ライフサイエンスコーパス: quasispecies

1 mucosal challenge with the diverse SIVsmE660 quasispecies.

2 of the mutant epitope sequences in the viral quasispecies.

3 a genetic bottleneck is imposed on the virus quasispecies.

4 tis C viruses exist as a dynamic and complex quasispecies.

5 and is qualitatively similar to an RNA virus quasispecies.

6 ated by PCR errors and the presence of viral quasispecies.

7 ection of influenza A virus N1 neuraminidase quasispecies.

8 ed site that fosters replication of M-tropic quasispecies.

9 genotyping algorithm based on the theory of quasispecies.

10 each population contained a diversity of HBV quasispecies.

11 particular codon at this locus in the viral quasispecies.

12 eraction between defined variants in a viral quasispecies.

13 cell responses in the evolution of the viral quasispecies.

14 is an ensemble of related sequences, termed quasispecies.

15 which in turn serves to constrain the viral quasispecies.

16 dimensionless parameters leading to distinct quasispecies.

17 erged at a frequency >20% of the serum viral quasispecies.

18 identical genotypes, commonly referred to as quasispecies.

19 nd R5X4 Envs derived from the HIV-1 89.6(PI) quasispecies.

20 about the potential members of the invading quasispecies.

21 stigated to better understand -1 PRF in this quasispecies.

22 composition and properties of the retrovirus quasispecies.

23 onserved among the various HCV genotypes and quasispecies.

24 th rate that exceeds that of the established quasispecies.

25 distribution of genetic variants known as a quasispecies.

26 infection with antigenically distinct viral quasispecies.

27 he distribution of adaptive mutations in RNA quasispecies.

28 ltiple viral variants that contribute to the quasispecies.

29 LA-B*0801-HSK in different HCV genotypes and quasispecies.

30 selection impacts on the evolution of viral quasispecies.

31 DMFE) is crucial to the evolutionary fate of quasispecies.

32 f related, but non-identical, genomes called quasispecies.

33 t is often referred to as sub-populations or quasispecies.

34 f reads to generate the most probable set of quasispecies.

35 or a small number of variants from the donor quasispecies.

36 tions of genetically close variants known as quasispecies.

37 s acting for the late selection of resistant quasispecies.

38 Changes in E2/HVR1 quasispecies 8-22 weeks after infection, likely caused b

39 the population level, which afford the viral quasispecies a greater probability to evolve and adapt t

40 Neither the Hamming distance nor the quasispecies affected the results.

41 ognition of common mutations reported in HCV quasispecies, albeit to a varying degree.

42 ct all the individual sequences of the viral quasispecies--along with their prevalence--using a heuri

43 ients indicates the potential utility of HCV quasispecies analysis as a non-invasive biomarker of HCC

44 Quasispecies analysis in one case indicated that 68% of

45 Quasispecies analysis revealed that several mutations pr

46 and anesthesia procedures were reviewed; HCV quasispecies analysis was performed.

47 The relationship between the HCV quasispecies and clinical and demographic features were

48 to the origins of plant viruses, analyses of quasispecies and mutation frequencies, population studie

49 t naive patients provides insight into viral quasispecies and the pre-existence of some drug-resistan

50 in these epitopes again predominated in the quasispecies and viral load dropped sharply.

51 g tier 2 or 3 strains, transmitted founders, quasispecies, and soluble sdAb JM4-resistant strains, bu

52 g tier 2 or 3 strains, transmitted founders, quasispecies, and soluble single domain antibody (sdAb)

53 ) mutates, diverging into a "swarm" of viral quasispecies, and the predominance of CCR5- or CXCR4-uti

54 in BP, and dynamics between their respective quasispecies are associated with changes in CD4(+) cell

55 ses of all potential members of the invading quasispecies are known.

56 Mathematical models predict that viral quasispecies are not simply a collection of diverse muta

57 cteria, i.e., functional differences between quasispecies arise endogenously within the evolutionary

58 Quasispecies arise from rapid genomic evolution powered

59 olated from the patient's pretreatment viral quasispecies as well as after therapy.

