메뉴 건너뛰기




Volumn 91, Issue 5, 2017, Pages

On the analysis of intrahost and interhost viral populations: Human cytomegalovirus as a case study of pitfalls and expectations

Author keywords

Human cytomegalovirus; Interhost diversity; Intrahost diversity; Population genetics

Indexed keywords

ARTICLE; GENETIC POLYMORPHISM; HUMAN CYTOMEGALOVIRUS; INTERHOST VIRAL POPULATION; INTRAHOST VIRAL POPULATION; MICROBIAL DIVERSITY; MODEL; MOLECULAR EVOLUTION; NONHUMAN; POPULATION GENETICS; QUANTITATIVE ANALYSIS; VIRAL DIVERSITY; VIRUS CELL INTERACTION; VIRUS LOAD; VIRUS MUTATION; ALLELE; BIOLOGICAL MODEL; CYTOMEGALOVIRUS; CYTOMEGALOVIRUS INFECTION; GENE FREQUENCY; GENETICS; HUMAN; PHYLOGENY; REPRODUCTIVE FITNESS; VIROLOGY; VIRUS GENE;

EID: 85013988114     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.01976-16     Document Type: Article
Times cited : (32)

References (23)
  • 1
    • 84937721609 scopus 로고    scopus 로고
    • High-throughput analysis of human cytomegalovirus genome diversity highlights the widespread occurrence of gene-disrupting mutations and pervasive recombination
    • Sijmons S, Thys K, Mbong Ngwese M, Van Damme E, Dvorak J, Van Loock M, Li G, Tachezy R, Busson L, Aerssens J, Van Ranst M, Maes P. 2015. High-throughput analysis of human cytomegalovirus genome diversity highlights the widespread occurrence of gene-disrupting mutations and pervasive recombination. J Virol 89:7673-7695. https://doi.org/10.1128/JVI.00578-15.
    • (2015) J Virol , vol.89 , pp. 7673-7695
    • Sijmons, S.1    Thys, K.2    Mbong Ngwese, M.3    Van Damme, E.4    Dvorak, J.5    Van Loock, M.6    Li, G.7    Tachezy, R.8    Busson, L.9    Aerssens, J.10    Van Ranst, M.11    Maes, P.12
  • 2
    • 0141565071 scopus 로고    scopus 로고
    • Patterns of intra-and interhost nonsynonymous variation reveal strong purifying selection in Dengue virus
    • Holmes EC. 2003. Patterns of intra-and interhost nonsynonymous variation reveal strong purifying selection in Dengue virus. J Virol 77: 11296-11298. https://doi.org/10.1128/JVI.77.20.11296-11298.2003.
    • (2003) J Virol , vol.77 , pp. 11296-11298
    • Holmes, E.C.1
  • 3
    • 0014421064 scopus 로고
    • Evolutionary rate at the molecular level
    • Kimura M. 1968. Evolutionary rate at the molecular level. Nature 217: 624-626. https://doi.org/10.1038/217624a0.
    • (1968) Nature , vol.217 , pp. 624-626
    • Kimura, M.1
  • 4
    • 0015722319 scopus 로고
    • Slightly deleterious mutant substitutions in evolution
    • Ohta T. 1973. Slightly deleterious mutant substitutions in evolution. Nature 246:96-98. https://doi.org/10.1038/246096a0.
    • (1973) Nature , vol.246 , pp. 96-98
    • Ohta, T.1
  • 5
    • 0008540928 scopus 로고
    • Statistical method for testing the neutral mutation hypothesis
    • Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis. Genetics 123:437-460.
    • (1989) Genetics , vol.123 , pp. 437-460
    • Tajima, F.1
  • 6
    • 0033911640 scopus 로고    scopus 로고
    • Hitchhiking under positive Darwinian selection
    • Fay J, Wu C-I. 2000. Hitchhiking under positive Darwinian selection. Genetics 155:1405-1413.
    • (2000) Genetics , vol.155 , pp. 1405-1413
    • Fay, J.1    Wu, C.-I.2
  • 7
    • 84907325378 scopus 로고    scopus 로고
    • Human cytomegalovirus intrahost evolution-a new avenue for understanding and controlling herpesvirus infections
    • Renzette N, Gibson L, Jensen JD, Kowalik TF. 2014. Human cytomegalovirus intrahost evolution-a new avenue for understanding and controlling herpesvirus infections. Curr Opin Virol 8:109-115. https://doi.org/10.1016/j.coviro.2014.08.001.
    • (2014) Curr Opin Virol , vol.8 , pp. 109-115
    • Renzette, N.1    Gibson, L.2    Jensen, J.D.3    Kowalik, T.F.4
  • 8
    • 0016220238 scopus 로고
    • The hitch-hiking effect of a favorable gene
    • Maynard Smith J, Haigh J. 1974. The hitch-hiking effect of a favorable gene. Genet Res 23:23-25. https://doi.org/10.1017/S0016672300014634.
    • (1974) Genet Res , vol.23 , pp. 23-25
    • Maynard Smith, J.1    Haigh, J.2
  • 9
    • 0027305597 scopus 로고
    • The effect of deleterious mutations on neutral molecular variation
    • Charlesworth B, Morgan MT, Charlesworth D. 1993. The effect of deleterious mutations on neutral molecular variation. Genetics 134: 1289-1303.
    • (1993) Genetics , vol.134 , pp. 1289-1303
    • Charlesworth, B.1    Morgan, M.T.2    Charlesworth, D.3
