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Volumn 8, Issue JAN, 2017, Pages

Characterization of the genomic diversity of norovirus in linked patients using a metagenomic deep sequencing approach

Author keywords

Antigenic variation; Genetic variation; Linked patients; Next generation sequencing (NGS); Norovirus; Recombination

Indexed keywords

ARTICLE; DIARRHEA; FECES ANALYSIS; GENETIC RECOMBINATION; GENETIC VARIABILITY; GENOME ANALYSIS; METAGENOMICS; MICROBIAL DIVERSITY; NEXT GENERATION SEQUENCING; NONHUMAN; NOROVIRUS; NOROVIRUS INFECTION; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; VIRAL GASTROENTERITIS; VIRUS CHARACTERIZATION; VIRUS GENOME; VIRUS LOAD; VOMITING;

EID: 85011966105     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2017.00073     Document Type: Article
Times cited : (27)

References (74)
  • 1
    • 84931571832 scopus 로고    scopus 로고
    • Functions of the 5' and 3' ends of calicivirus genomes
    • Alhatlani, B., Vashist, S., and Goodfellow, I. (2015). Functions of the 5' and 3' ends of calicivirus genomes. Virus Res. 206, 134-143. doi: 10.1016/j.virusres.2015.02.002
    • (2015) Virus Res , vol.206 , pp. 134-143
    • Alhatlani, B.1    Vashist, S.2    Goodfellow, I.3
  • 2
    • 77951297972 scopus 로고    scopus 로고
    • Duration of norovirus excretion and the longitudinal course of viral load in norovirus-infected elderly patients
    • Aoki, Y., Suto, A., Mizuta, K., Ahiko, T., Osaka, K., and Matsuzaki, Y. (2010). Duration of norovirus excretion and the longitudinal course of viral load in norovirus-infected elderly patients. J. Hosp. Infect. 75, 42-46. doi: 10.1016/j.jhin.2009.12.016
    • (2010) J. Hosp. Infect , vol.75 , pp. 42-46
    • Aoki, Y.1    Suto, A.2    Mizuta, K.3    Ahiko, T.4    Osaka, K.5    Matsuzaki, Y.6
  • 3
    • 84860771820 scopus 로고    scopus 로고
    • SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing
    • Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., et al. (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455-477. doi: 10.1089/cmb.2012.0021
    • (2012) J. Comput. Biol , vol.19 , pp. 455-477
    • Bankevich, A.1    Nurk, S.2    Antipov, D.3    Gurevich, A.A.4    Dvorkin, M.5    Kulikov, A.S.6
  • 5
    • 84878837128 scopus 로고    scopus 로고
    • A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples
    • Batty, E. M., Wong, T. H., Trebes, A., Argoud, K., Attar, M., Buck, D., et al. (2013). A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples. PLoS ONE 8:e66129. doi: 10.1371/journal.pone.0066129
    • (2013) PLoS ONE , vol.8
    • Batty, E.M.1    Wong, T.H.2    Trebes, A.3    Argoud, K.4    Attar, M.5    Buck, D.6
  • 6
    • 84874964797 scopus 로고    scopus 로고
    • Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data
    • Beerenwinkel, N., Gunthard, H. F., Roth, V., and Metzner, K. J. (2012). Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data. Front. Microbiol. 3:329. doi: 10.3389/fmicb.2012.00329
    • (2012) Front. Microbiol , vol.3 , pp. 329
    • Beerenwinkel, N.1    Gunthard, H.F.2    Roth, V.3    Metzner, K.J.4
  • 7
    • 84906505740 scopus 로고    scopus 로고
    • The burden of norovirus gastroenteritis: an important foodborne and healthcare-related infection
    • Belliot, G., Lopman, B. A., Ambert-Balay, K., and Pothier, P. (2014). The burden of norovirus gastroenteritis: an important foodborne and healthcare-related infection. Clin. Microbiol. Infect. 20, 724-730. doi: 10.1111/1469-0691.12722
    • (2014) Clin. Microbiol. Infect , vol.20 , pp. 724-730
    • Belliot, G.1    Lopman, B.A.2    Ambert-Balay, K.3    Pothier, P.4
  • 8
    • 84979713814 scopus 로고    scopus 로고
    • PR2S2Clust: patched RNA-seq read segments' structure-oriented clustering
    • Biswas, A. K., and Gao, J. X. (2016). PR2S2Clust: patched RNA-seq read segments' structure-oriented clustering. J. Bioinform. Comput. Biol. 14:1650027. doi: 10.1142/S021972001650027X
    • (2016) J. Bioinform. Comput. Biol , vol.14
    • Biswas, A.K.1    Gao, J.X.2
  • 9
    • 80052294511 scopus 로고    scopus 로고
    • Comparative evolution of GII.3 and GII.4 norovirus over a 31-year period
