메뉴 건너뛰기




Volumn 87, Issue 21, 2013, Pages 11843-11850

Quantifying selection against synonymous mutations in HIV-1 env evolution

Author keywords

[No Author keywords available]

Indexed keywords

ENVELOPE PROTEIN; VIRUS ENVELOPE PROTEIN; VIRUS RNA;

EID: 84925558761     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.01529-13     Document Type: Article
Times cited : (21)

References (48)
  • 2
    • 0029075130 scopus 로고
    • Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase
    • Mansky LM, Temin HM. 1995. Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase. J. Virol. 69:5087-5094.
    • (1995) J. Virol. , vol.69 , pp. 5087-5094
    • Mansky, L.M.1    Temin, H.M.2
  • 3
    • 77956820495 scopus 로고    scopus 로고
    • Nature, position, and frequency of mutations made in a single cycle of HIV-1 replication
    • Abram ME, Ferris AL, Shao W, Alvord WG, Hughes SH. 2010. Nature, position, and frequency of mutations made in a single cycle of HIV-1 replication. J. Virol. 84:9864-9878.
    • (2010) J. Virol. , vol.84 , pp. 9864-9878
    • Abram, M.E.1    Ferris, A.L.2    Shao, W.3    Alvord, W.G.4    Hughes, S.H.5
  • 6
    • 80052153094 scopus 로고    scopus 로고
    • The genomic rate of molecular adaptation of the human influenza A virus
    • Bhatt S, Holmes EC, Pybus OG. 2011. The genomic rate of molecular adaptation of the human influenza A virus. Mol. Biol. Evol. 28:2443-2451.
    • (2011) Mol. Biol. Evol. , vol.28 , pp. 2443-2451
    • Bhatt, S.1    Holmes, E.C.2    Pybus, O.G.3
  • 7
    • 0036720020 scopus 로고    scopus 로고
    • The Ka/Ks ratio: diagnosing the form of sequence evolution
    • Hurst LD. 2002. The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends Genet. 18:486-487.
    • (2002) Trends Genet. , vol.18 , pp. 486-487
    • Hurst, L.D.1
  • 8
    • 1842509978 scopus 로고    scopus 로고
    • Positive selection detection in 40,000 human immunodeficiency virus (HIV) type 1 sequences automatically identifies drug resistance and positive fitness mutations in HIV protease and reverse transcriptase
    • Chen L, Perlina A, Lee CJ. 2004. Positive selection detection in 40,000 human immunodeficiency virus (HIV) type 1 sequences automatically identifies drug resistance and positive fitness mutations in HIV protease and reverse transcriptase. J. Virol. 78:3722-3732.
    • (2004) J. Virol. , vol.78 , pp. 3722-3732
    • Chen, L.1    Perlina, A.2    Lee, C.J.3
  • 9
    • 84856804646 scopus 로고    scopus 로고
    • The HIV-1 rev response element: anRNAscaffold that directs the cooperative assembly of a homooligomeric ribonucleoprotein complex
    • Fernandes J, Jayaraman B, Frankel A. 2012. The HIV-1 rev response element: anRNAscaffold that directs the cooperative assembly of a homooligomeric ribonucleoprotein complex. RNA Biol. 9:4-9.
    • (2012) RNA Biol. , vol.9 , pp. 4-9
    • Fernandes, J.1    Jayaraman, B.2    Frankel, A.3
  • 12
    • 0029619270 scopus 로고
    • Reciprocal relationship between stem-loop potential and substitution density in retroviral quasispecies under positive Darwinian selection
    • Forsdyke DR. 1995. Reciprocal relationship between stem-loop potential and substitution density in retroviral quasispecies under positive Darwinian selection. J. Mol. Evol. 41:1022-1037.
    • (1995) J. Mol. Evol. , vol.41 , pp. 1022-1037
    • Forsdyke, D.R.1
  • 13
    • 80055055652 scopus 로고    scopus 로고
    • Mapping of positive selection sites in the HIV-1 genome in the context of RNA and protein structural constraints
    • Snoeck J, Fellay J, Bartha I, Douek DC, Telenti A. 2011. Mapping of positive selection sites in the HIV-1 genome in the context of RNA and protein structural constraints. Retrovirology 8:87.
    • (2011) Retrovirology , vol.8 , pp. 87
    • Snoeck, J.1    Fellay, J.2    Bartha, I.3    Douek, D.C.4    Telenti, A.5
  • 14
    • 84876844318 scopus 로고    scopus 로고
    • Comparison of SIV and HIV-1 genomic RNA structures reveals impact of sequence evolution on conserved and nonconserved structural motifs
