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...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-10-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/13/11/2122 |
| _version_ | 1827675208278867968 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-10T04:58:54Z |
| format | Article |
| id | doaj.art-26fe32661d5345259206d634ac46be20 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T04:58:54Z |
| publishDate | 2021-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-26fe32661d5345259206d634ac46be202023-11-23T01:55:13ZengMDPI AGViruses1999-49152021-10-011311212210.3390/v13112122Metagenomic Identification of Viral Sequences in Laboratory ReagentsAshleigh F. Porter0Joanna Cobbin1Ci-Xiu Li2John-Sebastian Eden3Edward C. Holmes4The Peter Doherty Institute of Immunity and Infection, Department of Microbiology and Immunity, University of Melbourne, Melbourne, VIC 3000, AustraliaSydney Institute for Infectious Diseases, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, AustraliaKey Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian 271000, ChinaSydney Institute for Infectious Diseases, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, AustraliaSydney Institute for Infectious Diseases, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, AustraliaMetagenomic 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.https://www.mdpi.com/1999-4915/13/11/2122reagent contaminationvirologymetatranscriptomics<i>Circoviridae</i><i>Totiviridae</i><i>Tombusviridae</i> |
| spellingShingle | Ashleigh F. Porter Joanna Cobbin Ci-Xiu Li John-Sebastian Eden Edward C. Holmes Metagenomic Identification of Viral Sequences in Laboratory Reagents Viruses reagent contamination virology metatranscriptomics <i>Circoviridae</i> <i>Totiviridae</i> <i>Tombusviridae</i> |
| title | 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_short | Metagenomic Identification of Viral Sequences in Laboratory Reagents |
| title_sort | metagenomic identification of viral sequences in laboratory reagents |
| topic | reagent contamination virology metatranscriptomics <i>Circoviridae</i> <i>Totiviridae</i> <i>Tombusviridae</i> |
| url | https://www.mdpi.com/1999-4915/13/11/2122 |
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