    • Boon, D., Mahar, J. E., Abente, E. J., Kirkwood, C. D., Purcell, R. H., Kapikian, A. Z., et al. (2011). Comparative evolution of GII.3 and GII.4 norovirus over a 31-year period. J. Virol. 85, 8656-8666. doi: 10.1128/JVI.00472-11
    • (2011) J. Virol , vol.85 , pp. 8656-8666
    • Boon, D.1    Mahar, J.E.2    Abente, E.J.3    Kirkwood, C.D.4    Purcell, R.H.5    Kapikian, A.Z.6
  • 10
    • 77956837921 scopus 로고    scopus 로고
    • Model-based quality assessment and base-calling for second-generation sequencing data
    • Bravo, H. C., and Irizarry, R. A. (2010). Model-based quality assessment and base-calling for second-generation sequencing data. Biometrics 66, 665-674. doi: 10.1111/j.1541-0420.2009.01353.x
    • (2010) Biometrics , vol.66 , pp. 665-674
    • Bravo, H.C.1    Irizarry, R.A.2
  • 11
    • 84991219412 scopus 로고    scopus 로고
    • Norovirus whole-genome sequencing by sureselect target enrichment: a robust and sensitive method
    • Brown, J. R., Roy, S., Ruis, C., Yara Romero, E., Shah, D., Williams, R., et al. (2016). Norovirus whole-genome sequencing by sureselect target enrichment: a robust and sensitive method. J. Clin. Microbiol. 54, 2530-2537. doi: 10.1128/JCM.01052-16
    • (2016) J. Clin. Microbiol , vol.54 , pp. 2530-2537
    • Brown, J.R.1    Roy, S.2    Ruis, C.3    Yara Romero, E.4    Shah, D.5    Williams, R.6
  • 12
    • 84857961991 scopus 로고    scopus 로고
    • Contribution of intra-and interhost dynamics to norovirus evolution
    • Bull, R. A., Eden, J. S., Luciani, F., McElroy, K., Rawlinson, W. D., and White, P. A. (2012). Contribution of intra-and interhost dynamics to norovirus evolution. J. Virol. 86, 3219-3229. doi: 10.1128/JVI.06712-11
    • (2012) J. Virol , vol.86 , pp. 3219-3229
    • Bull, R.A.1    Eden, J.S.2    Luciani, F.3    McElroy, K.4    Rawlinson, W.D.5    White, P.A.6
  • 13
    • 77950397317 scopus 로고    scopus 로고
    • Rapid evolution of pandemic noroviruses of the GII.4 lineage
    • Bull, R. A., Eden, J. S., Rawlinson, W. D., and White, P. A. (2010). Rapid evolution of pandemic noroviruses of the GII.4 lineage. PLoS Pathog. 6:e1000831. doi: 10.1371/journal.ppat.1000831
    • (2010) PLoS Pathog , vol.6
    • Bull, R.A.1    Eden, J.S.2    Rawlinson, W.D.3    White, P.A.4
  • 14
    • 79955476677 scopus 로고    scopus 로고
    • Mechanisms of GII.4 norovirus evolution
    • Bull, R. A., and White, P. A. (2011). Mechanisms of GII.4 norovirus evolution. Trends Microbiol. 19, 233-240. doi: 10.1016/j.tim.2011.01.002
    • (2011) Trends Microbiol , vol.19 , pp. 233-240
    • Bull, R.A.1    White, P.A.2
  • 15
    • 84949034565 scopus 로고    scopus 로고
    • Rapid emergence and predominance of a broadly recognizing and fast-evolving norovirus GII.17 variant in late 2014
    • Chan, M. C., Lee, N., Hung, T. N., Kwok, K., Cheung, K., Tin, E. K., et al. (2015). Rapid emergence and predominance of a broadly recognizing and fast-evolving norovirus GII.17 variant in late 2014. Nat. Commun. 6:10061. doi: 10.1038/ncomms10061
    • (2015) Nat. Commun , vol.6 , pp. 10061
    • Chan, M.C.1    Lee, N.2    Hung, T.N.3    Kwok, K.4    Cheung, K.5    Tin, E.K.6
  • 17
    • 85016399336 scopus 로고    scopus 로고
    • A novel norovirus GII.17 lineage contributed to adult gastroenteritis in Shanghai, China, during the winter of 2014-2015
    • Chen, H., Qian, F., Xu, J., Chan, M., Shen, Z., Zai, S., et al. (2015). A novel norovirus GII.17 lineage contributed to adult gastroenteritis in Shanghai, China, during the winter of 2014-2015. Emerg. Microbes Infect. 4:e67. doi: 10.1038/emi.2015.67
    • (2015) Emerg. Microbes Infect , vol.4
    • Chen, H.1    Qian, F.2    Xu, J.3    Chan, M.4    Shen, Z.5    Zai, S.6
  • 18
    • 84906969109 scopus 로고    scopus 로고
    • Deep sequencing of norovirus genomes defines evolutionary patterns in an urban tropical setting
    • Cotten, M., Petrova, V., Phan, M. V., Rabaa, M. A., Watson, S. J., Ong, S. H., et al. (2014). Deep sequencing of norovirus genomes defines evolutionary patterns in an urban tropical setting. J. Virol. 88, 11056-11069. doi: 10.1128/JVI.01333-14
    • (2014) J. Virol , vol.88 , pp. 11056-11069
    • Cotten, M.1    Petrova, V.2    Phan, M.V.3    Rabaa, M.A.4    Watson, S.J.5    Ong, S.H.6
  • 19
