1
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Da Silva AG, Bach E, Ellwanger JH, Chies JAB. Tips and tools to obtain and assess mosquito viromes. Arch Microbiol 2024; 206:132. [PMID: 38436750 DOI: 10.1007/s00203-023-03813-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/06/2023] [Accepted: 12/22/2023] [Indexed: 03/05/2024]
Abstract
Due to their vectorial capacity, mosquitoes (Diptera: Culicidae) receive special attention from health authorities and entomologists. These cosmopolitan insects are responsible for the transmission of many viral diseases, such as dengue and yellow fever, causing huge impacts on human health and justifying the intensification of research focused on mosquito-borne diseases. In this context, the study of the virome of mosquitoes can contribute to anticipate the emergence and/or the reemergence of infectious diseases. The assessment of mosquito viromes also contributes to the surveillance of a wide variety of viruses found in these insects, allowing the early detection of pathogens with public health importance. However, the study of mosquito viromes can be challenging due to the number and complexities of steps involved in this type of research. Therefore, this article aims to describe, in a straightforward and simplified way, the steps necessary for obtention and assessment of mosquito viromes. In brief, this article explores: the capture and preservation of specimens; sampling strategies; treatment of samples before DNA/RNA extraction; extraction methodologies; enrichment and purification processes; sequencing choices; and bioinformatics analysis.
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Affiliation(s)
- Amanda Gonzalez Da Silva
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Postgraduate Program in Genetics and Molecular Biology (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), UFRGS. Av. Bento Gonçalves, 9500, Porto Alegre, Rio Grande do Sul, Brazil
| | - Evelise Bach
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Postgraduate Program in Genetics and Molecular Biology (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), UFRGS. Av. Bento Gonçalves, 9500, Porto Alegre, Rio Grande do Sul, Brazil
| | - Joel Henrique Ellwanger
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Postgraduate Program in Genetics and Molecular Biology (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), UFRGS. Av. Bento Gonçalves, 9500, Porto Alegre, Rio Grande do Sul, Brazil
| | - José Artur Bogo Chies
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Postgraduate Program in Genetics and Molecular Biology (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), UFRGS. Av. Bento Gonçalves, 9500, Porto Alegre, Rio Grande do Sul, Brazil.
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2
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Xu T, Deng LS, Jian ZJ, Xu L, Li FQ, Lai SY, Ai YR, Zhu L, Xu ZW. First report on identification and genomic analysis of a novel porcine circovirus (porcine circovirus 4) in cats. Front Microbiol 2023; 14:1258484. [PMID: 37808320 PMCID: PMC10556453 DOI: 10.3389/fmicb.2023.1258484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 08/31/2023] [Indexed: 10/10/2023] Open
Abstract
Porcine circovirus type 4 (PCV4) is an emerging circovirus, which has been detected in domestic pigs across various provinces in China and Korea. In this study, we aimed to investigate whether cats are susceptible to PCV4. For this purpose, we collected 116 cat samples from animal hospitals in Sichuan Province, China, between 2021 and 2022. Using a SYBR Green-based real-time PCR assay, we detected PCV4 in 5 out of the 116 clinical samples, indicating a positive rate of 4.31% (5/116) and confirming the presence of PCV4 in cats from Sichuan Province, China. Moreover, we successfully sequenced and analyzed the complete genome of one PCV4 strain (SCGA-Cat) along with 60 reference sequences deposited in the GenBank database. SCGA-Cat exhibited high nucleotide homology (98.2-99.0%) with PCV4 strains from other species, including dogs, pigs, dairy cows, and fur animals. Notably, the SCGA-Cat strain from cats clustered closely with a PCV4 strain derived from a pig collected in Fujian Province, China. To the best of our knowledge, this study represents the first report on the molecular detection of PCV4 in cats worldwide, which prompted us to understand the genetic diversity and cross-species transmission of the ongoing PCV4 cases. However, further investigations are needed to explore the association between PCV4 infection and clinical syndromes in cats.
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Affiliation(s)
- Tong Xu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Li-Shuang Deng
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhi-Jie Jian
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Lei Xu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Feng-Qin Li
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Si-Yuan Lai
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yan-Ru Ai
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- College of Veterinary Medicine Sichuan Key Laboratory of Animal Epidemic Disease and Human Health, Sichuan Agricultural University, Chengdu, China
| | - Zhi-Wen Xu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- College of Veterinary Medicine Sichuan Key Laboratory of Animal Epidemic Disease and Human Health, Sichuan Agricultural University, Chengdu, China
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3
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A k-mer based approach for classifying viruses without taxonomy identifies viral associations in human autism and plant microbiomes. Comput Struct Biotechnol J 2021; 19:5911-5919. [PMID: 34849195 PMCID: PMC8605058 DOI: 10.1016/j.csbj.2021.10.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/17/2021] [Accepted: 10/20/2021] [Indexed: 12/25/2022] Open
Abstract
Viruses are an underrepresented taxa in the study and identification of microbiome constituents; however, they play an essential role in health, microbiome regulation, and transfer of genetic material. Only a few thousand viruses have been isolated, sequenced, and assigned a taxonomy, which limits the ability to identify and quantify viruses in the microbiome. Additionally, the vast diversity of viruses represents a challenge for classification, not only in constructing a viral taxonomy, but also in identifying similarities between a virus' genotype and its phenotype. However, the diversity of viral sequences can be leveraged to classify their sequences in metagenomic and metatranscriptomic samples, even if they do not have a taxonomy. To identify and quantify viruses in transcriptomic and genomic samples, we developed a dynamic programming algorithm for creating a classification tree out of 715,672 metagenome viruses. To create the classification tree, we clustered proportional similarity scores generated from the k-mer profiles of each of the metagenome viruses to create a database of metagenomic viruses. The resulting Kraken2 database of the metagenomic viruses can be found here: https://www.osti.gov/biblio/1615774 and is compatible with Kraken2. We then integrated the viral classification database with databases created with genomes from NCBI for use with ParaKraken (a parallelized version of Kraken provided in Supplemental Zip 1), a metagenomic/transcriptomic classifier. To illustrate the breadth of our utility for classifying metagenome viruses, we analyzed data from a plant metagenome study identifying genotypic and compartment specific differences between two Populus genotypes in three different compartments. We also identified a significant increase in abundance of eight viral sequences in post mortem brains in a human metatranscriptome study comparing Autism Spectrum Disorder patients and controls. We also show the potential accuracy for classifying viruses by utilizing both the JGI and NCBI viral databases to identify the uniqueness of viral sequences. Finally, we validate the accuracy of viral classification with NCBI databases containing viruses with taxonomy to identify pathogenic viruses in known COVID-19 and cassava brown streak virus infection samples. Our method represents the compulsory first step in better understanding the role of viruses in the microbiome by allowing for a more complete identification of sequences without taxonomy. Better classification of viruses will improve identifying associations between viruses and their hosts as well as viruses and other microbiome members. Despite the lack of taxonomy, this database of metagenomic viruses can be used with any tool that utilizes a taxonomy, such as Kraken, for accurate classification of viruses.
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4
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Abstract
Viruses are the most abundant biological entity on Earth, infect cellular organisms from all domains of life, and are central players in the global biosphere. Over the last century, the discovery and characterization of viruses have progressed steadily alongside much of modern biology. In terms of outright numbers of novel viruses discovered, however, the last few years have been by far the most transformative for the field. Advances in methods for identifying viral sequences in genomic and metagenomic datasets, coupled to the exponential growth of environmental sequencing, have greatly expanded the catalog of known viruses and fueled the tremendous growth of viral sequence databases. Development and implementation of new standards, along with careful study of the newly discovered viruses, have transformed and will continue to transform our understanding of microbial evolution, ecology, and biogeochemical cycles, leading to new biotechnological innovations across many diverse fields, including environmental, agricultural, and biomedical sciences.
