PMID- 17287328
OWN - NLM
STAT- MEDLINE
DCOM- 20071011
LR  - 20220408
IS  - 0095-1137 (Print)
IS  - 1098-660X (Electronic)
IS  - 0095-1137 (Linking)
VI  - 45
IP  - 4
DP  - 2007 Apr
TI  - Use of sequence analysis of the NS5B region for routine genotyping of hepatitis C 
      virus with reference to C/E1 and 5' untranslated region sequences.
PG  - 1102-12
AB  - Nucleotide sequence analysis of the NS5B region was performed to identify 
      genotypes of 8,479 hepatitis C virus (HCV) RNA-positive patient samples collected 
      in the Canadian province of Quebec. Genotypes could be determined for 97.3% of 
      patients. Genotypes 1 to 6 were found in 59.4, 9.0, 25.7, 3.6, 0.6, and 1.8% of 
      patients, respectively. Two isolates did not classify within the six genotypes. 
      The subtype 1 distribution was 76.7% 1a, 22.6% 1b, and 0.7% others, while the 
      subtype 2 distribution was 31.8% 2a, 47.6% 2b, 10.9% 2c, 4.1% 2i, and 5.6% 
      others. Subtype 3a accounted for 99.1% of genotype 3 strains, while all genotype 
      5 samples were of subtype 5a. The subtype 4 distribution was 39.2% 4a, 15.4% 4k, 
      11.6% 4d, 10.2% 4r, and 23.6% others. The subtype 6 distribution was 40.4% 6e, 
      20.5% 6a, and 39.1% others. The 5' untranslated region (5'UTR) sequences of 
      subtype 6e were indistinguishable from those of genotype 1. All samples that did 
      not classify within the established subtypes were also sequenced in C/E1 and 
      5'UTR. C/E1 phylogenetic reconstructions were analogous to those of NS5B. The 
      sequences identified in this study allowed the provisional assignments of 
      subtypes 1j, 1k, 2m, 2r, 3i, 4q, 6q, 6r, and 6s. Sixty-four (0.8%) isolates 
      classifying within genotypes 1 to 6 could not be assigned to one of the 
      recognized subtypes. Our results show that genotyping of HCV by nucleotide 
      sequence analysis of NS5B is efficient, allows the accurate discrimination of 
      subtypes, and is an effective tool for studying the molecular epidemiology of 
      HCV.
FAU - Murphy, Donald G
AU  - Murphy DG
AD  - Laboratoire de Sante Publique du Quebec, Institut National de Sante Publique du 
      Quebec, 20045 Chemin Sainte Marie, Sainte Anne de Bellevue H9X 3R5, Quebec, 
      Canada. donald.murphy@inspq.qc.ca
FAU - Willems, Bernard
AU  - Willems B
FAU - Deschenes, Marc
AU  - Deschenes M
FAU - Hilzenrat, Nir
AU  - Hilzenrat N
FAU - Mousseau, Roger
AU  - Mousseau R
FAU - Sabbah, Sidney
AU  - Sabbah S
LA  - eng
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SI  - GENBANK/EF116005
SI  - GENBANK/EF116006
SI  - GENBANK/EF116007
SI  - GENBANK/EF116008
SI  - GENBANK/EF116009
SI  - GENBANK/EF116010