60 cilitating genetic cooperativity among viral quasispecies as well as enhancing viral replication.

61 /=2% mutant frequency in a participant's HIV quasispecies at pol codons K103N, Y181C, G190A, M184 V,

62 Discovery of quasispecies at position 222 (Q/L), in addition to the a

63 plicates and, as a result, multiple emerging quasispecies become rapidly resistant to anti-virals, in

64 characteristics distinct from those of donor quasispecies, but the biological factors favoring their

65 e genetic imprint left on the evolving virus quasispecies by a composite of host selection pressures.

66 ffect of the DMFE on the dynamics of a large quasispecies by means of a phenotypic version of the cla

67 the respective serum HBV DNAs of the cloned quasispecies by population sequencing.

68 s, in which we assessed the diversity of the quasispecies by single-genome amplification (SGA) and do

69 solates and protect against heterologous HCV quasispecies challenge in a human liver-chimeric mouse m

70 Quasispecies changes over time were associated with fluc

71 Active drug use is associated with quasispecies changes probably due to repeated superinfec

72 drugs were 3 times more likely to experience quasispecies changes than their noninjecting counterpart

73 entivirus data, the Rev variants exhibited a quasispecies character.

74 to 2280) was assessed by sequencing 10 to 15 quasispecies clones per patient from serum-derived PCR p

75 ated with human immunodeficiency virus (HIV) quasispecies compartmentalization within the cerebrospin

76 Nucleotide and amino acid quasispecies complexities of the hypervariable region 1

77 We determined HCV quasispecies complexity and diversity in 69 subjects, 28

78 T-naive subjects had significantly lower HCV quasispecies complexity and diversity than did both HIV-

79 among HIV/HCV coinfected patients, HCV quasispecies complexity and dynamics correlate more clos

80 In conclusion, low pretreatment quasispecies complexity may predict peg-IFN response; ea

81 ature) and (ii) interrogate the longitudinal quasispecies complexity of the virome.

82 would be associated with differences in HCV quasispecies complexity over time and with treatment res

83 Patients with SVR had lower baseline quasispecies complexity than those without SVR (P = .07)

84 Quasispecies complexity was a mean of 2.24 bands for HCV

85 e only factors significantly associated with quasispecies complexity, assessed as the number of SSCP

86 Quasispecies complexity, determined by using this novel

87 nd partition analyses suggested that the Rev quasispecies comprised two distinct subpopulations that

88 fitness landscape occupied by an artificial quasispecies consisting of 48 randomly mutagenized clone

89 In each case, the donor viral quasispecies contained Envs that were resistant to autol

90 culture system in which naturally occurring quasispecies could be studied.

91 able renal transplant recipients, with JCPyV quasispecies detected in 5 samples.

92 to chronicity, major changes in the E2/HVR1 quasispecies developed at 8-22 weeks (mean, 13.1 wk).

93 In 2 of 4 patients studied temporally, core quasispecies did not change over time.

94 The quasispecies distribution in plasma and liver samples sh

95 s of hepatitis C virus (HCV) replication and quasispecies distribution within the tumor of patients w

96 cies diversity (P=.001), and higher rates of quasispecies diversification (P=.004) than did subjects

97 .3-99.6) times higher among persons with low quasispecies diversification rates compared with the odd

98 vels over time (P=.04), higher intraspecimen quasispecies diversity (P=.001), and higher rates of qua

99 genomes, we quantified West Nile virus (WNV) quasispecies diversity after passage in Drosophila cells

100 first time a system to investigate RNA virus quasispecies diversity at the cellular level utilizing h

101 status, on hepatitis C virus (HCV) load and quasispecies diversity in patients coinfected with the h

102 Nonstructural 5A sequences exhibited quasispecies diversity initially but, after 8.5 years, h

103 Overt quasispecies diversity is a feature of the parental stra

104 Hepatitis C virus (HCV) quasispecies diversity is more likely to affect early vi

105 otably, using chemical mutagenesis to expand quasispecies diversity of the high-fidelity virus before

106 We propose that restricting viral quasispecies diversity provides a general approach for t

107 HCV quasispecies diversity varied greatly between cells in v

108 HCV quasispecies diversity was analyzed by sequencing hyperv

109 Viral quasispecies diversity was analyzed in 187 specimens (me

110 Metrics of sequence coverage and depth, quasispecies diversity, and detection of DAA resistance-

111 ral emergence, host jumps, mutation effects, quasispecies diversity, and mathematical models of viral

112 Vs, comprehensive viral strain analysis, and quasispecies diversity.

113 ation results in an increase in HCV load and quasispecies diversity.