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Affiliation(s)
- Lee Call
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; ,
| | - Stephen Nayfach
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; ,
| | - Nikos C Kyrpides
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; ,
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5
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Kockler ZW, Gordenin DA. From RNA World to SARS-CoV-2: The Edited Story of RNA Viral Evolution. Cells 2021; 10:1557. [PMID: 34202997 PMCID: PMC8234929 DOI: 10.3390/cells10061557] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/11/2021] [Accepted: 06/17/2021] [Indexed: 12/13/2022] Open
Abstract
The current SARS-CoV-2 pandemic underscores the importance of understanding the evolution of RNA genomes. While RNA is subject to the formation of similar lesions as DNA, the evolutionary and physiological impacts RNA lesions have on viral genomes are yet to be characterized. Lesions that may drive the evolution of RNA genomes can induce breaks that are repaired by recombination or can cause base substitution mutagenesis, also known as base editing. Over the past decade or so, base editing mutagenesis of DNA genomes has been subject to many studies, revealing that exposure of ssDNA is subject to hypermutation that is involved in the etiology of cancer. However, base editing of RNA genomes has not been studied to the same extent. Recently hypermutation of single-stranded RNA viral genomes have also been documented though its role in evolution and population dynamics. Here, we will summarize the current knowledge of key mechanisms and causes of RNA genome instability covering areas from the RNA world theory to the SARS-CoV-2 pandemic of today. We will also highlight the key questions that remain as it pertains to RNA genome instability, mutations accumulation, and experimental strategies for addressing these questions.
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Affiliation(s)
| | - Dmitry A. Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC 27709, USA;
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6
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Mechanisms Underlying Host Range Variation in Flavivirus: From Empirical Knowledge to Predictive Models. J Mol Evol 2021; 89:329-340. [PMID: 34059925 DOI: 10.1007/s00239-021-10013-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 05/13/2021] [Indexed: 12/22/2022]
Abstract
Preventing and controlling epidemics caused by vector-borne viruses are particularly challenging due to their diverse pool of hosts and highly adaptive nature. Many vector-borne viruses belong to the Flavivirus genus, whose members vary greatly in host range and specificity. Members of the Flavivirus genus can be categorized to four main groups: insect-specific viruses that are maintained solely in arthropod populations, mosquito-borne viruses and tick-borne viruses that are transmitted to vertebrate hosts by mosquitoes or ticks via blood feeding, and those with no-known vector. The mosquito-borne group encompasses the yellow fever, dengue, and West Nile viruses, all of which are globally spread and cause severe morbidity in humans. The Flavivirus genus is genetically diverse, and its members are subject to different host-specific and vector-specific selective constraints, which do not always align. Thus, understanding the underlying genetic differences that led to the diversity in host range within this genus is an important aspect in deciphering the mechanisms that drive host compatibility and can aid in the constant arms-race against viral threats. Here, we review the phylogenetic relationships between members of the genus, their infection bottlenecks, and phenotypic and genomic differences. We further discuss methods that utilize these differences for prediction of host shifts in flaviviruses and can contribute to viral surveillance efforts.
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7
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Abril AG, Carrera M, Böhme K, Barros-Velázquez J, Cañas B, Rama JLR, Villa TG, Calo-Mata P. Proteomic Characterization of Bacteriophage Peptides from the Mastitis Producer Staphylococcus aureus by LC-ESI-MS/MS and the Bacteriophage Phylogenomic Analysis. Foods 2021; 10:799. [PMID: 33917943 PMCID: PMC8068337 DOI: 10.3390/foods10040799] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/28/2021] [Accepted: 04/06/2021] [Indexed: 01/21/2023] Open
Abstract
The present work describes LC-ESI-MS/MS MS (liquid chromatography-electrospray ionization-tandem mass spectrometry) analyses of tryptic digestion peptides from phages that infect mastitis-causing Staphylococcus aureus isolated from dairy products. A total of 1933 nonredundant peptides belonging to 1282 proteins were identified and analyzed. Among them, 79 staphylococcal peptides from phages were confirmed. These peptides belong to proteins such as phage repressors, structural phage proteins, uncharacterized phage proteins and complement inhibitors. Moreover, eighteen of the phage origin peptides found were specific to S. aureus strains. These diagnostic peptides could be useful for the identification and characterization of S. aureus strains that cause mastitis. Furthermore, a study of bacteriophage phylogeny and the relationship among the identified phage peptides and the bacteria they infect was also performed. The results show the specific peptides that are present in closely related phages and the existing links between bacteriophage phylogeny and the respective Staphylococcus spp. infected.
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Affiliation(s)
- Ana G. Abril
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain; (A.G.A.); (J.-L.R.R.); (T.G.V.)
| | - Mónica Carrera
- Department of Food Technology, Spanish National Research Council, Marine Research Institute, 36208 Vigo, Spain
| | - Karola Böhme
- Agroalimentary Technological Center of Lugo, 27002 Lugo, Spain;
| | - Jorge Barros-Velázquez
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, 27002 Lugo, Spain;
| | - Benito Cañas
- Department of Analytical Chemistry, Complutense University of Madrid, 28040 Madrid, Spain;
| | - José-Luis R. Rama
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain; (A.G.A.); (J.-L.R.R.); (T.G.V.)
| | - Tomás G. Villa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain; (A.G.A.); (J.-L.R.R.); (T.G.V.)
| | - Pilar Calo-Mata
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, 27002 Lugo, Spain;
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8
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Kudla M, Gutowska K, Synak J, Weber M, Bohnsack KS, Lukasiak P, Villmann T, Blazewicz J, Szachniuk M. Virxicon: A Lexicon Of Viral Sequences. Bioinformatics 2020; 36:5507-5513. [PMID: 33367605 PMCID: PMC8016492 DOI: 10.1093/bioinformatics/btaa1066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/18/2020] [Accepted: 12/11/2020] [Indexed: 11/12/2022] Open
Abstract
Motivation Viruses are the most abundant biological entities and constitute a large reservoir of genetic diversity. In recent years, knowledge about them has increased significantly as a result of dynamic development in life sciences and rapid technological progress. This knowledge is scattered across various data repositories, making a comprehensive analysis of viral data difficult. Results In response to the need for gathering a comprehensive knowledge of viruses and viral sequences, we developed Virxicon, a lexicon of all experimentally acquired sequences for RNA and DNA viruses. The ability to quickly obtain data for entire viral groups, searching sequences by levels of taxonomic hierarchy—according to the Baltimore classification and ICTV taxonomy—and tracking the distribution of viral data and its growth over time are unique features of our database compared to the other tools. Availabilityand implementation Virxicon is a publicly available resource, updated weekly. It has an intuitive web interface and can be freely accessed at http://virxicon.cs.put.poznan.pl/.