SI  - GENBANK/EF116011
SI  - GENBANK/EF116012
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SI  - GENBANK/EF116014
SI  - GENBANK/EF116015
SI  - GENBANK/EF116016
SI  - GENBANK/EF116017
SI  - GENBANK/EF116018
SI  - GENBANK/EF116019
SI  - GENBANK/EF116020
SI  - GENBANK/EF116021
SI  - GENBANK/EF116022
SI  - GENBANK/EF116023
SI  - GENBANK/EF116024
SI  - GENBANK/EF116025
SI  - GENBANK/EF116026
SI  - GENBANK/EF116027
SI  - GENBANK/EF116028
SI  - GENBANK/EF116029
SI  - GENBANK/EF116030
SI  - GENBANK/EF116031
SI  - GENBANK/EF116032
SI  - GENBANK/EF116033
SI  - GENBANK/EF116034
SI  - GENBANK/EF116035
SI  - GENBANK/EF116036
SI  - GENBANK/EF116037
SI  - GENBANK/EF116038
SI  - GENBANK/EF116039
SI  - GENBANK/EF116040
SI  - GENBANK/EF116041
SI  - GENBANK/EF116042
SI  - GENBANK/EF116043
SI  - GENBANK/EF116044
SI  - GENBANK/EF116045
SI  - GENBANK/EF116046
SI  - GENBANK/EF116047
SI  - GENBANK/EF116048
SI  - GENBANK/EF116049
SI  - GENBANK/EF116050
SI  - GENBANK/EF116051
SI  - GENBANK/EF116052
SI  - GENBANK/EF116053
SI  - GENBANK/EF116054
SI  - GENBANK/EF116055
SI  - GENBANK/EF116056
SI  - GENBANK/EF116057
SI  - GENBANK/EF116058
SI  - GENBANK/EF116059
SI  - GENBANK/EF116060
SI  - GENBANK/EF116061
SI  - GENBANK/EF116062
SI  - GENBANK/EF116063
SI  - GENBANK/EF116064
SI  - GENBANK/EF116065
SI  - GENBANK/EF116066
SI  - GENBANK/EF116067
SI  - GENBANK/EF116068
SI  - GENBANK/EF116069
SI  - GENBANK/EF116070
SI  - GENBANK/EF116071
SI  - GENBANK/EF116072
SI  - GENBANK/EF116073
SI  - GENBANK/EF116074
SI  - GENBANK/EF116075
SI  - GENBANK/EF116076
SI  - GENBANK/EF116077
SI  - GENBANK/EF116078
SI  - GENBANK/EF116079
SI  - GENBANK/EF116080
SI  - GENBANK/EF116081
SI  - GENBANK/EF116082
SI  - GENBANK/EF116083
SI  - GENBANK/EF116084
SI  - GENBANK/EF116085
SI  - GENBANK/EF116086
SI  - GENBANK/EF116087
SI  - GENBANK/EF116088
SI  - GENBANK/EF116089
SI  - GENBANK/EF116090
SI  - GENBANK/EF116091
SI  - GENBANK/EF116092
SI  - GENBANK/EF116093
SI  - GENBANK/EF116094
SI  - GENBANK/EF116095
SI  - GENBANK/EF116096
SI  - GENBANK/EF116097
SI  - GENBANK/EF116098
SI  - GENBANK/EF116099
SI  - GENBANK/EF116100
SI  - GENBANK/EF116101
SI  - GENBANK/EF116102
SI  - GENBANK/EF116103
SI  - GENBANK/EF116104
SI  - GENBANK/EF116105
SI  - GENBANK/EF116106
SI  - GENBANK/EF116107
SI  - GENBANK/EF116108
SI  - GENBANK/EF116109
SI  - GENBANK/EF116110
SI  - GENBANK/EF116111
SI  - GENBANK/EF116112
SI  - GENBANK/EF116113
SI  - GENBANK/EF116114
SI  - GENBANK/EF116115
SI  - GENBANK/EF116116
SI  - GENBANK/EF116117
SI  - GENBANK/EF116118
SI  - GENBANK/EF116119
SI  - GENBANK/EF116120
SI  - GENBANK/EF116121
SI  - GENBANK/EF116122
SI  - GENBANK/EF116123
SI  - GENBANK/EF116124
SI  - GENBANK/EF116125
SI  - GENBANK/EF116126
