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Volumn 236, Issue , 2016, Pages 221-230

Towards next-generation sequencing analytics for foodborne RNA viruses: Examining the effect of RNA input quantity and viral RNA purity

Author keywords

Detection; Foodborne viruses; Next generation sequences; RNA isolation

Indexed keywords

VIRUS RNA;

EID: 84980320636     PISSN: 01660934     EISSN: 18790984     Source Type: Journal    
DOI: 10.1016/j.jviromet.2016.07.013     Document Type: Article
Times cited : (11)

References (34)
  • 2
    • 1642565067 scopus 로고    scopus 로고
    • Use of reverse transcription and PCR to discriminate between infectious and non-infectious hepatitis A virus
    • Bhattacharya, S.S., Kulka, M., Lampel, K.A., Cebula, T.A., Goswami, B.B., Use of reverse transcription and PCR to discriminate between infectious and non-infectious hepatitis A virus. J. Virol. Methods 116 (2004), 181–187.
    • (2004) J. Virol. Methods , vol.116 , pp. 181-187
    • Bhattacharya, S.S.1    Kulka, M.2    Lampel, K.A.3    Cebula, T.A.4    Goswami, B.B.5
  • 6
    • 0023214707 scopus 로고
    • Hepatitis A virus cDNA and its RNA transcripts are infectious in cell culture
    • Cohen, J.I., Ticehurst, J.R., Feinstone, S.M., Rosenblum, B., Purcell, R.H., Hepatitis A virus cDNA and its RNA transcripts are infectious in cell culture. J. Virol. 61 (1987), 3035–3039.
    • (1987) J. Virol. , vol.61 , pp. 3035-3039
    • Cohen, J.I.1    Ticehurst, J.R.2    Feinstone, S.M.3    Rosenblum, B.4    Purcell, R.H.5
  • 7
    • 84875423891 scopus 로고    scopus 로고
    • Detection of replication-defective hepatitis A virus based on the correlation between real-time polymerase chain reaction and ELISA in situ results
    • Costa, A.M., Amado, L.A., Paula, V.S.d., Detection of replication-defective hepatitis A virus based on the correlation between real-time polymerase chain reaction and ELISA in situ results. Memórias Inst. Oswaldo Cruz 108 (2013), 36–40.
    • (2013) Memórias Inst. Oswaldo Cruz , vol.108 , pp. 36-40
    • Costa, A.M.1    Amado, L.A.2    Paula, V.S.D.3
  • 9
    • 84879165866 scopus 로고    scopus 로고
    • Comparison of two extraction methods for the detection of hepatitis A virus in lettuces using the murine norovirus as a process control
    • Coudray, C., Merle, G., Martin-Latil, S., Guillier, L., Perelle, S., Comparison of two extraction methods for the detection of hepatitis A virus in lettuces using the murine norovirus as a process control. J. Virol. Methods 193 (2013), 96–102.
    • (2013) J. Virol. Methods , vol.193 , pp. 96-102
    • Coudray, C.1    Merle, G.2    Martin-Latil, S.3    Guillier, L.4    Perelle, S.5
  • 10
    • 0024412996 scopus 로고
    • Replication kinetics and cytopathic effect of hepatitis A virus
    • Cromeans, T., Fields, H.A., Sobsey, M.D., Replication kinetics and cytopathic effect of hepatitis A virus. J. Gen. Virol. 70:Pt 8 (1989), 2051–2062.
    • (1989) J. Gen. Virol. , vol.70 , pp. 2051-2062
    • Cromeans, T.1    Fields, H.A.2    Sobsey, M.D.3
  • 11
    • 0019461029 scopus 로고
    • Propagation of human hepatitis A virus in African green monkey kidney cell culture: primary isolation and serial passage
    • Daemer, R.J., Feinstone, S.M., Gust, I.D., Purcell, R.H., Propagation of human hepatitis A virus in African green monkey kidney cell culture: primary isolation and serial passage. Infect. Immun. 32 (1981), 388–393.
    • (1981) Infect. Immun. , vol.32 , pp. 388-393
    • Daemer, R.J.1    Feinstone, S.M.2    Gust, I.D.3    Purcell, R.H.4
  • 13
    • 0034467243 scopus 로고    scopus 로고
    • Hepatitis A virus-specific immunoglobulin A mediates infection of hepatocytes with hepatitis A virus via the asialoglycoprotein receptor
    • Dotzauer, A., Gebhardt, U., Bieback, K., Gottke, U., Kracke, A., Mages, J., Lemon, S.M., Vallbracht, A., Hepatitis A virus-specific immunoglobulin A mediates infection of hepatocytes with hepatitis A virus via the asialoglycoprotein receptor. J. Virol. 74 (2000), 10950–10957.
    • (2000) J. Virol. , vol.74 , pp. 10950-10957