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Affiliation(s)
- Mateusz Kudla
- Institute of Computing Science and European Centre for Bioinformatics and Genomics, Poznan University of Technology, Poznan, 60-965, Poland.,Saxon Institute for Computational Intelligence and Machine Learning, University of Applied Sciences Mittweida, Mittweida, 09648, Germany
| | - Kaja Gutowska
- Institute of Computing Science and European Centre for Bioinformatics and Genomics, Poznan University of Technology, Poznan, 60-965, Poland.,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Jaroslaw Synak
- Institute of Computing Science and European Centre for Bioinformatics and Genomics, Poznan University of Technology, Poznan, 60-965, Poland
| | - Mirko Weber
- Saxon Institute for Computational Intelligence and Machine Learning, University of Applied Sciences Mittweida, Mittweida, 09648, Germany
| | - Katrin Sophie Bohnsack
- Saxon Institute for Computational Intelligence and Machine Learning, University of Applied Sciences Mittweida, Mittweida, 09648, Germany
| | - Piotr Lukasiak
- Institute of Computing Science and European Centre for Bioinformatics and Genomics, Poznan University of Technology, Poznan, 60-965, Poland.,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Thomas Villmann
- Saxon Institute for Computational Intelligence and Machine Learning, University of Applied Sciences Mittweida, Mittweida, 09648, Germany
| | - Jacek Blazewicz
- Institute of Computing Science and European Centre for Bioinformatics and Genomics, Poznan University of Technology, Poznan, 60-965, Poland.,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Marta Szachniuk
- Institute of Computing Science and European Centre for Bioinformatics and Genomics, Poznan University of Technology, Poznan, 60-965, Poland.,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
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9
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Maclot F, Candresse T, Filloux D, Malmstrom CM, Roumagnac P, van der Vlugt R, Massart S. Illuminating an Ecological Blackbox: Using High Throughput Sequencing to Characterize the Plant Virome Across Scales. Front Microbiol 2020; 11:578064. [PMID: 33178159 PMCID: PMC7596190 DOI: 10.3389/fmicb.2020.578064] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/24/2020] [Indexed: 01/08/2023] Open
Abstract
The ecology of plant viruses began to be explored at the end of the 19th century. Since then, major advances have revealed mechanisms of virus-host-vector interactions in various environments. These advances have been accelerated by new technlogies for virus detection and characterization, most recently including high throughput sequencing (HTS). HTS allows investigators, for the first time, to characterize all or nearly all viruses in a sample without a priori information about which viruses might be present. This powerful approach has spurred new investigation of the viral metagenome (virome). The rich virome datasets accumulated illuminate important ecological phenomena such as virus spread among host reservoirs (wild and domestic), effects of ecosystem simplification caused by human activities (and agriculture) on the biodiversity and the emergence of new viruses in crops. To be effective, however, HTS-based virome studies must successfully navigate challenges and pitfalls at each procedural step, from plant sampling to library preparation and bioinformatic analyses. This review summarizes major advances in plant virus ecology associated with technological developments, and then presents important considerations and best practices for HTS use in virome studies.
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Affiliation(s)
- François Maclot
- Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | | | - Denis Filloux
- CIRAD, BGPI, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Montpellier University, Montpellier, France
| | - Carolyn M Malmstrom
- Department of Plant Biology and Graduate Program in Ecology, Evolution and Behavior, Michigan State University, East Lansing, MI, United States
| | - Philippe Roumagnac
- CIRAD, BGPI, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Montpellier University, Montpellier, France
| | - René van der Vlugt
- Laboratory of Virology, Wageningen University and Research Centre (WUR-PRI), Wageningen, Netherlands
| | - Sébastien Massart
- Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
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10
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Pérez-Cobas AE, Gomez-Valero L, Buchrieser C. Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses. Microb Genom 2020; 6:mgen000409. [PMID: 32706331 PMCID: PMC7641418 DOI: 10.1099/mgen.0.000409] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/30/2020] [Indexed: 12/23/2022] Open
Abstract
Metagenomics and marker gene approaches, coupled with high-throughput sequencing technologies, have revolutionized the field of microbial ecology. Metagenomics is a culture-independent method that allows the identification and characterization of organisms from all kinds of samples. Whole-genome shotgun sequencing analyses the total DNA of a chosen sample to determine the presence of micro-organisms from all domains of life and their genomic content. Importantly, the whole-genome shotgun sequencing approach reveals the genomic diversity present, but can also give insights into the functional potential of the micro-organisms identified. The marker gene approach is based on the sequencing of a specific gene region. It allows one to describe the microbial composition based on the taxonomic groups present in the sample. It is frequently used to analyse the biodiversity of microbial ecosystems. Despite its importance, the analysis of metagenomic sequencing and marker gene data is quite a challenge. Here we review the primary workflows and software used for both approaches and discuss the current challenges in the field.
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Affiliation(s)
- Ana Elena Pérez-Cobas
- Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris, France and CNRS UMR 3525, 675724, Paris, France
| | - Laura Gomez-Valero
- Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris, France and CNRS UMR 3525, 675724, Paris, France
| | - Carmen Buchrieser
- Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris, France and CNRS UMR 3525, 675724, Paris, France
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11
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Pratas D, Toppinen M, Pyöriä L, Hedman K, Sajantila A, Perdomo MF. A hybrid pipeline for reconstruction and analysis of viral genomes at multi-organ level. Gigascience 2020; 9:giaa086. [PMID: 32815536 PMCID: PMC7439602 DOI: 10.1093/gigascience/giaa086] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/25/2020] [Accepted: 07/23/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Advances in sequencing technologies have enabled the characterization of multiple microbial and host genomes, opening new frontiers of knowledge while kindling novel applications and research perspectives. Among these is the investigation of the viral communities residing in the human body and their impact on health and disease. To this end, the study of samples from multiple tissues is critical, yet, the complexity of such analysis calls for a dedicated pipeline. We provide an automatic and efficient pipeline for identification, assembly, and analysis of viral genomes that combines the DNA sequence data from multiple organs. TRACESPipe relies on cooperation among 3 modalities: compression-based prediction, sequence alignment, and de novo assembly. The pipeline is ultra-fast and provides, additionally, secure transmission and storage of sensitive data. FINDINGS TRACESPipe performed outstandingly when tested on synthetic and ex vivo datasets, identifying and reconstructing all the viral genomes, including those with high levels of single-nucleotide polymorphisms. It also detected minimal levels of genomic variation between different organs. CONCLUSIONS TRACESPipe's unique ability to simultaneously process and analyze samples from different sources enables the evaluation of within-host variability. This opens up the possibility to investigate viral tissue tropism, evolution, fitness, and disease associations. Moreover, additional features such as DNA damage estimation and mitochondrial DNA reconstruction and analysis, as well as exogenous-source controls, expand the utility of this pipeline to other fields such as forensics and ancient DNA studies. TRACESPipe is released under GPLv3 and is available for free download at https://github.com/viromelab/tracespipe.
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Affiliation(s)
- Diogo Pratas
- Department of Virology, University of Helsinki, Haartmaninkatu 3, Helsinki, 00290, Finland
- Department of Electronics, Telecommunications and Informatics, University of Aveiro, Campus Universitario de Santiago, 3810-193 Aveiro, Portugal
- Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, Campus Universitario de Santiago, 3810-193 Aveiro, Portugal
| | - Mari Toppinen
- Department of Virology, University of Helsinki, Haartmaninkatu 3, Helsinki, 00290, Finland
| | - Lari Pyöriä
- Department of Virology, University of Helsinki, Haartmaninkatu 3, Helsinki, 00290, Finland
| | - Klaus Hedman
- Department of Virology, University of Helsinki, Haartmaninkatu 3, Helsinki, 00290, Finland
- HUSLAB, Helsinki University Hospital, Topeliuksenkatu 32, 00290 Helsinki, Finland
| | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Kytösuontie 11, 00300, Helsinki, Finland
- Forensic Medicine Unit, Finnish Institute of Health and Welfare, PO Box 30 FI-00271 Helsinki, Finland
| | - Maria F Perdomo
- Department of Virology, University of Helsinki, Haartmaninkatu 3, Helsinki, 00290, Finland
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12
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Abril AG, Carrera M, Böhme K, Barros-Velázquez J, Cañas B, Rama JLR, Villa TG, Calo-Mata P. Characterization of Bacteriophage Peptides of Pathogenic Streptococcus by LC-ESI-MS/MS: Bacteriophage Phylogenomics and Their Relationship to Their Host. Front Microbiol 2020; 11:1241. [PMID: 32582130 PMCID: PMC7296060 DOI: 10.3389/fmicb.2020.01241] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/14/2020] [Indexed: 01/21/2023] Open
Abstract
The present work focuses on LC-ESI-MS/MS (liquid chromatography-electrospray ionization-tandem mass spectrometry) analysis of phage-origin tryptic digestion peptides from mastitis-causing Streptococcus spp. isolated from milk. A total of 2,546 non-redundant peptides belonging to 1,890 proteins were identified and analyzed. Among them, 65 phage-origin peptides were determined as specific Streptococcus spp. peptides. These peptides belong to proteins such as phage repressors, phage endopeptidases, structural phage proteins, and uncharacterized phage proteins. Studies involving bacteriophage phylogeny and the relationship between phages encoding the peptides determined and the bacteria they infect were also performed. The results show how specific peptides are present in closely related phages, and a link exists between bacteriophage phylogeny and the Streptococcus spp. they infect. Moreover, the phage peptide M∗ATNLGQAYVQIM∗PSAK is unique and specific for Streptococcus agalactiae. These results revealed that diagnostic peptides, among others, could be useful for the identification and characterization of mastitis-causing Streptococcus spp., particularly peptides that belong to specific functional proteins, such as phage-origin proteins, because of their specificity to bacterial hosts.
