B)
T Mbisa
(T)
J McHutchison
(J)
J McKeating
(J)
A Miners
(A)
A Murray
(A)
P Shaw
(P)
C Spencer
(C)
E Thomson
(E)
P Vickerman
(P)
N Zitzmann
(N)
Informations de copyright
© 2020 Simmonds et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
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