Abstract
The protocol presented here allows the isolation, purification, nucleic acid extraction, and amplification of DNA/RNA from viruses present in human sera samples. The method allows the random amplification of the viral genomes present by using a Sequence-Independent, Single-Primer Amplification (SISPA) approach enabling the study of both DNA/RNA viruses. An amplification step is needed, as the concentration of viral DNA/RNA in serum samples is low for direct library preparation. The application of the described protocol guarantees enough randomly amplified double-strand DNA for further library preparation using Nextera XT kit from Illumina.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Gonzales-Gustavson E, Timoneda N, Fernandez-Cassi X et al (2017) Identification of sapovirus GV.2, astrovirus VA3 and novel anelloviruses in serum from patients with acute hepatitis of unknown aetiology. PLoS One 12:e0185911
Moustafa A, Xie C, Kirkness E et al (2017) The blood DNA virome in 8,000 humans. PLoS Pathog 13:e1006292
Reyes GR, Kim JP (1991) Sequence-independent, single-primer amplification (SISPA) of complex DNA populations. Mol Cell Probes 5:473–481
Froussard P (1993) rPCR: a powerful tool for random amplification of whole RNA sequences. Genome Res 2:185–190
Wang D, Urisman A, Liu YT et al (2003) Viral discovery and sequence recovery using DNA microarrays. PLoS Biol 1:E2
Allander T, Emerson SU, Engle RE, Purcell RH, Bukh J (2001) A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species. Proc Natl Acad Sci 98:11609–11614
Illumina (2014) Nextera® XT DNA library preparation kit. Reporter:8–11
Wylie TN, Wylie KM, Herter BN et al (2015) Enhanced virome sequencing using targeted sequence capture. Genome Res 25:1910–1920
Kapoor A, Li L, Victoria J et al (2009) Multiple novel astrovirus species in human stool. J Gen Virol 90:2965–2972
Fernandez-Cassi X, Timoneda N, Martínez-Puchol S et al (2017) Metagenomics for the study of viruses in urban sewage as a tool for public health surveillance. Sci Total Environ 618:870–880
Thorburn F, Bennett S, Modha S et al (2015) The use of next generation sequencing in the diagnosis and typing of respiratory infections. J Clin Virol 69:96–100
Blomström AL, Widén F, Hammer AS et al (2010) Detection of a novel astrovirus in brain tissue of mink suffering from shaking mink syndrome by use of viral metagenomics. J Clin Microbiol 48:4392–4396
Choi WS, Rodríguez RA, Sobsey MD (2014) Persistence of viral genomes after autoclaving. J Virol Methods 198:37–40
Duhaime MB, Deng L, Poulos BT et al (2012) Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method. Environ Microbiol 14:2526–2537
Karlsson OE, Belák S, Granberg F (2013) The effect of preprocessing by sequence-independent, single-primer amplification (SISPA) on metagenomic detection of viruses. Biosecur Bioterror 11(Suppl 1):S227–S234
Fernandez-Cassi X, Timoneda N, Gonzales-Gustavson E et al (2017) A metagenomic assessment of viral contamination on fresh parsley plants irrigated with fecally tainted river water. Int J Food Microbiol 257:80–90
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Fernandez-Cassi, X., Rusiñol, M., Martínez-Puchol, S. (2018). Viral Concentration and Amplification from Human Serum Samples Prior to Application of Next-Generation Sequencing Analysis. In: Moya, A., Pérez Brocal, V. (eds) The Human Virome. Methods in Molecular Biology, vol 1838. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8682-8_13
Download citation
DOI: https://doi.org/10.1007/978-1-4939-8682-8_13
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-8681-1
Online ISBN: 978-1-4939-8682-8
eBook Packages: Springer Protocols