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Affiliation(s)
- Ana G. Abril
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Mónica Carrera
- Department of Food Technology, Spanish National Research Council, Marine Research Institute, Vigo, Spain
| | - Karola Böhme
- Agroalimentary Technological Center of Lugo, Lugo, Spain
| | - Jorge Barros-Velázquez
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Lugo, Spain
| | - Benito Cañas
- Department of Analytical Chemistry, Complutense University of Madrid, Madrid, Spain
| | - Jose L. R. Rama
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Tomás G. Villa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Pilar Calo-Mata
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Lugo, Spain
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13
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Genotyping Porcine Circovirus 3 (PCV-3) Nowadays: Does It Make Sense? Viruses 2020; 12:v12030265. [PMID: 32121102 PMCID: PMC7150946 DOI: 10.3390/v12030265] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/20/2020] [Accepted: 02/25/2020] [Indexed: 02/07/2023] Open
Abstract
The discovery of a globally distributed porcine circovirus (Porcine circovirus 3; PCV-3) has led to intense research activity and the production of a large amount of molecular data. Different research groups have proposed several, not always concordant, genotypes for this virus. While such categories could aid an easier interpretation of PCV-3 molecular epidemiology, any classification, to be useful in practical settings, must be univocal and of help in the understanding of underlying biological features and epidemiology. Based on these premises, the possibility of defining PCV-3 genotypes was evaluated on the broadest available dataset of PCV-3 complete genome (n = 357) and open reading frame 2 (ORF2, n = 653) sequences. Genetic distance and phylogenetic clustering were selected as the main objective criteria. Additional factors, including the number of within-cluster sequences, host and geographic clustering, concordance between different genomic regions, and analysis method were also taken in account to generate a classification that could be effectively applied in research and diagnostic settings. A maximum within-genotype genetic distance of 3% at the complete genome and 6% at the ORF2 levels, bootstrap support higher than 90%, and concordance between analysis methods allowed us to clearly define two clades which could be potentially defined as genotypes. Further subdivision was not suggested due to the absence of a meaningful association between PCV-3 and its biological/epidemiological features. Nevertheless, since one of the clades included two strains only, thus far we formally propose the definition of only one PCV-3 genotype (PCV-3a). The established criteria will allow us to automatically recognize other genotypes when more strain sequences are characterized.
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14
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Moore RM, Harrison AO, McAllister SM, Polson SW, Wommack KE. Iroki: automatic customization and visualization of phylogenetic trees. PeerJ 2020; 8:e8584. [PMID: 32149022 PMCID: PMC7049256 DOI: 10.7717/peerj.8584] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/17/2020] [Indexed: 12/26/2022] Open
Abstract
Phylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Iroki’s utility for exploring biological and ecological trends in sequencing data was demonstrated through a variety of microbial ecology applications in which trees with hundreds to thousands of leaf nodes were customized according to extensive collections of metadata. The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal http://virome.dbi.udel.edu. Iroki’s source code is released under the MIT license and is available at https://github.com/mooreryan/iroki.
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Affiliation(s)
- Ryan M Moore
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States of America
| | - Amelia O Harrison
- School of Marine Science and Policy, University of Delaware, Newark, DE, United States of America
| | - Sean M McAllister
- School of Marine Science and Policy, University of Delaware, Newark, DE, United States of America
| | - Shawn W Polson
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States of America
| | - K Eric Wommack
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States of America
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15
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Virus Metagenomics in Farm Animals: A Systematic Review. Viruses 2020; 12:v12010107. [PMID: 31963174 PMCID: PMC7019290 DOI: 10.3390/v12010107] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/12/2020] [Accepted: 01/14/2020] [Indexed: 02/07/2023] Open
Abstract
A majority of emerging infectious diseases are of zoonotic origin. Metagenomic Next-Generation Sequencing (mNGS) has been employed to identify uncommon and novel infectious etiologies and characterize virus diversity in human, animal, and environmental samples. Here, we systematically reviewed studies that performed viral mNGS in common livestock (cattle, small ruminants, poultry, and pigs). We identified 2481 records and 120 records were ultimately included after a first and second screening. Pigs were the most frequently studied livestock and the virus diversity found in samples from poultry was the highest. Known animal viruses, zoonotic viruses, and novel viruses were reported in available literature, demonstrating the capacity of mNGS to identify both known and novel viruses. However, the coverage of metagenomic studies was patchy, with few data on the virome of small ruminants and respiratory virome of studied livestock. Essential metadata such as age of livestock and farm types were rarely mentioned in available literature, and only 10.8% of the datasets were publicly available. Developing a deeper understanding of livestock virome is crucial for detection of potential zoonotic and animal pathogens and One Health preparedness. Metagenomic studies can provide this background but only when combined with essential metadata and following the “FAIR” (Findable, Accessible, Interoperable, and Reusable) data principles.
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16
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Phytovirome Analysis of Wild Plant Populations: Comparison of Double-Stranded RNA and Virion-Associated Nucleic Acid Metagenomic Approaches. J Virol 2019; 94:JVI.01462-19. [PMID: 31597769 DOI: 10.1128/jvi.01462-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/01/2019] [Indexed: 12/29/2022] Open
Abstract
Metagenomic studies have indicated that the diversity of plant viruses was until recently far underestimated. As important components of ecosystems, there is a need to explore the diversity and richness of the viruses associated with plant populations and to understand the drivers shaping their diversity in space and time. Two viral sequence enrichment approaches, double-stranded RNA (dsRNA) and virion-associated nucleic acids (VANA), have been used and compared here for the description of the virome of complex plant pools representative of the most prevalent plant species in unmanaged and cultivated ecosystems. A novel bioinformatics strategy was used to assess viral richness not only at the family level but also by determining operational taxonomic units (OTU) following the clustering of conserved viral domains. A large viral diversity dominated by novel dsRNA viruses was detected in all sites, while a large between-site variability limited the ability to draw a clear conclusion on the impact of cultivation. A trend for a higher diversity of dsRNA viruses was nevertheless detected in unmanaged sites (118 versus 77 unique OTUs). The dsRNA-based approach consistently revealed a broader and more comprehensive diversity for RNA viruses than the VANA approach, whatever the assessment criterion. In addition, dissimilarity analyses indicated both approaches to be largely reproducible but not necessarily convergent. These findings illustrate features of phytoviromes in various ecosystems and a novel strategy for precise virus richness estimation. These results allow us to reason methodological choices in phytovirome studies and likely in other virome studies where RNA viruses are the focal taxa.IMPORTANCE There are today significant knowledge gaps on phytovirus populations and on the drivers impacting them but also on the comparative performance-methodological approaches for their study. We used and compared two viral sequence enrichment approaches, double-stranded RNAs (dsRNA) and virion-associated nucleic acids (VANA), for phytovirome description in complex pools representative of the most prevalent plant species in unmanaged and cultivated ecosystems. Viral richness was assessed by determining operational taxonomic units (OTU) following the clustering of conserved viral domains. There is some limited evidence of an impact of cultivation on viral populations. These results provide data allowing us to reason the methodological choices in virome studies. For researchers primarily interested in RNA viruses, the dsRNA approach is recommended because it consistently provided a more comprehensive description of the analyzed phytoviromes, but it understandably underrepresented DNA viruses and bacteriophages.