    • Pollom E, Dang KK, Potter EL, Gorelick RJ, Burch CL, Weeks KM, Swanstrom R. 2013. Comparison of SIV and HIV-1 genomic RNA structures reveals impact of sequence evolution on conserved and nonconserved structural motifs. PLoS Pathog. 9:e1003294. doi:10.1371/journal.ppat.1003294.
    • (2013) PLoS Pathog. , vol.9
    • Pollom, E.1    Dang, K.K.2    Potter, E.L.3    Gorelick, R.J.4    Burch, C.L.5    Weeks, K.M.6    Swanstrom, R.7
  • 15
    • 76749139978 scopus 로고    scopus 로고
    • Recombination rate and selection strength in HIV intra-patient evolution
    • Neher RA, Leitner T. 2010. Recombination rate and selection strength in HIV intra-patient evolution. PLoS Comput. Biol. 6:e1000660. doi:10.1371/journal.pcbi.1000660.
    • (2010) PLoS Comput. Biol. , vol.6
    • Neher, R.A.1    Leitner, T.2
  • 19
    • 49149118421 scopus 로고    scopus 로고
    • Autologous neutralizing humoral immunity and evolution of the viral envelope in the course of subtype B human immunodeficiency virus type 1 infection
    • Bunnik EM, Pisas L, Van Nuenen AC, Schuitemaker H. 2008. Autologous neutralizing humoral immunity and evolution of the viral envelope in the course of subtype B human immunodeficiency virus type 1 infection. J. Virol. 82:7932-7941.
    • (2008) J. Virol. , vol.82 , pp. 7932-7941
    • Bunnik, E.M.1    Pisas, L.2    Van Nuenen, A.C.3    Schuitemaker, H.4
  • 21
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 22
    • 84870840869 scopus 로고    scopus 로고
    • FFPopSim: an efficient forward simulation package for the evolution of large populations
    • Zanini F, Neher RA. 2012. FFPopSim: an efficient forward simulation package for the evolution of large populations. Bioinformatics 28:3332-3333.
    • (2012) Bioinformatics , vol.28 , pp. 3332-3333
    • Zanini, F.1    Neher, R.A.2
  • 23
    • 0029967721 scopus 로고    scopus 로고
    • HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time
    • Perelson AS, Neumann AU, Markowitz M, Leonard JM, Ho DD. 1996. HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time. Science 271:1582-1586.
    • (1996) Science , vol.271 , pp. 1582-1586
    • Perelson, A.S.1    Neumann, A.U.2    Markowitz, M.3    Leonard, J.M.4    Ho, D.D.5
  • 24
    • 0037385686 scopus 로고    scopus 로고
    • A novel antiviral intervention results in more accurate assessment of human immunodeficiency virus type 1 replication dynamics and T-cell decay in vivo
    • Markowitz M, Louie M, Hurley A, Sun E, Di Mascio M, Perelson AS, Ho DD. 2003. A novel antiviral intervention results in more accurate assessment of human immunodeficiency virus type 1 replication dynamics and T-cell decay in vivo. J. Virol. 77:5037-5038.
    • (2003) J. Virol. , vol.77 , pp. 5037-5038
    • Markowitz, M.1    Louie, M.2    Hurley, A.3    Sun, E.4    Di Mascio, M.5    Perelson, A.S.6    Ho, D.D.7
  • 27
    • 84869234001 scopus 로고    scopus 로고
    • Ultrasensitive allele-specific PCR reveals rare preexisting drug-resistant variants and a large replicating virus population in macaques infected with a simian immunodeficiency virus containing human immunodeficiency virus reverse transcriptase
    • Boltz VF, Ambrose Z, Kearney MF, Shao W, KewalRamani VN, Maldarelli F, Mellors JW, Coffin JM. 2012. Ultrasensitive allele-specific PCR reveals rare preexisting drug-resistant variants and a large replicating virus population in macaques infected with a simian immunodeficiency virus containing human immunodeficiency virus reverse transcriptase. J. Virol. 86:12525-12530.
    • (2012) J. Virol. , vol.86 , pp. 12525-12530
    • Boltz, V.F.1    Ambrose, Z.2    Kearney, M.F.3    Shao, W.4    KewalRamani, V.N.5    Maldarelli, F.6    Mellors, J.W.7    Coffin, J.M.8
  • 28
    • 80051478113 scopus 로고    scopus 로고
    • Genetic draft and quasi-neutrality in large facultatively sexual populations
    • Neher RA, Shraiman B. 2011. Genetic draft and quasi-neutrality in large facultatively sexual populations. Genetics 188:975-996.
    • (2011) Genetics , vol.188 , pp. 975-996
    • Neher, R.A.1    Shraiman, B.2
  • 29
    • 33645768069 scopus 로고    scopus 로고
