Metagenomic Snapshots of Viral Components in Guinean Bats

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Abstract

To prevent the emergence of zoonotic infectious diseases and reduce their epidemic potential, we need to understand their origins in nature. Bats in the order Chiroptera are widely distributed worldwide and are natural reservoirs of prominent zoonotic viruses, including Nipah virus, Marburg virus, and possibly SARS-CoV-2. In this study, we applied unbiased metagenomic and metatranscriptomic approaches to decipher the virosphere of frugivorous and insectivorous bat species captured in Guéckédou, Guinea, the epicenter of the West African Ebola virus disease epidemic in 2013–2016. Our study provides a snapshot of the viral diversity present in these bat species, with several novel viruses reported for the first time in bats, as well as some bat viruses closely related to known human or animal pathogens. In addition, analysis of Mops condylurus genomic DNA samples revealed the presence of an Ebola virus nucleoprotein (NP)-derived pseudogene inserted in its genome. These findings provide insight into the evolutionary traits of several virus families in bats and add evidence that nonretroviral integrated RNA viruses (NIRVs) derived from filoviruses may be common in bat genomes.

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New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

Stéphane Guindon, Jean-François Dufayard, Vincent Lefort … (2010)

PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.

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Global trends in emerging infectious diseases

Kate E. Jones, Nikkita G Patel, Marc A. Levy … (2008)

The next new disease Emerging infectious diseases are a major threat to health: AIDS, SARS, drug-resistant bacteria and Ebola virus are among the more recent examples. By identifying emerging disease 'hotspots', the thinking goes, it should be possible to spot health risks at an early stage and prepare containment strategies. An analysis of over 300 examples of disease emerging between 1940 and 2004 suggests that these hotspots can be accurately mapped based on socio-economic, environmental and ecological factors. The data show that the surveillance effort, and much current research spending, is concentrated in developed economies, yet the risk maps point to developing countries as the more likely source of new diseases. Supplementary information The online version of this article (doi:10.1038/nature06536) contains supplementary material, which is available to authorized users.

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A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents

Matthieu Leray, Joy Y Yang, Christopher Meyer … (2013)

Introduction The PCR-based analysis of homologous genes has become one of the most powerful approaches for species detection and identification, particularly with the recent availability of Next Generation Sequencing platforms (NGS) making it possible to identify species composition from a broad range of environmental samples. Identifying species from these samples relies on the ability to match sequences with reference barcodes for taxonomic identification. Unfortunately, most studies of environmental samples have targeted ribosomal markers, despite the fact that the mitochondrial Cytochrome c Oxidase subunit I gene (COI) is by far the most widely available sequence region in public reference libraries. This is largely because the available versatile (“universal”) COI primers target the 658 barcoding region, whose size is considered too large for many NGS applications. Moreover, traditional barcoding primers are known to be poorly conserved across some taxonomic groups. Results We first design a new PCR primer within the highly variable mitochondrial COI region, the “mlCOIintF” primer. We then show that this newly designed forward primer combined with the “jgHCO2198” reverse primer to target a 313 bp fragment performs well across metazoan diversity, with higher success rates than versatile primer sets traditionally used for DNA barcoding (i.e. LCO1490/HCO2198). Finally, we demonstrate how the shorter COI fragment coupled with an efficient bioinformatics pipeline can be used to characterize species diversity from environmental samples by pyrosequencing. We examine the gut contents of three species of planktivorous and benthivorous coral reef fish (family: Apogonidae and Holocentridae). After the removal of dubious COI sequences, we obtained a total of 334 prey Operational Taxonomic Units (OTUs) belonging to 14 phyla from 16 fish guts. Of these, 52.5% matched a reference barcode (>98% sequence similarity) and an additional 32% could be assigned to a higher taxonomic level using Bayesian assignment. Conclusions The molecular analysis of gut contents targeting the 313 COI fragment using the newly designed mlCOIintF primer in combination with the jgHCO2198 primer offers enormous promise for metazoan metabarcoding studies. We believe that this primer set will be a valuable asset for a range of applications from large-scale biodiversity assessments to food web studies.

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Author and article information

Contributors

Anne Balkema-Buschmann: Role: Academic Editor

Journal

Journal ID (nlm-ta): Microorganisms

Journal ID (iso-abbrev): Microorganisms

Journal ID (publisher-id): microorganisms

Title: Microorganisms

Publisher: MDPI

ISSN (Electronic): 2076-2607

Publication date (Electronic): 15 March 2021

Publication date Collection: March 2021

Volume: 9

Issue: 3

Electronic Location Identifier: 599

Affiliations

[1 ]Morcegos de Galicia, Magdalena G-2, 2o izq, 15320 As Pontes de García Rodríguez (A Coruña), Spain; robertox.hermida@ 123456gmail.com

[2 ]WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany; danielcadar@ 123456gmail.com (D.C.); bialonski@ 123456bnitm.de (A.B.); baum@ 123456bnitm.de (H.B.); hhakamak@ 123456emich.edu (H.H.); bencsik@ 123456bnitm.de (A.B.); nelson@ 123456bnitm.de (E.V.N.); guenther@ 123456bni.uni-hamburg.de (S.G.); jonassi@ 123456gmx.de (J.S.-C.); munoz-fontela@ 123456bnitm.de (C.M.F.)

[3 ]Laboratoire des Fièvres Hémorragiques en Guinée, Université Gamal Abdel Nasser de Conakry, Commune de Matoto, Conakry, Guinea; koundounofr@ 123456yahoo.fr (F.R.K.); cmagassouba01@ 123456gmail.com (N.M.)

[4 ]Estación Biológica de Doñana, CSIC, 41092 Seville, Spain; juste@ 123456ebd.csic.es (J.J.); juanele@ 123456ebd.csic.es (J.L.G.-M.)

[5 ]CIBER Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain

[6 ]Public Health England, Porton Down, Wiltshire SP4 0JG, UK; Miles.Carroll@ 123456phe.gov.uk

[7 ]Wellcome Centre for Human Genetics, Nuffield Department of Medicine, Oxford University, Oxford OX3 7BN, UK

[8 ]German Centre for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel, 38124 Braunschweig, Germany

[9 ]Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, 20148 Hamburg, Germany

Author notes

[* ]Correspondence: beatriz.escudero@ 123456bnitm.de

[†]

These authors contributed equally to this work.

Author information

Dániel Cadar https://orcid.org/0000-0002-8063-2766

Javier Juste https://orcid.org/0000-0003-1383-8462

Jonas Schmidt-Chanasit https://orcid.org/0000-0003-4433-0231

César Muñoz Fontela https://orcid.org/0000-0002-7725-2586

Beatriz Escudero-Pérez https://orcid.org/0000-0003-3655-0525

Article

Publisher ID: microorganisms-09-00599

DOI: 10.3390/microorganisms9030599

PMC ID: 7999534

PubMed ID: 33803988

SO-VID: e97e2e2f-f666-4a3e-9a8c-c8fc190b60eb

License:

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 ( http://creativecommons.org/licenses/by/4.0/).

Metagenomic Snapshots of Viral Components in Guinean Bats

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Abstract

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Novel Coronavirus Disease COVID-19

Most cited references 35

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

Global trends in emerging infectious diseases

A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents

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