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17
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Käfer S, Paraskevopoulou S, Zirkel F, Wieseke N, Donath A, Petersen M, Jones TC, Liu S, Zhou X, Middendorf M, Junglen S, Misof B, Drosten C. Re-assessing the diversity of negative strand RNA viruses in insects. PLoS Pathog 2019; 15:e1008224. [PMID: 31830128 PMCID: PMC6932829 DOI: 10.1371/journal.ppat.1008224] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 12/26/2019] [Accepted: 11/19/2019] [Indexed: 12/21/2022] Open
Abstract
The spectrum of viruses in insects is important for subjects as diverse as public health, veterinary medicine, food production, and biodiversity conservation. The traditional interest in vector-borne diseases of humans and livestock has drawn the attention of virus studies to hematophagous insect species. However, these represent only a tiny fraction of the broad diversity of Hexapoda, the most speciose group of animals. Here, we systematically probed the diversity of negative strand RNA viruses in the largest and most representative collection of insect transcriptomes from samples representing all 34 extant orders of Hexapoda and 3 orders of Entognatha, as well as outgroups, altogether representing 1243 species. Based on profile hidden Markov models we detected 488 viral RNA-directed RNA polymerase (RdRp) sequences with similarity to negative strand RNA viruses. These were identified in members of 324 arthropod species. Selection for length, quality, and uniqueness left 234 sequences for analyses, showing similarity to genomes of viruses classified in Bunyavirales (n = 86), Articulavirales (n = 54), and several orders within Haploviricotina (n = 94). Coding-complete genomes or nearly-complete subgenomic assemblies were obtained in 61 cases. Based on phylogenetic topology and the availability of coding-complete genomes we estimate that at least 20 novel viral genera in seven families need to be defined, only two of them monospecific. Seven additional viral clades emerge when adding sequences from the present study to formerly monospecific lineages, potentially requiring up to seven additional genera. One long sequence may indicate a novel family. For segmented viruses, cophylogenies between genome segments were generally improved by the inclusion of viruses from the present study, suggesting that in silico misassembly of segmented genomes is rare or absent. Contrary to previous assessments, significant virus-host codivergence was identified in major phylogenetic lineages based on two different approaches of codivergence analysis in a hypotheses testing framework. In spite of these additions to the known spectrum of viruses in insects, we caution that basing taxonomic decisions on genome information alone is challenging due to technical uncertainties, such as the inability to prove integrity of complete genome assemblies of segmented viruses.
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Affiliation(s)
- Simon Käfer
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University, Humboldt-University and Berlin Institute of Health, Berlin, Germany
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Sofia Paraskevopoulou
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University, Humboldt-University and Berlin Institute of Health, Berlin, Germany
| | - Florian Zirkel
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Nicolas Wieseke
- Swarm Intelligence and Complex Systems Group, Department of Computer Science, Leipzig University, Leipzig, Germany
| | - Alexander Donath
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Malte Petersen
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Terry C. Jones
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University, Humboldt-University and Berlin Institute of Health, Berlin, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Shanlin Liu
- BGI-Shenzhen, China Beishan Industrial Zone, Shenzhen, Guangdong Province, China
| | - Xin Zhou
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, China
| | - Martin Middendorf
- Swarm Intelligence and Complex Systems Group, Department of Computer Science, Leipzig University, Leipzig, Germany
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University, Humboldt-University and Berlin Institute of Health, Berlin, Germany
- German Center for Infection Research (DZIF), associated partner site Charité, Berlin, Germany
| | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University, Humboldt-University and Berlin Institute of Health, Berlin, Germany
- German Center for Infection Research (DZIF), associated partner site Charité, Berlin, Germany
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18
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Serdari D, Kostaki EG, Paraskevis D, Stamatakis A, Kapli P. Automated, phylogeny-based genotype delimitation of the Hepatitis Viruses HBV and HCV. PeerJ 2019; 7:e7754. [PMID: 31667012 PMCID: PMC6816385 DOI: 10.7717/peerj.7754] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/26/2019] [Indexed: 12/15/2022] Open
Abstract
Background The classification of hepatitis viruses still predominantly relies on ad hoc criteria, i.e., phenotypic traits and arbitrary genetic distance thresholds. Given the subjectivity of such practices coupled with the constant sequencing of samples and discovery of new strains, this manual approach to virus classification becomes cumbersome and impossible to generalize. Methods Using two well-studied hepatitis virus datasets, HBV and HCV, we assess if computational methods for molecular species delimitation that are typically applied to barcoding biodiversity studies can also be successfully deployed for hepatitis virus classification. For comparison, we also used ABGD, a tool that in contrast to other distance methods attempts to automatically identify the barcoding gap using pairwise genetic distances for a set of aligned input sequences. Results—Discussion We found that the mPTP species delimitation tool identified even without adapting its default parameters taxonomic clusters that either correspond to the currently acknowledged genotypes or to known subdivision of genotypes (subtypes or subgenotypes). In the cases where the delimited cluster corresponded to subtype or subgenotype, there were previous concerns that their status may be underestimated. The clusters obtained from the ABGD analysis differed depending on the parameters used. However, under certain values the results were very similar to the taxonomy and mPTP which indicates the usefulness of distance based methods in virus taxonomy under appropriate parameter settings. The overlap of predicted clusters with taxonomically acknowledged genotypes implies that virus classification can be successfully automated.
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Affiliation(s)
- Dora Serdari
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Evangelia-Georgia Kostaki
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Alexandros Stamatakis
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.,Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Paschalia Kapli
- Centre for Life's Origins and Evolution, Department of Genetics Evolution and Environment, University College London, University of London, London, United Kingdom
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19
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Dávila-Ramos S, Castelán-Sánchez HG, Martínez-Ávila L, Sánchez-Carbente MDR, Peralta R, Hernández-Mendoza A, Dobson ADW, Gonzalez RA, Pastor N, Batista-García RA. A Review on Viral Metagenomics in Extreme Environments. Front Microbiol 2019; 10:2403. [PMID: 31749771 PMCID: PMC6842933 DOI: 10.3389/fmicb.2019.02403] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 10/04/2019] [Indexed: 12/22/2022] Open
Abstract
Viruses are the most abundant biological entities in the biosphere, and have the ability to infect Bacteria, Archaea, and Eukaryotes. The virome is estimated to be at least ten times more abundant than the microbiome with 107 viruses per milliliter and 109 viral particles per gram in marine waters and sediments or soils, respectively. Viruses represent a largely unexplored genetic diversity, having an important role in the genomic plasticity of their hosts. Moreover, they also play a significant role in the dynamics of microbial populations. In recent years, metagenomic approaches have gained increasing popularity in the study of environmental viromes, offering the possibility of extending our knowledge related to both virus diversity and their functional characterization. Extreme environments represent an interesting source of both microbiota and their virome due to their particular physicochemical conditions, such as very high or very low temperatures and >1 atm hydrostatic pressures, among others. Despite the fact that some progress has been made in our understanding of the ecology of the microbiota in these habitats, few metagenomic studies have described the viromes present in extreme ecosystems. Thus, limited advances have been made in our understanding of the virus community structure in extremophilic ecosystems, as well as in their biotechnological potential. In this review, we critically analyze recent progress in metagenomic based approaches to explore the viromes in extreme environments and we discuss the potential for new discoveries, as well as methodological challenges and perspectives.
