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Volumn 5, Issue , 2015, Pages

Inferring the hosts of coronavirus using dual statistical models based on nucleotide composition

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE;

EID: 84948401744     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep17155     Document Type: Article
Times cited : (97)

References (40)
  • 1
    • 84884978170 scopus 로고    scopus 로고
    • Interspecies transmission and emergence of novel viruses: Lessons from bats and birds
    • Chan, J. F. W., To, K. K. W., Tse, H., Jin, D. Y. & Yuen, K. Y. Interspecies transmission and emergence of novel viruses: lessons from bats and birds. Trends Microbiol. 21, 544-555 (2013).
    • (2013) Trends Microbiol. , vol.21 , pp. 544-555
    • Chan, J.F.W.1    To, K.K.W.2    Tse, H.3    Jin, D.Y.4    Yuen, K.Y.5
  • 3
    • 84880593983 scopus 로고    scopus 로고
    • Genetic characterization of betacoronavirus lineage C viruses in bats reveals marked sequence divergence in the spike protein of pipistrellus bat coronavirus HKU5 in Japanese pipistrelle: Implications for the origin of the novel middle east respiratory syndrome coronavirus
    • Lau, S. K. P. et al. Genetic characterization of betacoronavirus lineage C viruses in bats reveals marked sequence divergence in the spike protein of Pipistrellus bat coronavirus HKU5 in Japanese Pipistrelle: Implications for the origin of the novel Middle East Respiratory Syndrome Coronavirus. J. Virol. 87, 8638-8650 (2013).
    • (2013) J. Virol. , vol.87 , pp. 8638-8650
    • Lau, S.K.P.1
  • 4
    • 84888011629 scopus 로고    scopus 로고
    • A decade after SARS: Strategies for controlling emerging coronaviruses
    • Graham, R. L., Donaldson, E. F. & Baric, R. S. A decade after SARS: strategies for controlling emerging coronaviruses. Nat. Rev. Microbiol. 11, 836-848 (2013).
    • (2013) Nat. Rev. Microbiol. , vol.11 , pp. 836-848
    • Graham, R.L.1    Donaldson, E.F.2    Baric, R.S.3
  • 5
    • 79952156407 scopus 로고    scopus 로고
    • Coronavirus genomics and bioinformatics analysis
    • Woo, P. C. Y., Huang, Y., Lau, S. K. P. & Yuen, K. Y. Coronavirus genomics and bioinformatics analysis. Viruses-Basel. 2, 1804-1820 (2010).
    • (2010) Viruses-Basel. , vol.2 , pp. 1804-1820
    • Woo, P.C.Y.1    Huang, Y.2    Lau, S.K.P.3    Yuen, K.Y.4
  • 6
    • 24944498409 scopus 로고    scopus 로고
    • Structure of SARS coronavirus spike receptor-binding domain complexed with receptor
    • Li, F., Li, W., Farzan, M. & Harrison, S. C. Structure of SARS coronavirus spike receptor-binding domain complexed with receptor. Science 309, 1864-1868 (2005).
    • (2005) Science , vol.309 , pp. 1864-1868
    • Li, F.1    Li, W.2    Farzan, M.3    Harrison, S.C.4
  • 7
    • 84883712861 scopus 로고    scopus 로고
    • Receptor recognition and cross-species infections of SARS coronavirus
    • Li, F. Receptor recognition and cross-species infections of SARS coronavirus. Antivir. Res. 100, 246-254 (2013).
    • (2013) Antivir. Res. , vol.100 , pp. 246-254
    • Li, F.1
  • 8
    • 67349158649 scopus 로고    scopus 로고
    • Coronaviruses post-SARS: Update on replication and pathogenesis
    • Perlman, S. & Netland, J. Coronaviruses post-SARS: update on replication and pathogenesis. Nat. Rev. Microbiol. 7, 439-450 (2009).
    • (2009) Nat. Rev. Microbiol. , vol.7 , pp. 439-450
    • Perlman, S.1    Netland, J.2
  • 9
    • 67651085081 scopus 로고    scopus 로고
    • Virus-host coevolution: Common patterns of nucleotide motif usage in flaviviridae and their hosts
    • Lobo, F. P. et al. Virus-host coevolution: common patterns of nucleotide motif usage in Flaviviridae and their hosts. PLoS ONE 4, 1-14 (2009).