114 sibility, we characterized circulating viral quasispecies during and after consecutive pregnancies in

115 infants and showed no further restriction in quasispecies during perinatal transmission.

116 characterize genomic changes in coronavirus quasispecies during simulated host-switching.

117 The virus quasispecies dynamics are explicitly represented by muta

118 We studied viral quasispecies dynamics in patients who failed standard of

119 Studies on hepatitis C virus (HCV) quasispecies dynamics in the natural course of infection

120 No affect on HCV quasispecies dynamics was noted in relation to CD4 count

121 Our results show that quasispecies effects and neutral drift can occur concurr

122 Quasispecies emergence was determined via heteroduplex c

123 ponse by sequential exposure to native HIV-1 quasispecies env variants derived from an individual wit

124 , with only one or few variants of the donor quasispecies establishing the new infection.

125 nses in virus neutralization and local virus quasispecies evolution has not been characterized.

126 We evaluated HCV quasispecies evolution in longitudinally collected speci

127 ts with inherited bleeding disorders undergo quasispecies evolution over time.

128 Viral quasispecies evolution upon long-term virus replication

129 s of response to antiviral therapy and viral quasispecies evolution.

130 viral population dynamics has been shaped by quasispecies evolutionary theory.

131 at de novo mutation, and not selection among quasispecies existing in a strain, is the primary drivin

132 ing formulation, identifies a minimal set of quasispecies explaining all observed reads, ShotMCS, bas

133 ontrol and several OBIs, variants of a given quasispecies expressed HBsAg according to different patt

134 Quasispecies fixation has two important characteristics:

135 ption-PCR, cloning, and sequencing to define quasispecies for the HCV internal ribosomal entry site (

136 These data suggest that of the viral quasispecies found in mothers, the HIV mother-to-child t

137 th algorithms were accurate in estimation of quasispecies frequencies, especially from large datasets

138 racking assay (RNA-HTA) was tested on plasma quasispecies from 21 HIV-1-infected persons in whom one

139 To approach this issue, nef quasispecies from chronically HIV-1-infected individuals

140 Comparison of the quasispecies from different body compartments within a g

141 To address this issue, nef quasispecies from nine chronically HIV-1-infected person

142 Deep sequencing of viral quasispecies from the ninth passage found five consensus

143 f closely related envelope protein variants (quasispecies) from an extremely neutralization-resistant

144 The high level of viral quasispecies genetic diversity found in at least a third

145 atistically significant, among patients with quasispecies >/=42% non-R(70) (P = 0.08), while HCC inci

146 as significantly reduced among patients with quasispecies >/=98.5% non-L(91) (P = 0.01).

147 ced viruses indicated that distinct proviral quasispecies had been activated by IL-7, as compared wit

148 changes (P = 0.05), and women with evolving quasispecies had greater decreases in CD4(+) cell levels

149 was abolished due to the emergence of viral quasispecies harboring a point mutation in the shRNA tar

150 CD8(+) T lymphocytes contain evolving viral quasispecies has not been characterized fully.

151 to tolerate Varroa and DWV, rather the viral quasispecies has simply not yet evolved the necessary mu

152 Because most studies of the HCV quasispecies have focused on a relatively small genomic

153 Hence, great quasispecies heterogeneity in the regions encoding the P

154 model that positive host pressure drives HCV quasispecies heterogeneity, although data favoring the h

155 ition of the JC polyomavirus population (the quasispecies, i.e., the whole of the consensus populatio

156 n, we evaluated the genetic diversity of HCV quasispecies in 12 seronegative subjects with primary in

157 bs) against individual viral variants of the quasispecies in a cohort of drug-naive subjects with lon

158 otease mutation was reported as the dominant quasispecies in a treatment-naive individual, raising co

159 en the percentage of 70 and/or 91 mutant HCV quasispecies in baseline serum samples of chronic HCV pa

160 hat suggested long-term persistence of viral quasispecies in CD4(+) TSCM cells.