    • 84856907832 scopus 로고    scopus 로고
    • Genetic mapping of a highly variable norovirus GII.4 blockade epitope: potential role in escape from human herd immunity
    • Debbink, K., Donaldson, E. F., Lindesmith, L. C., and Baric, R. S. (2012). Genetic mapping of a highly variable norovirus GII.4 blockade epitope: potential role in escape from human herd immunity. J. Virol. 86, 1214-1226. doi: 10.1128/JVI.06189-11
    • (2012) J. Virol , vol.86 , pp. 1214-1226
    • Debbink, K.1    Donaldson, E.F.2    Lindesmith, L.C.3    Baric, R.S.4
  • 20
    • 84969791255 scopus 로고    scopus 로고
    • Human norovirus transmission and evolution in a changing world
    • de Graaf, M., van Beek, J., and Koopmans, M. P. (2016). Human norovirus transmission and evolution in a changing world. Nat. Rev. Microbiol. 14, 421-433. doi: 10.1038/nrmicro.2016.48
    • (2016) Nat. Rev. Microbiol , vol.14 , pp. 421-433
    • de Graaf, M.1    van Beek, J.2    Koopmans, M.P.3
  • 21
  • 22
    • 84878165314 scopus 로고    scopus 로고
    • Recombination within the pandemic norovirus GII.4 lineage
    • Eden, J. S., Tanaka, M. M., Boni, M. F., Rawlinson, W. D., and White, P. A. (2013). Recombination within the pandemic norovirus GII.4 lineage. J. Virol. 87, 6270-6282. doi: 10.1128/JVI.03464-12
    • (2013) J. Virol , vol.87 , pp. 6270-6282
    • Eden, J.S.1    Tanaka, M.M.2    Boni, M.F.3    Rawlinson, W.D.4    White, P.A.5
  • 23
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797. doi: 10.1093/nar/gkh340
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 25
    • 84904430769 scopus 로고    scopus 로고
    • Whole genome single-nucleotide variation profile-based phylogenetic tree building methods for analysis of viral, bacterial and human genomes
    • Faison, W. J., Rostovtsev, A., Castro-Nallar, E., Crandall, K. A., Chumakov, K., Simonyan, V., et al. (2014). Whole genome single-nucleotide variation profile-based phylogenetic tree building methods for analysis of viral, bacterial and human genomes. Genomics 104, 1-7. doi: 10.1016/j.ygeno.2014.06.001
    • (2014) Genomics , vol.104 , pp. 1-7
    • Faison, W.J.1    Rostovtsev, A.2    Castro-Nallar, E.3    Crandall, K.A.4    Chumakov, K.5    Simonyan, V.6
  • 26
    • 84964777952 scopus 로고    scopus 로고
    • Norovirus recombinant strains isolated from gastroenteritis outbreaks in Southern Brazil, 2004-2011
    • Fumian, T. M., da Silva Ribeiro de Andrade, J., Leite, J. P., and Miagostovich, M. P. (2016). Norovirus recombinant strains isolated from gastroenteritis outbreaks in Southern Brazil, 2004-2011. PLoS ONE 11:e0145391. doi: 10.1371/journal.pone.0145391
    • (2016) PLoS ONE , vol.11
    • Fumian, T.M.1    da Silva Ribeiro de Andrade, J.2    Leite, J.P.3    Miagostovich, M.P.4
  • 27
    • 84892520167 scopus 로고    scopus 로고
    • Analysis of early strains of the norovirus pandemic variant GII.4 Sydney 2012 identifies mutations in adaptive sites of the capsid protein
    • Giammanco, G. M., De Grazia, S., Terio, V., Lanave, G., Catella, C., Bonura, F., et al. (2014). Analysis of early strains of the norovirus pandemic variant GII.4 Sydney 2012 identifies mutations in adaptive sites of the capsid protein. Virology 450-451, 355-358. doi: 10.1016/j.virol.2013.12.007
    • (2014) Virology , vol.450-451 , pp. 355-358
    • Giammanco, G.M.1    De Grazia, S.2    Terio, V.3    Lanave, G.4    Catella, C.5    Bonura, F.6
  • 28
    • 84907193791 scopus 로고    scopus 로고
    • Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak
    • Gire, S. K., Goba, A., Andersen, K. G., Sealfon, R. S., Park, D. J., Kanneh, L., et al. (2014). Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science 345, 1369-1372. doi: 10.1126/science.1259657
    • (2014) Science , vol.345 , pp. 1369-1372
    • Gire, S.K.1    Goba, A.2    Andersen, K.G.3    Sealfon, R.S.4    Park, D.J.5    Kanneh, L.6
  • 29
    • 34548415971 scopus 로고    scopus 로고
    • 'Caliciviridae: the noroviruses'
    • eds D. M. Knipe and P. Howley (Philadelphia, PA: Lippincott Williams & Wilkins)
    • Green, K. (2013). "Caliciviridae: the noroviruses, "in Fields, 6th Edn., eds D. M. Knipe and P. Howley (Philadelphia, PA: Lippincott Williams & Wilkins), 949.