    • Inefficient cytotoxic T lymphocyte-mediated killing of HIV-1-infected cells in vivo
    • Asquith B, Edwards CTT, Lipsitch M, McLean AR. 2006. Inefficient cytotoxic T lymphocyte-mediated killing of HIV-1-infected cells in vivo. PLoS Biol. 4:e90. doi:10.1371/journal.pbio.0040090.
    • (2006) PLoS Biol. , vol.4
    • Asquith, B.1    Edwards, C.T.T.2    Lipsitch, M.3    McLean, A.R.4
  • 31
    • 0018468345 scopus 로고
    • A comparison of three methods for selecting values of input variables in the analysis of output from a computer code
    • McKay MD, Beckman RJ, Conover WJ. 1979. A comparison of three methods for selecting values of input variables in the analysis of output from a computer code. Technometrics 21:239-245.
    • (1979) Technometrics , vol.21 , pp. 239-245
    • McKay, M.D.1    Beckman, R.J.2    Conover, W.J.3
  • 32
    • 0028952146 scopus 로고
    • HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy
    • Coffin JM. 1995. HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy. Science 267:483-489.
    • (1995) Science , vol.267 , pp. 483-489
    • Coffin, J.M.1
  • 33
    • 79952856172 scopus 로고    scopus 로고
    • Interplay between RNA structure and protein evolution in HIV-1
    • Sanjuan R, Borderia AV. 2011. Interplay between RNA structure and protein evolution in HIV-1. Mol. Biol. Evol. 28:1333-1338.
    • (2011) Mol. Biol. Evol. , vol.28 , pp. 1333-1338
    • Sanjuan, R.1    Borderia, A.V.2
  • 34
    • 0037372775 scopus 로고    scopus 로고
    • The extent of codon usage bias in human RNA viruses and its evolutionary origin
    • Jenkins GM, Holmes EC. 2003. The extent of codon usage bias in human RNA viruses and its evolutionary origin. Virus Res. 92:1-7.
    • (2003) Virus Res. , vol.92 , pp. 1-7
    • Jenkins, G.M.1    Holmes, E.C.2
  • 35
    • 84868267075 scopus 로고    scopus 로고
    • The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus
    • van der Kuyl AC, Berkhout B. 2012. The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus. Retrovirology 9:92.
    • (2012) Retrovirology , vol.9 , pp. 92
    • van der Kuyl, A.C.1    Berkhout, B.2
  • 36
    • 0041571679 scopus 로고    scopus 로고
    • Adaptation in the env gene of HIV-1 and evolutionary theories of disease progression
    • Williamson S. 2003. Adaptation in the env gene of HIV-1 and evolutionary theories of disease progression. Mol. Biol. Evol. 20:1318-1325.
    • (2003) Mol. Biol. Evol. , vol.20 , pp. 1318-1325
    • Williamson, S.1
  • 38
    • 0016220238 scopus 로고
    • The hitch-hiking effect of a favourable gene
    • Smith JM, Haigh J. 1974. The hitch-hiking effect of a favourable gene. Genet. Res. 23:23-35.
    • (1974) Genet. Res. , vol.23 , pp. 23-35
    • Smith, J.M.1    Haigh, J.2
  • 43
    • 84879018021 scopus 로고    scopus 로고
    • On the role of four small hairpins in the HIV-1 RNA genome
    • Knoepfel SA, Berkhout B. 2013. On the role of four small hairpins in the HIV-1 RNA genome. RNA Biol. 10:512-524.
    • (2013) RNA Biol. , vol.10 , pp. 512-524
    • Knoepfel, S.A.1    Berkhout, B.2
  • 44
    • 34547844134 scopus 로고    scopus 로고
    • Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates
    • Mayrose I, Doron-Faigenboim A, Bacharach E, Pupko T. 2007. Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates. Bioinformatics 23:i319 -i327.
    • (2007) Bioinformatics , vol.23 , pp. 1319-1327
    • Mayrose, I.1    Doron-Faigenboim, A.2    Bacharach, E.3    Pupko, T.4
  • 45
  • 46
    • 84875546274 scopus 로고    scopus 로고
    • Translating HIV sequences into quantitative fitness landscapes predicts viral vulnerabilities for rational immunogen design
    • Ferguson AL, Mann JK, Omarjee S, Ndung'u T, Walker BD, Chakraborty AK. 2013. Translating HIV sequences into quantitative fitness landscapes predicts viral vulnerabilities for rational immunogen design. Immunity 38:606-617.
    • (2013) Immunity , vol.38 , pp. 606-617
    • Ferguson, A.L.1    Mann, J.K.2    Omarjee, S.3    Ndung'u, T.4    Walker, B.D.5    Chakraborty, A.K.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.