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Affiliation(s)
- Sonia Dávila-Ramos
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Hugo G. Castelán-Sánchez
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Liliana Martínez-Ávila
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | | | - Raúl Peralta
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Armando Hernández-Mendoza
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Alan D. W. Dobson
- School of Microbiology, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
| | - Ramón A. Gonzalez
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Nina Pastor
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
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20
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Laenen L, Vergote V, Calisher CH, Klempa B, Klingström J, Kuhn JH, Maes P. Hantaviridae: Current Classification and Future Perspectives. Viruses 2019; 11:v11090788. [PMID: 31461937 PMCID: PMC6784073 DOI: 10.3390/v11090788] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 08/23/2019] [Indexed: 01/19/2023] Open
Abstract
In recent years, negative-sense RNA virus classification and taxon nomenclature have undergone considerable transformation. In 2016, the new order Bunyavirales was established, elevating the previous genus Hantavirus to family rank, thereby creating Hantaviridae. Here we summarize affirmed taxonomic modifications of this family from 2016 to 2019. Changes involve the admission of >30 new hantavirid species and the establishment of subfamilies and novel genera based on DivErsity pArtitioning by hieRarchical Clustering (DEmARC) analysis of genomic sequencing data. We outline an objective framework that can be used in future classification schemes when more hantavirids sequences will be available. Finally, we summarize current taxonomic proposals and problems in hantavirid taxonomy that will have to be addressed shortly.
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Affiliation(s)
- Lies Laenen
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Zoonotic Infectious Diseases Unit, 3000 Leuven, Belgium
- Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Valentijn Vergote
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Zoonotic Infectious Diseases Unit, 3000 Leuven, Belgium
| | | | - Boris Klempa
- Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
| | - Jonas Klingström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, SE-141 86 Stockholm, Sweden
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Frederick, MD 21702, USA
| | - Piet Maes
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Zoonotic Infectious Diseases Unit, 3000 Leuven, Belgium.
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21
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Breitwieser FP, Lu J, Salzberg SL. A review of methods and databases for metagenomic classification and assembly. Brief Bioinform 2019; 20:1125-1136. [PMID: 29028872 PMCID: PMC6781581 DOI: 10.1093/bib/bbx120] [Citation(s) in RCA: 261] [Impact Index Per Article: 52.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 08/22/2017] [Indexed: 12/13/2022] Open
Abstract
Microbiome research has grown rapidly over the past decade, with a proliferation of new methods that seek to make sense of large, complex data sets. Here, we survey two of the primary types of methods for analyzing microbiome data: read classification and metagenomic assembly, and we review some of the challenges facing these methods. All of the methods rely on public genome databases, and we also discuss the content of these databases and how their quality has a direct impact on our ability to interpret a microbiome sample.
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Affiliation(s)
| | | | - Steven L Salzberg
- Corresponding author: Steven L. Salzberg, Center for Computational Biology, Johns Hopkins University, 1900 E. Monument St., Baltimore, MD, 21205, USA. E-mail:
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22
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Vasilakis N, Tesh RB, Popov VL, Widen SG, Wood TG, Forrester NL, Gonzalez JP, Saluzzo JF, Alkhovsky S, Lam SK, Mackenzie JS, Walker PJ. Exploiting the Legacy of the Arbovirus Hunters. Viruses 2019; 11:E471. [PMID: 31126128 PMCID: PMC6563318 DOI: 10.3390/v11050471] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/15/2019] [Accepted: 05/21/2019] [Indexed: 12/13/2022] Open
Abstract
In recent years, it has become evident that a generational gap has developed in the community of arbovirus research. This apparent gap is due to the dis-investment of training for the next generation of arbovirologists, which threatens to derail the rich history of virus discovery, field epidemiology, and understanding of the richness of diversity that surrounds us. On the other hand, new technologies have resulted in an explosion of virus discovery that is constantly redefining the virosphere and the evolutionary relationships between viruses. This paradox presents new challenges that may have immediate and disastrous consequences for public health when yet to be discovered arboviruses emerge. In this review we endeavor to bridge this gap by providing a historical context for the work being conducted today and provide continuity between the generations. To this end, we will provide a narrative of the thrill of scientific discovery and excitement and the challenges lying ahead.
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Affiliation(s)
- Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
| | - Robert B Tesh
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
| | - Vsevolod L Popov
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
| | - Steve G Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Blvd, Galveston TX 77555, USA.
| | - Thomas G Wood
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Blvd, Galveston TX 77555, USA.
| | - Naomi L Forrester
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
| | - Jean Paul Gonzalez
- Center of Excellence for Emerging & Zoonotic Animal Disease, Kansas State University, Manhattan, KS 66502, USA.
| | | | - Sergey Alkhovsky
- Ivanovsky Institute of Virology, N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, 123098, 18 Gamaleya str., Moscow, Russia.
| | - Sai Kit Lam
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur 50603, Malaysia.
| | - John S Mackenzie
- Faculty of Medical Sciences, Curtin University, Perth, Western Australia 6102, Australia.
| | - Peter J Walker
- School of Biological Sciences, The University of Queensland, St Lucia, QLD 4072, Australia.
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23
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The First Complete Genome Sequence of a Novel Tetrastichus brontispae RNA Virus-1 (TbRV-1). Viruses 2019; 11:v11030257. [PMID: 30871248 PMCID: PMC6466307 DOI: 10.3390/v11030257] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 03/09/2019] [Accepted: 03/10/2019] [Indexed: 11/17/2022] Open
Abstract
The complete sequence of a novel RNA virus isolated from Tetrastichus brontispae (TbRV-1) was determined to be 12,239 nucleotides in length with five non-overlapping, linearly arranged coding sequences (CDS), potentially encoding nucleoproteins, hypothetical proteins, matrix proteins, glycoproteins, and RNA-dependent RNA polymerases. Sequence analysis indicated that the RNA-dependent RNA polymerase of TbRV-1 shares a 65% nucleotide and 67% amino acid sequence identity with Hubei dimarhabdovirus 2, suggesting that TbRV-1 is a member of the dimarhabdovirus supergroup. This corresponded to the result of the phylogenetic analysis. The affiliation of TbRV-1 with members of the family Rhabdoviridae was further validated by similar transcription termination motifs (GGAACUUUUUUU) to the Drosophila sigmavirus. The prevalence of TbRV-1 in all tissues suggested that the virus was constitutive of, and not specific to, any wasp tissue. To our knowledge, this is the first report on the complete genome sequence of a dimarhabdovirus in parasitoids.
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Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism. mBio 2019; 10:mBio.02497-18. [PMID: 30837339 PMCID: PMC6401483 DOI: 10.1128/mbio.02497-18] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Genomics and evolution of giant viruses are two of the most vigorously developing areas of virus research. Lately, metagenomics has become the main source of new virus genomes. Here we describe a metagenomic analysis of the genomes of large and giant viruses from deep sea sediments. The assembled new virus genomes substantially expand the known diversity of the nucleocytoplasmic large DNA viruses of eukaryotes. The results support the concept of independent evolution of giant viruses from smaller ancestors in different virus branches. The nucleocytoplasmic large DNA viruses (NCLDV) of eukaryotes (proposed order, “Megavirales”) include the families Poxviridae, Asfarviridae, Iridoviridae, Ascoviridae, Phycodnaviridae, Marseilleviridae, and Mimiviridae, as well as still unclassified pithoviruses, pandoraviruses, molliviruses, and faustoviruses. Several of these virus groups include giant viruses, with genome and particle sizes exceeding those of many bacterial and archaeal cells. We explored the diversity of the NCLDV in deep sea sediments from the Loki’s Castle hydrothermal vent area. Using metagenomics, we reconstructed 23 high-quality genomic bins of novel NCLDV, 15 of which are related to pithoviruses, 5 to marseilleviruses, 1 to iridoviruses, and 2 to klosneuviruses. Some of the identified pithovirus-like and marseillevirus-like genomes belong to deep branches in the phylogenetic tree of core NCLDV genes, substantially expanding the diversity and phylogenetic depth of the respective groups. The discovered viruses, including putative giant members of the family Marseilleviridae, have a broad range of apparent genome sizes, in agreement with the multiple, independent origins of gigantism in different branches of the NCLDV. Phylogenomic analysis reaffirms the monophyly of the pithovirus-iridovirus-marseillevirus branch of the NCLDV. Similarly to other giant viruses, the pithovirus-like viruses from Loki’s Castle encode translation systems components. Phylogenetic analysis of these genes indicates a greater bacterial contribution than had been detected previously. Genome comparison suggests extensive gene exchange between members of the pithovirus-like viruses and Mimiviridae. Further exploration of the genomic diversity of Megavirales in additional sediment samples is expected to yield new insights into the evolution of giant viruses and the composition of the ocean megavirome.