  • 10
    • 84954077343 scopus 로고    scopus 로고
    • On the relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus genetic diversity
    • Renzette N, Kowalik TF, Jensen JD. 2016. On the relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus genetic diversity. Mol Ecol 25:403-413. https://doi.org/10.1111/mec.13331.
    • (2016) Mol Ecol , vol.25 , pp. 403-413
    • Renzette, N.1    Kowalik, T.F.2    Jensen, J.D.3
  • 11
  • 12
    • 79958069377 scopus 로고    scopus 로고
    • Extensive genome-wide variability of human cytomegalovirus in congenitally infected infants
    • Renzette N, Bhattacharjee B, Jensen JD, Gibson L, Kowalik TF. 2011. Extensive genome-wide variability of human cytomegalovirus in congenitally infected infants. PLoS Pathog 7:e1001344. https://doi.org/10.1371/journal.ppat.1001344.
    • (2011) PLoS Pathog , vol.7
    • Renzette, N.1    Bhattacharjee, B.2    Jensen, J.D.3    Gibson, L.4    Kowalik, T.F.5
  • 13
    • 68949202924 scopus 로고    scopus 로고
    • Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change
    • Eyre-Walker A, Keightley PD. 2009. Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change. Mol Biol Evol 26:2097-2108. https://doi.org/10.1093/molbev/msp119.
    • (2009) Mol Biol Evol , vol.26 , pp. 2097-2108
    • Eyre-Walker, A.1    Keightley, P.D.2
  • 15
    • 0033117745 scopus 로고    scopus 로고
    • The role of population size in molecular evolution
    • Gillespie JH. 1999. The role of population size in molecular evolution. Theor Popul Biol 55:145-156. https://doi.org/10.1006/tpbi.1998.1391.
    • (1999) Theor Popul Biol , vol.55 , pp. 145-156
    • Gillespie, J.H.1
  • 16
    • 80053626924 scopus 로고    scopus 로고
    • Characterizing the influence of effective population size on the rate of adaptation: Gillespie's Darwin domain
    • Jensen JD, Bachtrog D. 2011. Characterizing the influence of effective population size on the rate of adaptation: Gillespie's Darwin domain. Genome Biol Ecol 3:687-701. https://doi.org/10.1093/gbe/evr063.
    • (2011) Genome Biol Ecol , vol.3 , pp. 687-701
    • Jensen, J.D.1    Bachtrog, D.2
  • 17
    • 84923108157 scopus 로고    scopus 로고
    • WFABC: a Wright-Fisher ABC-based approach for inferring effective population sizes and selection coefficients from time-sampled data
    • Foll M, Shim H, Jensen JD. 2015. WFABC: a Wright-Fisher ABC-based approach for inferring effective population sizes and selection coefficients from time-sampled data. Mol Ecol Resour 15:87-98. https://doi.org/10.1111/1755-0998.12280.
    • (2015) Mol Ecol Resour , vol.15 , pp. 87-98
    • Foll, M.1    Shim, H.2    Jensen, J.D.3
  • 19
    • 84954077710 scopus 로고    scopus 로고
    • The consequences of not accounting for background selection in demographic inference
    • Ewing GB, Jensen JD. 2016. The consequences of not accounting for background selection in demographic inference. Mol Ecol 25:135-141. https://doi.org/10.1111/mec.13390.
    • (2016) Mol Ecol , vol.25 , pp. 135-141
    • Ewing, G.B.1    Jensen, J.D.2
  • 21
    • 84963983934 scopus 로고    scopus 로고
    • Detecting and quantifying changing selection intensities from time-sampled polymorphism data
    • Shim H, Laurent S, Matuszewski S, Foll M, Jensen JD. 2016. Detecting and quantifying changing selection intensities from time-sampled polymorphism data. G3 6:893-904. https://doi.org/10.1534/g3.115.023200.
    • (2016) G3 , vol.6 , pp. 893-904
    • Shim, H.1    Laurent, S.2    Matuszewski, S.3    Foll, M.4    Jensen, J.D.5
  • 22
    • 33745347447 scopus 로고    scopus 로고
    • The distribution of fitness effects of new deleterious amino acid mutations in humans
    • Eyre-Walker A, Woolfit M, Phelps T. 2006. The distribution of fitness effects of new deleterious amino acid mutations in humans. Genetics 173:891-900. https://doi.org/10.1534/genetics.106.057570.
    • (2006) Genetics , vol.173 , pp. 891-900
    • Eyre-Walker, A.1    Woolfit, M.2    Phelps, T.3
  • 23
    • 56649111423 scopus 로고    scopus 로고
    • A flexible forward simulator for populations subject to selection and demography
    • Hernandez R. 2008. A flexible forward simulator for populations subject to selection and demography. Bioinformatics 24:2786-2787. https://doi.org/10.1093/bioinformatics/btn522.
    • (2008) Bioinformatics , vol.24 , pp. 2786-2787
    • Hernandez, R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.