SI  - GENBANK/EF116127
SI  - GENBANK/EF116128
SI  - GENBANK/EF116129
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SI  - GENBANK/EF116149
SI  - GENBANK/EF116150
SI  - GENBANK/EF116151
SI  - GENBANK/EF116152
SI  - GENBANK/EF116153
SI  - GENBANK/EF116154
SI  - GENBANK/EF116155
SI  - GENBANK/EF116156
SI  - GENBANK/EF116157
SI  - GENBANK/EF116158
SI  - GENBANK/EF116159
SI  - GENBANK/EF116160
SI  - GENBANK/EF116161
SI  - GENBANK/EF116162
SI  - GENBANK/EF116163
SI  - GENBANK/EF116164
SI  - GENBANK/EF116165
SI  - GENBANK/EF116166
SI  - GENBANK/EF116167
SI  - GENBANK/EF116168
SI  - GENBANK/EF116169
SI  - GENBANK/EF116170
SI  - GENBANK/EF116171
SI  - GENBANK/EF116172
SI  - GENBANK/EF116173
SI  - GENBANK/EF116174
SI  - GENBANK/EF116175
SI  - GENBANK/EF116176
SI  - GENBANK/EF116177
SI  - GENBANK/EF116178
SI  - GENBANK/EF116179
SI  - GENBANK/EF116180
SI  - GENBANK/EF116181
SI  - GENBANK/EF116182
SI  - GENBANK/EF116183
SI  - GENBANK/EF116184
SI  - GENBANK/EF116185
SI  - GENBANK/EF116186
SI  - GENBANK/EF116187
SI  - GENBANK/EF116188
SI  - GENBANK/EF116189
SI  - GENBANK/EF116190
SI  - GENBANK/EF116191
SI  - GENBANK/EF116192
SI  - GENBANK/EF116193
SI  - GENBANK/EF116194
SI  - GENBANK/EF116195
SI  - GENBANK/EF116196
SI  - GENBANK/EF116197
SI  - GENBANK/EF116198
SI  - GENBANK/EF116199
SI  - GENBANK/EF116200
SI  - GENBANK/EF116201
PT  - Journal Article
DEP - 20070207
PL  - United States
TA  - J Clin Microbiol
JT  - Journal of clinical microbiology
JID - 7505564
RN  - 0 (5' Untranslated Regions)
RN  - 0 (E1 protein, Hepatitis C virus)
RN  - 0 (RNA, Viral)
RN  - 0 (Viral Envelope Proteins)
RN  - 0 (Viral Nonstructural Proteins)
RN  - EC 2.7.7.48 (NS-5 protein, hepatitis C virus)
SB  - IM
MH  - 5' Untranslated Regions/genetics
MH  - Adult
MH  - Aged
MH  - Base Sequence
MH  - Female
MH  - Genotype
MH  - Hepacivirus/*classification/*genetics/isolation & purification
MH  - Hepatitis C/epidemiology/*virology
MH  - Humans
MH  - Male
MH  - Middle Aged
MH  - Molecular Epidemiology/methods
MH  - Molecular Sequence Data
MH  - Phylogeny
MH  - Quebec/epidemiology
MH  - RNA, Viral/*genetics
MH  - Sensitivity and Specificity
MH  - *Sequence Analysis, DNA
MH  - Sequence Homology
MH  - Viral Envelope Proteins/genetics
MH  - Viral Nonstructural Proteins/*genetics
PMC - PMC1865836
EDAT- 2007/02/09 09:00
MHDA- 2007/10/12 09:00
PMCR- 2007/08/01
CRDT- 2007/02/09 09:00
PHST- 2007/02/09 09:00 [pubmed]
PHST- 2007/10/12 09:00 [medline]
PHST- 2007/02/09 09:00 [entrez]
PHST- 2007/08/01 00:00 [pmc-release]
AID - JCM.02366-06 [pii]
AID - 2366-06 [pii]
AID - 10.1128/JCM.02366-06 [doi]
PST - ppublish
SO  - J Clin Microbiol. 2007 Apr;45(4):1102-12. doi: 10.1128/JCM.02366-06. Epub 2007 
      Feb 7.