    • (2009) PLoS ONE , vol.4 , pp. 1-14
    • Lobo, F.P.1
  • 10
    • 66149093121 scopus 로고    scopus 로고
    • Different evolutionary trajectories of European avian-like and classical swine H1N1 influenza A viruses
    • Dunham, E. J. et al. Different evolutionary trajectories of European Avian-Like and classical Swine H1N1 influenza A viruses. J. Virol. 83, 5485-5494 (2009).
    • (2009) J. Virol. , vol.83 , pp. 5485-5494
    • Dunham, E.J.1
  • 11
    • 46449083518 scopus 로고    scopus 로고
    • Patterns of evolution and host gene mimicry in influenza and other RNA viruses
    • Greenbaum, B. D., Levine, A. J., Bhanot, G. & Rabadan, R. Patterns of evolution and host gene mimicry in influenza and other RNA viruses. PLoS Pathog. 4, 1-9 (2008).
    • (2008) PLoS Pathog. , vol.4 , pp. 1-9
    • Greenbaum, B.D.1    Levine, A.J.2    Bhanot, G.3    Rabadan, R.4
  • 12
    • 43949113259 scopus 로고    scopus 로고
    • Convergent host-parasite codon usage between honeybee and bee associated viral genomes
    • Chantawannakul, P. & Cutler, R. W. Convergent host-parasite codon usage between honeybee and bee associated viral genomes. J. Invertebr. Pathol. 98, 206-210 (2008).
    • (2008) J. Invertebr. Pathol. , vol.98 , pp. 206-210
    • Chantawannakul, P.1    Cutler, R.W.2
  • 13
    • 33745654553 scopus 로고    scopus 로고
    • Evolutionary basis of codon usage and nucleotide composition bias in vertebrate DNA viruses
    • Shackelton, L. A., Parrish, C. R. & Holmes, E. C. Evolutionary basis of codon usage and nucleotide composition bias in vertebrate DNA viruses. J. Mol. Evol. 62, 551-563 (2006).
    • (2006) J. Mol. Evol. , vol.62 , pp. 551-563
    • Shackelton, L.A.1    Parrish, C.R.2    Holmes, E.C.3
  • 14
    • 1642412614 scopus 로고    scopus 로고
    • Analysis of synonymous codon usage in SARS coronavirus and other viruses in the nidovirales
    • Gu, W. J., Zhou, T., Ma, J. M., Sun, X. & Lu, Z. H. Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales. Virus Res. 101, 155-161 (2004).
    • (2004) Virus Res. , vol.101 , pp. 155-161
    • Gu, W.J.1    Zhou, T.2    Ma, J.M.3    Sun, X.4    Lu, Z.H.5
  • 15
    • 0036176330 scopus 로고    scopus 로고
    • Codon and amino acid usage in retroviral genomes is consistent with virus-specific nucleotide pressure
    • Berkhout, B., Grigoriev, A., Bakker, M. & Lukashov, V. V. Codon and amino acid usage in retroviral genomes is consistent with virus-specific nucleotide pressure. Aids Res. Hum. Retrov. 18, 133-141 (2002).
    • (2002) AIDS Res. Hum. Retrov. , vol.18 , pp. 133-141
    • Berkhout, B.1    Grigoriev, A.2    Bakker, M.3    Lukashov, V.V.4
  • 16
    • 0035036803 scopus 로고    scopus 로고
    • Evolution of base composition and codon usage bias in the genus flavivirus
    • Jenkins, G. M., Pagel, M., Gould, E. A., Zanotto, P. M. D. & Holmes, E. C. Evolution of base composition and codon usage bias in the genus Flavivirus. J. Mol. Evol. 52, 383-390 (2001).