    • (2013) Fields, 6th Edn , pp. 949
    • Green, K.1
  • 30
    • 84906515707 scopus 로고    scopus 로고
    • Norovirus infection in immunocompromised hosts
    • Green, K. Y. (2014). Norovirus infection in immunocompromised hosts. Clin. Microbiol. Infect. 20, 717-723. doi: 10.1111/1469-0691.12761
    • (2014) Clin. Microbiol. Infect , vol.20 , pp. 717-723
    • Green, K.Y.1
  • 31
    • 84880715196 scopus 로고    scopus 로고
    • Acute gastroenteritis surveillance through the National Outbreak Reporting System, United States
    • Hall, A. J., Wikswo, M. E., Manikonda, K., Roberts, V. A., Yoder, J. S., and Gould, L. H. (2013). Acute gastroenteritis surveillance through the National Outbreak Reporting System, United States. Emerg. Infect. Dis. 19, 1305-1309. doi: 10.3201/eid1908.130482
    • (2013) Emerg. Infect. Dis , vol.19 , pp. 1305-1309
    • Hall, A.J.1    Wikswo, M.E.2    Manikonda, K.3    Roberts, V.A.4    Yoder, J.S.5    Gould, L.H.6
  • 32
    • 84977123221 scopus 로고    scopus 로고
    • A next generation sequencing-based method to study the intra-host genetic diversity of norovirus in patients with acute and chronic infection
    • Hasing, M. E., Hazes, B., Lee, B. E., Preiksaitis, J. K., and Pang, X. L. (2016). A next generation sequencing-based method to study the intra-host genetic diversity of norovirus in patients with acute and chronic infection. BMC Genomics 17:480. doi: 10.1186/s12864-016-2831-y
    • (2016) BMC Genomics , vol.17 , pp. 480
    • Hasing, M.E.1    Hazes, B.2    Lee, B.E.3    Preiksaitis, J.K.4    Pang, X.L.5
  • 33
    • 84953218815 scopus 로고    scopus 로고
    • World health organization global estimates and regional comparisons of the burden of foodborne disease in 2010
    • Havelaar, A. H., Kirk, M. D., Torgerson, P. R., Gibb, H. J., Hald, T., Lake, R. J., et al. (2015). World health organization global estimates and regional comparisons of the burden of foodborne disease in 2010. PLoS Med. 12:e1001923. doi: 10.1371/journal.pmed.1001923
    • (2015) PLoS Med , vol.12
    • Havelaar, A.H.1    Kirk, M.D.2    Torgerson, P.R.3    Gibb, H.J.4    Hald, T.5    Lake, R.J.6
  • 34
    • 84921033923 scopus 로고    scopus 로고
    • Sequence analysis of the capsid gene during a genotype II.4 dominated norovirus season in one university hospital: identification of possible transmission routes
    • Holzknecht, B. J., Franck, K. T., Nielsen, R. T., Bottiger, B., Fischer, T. K., and Fonager, J. (2015). Sequence analysis of the capsid gene during a genotype II.4 dominated norovirus season in one university hospital: identification of possible transmission routes. PLoS ONE 10:e0115331. doi: 10.1371/journal.pone.0115331
    • (2015) PLoS ONE , vol.10
    • Holzknecht, B.J.1    Franck, K.T.2    Nielsen, R.T.3    Bottiger, B.4    Fischer, T.K.5    Fonager, J.6
  • 35
    • 84941985284 scopus 로고    scopus 로고
    • Characterization of hepatitis C virus recombination in cameroon by use of nonspecific next-generation sequencing
    • Iles, J. C., Njouom, R., Foupouapouognigni, Y., Bonsall, D., Bowden, R., Trebes, A., et al. (2015). Characterization of hepatitis C virus recombination in cameroon by use of nonspecific next-generation sequencing. J. Clin. Microbiol. 53, 3155-3164. doi: 10.1128/JCM.00483-15
    • (2015) J. Clin. Microbiol , vol.53 , pp. 3155-3164
    • Iles, J.C.1    Njouom, R.2    Foupouapouognigni, Y.3    Bonsall, D.4    Bowden, R.5    Trebes, A.6
  • 36
    • 0037388633 scopus 로고    scopus 로고
    • Broadly reactive and highly sensitive assay for Norwalk-like viruses based on real-time quantitative reverse transcription-PCR
    • Kageyama, T., Kojima, S., Shinohara, M., Uchida, K., Fukushi, S., Hoshino, F. B., et al. (2003). Broadly reactive and highly sensitive assay for Norwalk-like viruses based on real-time quantitative reverse transcription-PCR. J. Clin. Microbiol. 41, 1548-1557. doi: 10.1128/JCM.41.4.1548-1557.2003
    • (2003) J. Clin. Microbiol , vol.41 , pp. 1548-1557
    • Kageyama, T.1    Kojima, S.2    Shinohara, M.3    Uchida, K.4    Fukushi, S.5    Hoshino, F.B.6
  • 37
    • 84929649257 scopus 로고    scopus 로고
    • What is the reservoir of emergent human norovirus strains?
