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Novel Rhabdovirus and an almost complete drain fly transcriptome recovered from two independent contaminations of clinical samples

Francisco Brito, Mosè Manni, Florian Laubscher, Manuel Schibler, Mary-Anne Hartley, Kristina Keitel, Tarsis Mlaganile, Valerie d’Acremont, Samuel Cordey, Laurent Kaiser, Evgeny M Zdobnov
doi: https://doi.org/10.1101/645325
Francisco Brito
1Swiss Institute of Bioinformatics, Geneva, Switzerland
2Department of Genetic Medicine and Development, Faculty of Medicine, Geneva, Switzerland
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Mosè Manni
1Swiss Institute of Bioinformatics, Geneva, Switzerland
2Department of Genetic Medicine and Development, Faculty of Medicine, Geneva, Switzerland
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Florian Laubscher
3Laboratory of Virology, University Hospitals of Geneva, Switzerland
4University of Geneva Medical School, Geneva, Switzerland
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Manuel Schibler
3Laboratory of Virology, University Hospitals of Geneva, Switzerland
4University of Geneva Medical School, Geneva, Switzerland
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Mary-Anne Hartley
5Center for Primary Care and Public Health, University of Lausanne, Switzerland
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Kristina Keitel
6Swiss Tropical and Public Health Institute, University of Basel, Switzerland
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Tarsis Mlaganile
7Ifakara Health Institute, Dar es Salaam, Tanzania
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Valerie d’Acremont
5Center for Primary Care and Public Health, University of Lausanne, Switzerland
6Swiss Tropical and Public Health Institute, University of Basel, Switzerland
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Samuel Cordey
3Laboratory of Virology, University Hospitals of Geneva, Switzerland
4University of Geneva Medical School, Geneva, Switzerland
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  • For correspondence: evgeny.zdobnov@unige.ch
Laurent Kaiser
3Laboratory of Virology, University Hospitals of Geneva, Switzerland
4University of Geneva Medical School, Geneva, Switzerland
8Geneva Centre for Emerging Viral Diseases, Geneva, Switzerland
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  • For correspondence: evgeny.zdobnov@unige.ch
Evgeny M Zdobnov
1Swiss Institute of Bioinformatics, Geneva, Switzerland
2Department of Genetic Medicine and Development, Faculty of Medicine, Geneva, Switzerland
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  • For correspondence: evgeny.zdobnov@unige.ch
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Abstract

Metagenomic approaches enable an open exploration of microbial communities without requiring a priori knowledge of a sample’s composition by shotgun sequencing the total RNA or DNA of the sample. Such an approach is valuable for exploratory diagnostics of novel pathogens in clinical practice. Yet, one may also identify surprising off-target findings. Here we report a mostly complete transcriptome from a drain fly (likely Psychoda alternata) as well as a novel Rhabdovirus-like virus recovered from two independent contaminations of RNA sequencing libraries from clinical samples of cerebral spinal fluid (CSF) and serum, out of a total of 724 libraries sequenced at the same laboratory during a 2-year time span. This drain fly genome shows a considerable divergence from previously sequenced insects, which may obscure common clinical metagenomic analyses not expecting such contaminations. The classification of these contaminant sequences allowed us to identify infected drain flies as the likely origin of the novel Rhabdovirus-like sequence, which could have been erroneously linked to human pathology, had they been ignored.

Footnotes

  • ↵* joint first author.

  • http://cegg.unige.ch/contamination_metagenomics

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Posted May 23, 2019.
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Novel Rhabdovirus and an almost complete drain fly transcriptome recovered from two independent contaminations of clinical samples
Francisco Brito, Mosè Manni, Florian Laubscher, Manuel Schibler, Mary-Anne Hartley, Kristina Keitel, Tarsis Mlaganile, Valerie d’Acremont, Samuel Cordey, Laurent Kaiser, Evgeny M Zdobnov
bioRxiv 645325; doi: https://doi.org/10.1101/645325
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Novel Rhabdovirus and an almost complete drain fly transcriptome recovered from two independent contaminations of clinical samples
Francisco Brito, Mosè Manni, Florian Laubscher, Manuel Schibler, Mary-Anne Hartley, Kristina Keitel, Tarsis Mlaganile, Valerie d’Acremont, Samuel Cordey, Laurent Kaiser, Evgeny M Zdobnov
bioRxiv 645325; doi: https://doi.org/10.1101/645325

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