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

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Abstract

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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Acknowledgements

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.

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Authors and Affiliations

  1. Division of Gastroenterology and Hepatology, Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA

    Yi Ren, Yanjuan Xu, Adrian M. Di Bisceglie & Xiaofeng Fan

  2. Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA

    Adrian M. Di Bisceglie & Xiaofeng Fan

  3. Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA

    William M. Lee

  4. Wuhan Pulmonary Hospital, Wuhan, 430030, Hubei, China

    Yi Ren

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Contributions

Conceived and designed the experiments: XF, WML, AMD; performed the experiments: YR, YX; data interpretation: XF, AMD; analyzed the data: XF; wrote the paper: XF.

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Correspondence to Adrian M. Di Bisceglie or Xiaofeng Fan.

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Ren, Y., Xu, Y., Lee, W.M. et al. In-depth serum virome analysis in patients with acute liver failure with indeterminate etiology. Arch Virol 165, 127–135 (2020). https://doi.org/10.1007/s00705-019-04466-9

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