    • Karst, S. M., and Baric, R. S. (2015). What is the reservoir of emergent human norovirus strains? J. Virol. 89, 5756-5759. doi: 10.1128/JVI.03063-14
    • (2015) J. Virol , vol.89 , pp. 5756-5759
    • Karst, S.M.1    Baric, R.S.2
  • 38
    • 85011997401 scopus 로고    scopus 로고
    • Phylogeographic analysis of hemorrhagic fever with renal syndrome patients using multiplex PCR-based next generation sequencing
    • Kim, W. K., Kim, J. A., Song, D. H., Lee, D., Kim, Y. C., Lee, S. Y., et al. (2016). Phylogeographic analysis of hemorrhagic fever with renal syndrome patients using multiplex PCR-based next generation sequencing. Sci. Rep. 6:26017. doi: 10.1038/srep26017
    • (2016) Sci. Rep , vol.6 , pp. 26017
    • Kim, W.K.1    Kim, J.A.2    Song, D.H.3    Lee, D.4    Kim, Y.C.5    Lee, S.Y.6
  • 39
    • 84979299119 scopus 로고    scopus 로고
    • Investigating intra-host and intra-herd sequence diversity of foot-and-mouth disease virus
    • King, D. J., Freimanis, G. L., Orton, R. J., Waters, R. A., Haydon, D. T., and King, D. P. (2016). Investigating intra-host and intra-herd sequence diversity of foot-and-mouth disease virus. Infect. Genet. Evol. 44, 286-292. doi: 10.1016/j.meegid.2016.07.010
    • (2016) Infect. Genet. Evol , vol.44 , pp. 286-292
    • King, D.J.1    Freimanis, G.L.2    Orton, R.J.3    Waters, R.A.4    Haydon, D.T.5    King, D.P.6
  • 41
    • 84880377433 scopus 로고    scopus 로고
    • Next-generation whole genome sequencing identifies the direction of norovirus transmission in linked patients
    • Kundu, S., Lockwood, J., Depledge, D. P., Chaudhry, Y., Aston, A., Rao, K., et al. (2013). Next-generation whole genome sequencing identifies the direction of norovirus transmission in linked patients. Clin. Infect. Dis. 57, 407-414. doi: 10.1093/cid/cit287
    • (2013) Clin. Infect. Dis , vol.57 , pp. 407-414
    • Kundu, S.1    Lockwood, J.2    Depledge, D.P.3    Chaudhry, Y.4    Aston, A.5    Rao, K.6
  • 42
    • 80054915847 scopus 로고    scopus 로고
    • A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
    • Li, H. (2011). A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987-2993. doi: 10.1093/bioinformatics/btr509
    • (2011) Bioinformatics , vol.27 , pp. 2987-2993
    • Li, H.1
  • 43
    • 84964751833 scopus 로고    scopus 로고
    • A multi-site study of norovirus molecular epidemiology in Australia and New Zealand, 2013-2014
    • Lim, K. L., Hewitt, J., Sitabkhan, A., Eden, J. S., Lun, J., Levy, A., et al. (2016). A multi-site study of norovirus molecular epidemiology in Australia and New Zealand, 2013-2014. PLoS ONE 11:e0145254. doi: 10.1371/journal.pone.0145254
    • (2016) PLoS ONE , vol.11
    • Lim, K.L.1    Hewitt, J.2    Sitabkhan, A.3    Eden, J.S.4    Lun, J.5    Levy, A.6
  • 44
    • 84874689661 scopus 로고    scopus 로고
    • Emergence of a norovirus GII.4 strain correlates with changes in evolving blockade epitopes
    • Lindesmith, L. C., Costantini, V., Swanstrom, J., Debbink, K., Donaldson, E. F., Vinje, J., et al. (2013). Emergence of a norovirus GII.4 strain correlates with changes in evolving blockade epitopes. J. Virol. 87, 2803-2813. doi: 10.1128/JVI.03106-12
    • (2013) J. Virol , vol.87 , pp. 2803-2813
    • Lindesmith, L.C.1    Costantini, V.2    Swanstrom, J.3    Debbink, K.4    Donaldson, E.F.5    Vinje, J.6
  • 45
    • 84988838406 scopus 로고    scopus 로고
    • A universal protocol to generate consensus level genome sequences for foot-and-mouth disease virus and other positive-sense polyadenylated RNA viruses using the Illumina MiSeq
    • Logan, G., Freimanis, G. L., King, D. J., Valdazo-Gonzalez, B., Bachanek-Bankowska, K., Sanderson, N. D., et al. (2014). A universal protocol to generate consensus level genome sequences for foot-and-mouth disease virus and other positive-sense polyadenylated RNA viruses using the Illumina MiSeq. BMC Genomics 15:828. doi: 10.1186/1471-2164-15-828
    • (2014) BMC Genomics , vol.15 , pp. 828
    • Logan, G.1    Freimanis, G.L.2    King, D.J.3    Valdazo-Gonzalez, B.4    Bachanek-Bankowska, K.5    Sanderson, N.D.6
  • 46
    • 0032889281 scopus 로고    scopus 로고
    • Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination
    • Lole, K. S., Bollinger, R. C., Paranjape, R. S., Gadkari, D., Kulkarni, S. S., Novak, N. G., et al. (1999). Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J. Virol. 73, 152-160.
