Metagenomic Identification of Viral Sequences in Laboratory Reagents

Metagenomic next-generation sequencing has transformed the discovery and diagnosis of infectious disease, with the power to characterise the complete ‘infectome’ (bacteria, viruses, fungi, parasites) of an individual host organism. However, the identification of novel pathogens has been complicated...

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Autores principales:	Ashleigh F. Porter, Joanna Cobbin, Ci-Xiu Li, John-Sebastian Eden, Edward C. Holmes
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	reagent contamination virology metatranscriptomics <i>Circoviridae</i> <i>Totiviridae</i> <i>Tombusviridae</i> Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/26fe32661d5345259206d634ac46be20
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spelling	oai:doaj.org-article:26fe32661d5345259206d634ac46be202021-11-25T19:12:27ZMetagenomic Identification of Viral Sequences in Laboratory Reagents10.3390/v131121221999-4915https://doaj.org/article/26fe32661d5345259206d634ac46be202021-10-01T00:00:00Zhttps://www.mdpi.com/1999-4915/13/11/2122https://doaj.org/toc/1999-4915Metagenomic next-generation sequencing has transformed the discovery and diagnosis of infectious disease, with the power to characterise the complete ‘infectome’ (bacteria, viruses, fungi, parasites) of an individual host organism. However, the identification of novel pathogens has been complicated by widespread microbial contamination in commonly used laboratory reagents. Using total RNA sequencing (“metatranscriptomics”) we documented the presence of contaminant viral sequences in multiple ‘blank’ negative control sequencing libraries that comprise a sterile water and reagent mix. Accordingly, we identified 14 viral sequences in 7 negative control sequencing libraries. As in previous studies, several circular replication-associated protein encoding (CRESS) DNA virus-like sequences were recovered in the blank control libraries, as well as contaminating sequences from the <i>Totiviridae</i>, <i>Tombusviridae</i> and <i>Lentiviridae</i> families of RNA virus. These data suggest that viral contamination of common laboratory reagents is likely commonplace and can comprise a wide variety of viruses.Ashleigh F. PorterJoanna CobbinCi-Xiu LiJohn-Sebastian EdenEdward C. HolmesMDPI AGarticlereagent contaminationvirologymetatranscriptomics<i>Circoviridae</i><i>Totiviridae</i><i>Tombusviridae</i>MicrobiologyQR1-502ENViruses, Vol 13, Iss 2122, p 2122 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	reagent contamination virology metatranscriptomics <i>Circoviridae</i> <i>Totiviridae</i> <i>Tombusviridae</i> Microbiology QR1-502
spellingShingle	reagent contamination virology metatranscriptomics <i>Circoviridae</i> <i>Totiviridae</i> <i>Tombusviridae</i> Microbiology QR1-502 Ashleigh F. Porter Joanna Cobbin Ci-Xiu Li John-Sebastian Eden Edward C. Holmes Metagenomic Identification of Viral Sequences in Laboratory Reagents
description	Metagenomic next-generation sequencing has transformed the discovery and diagnosis of infectious disease, with the power to characterise the complete ‘infectome’ (bacteria, viruses, fungi, parasites) of an individual host organism. However, the identification of novel pathogens has been complicated by widespread microbial contamination in commonly used laboratory reagents. Using total RNA sequencing (“metatranscriptomics”) we documented the presence of contaminant viral sequences in multiple ‘blank’ negative control sequencing libraries that comprise a sterile water and reagent mix. Accordingly, we identified 14 viral sequences in 7 negative control sequencing libraries. As in previous studies, several circular replication-associated protein encoding (CRESS) DNA virus-like sequences were recovered in the blank control libraries, as well as contaminating sequences from the <i>Totiviridae</i>, <i>Tombusviridae</i> and <i>Lentiviridae</i> families of RNA virus. These data suggest that viral contamination of common laboratory reagents is likely commonplace and can comprise a wide variety of viruses.
format	article
author	Ashleigh F. Porter Joanna Cobbin Ci-Xiu Li John-Sebastian Eden Edward C. Holmes
author_facet	Ashleigh F. Porter Joanna Cobbin Ci-Xiu Li John-Sebastian Eden Edward C. Holmes
author_sort	Ashleigh F. Porter
title	Metagenomic Identification of Viral Sequences in Laboratory Reagents
title_short	Metagenomic Identification of Viral Sequences in Laboratory Reagents
title_full	Metagenomic Identification of Viral Sequences in Laboratory Reagents
title_fullStr	Metagenomic Identification of Viral Sequences in Laboratory Reagents
title_full_unstemmed	Metagenomic Identification of Viral Sequences in Laboratory Reagents
title_sort	metagenomic identification of viral sequences in laboratory reagents
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/26fe32661d5345259206d634ac46be20
work_keys_str_mv	AT ashleighfporter metagenomicidentificationofviralsequencesinlaboratoryreagents AT joannacobbin metagenomicidentificationofviralsequencesinlaboratoryreagents AT cixiuli metagenomicidentificationofviralsequencesinlaboratoryreagents AT johnsebastianeden metagenomicidentificationofviralsequencesinlaboratoryreagents AT edwardcholmes metagenomicidentificationofviralsequencesinlaboratoryreagents
_version_	1718410141833887744

Metagenomic Identification of Viral Sequences in Laboratory Reagents

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