title: Performance of VIDISCA-454 in feces-suspensions and serum.
abstract: Virus discovery combining sequence unbiased amplification with next generation sequencing is now state-of-the-art. We have previously determined that the performance of the unbiased amplification technique which is operational at our institute, VIDISCA-454, is efficient when respiratory samples are used as input. The performance of the assay is, however, not known for other clinical materials like blood or stool samples. Here, we investigated the sensitivity of VIDISCA-454 with feces-suspensions and serum samples that are positive and that have been quantified for norovirus and human immunodeficiency virus type 1, respectively. The performance of VIDISCA-454 in serum samples was equal to its performance in respiratory material, with an estimated lower threshold of 1,000 viral genome copies. The estimated threshold in feces-suspension is around 200,000 viral genome copies. The decreased sensitivity in feces suspension is mainly due to sequences that share no recognizable identity with known sequences. Most likely these sequences originate from bacteria and phages which are not completely sequenced.
authors.affiliation: Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105AZ, Amsterdam, The Netherlands.
authors.forename: Michel
authors.initials: M
authors.lastname: De Vries
authors.affiliation: Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105AZ, Amsterdam, The Netherlands.
authors.forename: Bas B
authors.initials: BB
authors.lastname: Oude Munnink
authors.affiliation: Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105AZ, Amsterdam, The Netherlands.
authors.forename: Martin
authors.initials: M
authors.lastname: Deijs
authors.affiliation: Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105AZ, Amsterdam, The Netherlands.
authors.forename: Marta
authors.initials: M
authors.lastname: Canuti
authors.affiliation: Laboratory of Clinical Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105AZ, Amsterdam, The Netherlands.
authors.forename: Sylvie M
authors.initials: SM
authors.lastname: Koekkoek
authors.affiliation: Laboratory of Clinical Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105AZ, Amsterdam, The Netherlands.
authors.forename: Richard
authors.initials: R
authors.lastname: Molenkamp
authors.affiliation: Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105AZ, Amsterdam, The Netherlands.
authors.forename: Margreet
authors.initials: M
authors.lastname: Bakker
authors.affiliation: Laboratory of Clinical Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105AZ, Amsterdam, The Netherlands.
authors.forename: Suzanne
authors.initials: S
authors.lastname: Jurriaans
authors.affiliation: Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Bioinformatics Laboratory, Academic Medical Center of the University of Amsterdam, 1105AZ, Amsterdam, The Netherlands.
authors.forename: Barbera D C
authors.initials: BDC
authors.lastname: Van Schaik
authors.affiliation: Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Bioinformatics Laboratory, Academic Medical Center of the University of Amsterdam, 1105AZ, Amsterdam, The Netherlands.
authors.forename: Angela C
authors.initials: AC
authors.lastname: Luyf
authors.affiliation: Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Bioinformatics Laboratory, Academic Medical Center of the University of Amsterdam, 1105AZ, Amsterdam, The Netherlands.
authors.forename: Silvia D
authors.initials: SD
authors.lastname: Olabarriaga
authors.affiliation: Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Bioinformatics Laboratory, Academic Medical Center of the University of Amsterdam, 1105AZ, Amsterdam, The Netherlands.|Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
authors.forename: Antoine H C
authors.initials: AHC
authors.lastname: Van Kampen
authors.affiliation: Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105AZ, Amsterdam, The Netherlands.
authors.forename: Lia
authors.initials: L
authors.lastname: Van der Hoek
mesh_terms: D000293:Adolescent; D000328:Adult; D017250:Caliciviridae Infections / Q000175:diagnosis* / Q000821:virology; D005243:Feces / Q000821:virology*; D015658:HIV Infections / Q000175:diagnosis* / Q000821:virology; D015497:HIV-1 / Q000235:genetics / Q000302:isolation & purification*; D006801:Humans; D008297:Male; D029322:Norovirus / Q000235:genetics / Q000302:isolation & purification*; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*; D044967:Serum / Q000821:virology*; D055815:Young Adult