    • (1999) J. Virol , vol.73 , pp. 152-160
    • Lole, K.S.1    Bollinger, R.C.2    Paranjape, R.S.3    Gadkari, D.4    Kulkarni, S.S.5    Novak, N.G.6
  • 47
    • 84929000081 scopus 로고    scopus 로고
    • Acute gastroenteritis outbreak caused by a GII.6 norovirus
    • Luo, L. F., Qiao, K., Wang, X. G., Ding, K. Y., Su, H. L., Li, C. Z., et al. (2015). Acute gastroenteritis outbreak caused by a GII.6 norovirus. World J. Gastroenterol. 21, 5295-5302. doi: 10.3748/wjg.v21.i17.5295
    • (2015) World J. Gastroenterol , vol.21 , pp. 5295-5302
    • Luo, L.F.1    Qiao, K.2    Wang, X.G.3    Ding, K.Y.4    Su, H.L.5    Li, C.Z.6
  • 49
    • 84886466653 scopus 로고    scopus 로고
    • Evidence for recombination between pandemic GII.4 norovirus strains New Orleans 2009 and Sydney 2012
    • Martella, V., Medici, M. C., De Grazia, S., Tummolo, F., Calderaro, A., Bonura, F., et al. (2013). Evidence for recombination between pandemic GII.4 norovirus strains New Orleans 2009 and Sydney 2012. J. Clin. Microbiol. 51, 3855-3857. doi: 10.1128/JCM.01847-13
    • (2013) J. Clin. Microbiol , vol.51 , pp. 3855-3857
    • Martella, V.1    Medici, M.C.2    De Grazia, S.3    Tummolo, F.4    Calderaro, A.5    Bonura, F.6
  • 50
    • 85013750548 scopus 로고    scopus 로고
    • RDP4: detection and analysis of recombination patterns in virus genomes
    • Martin, D. P., Murrell, B., Golden, M., Khoosal, A., and Muhire, B. (2015). RDP4: detection and analysis of recombination patterns in virus genomes. Virus Evol. 1:vev003. doi: 10.1093/ve/vev003
    • (2015) Virus Evol , vol.1
    • Martin, D.P.1    Murrell, B.2    Golden, M.3    Khoosal, A.4    Muhire, B.5
  • 51
    • 74549200287 scopus 로고    scopus 로고
    • Molecular detection and characterization of noroviruses from children in Botswana
    • Mattison, K., Sebunya, T. K., Shukla, A., Noliwe, L. N., and Bidawid, S. (2010). Molecular detection and characterization of noroviruses from children in Botswana. J. Med. Virol. 82, 321-324. doi: 10.1002/jmv.21682
    • (2010) J. Med. Virol , vol.82 , pp. 321-324
    • Mattison, K.1    Sebunya, T.K.2    Shukla, A.3    Noliwe, L.N.4    Bidawid, S.5
  • 52
    • 84928482095 scopus 로고    scopus 로고
    • Human norovirus as a foodborne pathogen: challenges and developments
    • Moore, M. D., Goulter, R. M., and Jaykus, L. A. (2015). Human norovirus as a foodborne pathogen: challenges and developments. Annu. Rev. Food Sci. Technol. 6, 411-433. doi: 10.1146/annurev-food-022814-015643
    • (2015) Annu. Rev. Food Sci. Technol , vol.6 , pp. 411-433
    • Moore, M.D.1    Goulter, R.M.2    Jaykus, L.A.3
  • 53
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcriptomes by RNA-Seq
    • Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., and Wold, B. (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621-628. doi: 10.1038/nmeth.1226
    • (2008) Nat. Methods , vol.5 , pp. 621-628
    • Mortazavi, A.1    Williams, B.A.2    McCue, K.3    Schaeffer, L.4    Wold, B.5
  • 54
    • 84937040982 scopus 로고    scopus 로고
    • Genome of emerging norovirus, GII.17, United States, 2014
    • Parra, G. I., and Green, K. Y. (2015). Genome of emerging norovirus, GII.17, United States, 2014. Emerg. Infect. Dis. 21, 1477-1479 doi: 10.3201/eid2108.150652
    • (2015) Emerg. Infect. Dis , vol.21 , pp. 1477-1479
    • Parra, G.I.1    Green, K.Y.2
  • 55
    • 84957109044 scopus 로고    scopus 로고
    • Assessment of the utility of whole genome sequencing of measles virus in the characterisation of outbreaks
    • Penedos, A. R., Myers, R., Hadef, B., Aladin, F., and Brown, K. E. (2015). Assessment of the utility of whole genome sequencing of measles virus in the characterisation of outbreaks. PLoS ONE 10:e0143081. doi: 10.1371/journal.pone.0143081
    • (2015) PLoS ONE , vol.10
    • Penedos, A.R.1    Myers, R.2    Hadef, B.3    Aladin, F.4    Brown, K.E.5
  • 56
    • 84911395833 scopus 로고    scopus 로고
    • Choice of reference sequence and assembler for alignment of Listeria monocytogenes short-read sequence data greatly influences rates of error in SNP analyses
    • Pightling, A. W., Petronella, N., and Pagotto, F. (2014). Choice of reference sequence and assembler for alignment of Listeria monocytogenes short-read sequence data greatly influences rates of error in SNP analyses. PLoS ONE 9:e104579. doi: 10.1371/journal.pone.0104579
    • (2014) PLoS ONE , vol.9
    • Pightling, A.W.1    Petronella, N.2    Pagotto, F.3
  • 57