    • Dotzauer, A.1    Gebhardt, U.2    Bieback, K.3    Gottke, U.4    Kracke, A.5    Mages, J.6    Lemon, S.M.7    Vallbracht, A.8
  • 14
    • 0037843191 scopus 로고    scopus 로고
    • Limitations of TaqMan PCR for detecting divergent viral pathogens illustrated by hepatitis A, B, C, and E viruses and human immunodeficiency virus
    • Gardner, S.N., Kuczmarski, T.A., Vitalis, E.A., Slezak, T.R., Limitations of TaqMan PCR for detecting divergent viral pathogens illustrated by hepatitis A, B, C, and E viruses and human immunodeficiency virus. J. Clin. Microbiol. 41 (2003), 2417–2427.
    • (2003) J. Clin. Microbiol. , vol.41 , pp. 2417-2427
    • Gardner, S.N.1    Kuczmarski, T.A.2    Vitalis, E.A.3    Slezak, T.R.4
  • 15
    • 4644317058 scopus 로고    scopus 로고
    • Apoptosis induced by a cytopathic hepatitis A virus is dependent on caspase activation following ribosomal RNA degradation but occurs in the absence of 2'–5' oligoadenylate synthetase
    • Goswami, B.B., Kulka, M., Ngo, D., Cebula, T.A., Apoptosis induced by a cytopathic hepatitis A virus is dependent on caspase activation following ribosomal RNA degradation but occurs in the absence of 2'–5' oligoadenylate synthetase. Antiviral Res. 63 (2004), 153–166.
    • (2004) Antiviral Res. , vol.63 , pp. 153-166
    • Goswami, B.B.1    Kulka, M.2    Ngo, D.3    Cebula, T.A.4
  • 17
    • 77955883388 scopus 로고    scopus 로고
    • Biases in Illumina transcriptome sequencing caused by random hexamer priming
    • Hansen, K.D., Brenner, S.E., Dudoit, S., Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res., 38, 2010, e131.
    • (2010) Nucleic Acids Res. , vol.38 , pp. e131
    • Hansen, K.D.1    Brenner, S.E.2    Dudoit, S.3
  • 18
    • 80053561448 scopus 로고    scopus 로고
    • Single nucleotide polymorphism (SNP)-based differentiation of Shigella isolates by pyrosequencing
    • Hayford, A.E., Mammel, M.K., Lacher, D.W., Brown, E.W., Single nucleotide polymorphism (SNP)-based differentiation of Shigella isolates by pyrosequencing. Infect. Genet. Evol. 11 (2011), 1761–1768.
    • (2011) Infect. Genet. Evol. , vol.11 , pp. 1761-1768
    • Hayford, A.E.1    Mammel, M.K.2    Lacher, D.W.3    Brown, E.W.4
  • 19
    • 70249146903 scopus 로고    scopus 로고
    • Advantages of next-generation sequencing versus the microarray in epigenetic research
    • Hurd, P.J., Nelson, C.J., Advantages of next-generation sequencing versus the microarray in epigenetic research. Briefings Funct. Genomics Proteomics 8 (2009), 174–183.
    • (2009) Briefings Funct. Genomics Proteomics , vol.8 , pp. 174-183
    • Hurd, P.J.1    Nelson, C.J.2
  • 20
    • 84867492800 scopus 로고    scopus 로고
    • SNP-based real-time pyrosequencing as a sensitive and specific tool for identification and differentiation of Rickettsia species in Ixodes ricinus ticks
    • Janecek, E., Streichan, S., Strube, C., SNP-based real-time pyrosequencing as a sensitive and specific tool for identification and differentiation of Rickettsia species in Ixodes ricinus ticks. BMC Infect. Dis. 12 (2012), 1471–2334.
    • (2012) BMC Infect. Dis. , vol.12 , pp. 1471-2334
    • Janecek, E.1    Streichan, S.2    Strube, C.3
  • 21
    • 0037931132 scopus 로고    scopus 로고
    • The cytopathic 18f strain of Hepatitis A virus induces RNA degradation in FrhK4 cells
    • Kulka, M., Chen, A., Ngo, D., Bhattacharya, S.S., Cebula, T.A., Goswami, B.B., The cytopathic 18f strain of Hepatitis A virus induces RNA degradation in FrhK4 cells. Arch. Virol. 148 (2003), 1275–1300.
    • (2003) Arch. Virol. , vol.148 , pp. 1275-1300
    • Kulka, M.1    Chen, A.2    Ngo, D.3    Bhattacharya, S.S.4    Cebula, T.A.5    Goswami, B.B.6
  • 22
    • 67349136468 scopus 로고    scopus 로고
    • Activation of the 2-5OAS/RNase L pathway in CVB1 or HAV/18f infected FRhK-4 cells does not require induction of OAS1 or OAS2 expression
    • Kulka, M., Calvo, M.S., Ngo, D.T., Wales, S.Q., Goswami, B.B., Activation of the 2-5OAS/RNase L pathway in CVB1 or HAV/18f infected FRhK-4 cells does not require induction of OAS1 or OAS2 expression. Virology 388 (2009), 169–184.
