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Article ; Online: Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery.

Pérot, Philippe / Bigot, Thomas / Temmam, Sarah / Regnault, Béatrice / Eloit, Marc

2022 Volume 14, Issue 9

Abstract: We present Microseek, a pipeline for virus identification and discovery based on RVDB-prot, a comprehensive, curated and regularly updated database of viral proteins. Microseek analyzes metagenomic Next Generation Sequencing (mNGS) raw data by performing ...

Abstract	We present Microseek, a pipeline for virus identification and discovery based on RVDB-prot, a comprehensive, curated and regularly updated database of viral proteins. Microseek analyzes metagenomic Next Generation Sequencing (mNGS) raw data by performing quality steps, de novo assembly, and by scoring the Lowest Common Ancestor (LCA) from translated reads and contigs. Microseek runs on a local computer. The outcome of the pipeline is displayed through a user-friendly and dynamic graphical interface. Based on two representative mNGS datasets derived from human tissue and plasma specimens, we illustrate how Microseek works, and we report its performances. In silico spikes of known viral sequences, but also spikes of fake
MeSH term(s)	High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; Metagenomics/methods ; Viral Proteins/genetics ; Viruses/genetics
Chemical Substances	Viral Proteins
Language	English
Publishing date	2022-09-08
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v14091990
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Virus Pop-Expanding Viral Databases by Protein Sequence Simulation.

Kende, Julia / Bonomi, Massimiliano / Temmam, Sarah / Regnault, Béatrice / Pérot, Philippe / Eloit, Marc / Bigot, Thomas

Viruses

2023 Volume 15, Issue 6

Abstract: The improvement of our knowledge of the virosphere, which includes unknown viruses, is a key area in virology. Metagenomics tools, which perform taxonomic assignation from high throughput sequencing datasets, are generally evaluated with datasets derived ...

Abstract	The improvement of our knowledge of the virosphere, which includes unknown viruses, is a key area in virology. Metagenomics tools, which perform taxonomic assignation from high throughput sequencing datasets, are generally evaluated with datasets derived from biological samples or in silico spiked samples containing known viral sequences present in public databases, resulting in the inability to evaluate the capacity of these tools to detect novel or distant viruses. Simulating realistic evolutionary directions is therefore key to benchmark and improve these tools. Additionally, expanding current databases with realistic simulated sequences can improve the capacity of alignment-based searching strategies for finding distant viruses, which could lead to a better characterization of the "dark matter" of metagenomics data. Here, we present Virus Pop, a novel pipeline for simulating realistic protein sequences and adding new branches to a protein phylogenetic tree. The tool generates simulated sequences with substitution rate variations that are dependent on protein domains and inferred from the input dataset, allowing for a realistic representation of protein evolution. The pipeline also infers ancestral sequences corresponding to multiple internal nodes of the input data phylogenetic tree, enabling new sequences to be inserted at various points of interest in the group studied. We demonstrated that Virus Pop produces simulated sequences that closely match the structural and functional characteristics of real protein sequences, taking as an example the spike protein of
MeSH term(s)	Humans ; Phylogeny ; Computational Biology/methods ; Computer Simulation ; Databases, Factual ; Viruses/genetics ; Metagenomics/methods
Language	English
Publishing date	2023-05-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v15061227
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery

Pérot, Philippe / Bigot, Thomas / Temmam, Sarah / Regnault, Béatrice / Eloit, Marc

Viruses. 2022 Sept. 08, v. 14, no. 9

2022

Abstract	We present Microseek, a pipeline for virus identification and discovery based on RVDB-prot, a comprehensive, curated and regularly updated database of viral proteins. Microseek analyzes metagenomic Next Generation Sequencing (mNGS) raw data by performing quality steps, de novo assembly, and by scoring the Lowest Common Ancestor (LCA) from translated reads and contigs. Microseek runs on a local computer. The outcome of the pipeline is displayed through a user-friendly and dynamic graphical interface. Based on two representative mNGS datasets derived from human tissue and plasma specimens, we illustrate how Microseek works, and we report its performances. In silico spikes of known viral sequences, but also spikes of fake Neopneumovirus viral sequences generated with variable evolutionary distances from known members of the Pneumoviridae family, were used. Results were compared to Chan Zuckerberg ID (CZ ID), a reference cloud-based mNGS pipeline. We show that Microseek reliably identifies known viral sequences and performs well for the detection of distant pseudoviral sequences, especially in complex samples such as in human plasma, while minimizing non-relevant hits.
Keywords	Pneumoviridae ; ancestry ; computer simulation ; computers ; data collection ; databases ; humans ; metagenomics ; viruses
Language	English
Dates of publication	2022-0908
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v14091990
Database	NAL-Catalogue (AGRICOLA)

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Article: A Search for Tick-Associated, Bronnoya-like Virus Spillover into Sheep.