    • 84894901261 scopus 로고    scopus 로고
    • One-step RT-droplet digital PCR: a breakthrough in the quantification of waterborne RNA viruses
    • Racki, N., Morisset, D., Gutierrez-Aguirre, I., and Ravnikar, M. (2014). One-step RT-droplet digital PCR: a breakthrough in the quantification of waterborne RNA viruses. Anal. Bioanal. Chem. 406, 661-667. doi: 10.1007/s00216-013-7476-y
    • (2014) Anal. Bioanal. Chem , vol.406 , pp. 661-667
    • Racki, N.1    Morisset, D.2    Gutierrez-Aguirre, I.3    Ravnikar, M.4
  • 58
    • 37449020884 scopus 로고    scopus 로고
    • Genotyping of GII.4 and GIIb norovirus RT-PCR amplicons by RFLP analysis
    • Ramirez, S., Giammanco, G. M., De Grazia, S., Colomba, C., Martella, V., and Arista, S. (2008). Genotyping of GII.4 and GIIb norovirus RT-PCR amplicons by RFLP analysis. J. Virol. Methods 147, 250-256. doi: 10.1016/j.jviromet.2007.09.005
    • (2008) J. Virol. Methods , vol.147 , pp. 250-256
    • Ramirez, S.1    Giammanco, G.M.2    De Grazia, S.3    Colomba, C.4    Martella, V.5    Arista, S.6
  • 59
    • 84986616760 scopus 로고    scopus 로고
    • Navigating microbiological food safety in the era of whole genome sequencing
    • Ronholm, J., Nasheri, N., Petronella, N., and Pagotto, F. (2016). Navigating microbiological food safety in the era of whole genome sequencing. Clin. Microbiol. Rev. 29, 837-857. doi: 10.1128/CMR.00056-16
    • (2016) Clin. Microbiol. Rev , vol.29 , pp. 837-857
    • Ronholm, J.1    Nasheri, N.2    Petronella, N.3    Pagotto, F.4
  • 60
    • 84964265402 scopus 로고    scopus 로고
    • Norovirus infection: replication, manipulation of host, and interaction with the host immune response
    • Sarvestani, S. T., Cotton, B., Fritzlar, S., O'Donnell, T. B., and Mackenzie, J. M. (2016). Norovirus infection: replication, manipulation of host, and interaction with the host immune response. J. Interferon Cytokine Res. 36, 215-225. doi: 10.1089/jir.2015.0124
    • (2016) J. Interferon Cytokine Res , vol.36 , pp. 215-225
    • Sarvestani, S.T.1    Cotton, B.2    Fritzlar, S.3    O'Donnell, T.B.4    Mackenzie, J.M.5
  • 62
    • 80052288988 scopus 로고    scopus 로고
    • Structural analysis of histo-blood group antigen binding specificity in a norovirus GII.4 epidemic variant: implications for epochal evolution
    • Shanker, S., Choi, J. M., Sankaran, B., Atmar, R. L., Estes, M. K., and Prasad, B. V. (2011). Structural analysis of histo-blood group antigen binding specificity in a norovirus GII.4 epidemic variant: implications for epochal evolution. J. Virol. 85, 8635-8645. doi: 10.1128/JVI.00848-11
    • (2011) J. Virol , vol.85 , pp. 8635-8645
    • Shanker, S.1    Choi, J.M.2    Sankaran, B.3    Atmar, R.L.4    Estes, M.K.5    Prasad, B.V.6
  • 63
    • 43349101238 scopus 로고    scopus 로고
    • Bioinformatic and functional analysis of RNA secondary structure elements among different genera of human and animal caliciviruses
    • Simmonds, P., Karakasiliotis, I., Bailey, D., Chaudhry, Y., Evans, D. J., and Goodfellow, I. G. (2008). Bioinformatic and functional analysis of RNA secondary structure elements among different genera of human and animal caliciviruses. Nucleic Acids Res. 36, 2530-2546. doi: 10.1093/nar/gkn096
    • (2008) Nucleic Acids Res , vol.36 , pp. 2530-2546
    • Simmonds, P.1    Karakasiliotis, I.2    Bailey, D.3    Chaudhry, Y.4    Evans, D.J.5    Goodfellow, I.G.6
  • 64
    • 84935009609 scopus 로고    scopus 로고
    • Evaluation of signature erosion in ebola virus due to genomic drift and its impact on the performance of diagnostic assays
    • Sozhamannan, S., Holland, M. Y., Hall, A. T., Negron, D. A., Ivancich, M., Koehler, J. W., et al. (2015). Evaluation of signature erosion in ebola virus due to genomic drift and its impact on the performance of diagnostic assays. Viruses 7, 3130-3154. doi: 10.3390/v7062763
    • (2015) Viruses , vol.7 , pp. 3130-3154
    • Sozhamannan, S.1    Holland, M.Y.2    Hall, A.T.3    Negron, D.A.4    Ivancich, M.5    Koehler, J.W.6
  • 65
    • 84899553363 scopus 로고    scopus 로고
    • RAxML version 8, a tool for phylogenetic analysis and post-analysis of large phylogenies
    • Stamatakis, A. (2014). RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312-1313. doi: 10.1093/bioinformatics/btu033
    • (2014) Bioinformatics , vol.30 , pp. 1312-1313
    • Stamatakis, A.1
  • 66
    • 84991280301 scopus 로고    scopus 로고