161 y do not give a full representation of HIV-1 quasispecies in cellular reservoirs, the major repositor

162 t variance with GSS, characterization of PrP quasispecies in different sCJD subtypes ruled out the pr

163 HCV exists as a quasispecies in each infected individual, and longitudin

164 ses contribute to the evolution of the viral quasispecies in HIV-1-infected women and their infants a

165 d HIV coinfection, little is known about HCV quasispecies in HIV-positive patients.

166 in two children, which pre-existed as minor quasispecies in maternal samples.

167 ion between the genetic heterogeneity of HEV quasispecies in ORF1 and the outcome of infection in sol

168 In a selected case, HCV quasispecies in serum, peripheral blood mononuclear cell

169 HBV transmission and the evolution of viral quasispecies in the context of MTCT.

170 understand better the dynamics between HIV-1 quasispecies in the genital tract and blood, we performe

171 Viral quasispecies in the second envelope hypervariable region

172 Serial passage of the quasispecies in vitro resulted in replacement of the ini

173 ovides an accurate representation of the env quasispecies in vivo, and has an overall error rate (inc

174 ved in 58% of the women; the loss or gain of quasispecies in VS or BP was always accompanied by such

175 addition, sustained compartmentalization of quasispecies in VS was found for four women, even as CD4

176 rus pool consisted of a donor-specific HSV-1 quasispecies, including one major ACV-sensitive (ACV(S))

177 phism and sequence analysis of the viral RNA quasispecies indicated that the virus present in SB cell

178 e for complementation between members in the quasispecies, indicating that selection indeed occurs at

179 ne response and escape mutation of the virus quasispecies inside a single host.

180 ction with the host is not confounded by the quasispecies invariably present in a natural infection.

181 Therefore, the HCV quasispecies is highly complex even during acute infecti

182 ntageous mutant rises to fixation in a viral quasispecies is investigated in the framework of multity

183 the predominance of CCR5- or CXCR4-utilizing quasispecies is strongly associated with the pattern of

184 Because HCV exists as a quasispecies, it is conceivable that a viral population

185 e requirement for a predominant S282T mutant quasispecies, its low replication capacity, and the low-

186 Sequential and mixture exposure to quasispecies led to epitope targeting similar to that ob

187 However, as a consequence of quasispecies-level negative frequency-dependent selectio

188 ronic infection, where the presence of viral quasispecies makes it difficult to ascertain the true na

189 ur study also showed that composition of HCV quasispecies may be preserved during transmission from h

190 NS3) protease inhibitors in <1% of the viral quasispecies may still allow >1000-fold viral load reduc

191 ction of env variants representing the viral quasispecies members isolated from an individual that de

192 tro selected functional Nef from the in vivo quasispecies mixtures that predominately lacked MHC-I do

193 inor viral variants and characterize complex quasispecies mixtures.

194 The quasispecies model is a very successful theoretical fram

195 We analyse the semiconservative quasispecies model of both MIN and CIN tumors.

196 Here, we present a within-host quasispecies model that incorporates a long-lived reserv

197 A quasispecies model with multiple subpopulations may prov

198 ed from infected CD8(+) cells from the viral quasispecies of 7 of 12 patients.

199 action upon the replication of two distinct quasispecies of an HCV replicon whose encoded NS5A prote

200 We find that multiple quasispecies of bacteria and phage can coexist in a homo

201 only a limited subset of the total number of quasispecies of bacteria, i.e., functional differences b

202 kage deep sequencing method and analyzed the quasispecies of four MTCT pairs that broke through immun

203 of novel strategies to block emergence of X4 quasispecies of human immunodeficiency virus type 1.

