ライフサイエンスコーパス: quasispecies

1 tions of genetically close variants known as quasispecies.

2 s acting for the late selection of resistant quasispecies.

3 mucosal challenge with the diverse SIVsmE660 quasispecies.

4 of the mutant epitope sequences in the viral quasispecies.

5 a genetic bottleneck is imposed on the virus quasispecies.

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

7 and is qualitatively similar to an RNA virus quasispecies.

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

9 ection of influenza A virus N1 neuraminidase quasispecies.

10 enetics system for an invertebrate RNA virus quasispecies.

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

12 genotyping algorithm based on the theory of quasispecies.

13 each population contained a diversity of HBV quasispecies.

14 particular codon at this locus in the viral quasispecies.

15 he distribution of adaptive mutations in RNA quasispecies.

16 cell responses in the evolution of the viral quasispecies.

17 is an ensemble of related sequences, termed quasispecies.

18 which in turn serves to constrain the viral quasispecies.

19 dimensionless parameters leading to distinct quasispecies.

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

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

22 identical genotypes, commonly referred to as quasispecies.

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

24 about the potential members of the invading quasispecies.

25 eraction between defined variants in a viral quasispecies.

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

27 distribution of genetic variants known as a quasispecies.

28 infection with antigenically distinct viral quasispecies.

29 ltiple viral variants that contribute to the quasispecies.

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

31 selection impacts on the evolution of viral quasispecies.

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

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

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

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

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

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

38 Viruses populate their hosts as a viral quasispecies: a collection of genetically related mutant

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

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

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

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

43 Quasispecies analysis in one case indicated that 68% of

44 Quasispecies analysis revealed that several mutations pr

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

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

47 ined proportions of artificial RNA and virus quasispecies and measured their relative proportions usi

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

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

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

56 Quasispecies arise from rapid genomic evolution powered

57 ges in the population structure of the viral quasispecies as it adapted to immune pressure.

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

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

60 rates compared to the state-of-the-art viral quasispecies assemblers.

61 Viral quasispecies assembly is the reconstruction of strain-sp

62 /=2% mutant frequency in a participant's HIV quasispecies at pol codons K103N, Y181C, G190A, M184 V,

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

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

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

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

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

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

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

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

71 Quasispecies changes over time were associated with fluc

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

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

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

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

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

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

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

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

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

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

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

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

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

85 Quasispecies complexity was a mean of 2.24 bands for HCV

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

87 Quasispecies complexity, determined by using this novel

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 s, from a phase 2b VCV clinical trial, whose quasispecies contained R5 and dual-mixed virions at the

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

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

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

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

95 The quasispecies distribution in plasma and liver samples sh

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

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

98 a, emergence of drug-resistant variants, and quasispecies diversification in the plasma compartment w

99 .3-99.6) times higher among persons with low quasispecies diversification rates compared with the odd

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

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

102 Low quasispecies diversity and inefficient neutralizing acti

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

104 Women with low quasispecies diversity displayed significantly higher me

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

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

107 Overt quasispecies diversity is a feature of the parental stra

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

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

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

111 HCV quasispecies diversity varied greatly between cells in v

112 HCV quasispecies diversity was analyzed by sequencing hyperv

113 Viral quasispecies diversity was analyzed in 187 specimens (me

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

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

116 nificant associations were found between HCV quasispecies diversity, selective pressure exerted on th

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

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

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

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

121 The virus quasispecies dynamics are explicitly represented by muta

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

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

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

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

126 Quasispecies emergence was determined via heteroduplex c

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

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

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

130 We evaluated HCV quasispecies evolution in longitudinally collected speci

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

132 Viral quasispecies evolution upon long-term virus replication

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

174 Viral quasispecies in the second envelope hypervariable region

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

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

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

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

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

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

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

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

183 of the genetic diversity present in the HIV quasispecies is critical for the development of a preven

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

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

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

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

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

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

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

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

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

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

194 inor viral variants and characterize complex quasispecies mixtures.

195 The quasispecies model is a very successful theoretical fram

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

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

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

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

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

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

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

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

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

205 RNA viruses rapidly diversify into quasispecies of related genotypes.

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

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

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

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

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

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

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

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

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

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

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

217 d with a significant bottleneck in the viral quasispecies population, yet the timing of that bottlene

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

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

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

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

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

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

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

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

226 pon treatment, the composition of the plasma quasispecies rapidly changed, leading to a majority of c

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

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

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

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

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

232 HCV quasispecies sequences from the patients were nearly ide

233 The HCV quasispecies sequences from this potential source patien

234 ributions and contig sizes, and also on mock quasispecies sequencing data.

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

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

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

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

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

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

244 he development of drug resistance with viral quasispecies that continued the use of CCR5 for entry.

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

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

251 The quasispecies theory by Eigen predicts the existence of a

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

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

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

255 While quasispecies theory has provided an intellectual framewo

256 Quasispecies theory is a case of mutation-selection bala

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

258 e functional landscapes predicted from viral 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 dicted to cleave the majority of HIV-1 viral quasispecies (vQS) observed within and among patients.

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

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

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

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 owed that minority variants present at 1% of quasispecies were detected reproducibly with minimal var

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

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

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

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

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

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

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

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