    • (2009) Virology , vol.388 , pp. 169-184
    • Kulka, M.1    Calvo, M.S.2    Ngo, D.T.3    Wales, S.Q.4    Goswami, B.B.5
  • 23
    • 0026069630 scopus 로고
    • Antigenic and genetic variation in cytopathic hepatitis A virus variants arising during persistent infection: evidence for genetic recombination
    • Lemon, S.M., Murphy, P.C., Shields, P.A., Ping, L.H., Feinstone, S.M., Cromeans, T., Jansen, R.W., Antigenic and genetic variation in cytopathic hepatitis A virus variants arising during persistent infection: evidence for genetic recombination. J. Virol. 65 (1991), 2056–2065.
    • (1991) J. Virol. , vol.65 , pp. 2056-2065
    • Lemon, S.M.1    Murphy, P.C.2    Shields, P.A.3    Ping, L.H.4    Feinstone, S.M.5    Cromeans, T.6    Jansen, R.W.7
  • 24
    • 0035126736 scopus 로고    scopus 로고
    • Typing and subtyping influenza virus using DNA microarrays and multiplex reverse transcriptase PCR
    • Li, J., Chen, S., Evans, D.H., Typing and subtyping influenza virus using DNA microarrays and multiplex reverse transcriptase PCR. J. Clin. Microbiol. 39 (2001), 696–704.
    • (2001) J. Clin. Microbiol. , vol.39 , pp. 696-704
    • Li, J.1    Chen, S.2    Evans, D.H.3
  • 25
    • 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-González, B., Bachanek-Bankowska, K., Sanderson, N.D., Knowles, N.J., King, D.P., Cottam, E.M., 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 (2014), 1–10.
    • (2014) BMC Genomics , vol.15 , pp. 1-10
    • Logan, G.1    Freimanis, G.L.2    King, D.J.3    Valdazo-González, B.4    Bachanek-Bankowska, K.5    Sanderson, N.D.6    Knowles, N.J.7    King, D.P.8    Cottam, E.M.9
  • 27
    • 45549088326 scopus 로고    scopus 로고
    • The transcriptional landscape of the yeast genome defined by RNA sequencing
    • Nagalakshmi, U., Wang, Z., Waern, K., Shou, C., Raha, D., Gerstein, M., Snyder, M., The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320 (2008), 1344–1349.
    • (2008) Science , vol.320 , pp. 1344-1349
    • Nagalakshmi, U.1    Wang, Z.2    Waern, K.3    Shou, C.4    Raha, D.5    Gerstein, M.6    Snyder, M.7
  • 29
    • 84962346011 scopus 로고    scopus 로고
    • Review: approaches to the viral extraction, detection, and identification of hepatitis viruses, HAV, and HEV, in foods
    • Papafragkou, E., Kulka, M., Review: approaches to the viral extraction, detection, and identification of hepatitis viruses, HAV, and HEV, in foods. J. AOAC Int. 99 (2016), 130–142.
    • (2016) J. AOAC Int. , vol.99 , pp. 130-142
    • Papafragkou, E.1    Kulka, M.2
  • 30
    • 84908276271 scopus 로고    scopus 로고
    • Detection and quantification of hepatitis A virus and norovirus in Spanish authorized shellfish harvesting areas
    • Polo, D., Varela, M.F., Romalde, J.L., Detection and quantification of hepatitis A virus and norovirus in Spanish authorized shellfish harvesting areas. Int. J. Food Microbiol. 193 (2015), 43–50.
    • (2015) Int. J. Food Microbiol. , vol.193 , pp. 43-50
    • Polo, D.1    Varela, M.F.2    Romalde, J.L.3
  • 33
    • 84861833100 scopus 로고    scopus 로고
    • Temperature and density dependent induction of a cytopathic effect following infection with non-cytopathic HAV strains
    • Wales, S.Q., Ngo, D., Hida, K., Kulka, M., Temperature and density dependent induction of a cytopathic effect following infection with non-cytopathic HAV strains. Virology 430 (2012), 30–42.
    • (2012) Virology , vol.430 , pp. 30-42
    • Wales, S.Q.1    Ngo, D.2    Hida, K.3    Kulka, M.4
  • 34
    • 84861571690 scopus 로고    scopus 로고
    • Application of enteric viruses for fecal pollution source tracking in environmental waters
    • Wong, K., Fong, T.-T., Bibby, K., Molina, M., Application of enteric viruses for fecal pollution source tracking in environmental waters. Environ. Int. 45 (2012), 151–164.
    • (2012) Environ. Int. , vol.45 , pp. 151-164
    • Wong, K.1    Fong, T.-T.2    Bibby, K.3    Molina, M.4


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