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Watson AK, Lannes R, Pathmanathan JS, Méheust R, Karkar S, Colson P, Corel E, Lopez P, Bapteste E. The Methodology Behind Network Thinking: Graphs to Analyze Microbial Complexity and Evolution. Methods Mol Biol 2019; 1910:271-308. [PMID: 31278668 DOI: 10.1007/978-1-4939-9074-0_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In the post genomic era, large and complex molecular datasets from genome and metagenome sequencing projects expand the limits of what is possible for bioinformatic analyses. Network-based methods are increasingly used to complement phylogenetic analysis in studies in molecular evolution, including comparative genomics, classification, and ecological studies. Using network methods, the vertical and horizontal relationships between all genes or genomes, whether they are from cellular chromosomes or mobile genetic elements, can be explored in a single expandable graph. In recent years, development of new methods for the construction and analysis of networks has helped to broaden the availability of these approaches from programmers to a diversity of users. This chapter introduces the different kinds of networks based on sequence similarity that are already available to tackle a wide range of biological questions, including sequence similarity networks, gene-sharing networks and bipartite graphs, and a guide for their construction and analyses.
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Affiliation(s)
- Andrew K Watson
- Sorbonne Universités, Institut de Biologie Paris-Seine, UPMC Université Paris 6, Paris, France
| | - Romain Lannes
- Sorbonne Universités, Institut de Biologie Paris-Seine, UPMC Université Paris 6, Paris, France
| | - Jananan S Pathmanathan
- Sorbonne Universités, Institut de Biologie Paris-Seine, UPMC Université Paris 6, Paris, France
| | - Raphaël Méheust
- Sorbonne Universités, Institut de Biologie Paris-Seine, UPMC Université Paris 6, Paris, France
| | - Slim Karkar
- Sorbonne Universités, Institut de Biologie Paris-Seine, UPMC Université Paris 6, Paris, France
- Department of Ecology, Evolution, and Natural Resources, School of Environmental and Biological Sciences, Rutgers, The State University of NJ, New Brunswick, NJ, USA
| | - Philippe Colson
- Fondation Institut Hospitalo-Universitaire Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Tione, Assistance Publique-Hôpitaux de Marseille, Marseille, France
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63, CNRS 7278, IRD 198, INSERM U1095, Aix-Marseille University, Marseille, France
| | - Eduardo Corel
- Sorbonne Universités, Institut de Biologie Paris-Seine, UPMC Université Paris 6, Paris, France
| | - Philippe Lopez
- Sorbonne Universités, Institut de Biologie Paris-Seine, UPMC Université Paris 6, Paris, France
| | - Eric Bapteste
- Sorbonne Universités, Institut de Biologie Paris-Seine, UPMC Université Paris 6, Paris, France.
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Warrilow D, Huang B, Newton ND, Harrison JJ, Johnson KN, Chow WK, Hall RA, Hobson-Peters J. The taxonomy of an Australian nodavirus isolated from mosquitoes. PLoS One 2018; 13:e0210029. [PMID: 30596795 PMCID: PMC6312370 DOI: 10.1371/journal.pone.0210029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/14/2018] [Indexed: 11/18/2022] Open
Abstract
We describe a virus isolated from Culex annulirostris mosquitoes in Australia. Phylogenetic analysis of its RNA-dependent RNA polymerase sequence and that of other related viruses revealed 6 clades, two of which corresponded wholly or partly with existing genera in the family Nodaviridae. There was greater genetic diversity within the family than previously recognized prompting us to suggest that additional genera should be considered within the family.
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Affiliation(s)
- David Warrilow
- Public Health Virology Laboratory, Queensland Health Forensic and Scientific Services, Archerfield, Queensland
- * E-mail: (DW); (JHP)
| | - Bixing Huang
- Public Health Virology Laboratory, Queensland Health Forensic and Scientific Services, Archerfield, Queensland
| | - Natalee D. Newton
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Jessica J. Harrison
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Karyn N. Johnson
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Weng Kong Chow
- Australian Defence Force Malaria and Infectious Disease Institute, Queensland, Australia
| | - Roy A. Hall
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Jody Hobson-Peters
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
- * E-mail: (DW); (JHP)
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Kang S, Kim YC. The Genome-Based Virus Taxonomy with ICTV Database Extension. Genomics Inform 2018; 16:e22. [PMID: 30602083 PMCID: PMC6440660 DOI: 10.5808/gi.2018.16.4.e22] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 12/23/2018] [Indexed: 11/29/2022] Open
Abstract
In 1966, the International Classification of Viruses (ICNV) was established to standardize the naming of viruses. In 1975, the organization was renamed “International Committee on Taxonomy of Viruses (ICTV),” by which it is still known today. The primary virus classification provided by ICTV in 1971 was for viruses infecting vertebrates, which includes 19 genera, 2 families, and 24 unclassified groups. Presently, the 10th virus taxonomy has been published. However, the early classification of viruses was based on clinical results “in vivo” and “in vitro,” as well as on the shape of the Phenotype virus. Due to the development of next-generation sequencing and the accompanying bioinformatics analysis pipelines, a reconstruction of the classification system has been proposed. At a meeting held in Boston, USA between June 9–11, 2016, there was even an in-depth discussion regarding the classification of viruses using metagenomic data. One suggested activity that arose from the meeting was that viral taxonomy should be reconstructed, based on genotype and bioinformatics analysis “in silico.” This article describes our efforts to achieve this goal by construction of a web-based system and the extension of an associated database, based on ICTV taxonomy. This virus taxonomy web system was designed specifically to extend the virus taxonomy up to strain and isolation, which was then connected with the NCBI database to facilitate searches for specific viral genes; there are also links to journals provided by the EMBL RESTful API that improves accessibility for academic groups.