Bratuleanu, Bianca Elena / Raileanu, Cristian / Chrétien, Delphine / Guardado-Calvo, Pablo / Bigot, Thomas / Savuta, Gheorghe / Temmam, Sarah / Eloit, Marc

Microorganisms

2023 Volume 11, Issue 1

Abstract: Tick-borne diseases are responsible for many vector-borne diseases within Europe. Recently, novel viruses belonging to a new viral family of the ... ...

Abstract	Tick-borne diseases are responsible for many vector-borne diseases within Europe. Recently, novel viruses belonging to a new viral family of the order
Language	English
Publishing date	2023-01-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms11010209
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Simulation data for the estimation of numerical constants for approximating pairwise evolutionary distances between amino acid sequences

Bigot, Thomas / Guglielmini, Julien / Criscuolo, Alexis

Data in Brief. 2019 Aug., v. 25

2019

Abstract: Estimating the number of substitution events per site that have occurred during the evolution of a pair of amino acid sequences is a common task in phylogenetics and comparative genomics that often requires quite slow maximum-likelihood procedures when ... ...

Abstract	Estimating the number of substitution events per site that have occurred during the evolution of a pair of amino acid sequences is a common task in phylogenetics and comparative genomics that often requires quite slow maximum-likelihood procedures when taking into account explicit evolutionary models. Data presented in this article are large sets of numbers of substitution events and associated numbers of observed differences between pairs of aligned amino acid sequences that have been generated through a simulation procedure of sequence evolution under a broad range of evolutionary models. These data are available at https://zenodo.org/record/2653704 (doi:10.5281/zenodo.2653704). They are accompanied in this paper by figures showing the strong relationship between the corresponding evolutionary and uncorrected distances, as well as estimated numerical constants that determine non-linear functions that fit the simulated data. These numerical constants can be useful to quickly estimate pairwise evolutionary distances directly from uncorrected distances between aligned amino acid sequences.
Keywords	amino acids ; genomics ; phylogeny ; statistical analysis
Language	English
Dates of publication	2019-08
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	2786545-9
ISSN	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2019.104212
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Simulation data for the estimation of numerical constants for approximating pairwise evolutionary distances between amino acid sequences.

Bigot, Thomas / Guglielmini, Julien / Criscuolo, Alexis

Data in brief

2019 Volume 25, Page(s) 104212

Abstract	Estimating the number of substitution events per site that have occurred during the evolution of a pair of amino acid sequences is a common task in phylogenetics and comparative genomics that often requires quite slow maximum-likelihood procedures when taking into account explicit evolutionary models. Data presented in this article are large sets of numbers of substitution events and associated numbers of observed differences between pairs of aligned amino acid sequences that have been generated through a simulation procedure of sequence evolution under a broad range of evolutionary models. These data are available at https://zenodo.org/record/2653704 (doi:10.5281/zenodo.2653704). They are accompanied in this paper by figures showing the strong relationship between the corresponding evolutionary and uncorrected distances, as well as estimated numerical constants that determine non-linear functions that fit the simulated data. These numerical constants can be useful to quickly estimate pairwise evolutionary distances directly from uncorrected distances between aligned amino acid sequences.
Language	English
Publishing date	2019-07-08
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2786545-9
ISSN	2352-3409 ; 2352-3409
ISSN (online)	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2019.104212
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: RVDB-prot, a reference viral protein database and its HMM profiles.

Bigot, Thomas / Temmam, Sarah / Pérot, Philippe / Eloit, Marc

F1000Research

2019 Volume 8, Page(s) 530

Abstract: We present RVDB-prot, a database corresponding to the protein equivalent of the nucleic acid reference virus database RVDB. Protein databases can be helpful to perform more sensitive protein sequence comparisons. Similarly to its homologous public ... ...

Abstract	We present RVDB-prot, a database corresponding to the protein equivalent of the nucleic acid reference virus database RVDB. Protein databases can be helpful to perform more sensitive protein sequence comparisons. Similarly to its homologous public repository, RVDB-prot aims to provide reliable and accurately annotated unique entries, while including also an Hidden Markov Model (HMM) protein profiles database for distant protein searching.
Language	English
Publishing date	2019-04-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2699932-8
ISSN	2046-1402 ; 2046-1402
ISSN (online)	2046-1402
ISSN	2046-1402
DOI	10.12688/f1000research.18776.2
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Deep Impact of Random Amplification and Library Construction Methods on Viral Metagenomics Results.

Regnault, Béatrice / Bigot, Thomas / Ma, Laurence / Pérot, Philippe / Temmam, Sarah / Eloit, Marc

Viruses

2021 Volume 13, Issue 2

Abstract: Clinical metagenomics is a broad-range agnostic detection method of pathogens, including novel microorganisms. A major limit is the low pathogen load compared to the high background of host nucleic acids. To overcome this issue, several solutions exist, ... ...

