Viral Categorization and Discovery in Human Circulation by Transcriptome Sequencing

Overview

Journal Biochem Biophys Res Commun

Publisher Elsevier

Specialty Biochemistry

Date 2013 Jun 15

PMID 23764402

Citations 4

Authors

Weihua Wang

Xiaoan Zhang

Yanjuan Xu

Adrian M Di Bisceglie

Xiaofeng Fan

Affiliations

Soon will be listed here.

Abstract

Serum is the most common and easily accessible patient specimen in a minimally invasive manner. As a biological resource, RNA in serum has been less explored for its clinical utilization due to prevailing concerns regarding its high degradable nature. In the current study, however, we have documented the use of human serum RNA for viral categorization and discovery through transcriptome sequencing and analysis using well-curated databases and advanced bioinformatic tools. Such an integrated approach may have an immediate application in any clinical situations concerning with viral etiology.

Citing Articles

In-depth serum virome analysis in patients with acute liver failure with indeterminate etiology.

Ren Y, Xu Y, Lee W, Di Bisceglie A, Fan X Arch Virol. 2019; 165(1):127-135.

PMID: 31741097 PMC: 6957702. DOI: 10.1007/s00705-019-04466-9.

Full annotation of serum virome in Chinese blood donors with elevated alanine aminotransferase levels.

Li G, Zhou Z, Yao L, Xu Y, Wang L, Fan X Transfusion. 2019; 59(10):3177-3185.

PMID: 31393615 PMC: 6785372. DOI: 10.1111/trf.15476.

Template-dependent multiple displacement amplification for profiling human circulating RNA.

Wang W, Ren Y, Lu Y, Xu Y, Crosby S, Di Bisceglie A Biotechniques. 2017; 63(1):21-27.

PMID: 28701144 PMC: 5762180. DOI: 10.2144/000114566.

Identification of the transcripts associated with spontaneous HCV clearance in individuals co-infected with HIV and HCV.

Chen Y, Shen C, Guha D, Ding M, Kulich S, Ashimkhanova A BMC Infect Dis. 2016; 16(1):693.

PMID: 27875997 PMC: 5120459. DOI: 10.1186/s12879-016-2044-7.

References

Niu B, Fu L, Sun S, Li W . Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinformatics. 2010; 11:187. PMC: 2874554. DOI: 10.1186/1471-2105-11-187. View

Jurka J, Kapitonov V, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J . Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005; 110(1-4):462-7. DOI: 10.1159/000084979. View

Fan X, Xu Y, Di Bisceglie A . Efficient amplification and cloning of near full-length hepatitis C virus genome from clinical samples. Biochem Biophys Res Commun. 2006; 346(4):1163-72. PMC: 7092855. DOI: 10.1016/j.bbrc.2006.06.039. View

Langmead B, Salzberg S . Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9(4):357-9. PMC: 3322381. DOI: 10.1038/nmeth.1923. View

Kent W, Sugnet C, Furey T, Roskin K, Pringle T, Zahler A . The human genome browser at UCSC. Genome Res. 2002; 12(6):996-1006. PMC: 186604. DOI: 10.1101/gr.229102. View

Moore R, Warren R, Freeman J, Gustavsen J, Chenard C, Friedman J . The sensitivity of massively parallel sequencing for detecting candidate infectious agents associated with human tissue. PLoS One. 2011; 6(5):e19838. PMC: 3094400. DOI: 10.1371/journal.pone.0019838. View

Flicek P, Amode M, Barrell D, Beal K, Brent S, Carvalho-Silva D . Ensembl 2012. Nucleic Acids Res. 2011; 40(Database issue):D84-90. PMC: 3245178. DOI: 10.1093/nar/gkr991. View

Kim J, Easley C . Isothermal DNA amplification in bioanalysis: strategies and applications. Bioanalysis. 2011; 3(2):227-39. DOI: 10.4155/bio.10.172. View

Skinner G . Transformation of primary hamster embryo fibroblasts by type 2 simplex virus: evidence for a "hit and run" mechanism. Br J Exp Pathol. 1976; 57(4):361-76. PMC: 2041152. View

10.

Berman A, Kamtekar S, Goodman J, Lazaro J, de Vega M, Blanco L . Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases. EMBO J. 2007; 26(14):3494-505. PMC: 1933411. DOI: 10.1038/sj.emboj.7601780. View

11.

Becher P, Thiel H, Collins M, Brownlie J, Orlich M . Cellular sequences in pestivirus genomes encoding gamma-aminobutyric acid (A) receptor-associated protein and Golgi-associated ATPase enhancer of 16 kilodaltons. J Virol. 2002; 76(24):13069-76. PMC: 136705. DOI: 10.1128/jvi.76.24.13069-13076.2002. View

12.

Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R . InterProScan: protein domains identifier. Nucleic Acids Res. 2005; 33(Web Server issue):W116-20. PMC: 1160203. DOI: 10.1093/nar/gki442. View

13.

Rice P, Longden I, Bleasby A . EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000; 16(6):276-7. DOI: 10.1016/s0168-9525(00)02024-2. View

14.

Briese T, Paweska J, McMullan L, Hutchison S, Street C, Palacios G . Genetic detection and characterization of Lujo virus, a new hemorrhagic fever-associated arenavirus from southern Africa. PLoS Pathog. 2009; 5(5):e1000455. PMC: 2680969. DOI: 10.1371/journal.ppat.1000455. View

15.

Feng H, Shuda M, Chang Y, Moore P . Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science. 2008; 319(5866):1096-100. PMC: 2740911. DOI: 10.1126/science.1152586. View

16.

Zhang X, Fan X, Xu Y, Di Bisceglie A . Enhanced protocol for determining the 3' terminus of hepatitis C virus. J Virol Methods. 2010; 167(2):158-64. PMC: 2916046. DOI: 10.1016/j.jviromet.2010.03.030. View

17.

Pruitt K, Tatusova T, Brown G, Maglott D . NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res. 2011; 40(Database issue):D130-5. PMC: 3245008. DOI: 10.1093/nar/gkr1079. View

18.

McIntyre L, Lopiano K, Morse A, Amin V, Oberg A, Young L . RNA-seq: technical variability and sampling. BMC Genomics. 2011; 12:293. PMC: 3141664. DOI: 10.1186/1471-2164-12-293. View

19.

Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P . The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2012; 41(Database issue):D590-6. PMC: 3531112. DOI: 10.1093/nar/gks1219. View

20.

Fan G, Li J . Regions identity between the genome of vertebrates and non-retroviral families of insect viruses. Virol J. 2011; 8:511. PMC: 3226645. DOI: 10.1186/1743-422X-8-511. View