    • Comparison of next-generation sequencing technologies for comprehensive assessment of full-length hepatitis C viral genomes
    • Thomson, E., Ip, C. L., Badhan, A., Christiansen, M. T., Adamson, W., Ansari, M. A., et al. (2016). Comparison of next-generation sequencing technologies for comprehensive assessment of full-length hepatitis C viral genomes. J. Clin. Microbiol. 54, 2470-2484. doi: 10.1128/JCM.00330-16
    • (2016) J. Clin. Microbiol , vol.54 , pp. 2470-2484
    • Thomson, E.1    Ip, C.L.2    Badhan, A.3    Christiansen, M.T.4    Adamson, W.5    Ansari, M.A.6
  • 67
    • 84891541960 scopus 로고    scopus 로고
    • Genotypic and epidemiologic trends of norovirus outbreaks in the United States, 2009 to 2013
    • Vega, E., Barclay, L., Gregoricus, N., Shirley, S. H., Lee, D., and Vinje, J. (2014). Genotypic and epidemiologic trends of norovirus outbreaks in the United States, 2009 to 2013. J. Clin. Microbiol. 52, 147-155. doi: 10.1128/JCM.02680-13
    • (2014) J. Clin. Microbiol , vol.52 , pp. 147-155
    • Vega, E.1    Barclay, L.2    Gregoricus, N.3    Shirley, S.H.4    Lee, D.5    Vinje, J.6
  • 68
    • 84924985007 scopus 로고    scopus 로고
    • Norovirus genotype profiles associated with foodborne transmission, 1999-2012
    • Verhoef, L., Hewitt, J., Barclay, L., Ahmed, S. M., Lake, R., Hall, A. J., et al. (2015). Norovirus genotype profiles associated with foodborne transmission, 1999-2012. Emerg. Infect. Dis. 21, 592-599. doi: 10.3201/eid2104.141073
    • (2015) Emerg. Infect. Dis , vol.21 , pp. 592-599
    • Verhoef, L.1    Hewitt, J.2    Barclay, L.3    Ahmed, S.M.4    Lake, R.5    Hall, A.J.6
  • 69
    • 84923053367 scopus 로고    scopus 로고
    • Advances in laboratory methods for detection and typing of norovirus
    • Vinje, J. (2015). Advances in laboratory methods for detection and typing of norovirus. J. Clin. Microbiol. 53, 373-381. doi: 10.1128/JCM.01535-14
    • (2015) J. Clin. Microbiol , vol.53 , pp. 373-381
    • Vinje, J.1
  • 70
    • 84876304977 scopus 로고    scopus 로고
    • Norwalk virus minor capsid protein VP2 associates within the VP1 shell domain
    • Vongpunsawad, S., Venkataram Prasad, B. V., and Estes, M. K. (2013). Norwalk virus minor capsid protein VP2 associates within the VP1 shell domain. J. Virol. 87, 4818-4825. doi: 10.1128/JVI.03508-12
    • (2013) J. Virol , vol.87 , pp. 4818-4825
    • Vongpunsawad, S.1    Venkataram Prasad, B.V.2    Estes, M.K.3
  • 71
    • 84906512769 scopus 로고    scopus 로고
    • Evolution of norovirus
    • White, P. A. (2014). Evolution of norovirus. Clin. Microbiol. Infect. 20, 741-745. doi: 10.1111/1469-0691.12746
    • (2014) Clin. Microbiol. Infect , vol.20 , pp. 741-745
    • White, P.A.1
  • 72
    • 84887354366 scopus 로고    scopus 로고
    • Whole genome sequencing and de novo assembly identifies Sydney-like variant noroviruses and recombinants during the winter 2012/2013 outbreak in England
    • Wong, T. H., Dearlove, B. L., Hedge, J., Giess, A. P., Piazza, P., Trebes, A., et al. (2013). Whole genome sequencing and de novo assembly identifies Sydney-like variant noroviruses and recombinants during the winter 2012/2013 outbreak in England. Virol. J. 10:335. doi: 10.1186/1743-422X-10-335
    • (2013) Virol. J , vol.10 , pp. 335
    • Wong, T.H.1    Dearlove, B.L.2    Hedge, J.3    Giess, A.P.4    Piazza, P.5    Trebes, A.6
  • 73
    • 84922580083 scopus 로고    scopus 로고
    • Genome characterization of a GII.6 norovirus strain identified in China
    • Xue, L., Wu, Q., Kou, X., Cai, W., Zhang, J., and Guo, W. (2015). Genome characterization of a GII.6 norovirus strain identified in China. Infect. Genet. Evol. 31, 110-117. doi: 10.1016/j.meegid.2015.01.027
    • (2015) Infect. Genet. Evol , vol.31 , pp. 110-117
    • Xue, L.1    Wu, Q.2    Kou, X.3    Cai, W.4    Zhang, J.5    Guo, W.6
  • 74
    • 84920767640 scopus 로고    scopus 로고
    • The murine norovirus core subgenomic RNA promoter consists of a stable stem-loop that can direct accurate initiation of RNA synthesis
    • Yunus, M. A., Lin, X., Bailey, D., Karakasiliotis, I., Chaudhry, Y., Vashist, S., et al. (2015). The murine norovirus core subgenomic RNA promoter consists of a stable stem-loop that can direct accurate initiation of RNA synthesis. J. Virol. 89, 1218-1229. doi: 10.1128/JVI.02432-14
    • (2015) J. Virol , vol.89 , pp. 1218-1229
    • Yunus, M.A.1    Lin, X.2    Bailey, D.3    Karakasiliotis, I.4    Chaudhry, Y.5    Vashist, S.6


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