204 d transfected into Huh7.5 cells to produce a quasispecies of hypervariable region 1 (HVR1) that mimic

205 CXCR4-tropic viruses are present within the quasispecies of patients infected with subtype C virus a

206 When diversification occurs, quasispecies of phage adsorb effectively to only a limit

207 RNA viruses rapidly diversify into quasispecies of related genotypes.

208 us (HCV) infection results in highly diverse quasispecies of related viruses over time, mutations acc

209 ispecies that was much less diverse than the quasispecies of the bulk cell population from which the

210 cally heterogeneous and consist of a pool of quasispecies of VACV.

211 e of the immune response yields the diverse "quasispecies" of chronic infection.

212 space of the general model that results in a quasispecies only composed by lethal phenotypes is extre

213 ed to that for women who maintained the same quasispecies (P < 0.05).

214 C-free control patients had >/=42% non-R(70) quasispecies (P = 0.06).

215 from the patient's spleen and had an HCV RNA quasispecies pattern distinct from that in the serum.

216 Quasispecies percentage cut-points, >/=42% of non-argini

217 ightly associated with homogenization of HCV quasispecies, perhaps reflecting immune failure and/or s

218 study virulence thresholds in the context of quasispecies population dynamics.

219 isolate, while the lamivudine-resistant HBV quasispecies population showed a >1,000-fold increase in

220 developed a procedure for cloning serum HBV quasispecies populations and for phenotypic analysis of

221 We found phylogenetically distinct quasispecies populations at different plasma time points

222 mmary, a strategy of cloning full genome HBV quasispecies populations from patient sera was developed

223 he supernatant following transfection of the quasispecies populations remained mostly unchanged from

224 ed for this task, accurate reconstruction of quasispecies populations remains greatly unresolved.

225 t rather as a population of variants termed "quasispecies." Preexisting variants resistant to specifi

226 that may affect therapeutic efficiency, HCV quasispecies (QS) characteristics have been a major focu

227 neutralizing antibody (NA) responses and HCV quasispecies (QS) diversity and complexity in a large co

228 QuRe is a program for viral quasispecies reconstruction, specifically developed to a

229 tion, suggesting ongoing viral evolution and quasispecies replacement over time.

230 ic clustering over time, suggesting frequent quasispecies replacement rather than simple diversificat

231 Two intra-host viral population 'quasispecies' samples (type-1 human immunodeficiency and

232 nvestigate the genotype and phenotype of MHV quasispecies selected for resistance to a broad-spectrum

233 HCV quasispecies sequences from the patients were nearly ide

234 The HCV quasispecies sequences from this potential source patien

235 d state-of-the-art algorithms for estimating quasispecies spectra from the NGS amplicon and shotgun r

236 IV and HCV plasma loads were associated with quasispecies stability over time, as reflected by stable

237 Relative quasispecies structure is a plausible correlate of atten

238 The quasispecies structure is characteristic of complex adap

239 ch we did not observe a complete loss of the quasispecies structure of the wild-type genome, although

240 These insights into RNA virus quasispecies structure provide guidance for selecting cl

241 tion of lethal mouse viruses from within the quasispecies sufficient to establish lethality in immuno

242 mber of variants that diverge into a diverse quasispecies swarm.

243 y more accelerated evolution rate of HCV RNA quasispecies than either the IFN-alpha or placebo group.

244 an overall transmission advantage for viral quasispecies that are dominated by viruses with high in

245 Despite the extensive viral quasispecies that develops in an individual during the c

246 sity of HCV and the rapid evolution of viral quasispecies that escape antibody-mediated neutralizatio

247 The swarm of quasispecies that evolves in each HIV-1-infected individ

248 Each cell contained a unique quasispecies that was much less diverse than the quasisp

249 le depends on the overall growth rate of the quasispecies that will form if invasion is successful ra

250 iral dynamics involved in the formation of a quasispecies, the choice of mutagenic nucleoside analogs

251 evidence for a fundamental prediction of the quasispecies theory and establishes a link between mutat

252 The quasispecies theory by Eigen predicts the existence of a

253 thus providing a genotype-phenotype map, the quasispecies theory can form the basis of a detailed seq

254 recent theoretical approach, we applied the quasispecies theory combined with kinetic/thermodynamic

255 ection pressure have been established by the quasispecies theory decades ago, its implications have l

256 While quasispecies theory has provided an intellectual framewo

257 Quasispecies theory is a case of mutation-selection bala

258 as been an invaluable tool to test models of quasispecies theory.

