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Enhanced Viral Metagenomics with Lazypipe 2

Viruses are the main agents causing emerging and re-emerging infectious diseases. It is therefore important to screen for and detect them and uncover the evolutionary processes that support their ability to jump species boundaries and establish themselves in new hosts. Metagenomic next-generation se...

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Autores principales: Plyusnin, Ilya, Vapalahti, Olli, Sironen, Tarja, Kant, Ravi, Smura, Teemu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9960287/
https://www.ncbi.nlm.nih.gov/pubmed/36851645
http://dx.doi.org/10.3390/v15020431
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author Plyusnin, Ilya
Vapalahti, Olli
Sironen, Tarja
Kant, Ravi
Smura, Teemu
author_facet Plyusnin, Ilya
Vapalahti, Olli
Sironen, Tarja
Kant, Ravi
Smura, Teemu
author_sort Plyusnin, Ilya
collection PubMed
description Viruses are the main agents causing emerging and re-emerging infectious diseases. It is therefore important to screen for and detect them and uncover the evolutionary processes that support their ability to jump species boundaries and establish themselves in new hosts. Metagenomic next-generation sequencing (mNGS) is a high-throughput, impartial technology that has enabled virologists to detect either known or novel, divergent viruses from clinical, animal, wildlife and environmental samples, with little a priori assumptions. mNGS is heavily dependent on bioinformatic analysis, with an emerging demand for integrated bioinformatic workflows. Here, we present Lazypipe 2, an updated mNGS pipeline with, as compared to Lazypipe1, significant improvements in code stability and transparency, with added functionality and support for new software components. We also present extensive benchmarking results, including evaluation of a novel canine simulated metagenome, precision and recall of virus detection at varying sequencing depth, and a low to extremely low proportion of viral genetic material. Additionally, we report accuracy of virus detection with two strategies: homology searches using nucleotide or amino acid sequences. We show that Lazypipe 2 with nucleotide-based annotation approaches near perfect detection for eukaryotic viruses and, in terms of accuracy, outperforms the compared pipelines. We also discuss the importance of homology searches with amino acid sequences for the detection of highly divergent novel viruses.
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spelling pubmed-99602872023-02-26 Enhanced Viral Metagenomics with Lazypipe 2 Plyusnin, Ilya Vapalahti, Olli Sironen, Tarja Kant, Ravi Smura, Teemu Viruses Article Viruses are the main agents causing emerging and re-emerging infectious diseases. It is therefore important to screen for and detect them and uncover the evolutionary processes that support their ability to jump species boundaries and establish themselves in new hosts. Metagenomic next-generation sequencing (mNGS) is a high-throughput, impartial technology that has enabled virologists to detect either known or novel, divergent viruses from clinical, animal, wildlife and environmental samples, with little a priori assumptions. mNGS is heavily dependent on bioinformatic analysis, with an emerging demand for integrated bioinformatic workflows. Here, we present Lazypipe 2, an updated mNGS pipeline with, as compared to Lazypipe1, significant improvements in code stability and transparency, with added functionality and support for new software components. We also present extensive benchmarking results, including evaluation of a novel canine simulated metagenome, precision and recall of virus detection at varying sequencing depth, and a low to extremely low proportion of viral genetic material. Additionally, we report accuracy of virus detection with two strategies: homology searches using nucleotide or amino acid sequences. We show that Lazypipe 2 with nucleotide-based annotation approaches near perfect detection for eukaryotic viruses and, in terms of accuracy, outperforms the compared pipelines. We also discuss the importance of homology searches with amino acid sequences for the detection of highly divergent novel viruses. MDPI 2023-02-04 /pmc/articles/PMC9960287/ /pubmed/36851645 http://dx.doi.org/10.3390/v15020431 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Plyusnin, Ilya
Vapalahti, Olli
Sironen, Tarja
Kant, Ravi
Smura, Teemu
Enhanced Viral Metagenomics with Lazypipe 2
title Enhanced Viral Metagenomics with Lazypipe 2
title_full Enhanced Viral Metagenomics with Lazypipe 2
title_fullStr Enhanced Viral Metagenomics with Lazypipe 2
title_full_unstemmed Enhanced Viral Metagenomics with Lazypipe 2
title_short Enhanced Viral Metagenomics with Lazypipe 2
title_sort enhanced viral metagenomics with lazypipe 2
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9960287/
https://www.ncbi.nlm.nih.gov/pubmed/36851645
http://dx.doi.org/10.3390/v15020431
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