Abstract	Clinical metagenomics is a broad-range agnostic detection method of pathogens, including novel microorganisms. A major limit is the low pathogen load compared to the high background of host nucleic acids. To overcome this issue, several solutions exist, such as applying a very high depth of sequencing, or performing a relative enrichment of viral genomes associated with capsids. At the end, the quantity of total nucleic acids is often below the concentrations recommended by the manufacturers of library kits, which necessitates to random amplify nucleic acids. Using a pool of 26 viruses representative of viral diversity, we observed a deep impact of the nature of sample (total nucleic acids versus RNA only), the reverse transcription, the random amplification and library construction method on virus recovery. We further optimized the two most promising methods and assessed their performance with fully characterized reference virus stocks. Good genome coverage and limit of detection lower than 100 or 1000 genome copies per mL of plasma, depending on the genome viral type, were obtained from a three million reads dataset. Our study reveals that optimized random amplification is a technique of choice when insufficient amounts of nucleic acid are available for direct libraries constructions.
MeSH term(s)	Genome, Viral/genetics ; Genomic Library ; Humans ; Limit of Detection ; Metagenomics/methods ; Nucleic Acid Amplification Techniques/methods ; Viruses/genetics ; Viruses/isolation & purification
Language	English
Publishing date	2021-02-07
Publishing country	Switzerland
Document type	Comparative Study ; Evaluation Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v13020253
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Detection of

Bratuleanu, Bianca Elena / Temmam, Sarah / Munier, Sandie / Chrétien, Delphine / Bigot, Thomas / van der Werf, Sylvie / Savuta, Gheorghe / Eloit, Marc

Frontiers in veterinary science

2022 Volume 9, Page(s) 863814

Abstract: Ticks are involved in the transmission of various pathogens and several tick-borne diseases cause significant problems for the health of humans and livestock. The members of ... ...

Abstract	Ticks are involved in the transmission of various pathogens and several tick-borne diseases cause significant problems for the health of humans and livestock. The members of the
Language	English
Publishing date	2022-04-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2834243-4
ISSN	2297-1769
ISSN	2297-1769
DOI	10.3389/fvets.2022.863814
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: The virome of Rhipicephalus, Dermacentor and Haemaphysalis ticks from Eastern Romania includes novel viruses with potential relevance for public health

Bratuleanu, Bianca Elena / Temmam, Sarah / Chrétien, Delphine / Regnault, Béatrice / Pérot, Philippe / Bouchier, Christiane / Bigot, Thomas / Savuța, Gheorghe / Eloit, Marc

Transboundary and emerging diseases. 2022 May, v. 69, no. 3

2022

Abstract: Ticks are involved in the transmission of various pathogens and several tick‐borne diseases cause significant problems for the health of humans and livestock. The composition of viral communities in ticks and their interactions with pathogens, is poorly ... ...

Abstract	Ticks are involved in the transmission of various pathogens and several tick‐borne diseases cause significant problems for the health of humans and livestock. The composition of viral communities in ticks and their interactions with pathogens, is poorly understood, particularly in Eastern Europe, an area that represents a major hub for animal‐arthropod vectors exchanges (e.g., via bird migrations). The aim of this study was to describe the virome of Dermacentor sp., Rhipicephalus sp. and Haemaphysalis sp. ticks collected from relatively little studied regions of Romania (Iasi and Tulcea counties) located at the intersection of various biotopes, countries and routes of migrations. We also focused the study on viruses that could potentially have relevance for human and animal health. In 2019, more than 500 ticks were collected from the vegetation and from small ruminants and analysed by high‐throughput transcriptome sequencing. Among the viral communities infecting Romanian ticks, viruses belonging to the Flaviviridae, Phenuiviridae and Nairoviridae families were identified and full genomes were derived. Phylogenetic analyses placed them in clades where mammalian isolates are found, suggesting that these viruses could constitute novel arboviruses. The characterization of these communities increase the knowledge of the diversity of viruses in Eastern Europe and provides a basis for further studies about the interrelationship between ticks and tick‐borne viruses.
Keywords	Dermacentor ; Flaviviridae ; Haemaphysalis ; Nairoviridae ; Phenuiviridae ; Rhipicephalus ; arboviruses ; biotopes ; birds ; genome ; phylogeny ; public health ; transcriptome ; vegetation ; Eastern European region ; Romania
Language	English
Dates of publication	2022-05
Size	p. 1387-1403.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2414822-2
ISSN	1865-1682 ; 1865-1674
ISSN (online)	1865-1682
ISSN	1865-1674
DOI	10.1111/tbed.14105
Database	NAL-Catalogue (AGRICOLA)

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