TY - JOUR
T1 - In-depth serum virome analysis in patients with acute liver failure with indeterminate etiology
AU - Ren, Yi
AU - Xu, Yanjuan
AU - Lee, William M.
AU - Di Bisceglie, Adrian M.
AU - Fan, Xiaofeng
N1 - Funding Information:
This work was supported by the US National Institutes of Health (NIH) Grants AI117128 (X.F.) and AI139835 (X.F.) and a seed Grant from the Saint Louis University Liver Center (X.F.). The ALFSG was supported by U01 DK58369. Special acknowledgment is given to all the patients, families, coordinators and PI’s that participated in this network, 1998-2019.
Funding Information:
This work was supported by the US National Institutes of Health (NIH) Grants AI117128 (X.F.) and AI139835 (X.F.) and a seed Grant from the Saint Louis University Liver Center (X.F.). The ALFSG was supported by U01 DK58369. Special acknowledgment is given to all the patients, families, coordinators and PI?s that participated in this network, 1998-2019.
Publisher Copyright:
© 2019, Springer-Verlag GmbH Austria, part of Springer Nature.
PY - 2020/1/1
Y1 - 2020/1/1
N2 - In clinical virome research, whole-genome/transcriptome amplification is required when starting material is limited. An improved method, named “template-dependent multiple displacement amplification” (tdMDA), has recently been developed in our lab (Wang et al. in BioTechniques 63:21–25. https://doi.org/10.2144/000114566, 2017). In combination with Illumina sequencing and bioinformatics pipelines, its application in virome sequencing was explored using a serum sample from a patient with chronic hepatitis C virus (HCV) infection. In comparison to an amplification-free procedure, virome sequencing via tdMDA showed a 9.47-fold enrichment for HCV-mapped reads and, accordingly, an increase in HCV genome coverage from 28.5% to 70.1%. Eight serum samples from acute patients liver failure (ALF) with or without known etiology were then used for virome sequencing with an average depth at 94,913x. Both similarity-based (mapping, NCBI BLASTn, BLASTp, and profile hidden Markov model analysis) and similarity-independent methods (machine-learning algorithms) identified viruses from multiple families, including Herpesviridae, Picornaviridae, Myoviridae, and Anelloviridae. However, their commensal nature and cross-detection ruled out an etiological interpretation. Together with a lack of detection of novel viruses in a comprehensive analysis at a resolution of single reads, these data indicate that viral agents might be rare in ALF cases with indeterminate etiology.
AB - In clinical virome research, whole-genome/transcriptome amplification is required when starting material is limited. An improved method, named “template-dependent multiple displacement amplification” (tdMDA), has recently been developed in our lab (Wang et al. in BioTechniques 63:21–25. https://doi.org/10.2144/000114566, 2017). In combination with Illumina sequencing and bioinformatics pipelines, its application in virome sequencing was explored using a serum sample from a patient with chronic hepatitis C virus (HCV) infection. In comparison to an amplification-free procedure, virome sequencing via tdMDA showed a 9.47-fold enrichment for HCV-mapped reads and, accordingly, an increase in HCV genome coverage from 28.5% to 70.1%. Eight serum samples from acute patients liver failure (ALF) with or without known etiology were then used for virome sequencing with an average depth at 94,913x. Both similarity-based (mapping, NCBI BLASTn, BLASTp, and profile hidden Markov model analysis) and similarity-independent methods (machine-learning algorithms) identified viruses from multiple families, including Herpesviridae, Picornaviridae, Myoviridae, and Anelloviridae. However, their commensal nature and cross-detection ruled out an etiological interpretation. Together with a lack of detection of novel viruses in a comprehensive analysis at a resolution of single reads, these data indicate that viral agents might be rare in ALF cases with indeterminate etiology.
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U2 - 10.1007/s00705-019-04466-9
DO - 10.1007/s00705-019-04466-9
M3 - Article
C2 - 31741097
AN - SCOPUS:85075130257
SN - 0304-8608
VL - 165
SP - 127
EP - 135
JO - Archives of Virology
JF - Archives of Virology
IS - 1
ER -