Performance of VIDISCA-454 in Feces-Suspensions and Serum

Viruses

Michel de Vries³  Bas B. Oude Munnink³  Martin Deijs³  Marta Canuti³  Sylvie M. Koekkoek¹  Richard Molenkamp¹  Margreet Bakker³  Suzanne Jurriaans¹  Barbera D. C. van Schaik²  Angela C. Luyf²  Silvia D. Olabarriaga²  Antoine H. C. van Kampen² 

[1] 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;Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Bioinformatics Laboratory, Academic Medical Center of the University of Amsterdam, 1105AZ, Amsterdam, The Netherlands;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;

关键词: virus discovery;    VIDISCA;    diarrhoea;    HIV-1;    norovirus;   

DOI  :  10.3390/v4081328

来源: mdpi

【 摘 要 】

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.

【 授权许可】

CC BY   
© 2012 by the authors; licensee MDPI, Basel, Switzerland.