    • (2001) J. Mol. Evol. , vol.52 , pp. 383-390
    • Jenkins, G.M.1    Pagel, M.2    Gould, E.A.3    Zanotto, P.M.D.4    Holmes, E.C.5
  • 17
    • 0030726485 scopus 로고    scopus 로고
    • Dinucleotide and stop codon frequencies in single-stranded RNA viruses
    • Rima, B. K. & McFerran, N. V. Dinucleotide and stop codon frequencies in single-stranded RNA viruses. J. Gen. Virol. 78, 2859-2870 (1997).
    • (1997) J. Gen. Virol. , vol.78 , pp. 2859-2870
    • Rima, B.K.1    McFerran, N.V.2
  • 18
    • 84948412921 scopus 로고
    • On a class of pattern-recognition learning algorithms
    • Vapnik, V. N. & Chervone, Ay. On a class of pattern-recognition learning algorithms. Automat. Rem. Contr+. 25, 838-& (1965).
    • (1965) Automat. Rem. Contr+. , vol.25 , pp. 838
    • Vapnik, V.N.1    Chervone, A.2
  • 19
    • 34249753618 scopus 로고
    • Support-vector networks
    • Cortes, C. & Vapnik, V. Support-vector networks. Mach. Learn. 20, 273-297 (1995).
    • (1995) Mach. Learn. , vol.20 , pp. 273-297
    • Cortes, C.1    Vapnik, V.2
  • 21
    • 0033636139 scopus 로고    scopus 로고
    • Support vector machine classification and validation of cancer tissue samples using microarray expression data
    • Furey, T. S. et al. Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics 16, 906-914 (2000).
    • (2000) Bioinformatics , vol.16 , pp. 906-914
    • Furey, T.S.1
  • 23
    • 77956846403 scopus 로고    scopus 로고
    • Use of nucleotide composition analysis to infer hosts for three novel picorna-like viruses
    • Kapoor, A., Simmonds, P., Lipkin, W. I., Zaidi, S. & Delwart, E. Use of nucleotide composition analysis to infer hosts for three novel Picorna-like viruses. J. Virol. 84, 10322-10328 (2010).
    • (2010) J. Virol. , vol.84 , pp. 10322-10328
    • Kapoor, A.1    Simmonds, P.2    Lipkin, W.I.3    Zaidi, S.4    Delwart, E.5
  • 24
    • 0030923586 scopus 로고    scopus 로고
    • Compositional differences within and between eukaryotic genomes
    • Karlin, S. & Mrazek, J. Compositional differences within and between eukaryotic genomes. P. Natl. Acad. Sci. USA 94, 10227-10232 (1997).
    • (1997) P. Natl. Acad. Sci. USA , vol.94 , pp. 10227-10232
    • Karlin, S.1    Mrazek, J.2
  • 25
    • 20044382817 scopus 로고    scopus 로고
    • Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human
    • Song, H. D. et al. Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human. P. Natl. Acad. Sci. USA 102, 2430-2435 (2005).
    • (2005) P. Natl. Acad. Sci. USA , vol.102 , pp. 2430-2435
    • Song, H.D.1
  • 26
    • 34247647376 scopus 로고    scopus 로고
    • Natural mutations in the receptor binding domain of spike glycoprotein determine the reactivity of crossneutralization between palm civet coronavirus and severe acute respiratory syndrome coronavirus
    • Liu, L. et al. Natural mutations in the receptor binding domain of spike glycoprotein determine the reactivity of crossneutralization between palm civet coronavirus and severe acute respiratory syndrome coronavirus. J. Virol. 81, 4694-4700 (2007).
    • (2007) J. Virol. , vol.81 , pp. 4694-4700
    • Liu, L.1
  • 27
    • 84871415482 scopus 로고    scopus 로고
    • Genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans
    • van Boheemen, S. et al. Genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans. Mbio. 3, 1-9 (2012).
    • (2012) Mbio , vol.3 , pp. 1-9
    • Van Boheemen, S.1
  • 28
    • 84881190964 scopus 로고    scopus 로고
    • Structure of MERS-CoV spike receptor-binding domain complexed with human receptor DPP4
    • Wang, N. S. et al. Structure of MERS-CoV spike receptor-binding domain complexed with human receptor DPP4. Cell Res. 23, 986-993 (2013).