259 ly related viral variants, termed the "viral quasispecies." These variants may display divergent repl

260 IV preserves sequence heterogeneity in viral quasispecies through genetic complementation.

261 romoting genetic interplay by enabling viral quasispecies to collectively infect a susceptible host c

262 esent at levels of >/=90% within a patient's quasispecies to confer low-level resistance.

263 However, the transition from a stable quasispecies to genetic drift and loss of information ca

264 y also illustrate the capacity of the SIVmac quasispecies to modify antigenic determinants in respons

265 ation does not totally push the entire viral quasispecies towards deleterious or lethal regions of th

266 molecular mass and isoelectric point of PrP quasispecies under two-dimensional electrophoresis.

267 he data suggest that upon transmission, core quasispecies undergo genetic homogenization associated w

268 Hepatitis C virus (HCV) quasispecies variability has been associated with liver

269 active antiretroviral therapy (HAART) on HCV quasispecies variability have not been firmly establishe

270 coinfection is associated with decreased HCV quasispecies variability, which appears to be reversed b

271 explore the use of a collection of HIV-1 env quasispecies variants as immunogens and to present evide

272 utation patterns were also observed in minor quasispecies variants at baseline.

273 ight be attributed to the selection of minor quasispecies variants at the baseline with or without ad

274 ative fitness of the predominant single-cell quasispecies variants indicated a modest reduction in fi

275 The emergence of drug-resistant HCV quasispecies variants is assumed to be a major mechanism

276 Comparative analyses of consensus dominant quasispecies variants revealed that most mutations, occu

277 in our lab, multiple nearly full-length HCV quasispecies variants were generated from 9.1-kb amplico

278 e to select populations of emerging envelope quasispecies variants.

279 mutant frequency within an individual's HIV quasispecies was 67%.

280 Evolution of quasispecies was observed in 58% of the women; the loss

281 llowing subsequent transmission, a synthetic quasispecies was reconstituted comprising molecular clon

282 RNA, such that the replication of both viral quasispecies was suppressed by IFN treatment of the Huh7

283 und that the baseline diversity of HIV-1 env quasispecies was the major difference between VS and TF

284 lymerase error rate, primary infection viral quasispecies were classified as genetically heterogeneou

285 Heterogeneous quasispecies were detected in 4 of 12 preseroconversion

286 tes differed slightly between patients, core quasispecies were relatively homogeneous within each pat

287 onment influences the character of the viral quasispecies when HIV-1 is transmitted in utero.

288 (P < .0001) and diversity (P = .001) of HCV quasispecies, whereas HAART predicted increased complexi

289 ion at epitope-containing sites in the viral quasispecies, which conferred escape by mechanisms inclu

290 CoVs) possess large RNA genomes and exist as quasispecies, which increases the possibility of adaptiv

291 etically distinct but related variants, or a quasispecies, whose complexity and sequence evolution ar

292 C and 54.7% of matched HCC-free patients had quasispecies with >/=98.5% non-L(91) (P = 0.06).

293 long as it has the potential to grow into a quasispecies with an overall growth rate that exceeds th

294 Viral quasispecies with D-X4 phenotypes were associated signif

295 e selection of viral variants from among the quasispecies with different genotypes than those of the

296 n is characterized by complex array of viral quasispecies with reduced antigenicity/immunogenicity an

297 he clinical value of hepatitis B virus (HBV) quasispecies with reverse transcriptase and HBV surface

298 STTV1 exists as a quasispecies, with several genome variants identified in

299 The evolution of HCV NS5A quasispecies within the first week was analyzed by compa

300 erized by acquisition of a homogeneous viral quasispecies, yet the selective factors responsible for