    • (2013) Cell Res. , vol.23 , pp. 986-993
    • Wang, N.S.1
  • 29
    • 20044388735 scopus 로고    scopus 로고
    • SARS-associated coronavirus transmitted from human to pig
    • Chen, W. J. et al. SARS-associated coronavirus transmitted from human to pig. Emerg. Infect. Dis. 11, 446-448 (2005).
    • (2005) Emerg. Infect. Dis. , vol.11 , pp. 446-448
    • Chen, W.J.1
  • 30
    • 84889573658 scopus 로고    scopus 로고
    • Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor
    • Ge, X. Y. et al. Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature 503, 535-+ (2013).
    • (2013) Nature , vol.503
    • Ge, X.Y.1
  • 31
    • 34250221097 scopus 로고    scopus 로고
    • Analysis of the genome sequence of an alpaca coronavirus
    • Jin, L. et al. Analysis of the genome sequence of an alpaca coronavirus. Virology 365, 198-203 (2007).
    • (2007) Virology , vol.365 , pp. 198-203
    • Jin, L.1
  • 32
  • 33
    • 33749020042 scopus 로고    scopus 로고
    • Genomic signatures of human versus avian influenza A viruses
    • Chen, G. W. et al. Genomic signatures of human versus avian influenza A viruses. Emerg. Infect. Dis. 12, 1353-1360 (2006).
    • (2006) Emerg. Infect. Dis. , vol.12 , pp. 1353-1360
    • Chen, G.W.1
  • 34
    • 84871007119 scopus 로고    scopus 로고
    • Adaptive mutations in NEP compensate for defective H5N1 RNA replication in cultured human cells
    • Manz, B., Brunotte, L., Reuther, P. & Schwemmle, M. Adaptive mutations in NEP compensate for defective H5N1 RNA replication in cultured human cells. Nat. Commun. 3, 802 (2012).
    • (2012) Nat. Commun. , vol.3 , pp. 802
    • Manz, B.1    Brunotte, L.2    Reuther, P.3    Schwemmle, M.4
  • 35
    • 84883168540 scopus 로고    scopus 로고
    • Virus-specific factors associated with zoonotic and pandemic potential
    • Romero-Tejeda, A. & Capua, I. Virus-specific factors associated with zoonotic and pandemic potential. Influenza Other Respi. Viruses 7 Suppl 2, 4-14 (2013).
    • (2013) Influenza Other Respi. Viruses , vol.7 , pp. 4-14
    • Romero-Tejeda, A.1    Capua, I.2
  • 36
    • 84861307149 scopus 로고    scopus 로고
    • Discovery of seven novel mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus
    • Woo, P. C. Y. et al. Discovery of seven novel mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus. J. Virol. 86, 3995-4008 (2012).
    • (2012) J. Virol. , vol.86 , pp. 3995-4008
    • Woo, P.C.Y.1
  • 37
    • 13744252665 scopus 로고    scopus 로고
    • Complete genomic sequence of human coronavirus OC43: Molecular clock analysis suggests a relatively recent zoonotic coronavirus transmission event
    • Vijgen, L. et al. Complete genomic sequence of human coronavirus OC43: Molecular clock analysis suggests a relatively recent zoonotic coronavirus transmission event. J. Virol. 79, 1595-1604 (2005).
    • (2005) J. Virol. , vol.79 , pp. 1595-1604
    • Vijgen, L.1
  • 38
    • 0026502711 scopus 로고
    • Over-representation and under-representation of short oligonucleotides in DNAsequences
    • Burge, C., Campbell, A. M. & Karlin, S. Over-representation and under-representation of short oligonucleotides in DNAsequences. P. Natl. Acad. Sci. USA 89, 1358-1362 (1992).
    • (1992) P. Natl. Acad. Sci. USA , vol.89 , pp. 1358-1362
    • Burge, C.1    Campbell, A.M.2    Karlin, S.3
  • 39
    • 78049497235 scopus 로고    scopus 로고
    • Mahalanobis distance
    • McLachlan, G. J. Mahalanobis distance. Resonance 4, 20-26 (1999).
    • (1999) Resonance , vol.4 , pp. 20-26
    • McLachlan, G.J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.