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Affiliation(s)
- Shinduck Kang
- Department of Microbiology, Chungbuk National University, Cheongju 28644, Korea
| | - Young-Chang Kim
- Department of Microbiology, Chungbuk National University, Cheongju 28644, Korea
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Modha S, Thanki AS, Cotmore SF, Davison AJ, Hughes J. ViCTree: an automated framework for taxonomic classification from protein sequences. Bioinformatics 2018; 34:2195-2200. [PMID: 29474519 PMCID: PMC6022645 DOI: 10.1093/bioinformatics/bty099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 01/08/2018] [Accepted: 02/20/2018] [Indexed: 11/14/2022] Open
Abstract
Motivation The increasing rate of submission of genetic sequences into public databases is providing a growing resource for classifying the organisms that these sequences represent. To aid viral classification, we have developed ViCTree, which automatically integrates the relevant sets of sequences in NCBI GenBank and transforms them into an interactive maximum likelihood phylogenetic tree that can be updated automatically. ViCTree incorporates ViCTreeView, which is a JavaScript-based visualization tool that enables the tree to be explored interactively in the context of pairwise distance data. Results To demonstrate utility, ViCTree was applied to subfamily Densovirinae of family Parvoviridae. This led to the identification of six new species of insect virus. Availability and implementation ViCTree is open-source and can be run on any Linux- or Unix-based computer or cluster. A tutorial, the documentation and the source code are available under a GPL3 license, and can be accessed at http://bioinformatics.cvr.ac.uk/victree_web/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sejal Modha
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Anil S Thanki
- Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
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Abstract
Due to their dependence on cellular organisms for metabolism and replication, viruses are typically named and assigned to species according to their genome structure and the original host that they infect. But because viruses often infect multiple hosts and the numbers of distinct lineages within a host can be vast, their delineation into species is often dictated by arbitrary sequence thresholds, which are highly inconsistent across lineages. Here we apply an approach to determine the boundaries of viral species based on the detection of gene flow within populations, thereby defining viral species according to the biological species concept (BSC). Despite the potential for gene transfer between highly divergent genomes, viruses, like the cellular organisms they infect, assort into reproductively isolated groups and can be organized into biological species. This approach revealed that BSC-defined viral species are often congruent with the taxonomic partitioning based on shared gene contents and host tropism, and that bacteriophages can similarly be classified in biological species. These results open the possibility to use a single, universal definition of species that is applicable across cellular and acellular lifeforms.
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Mahmoudabadi G, Phillips R. A comprehensive and quantitative exploration of thousands of viral genomes. eLife 2018; 7:31955. [PMID: 29624169 PMCID: PMC5908442 DOI: 10.7554/elife.31955] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 03/30/2018] [Indexed: 01/27/2023] Open
Abstract
The complete assembly of viral genomes from metagenomic datasets (short genomic sequences gathered from environmental samples) has proven to be challenging, so there are significant blind spots when we view viral genomes through the lens of metagenomics. One approach to overcoming this problem is to leverage the thousands of complete viral genomes that are publicly available. Here we describe our efforts to assemble a comprehensive resource that provides a quantitative snapshot of viral genomic trends – such as gene density, noncoding percentage, and abundances of functional gene categories – across thousands of viral genomes. We have also developed a coarse-grained method for visualizing viral genome organization for hundreds of genomes at once, and have explored the extent of the overlap between bacterial and bacteriophage gene pools. Existing viral classification systems were developed prior to the sequencing era, so we present our analysis in a way that allows us to assess the utility of the different classification systems for capturing genomic trends.
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Affiliation(s)
- Gita Mahmoudabadi
- Department of Bioengineering, California Institute of Technology, Pasadena, United States
| | - Rob Phillips
- Department of Bioengineering, California Institute of Technology, Pasadena, United States.,Department of Applied Physics, California Institute of Technology, Pasadena, United States
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Yutin N, Bäckström D, Ettema TJG, Krupovic M, Koonin EV. Vast diversity of prokaryotic virus genomes encoding double jelly-roll major capsid proteins uncovered by genomic and metagenomic sequence analysis. Virol J 2018; 15:67. [PMID: 29636073 PMCID: PMC5894146 DOI: 10.1186/s12985-018-0974-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/28/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Analysis of metagenomic sequences has become the principal approach for the study of the diversity of viruses. Many recent, extensive metagenomic studies on several classes of viruses have dramatically expanded the visible part of the virosphere, showing that previously undetected viruses, or those that have been considered rare, actually are important components of the global virome. RESULTS We investigated the provenance of viruses related to tail-less bacteriophages of the family Tectiviridae by searching genomic and metagenomics sequence databases for distant homologs of the tectivirus-like Double Jelly-Roll major capsid proteins (DJR MCP). These searches resulted in the identification of numerous genomes of virus-like elements that are similar in size to tectiviruses (10-15 kilobases) and have diverse gene compositions. By comparison of the gene repertoires, the DJR MCP-encoding genomes were classified into 6 distinct groups that can be predicted to differ in reproduction strategies and host ranges. Only the DJR MCP gene that is present by design is shared by all these genomes, and most also encode a predicted DNA-packaging ATPase; the rest of the genes are present only in subgroups of this unexpectedly diverse collection of DJR MCP-encoding genomes. Only a minority encode a DNA polymerase which is a hallmark of the family Tectiviridae and the putative family "Autolykiviridae". Notably, one of the identified putative DJR MCP viruses encodes a homolog of Cas1 endonuclease, the integrase involved in CRISPR-Cas adaptation and integration of transposon-like elements called casposons. This is the first detected occurrence of Cas1 in a virus. Many of the identified elements are individual contigs flanked by inverted or direct repeats and appear to represent complete, extrachromosomal viral genomes, whereas others are flanked by bacterial genes and thus can be considered as proviruses. These contigs come from metagenomes of widely different environments, some dominated by archaea and others by bacteria, suggesting that collectively, the DJR MCP-encoding elements have a broad host range among prokaryotes. CONCLUSIONS The findings reported here greatly expand the known host range of (putative) viruses of bacteria and archaea that encode a DJR MCP. They also demonstrate the extreme diversity of genome architectures in these viruses that encode no universal proteins other than the capsid protein that was used as the marker for their identification. From a supposedly minor group of bacterial and archaeal viruses, these viruses are emerging as a substantial component of the prokaryotic virome.
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Affiliation(s)
- Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD, 20894, USA
| | - Disa Bäckström
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Box 596, -75123, Uppsala, SE, Sweden
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Box 596, -75123, Uppsala, SE, Sweden
| | - Mart Krupovic
- Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Department of Microbiology, Institut Pasteur, Paris, France
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD, 20894, USA.
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Lefkowitz EJ, Dempsey DM, Hendrickson RC, Orton RJ, Siddell SG, Smith DB. Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV). Nucleic Acids Res 2018; 46:D708-D717. [PMID: 29040670 PMCID: PMC5753373 DOI: 10.1093/nar/gkx932] [Citation(s) in RCA: 617] [Impact Index Per Article: 102.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 09/13/2017] [Accepted: 10/02/2017] [Indexed: 11/13/2022] Open
Abstract
The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa; maintaining a database detailing the currently approved taxonomy; and providing the database, supporting proposals, and other virus-related information from an open-access, public web site. The ICTV web site (http://ictv.global) provides access to the current taxonomy database in online and downloadable formats, and maintains a complete history of virus taxa back to the first release in 1971. The ICTV has also published the ICTV Report on Virus Taxonomy starting in 1971. This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics. The ninth ICTV report, published in 2012, is available as an open-access online publication from the ICTV web site. The current, 10th report (http://ictv.global/report/), is being published online, and is replacing the previous hard-copy edition with a completely open access, continuously updated publication. No other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy.
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Affiliation(s)
- Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Donald M Dempsey
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | - Richard J Orton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Stuart G Siddell
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Donald B Smith
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Kinoti WM, Constable FE, Nancarrow N, Plummer KM, Rodoni B. Analysis of intra-host genetic diversity of Prunus necrotic ringspot virus (PNRSV) using amplicon next generation sequencing. PLoS One 2017; 12:e0179284. [PMID: 28632759 PMCID: PMC5478126 DOI: 10.1371/journal.pone.0179284] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 05/08/2017] [Indexed: 12/28/2022] Open
Abstract
PCR amplicon next generation sequencing (NGS) analysis offers a broadly applicable and targeted approach to detect populations of both high- or low-frequency virus variants in one or more plant samples. In this study, amplicon NGS was used to explore the diversity of the tripartite genome virus, Prunus necrotic ringspot virus (PNRSV) from 53 PNRSV-infected trees using amplicons from conserved gene regions of each of PNRSV RNA1, RNA2 and RNA3. Sequencing of the amplicons from 53 PNRSV-infected trees revealed differing levels of polymorphism across the three different components of the PNRSV genome with a total number of 5040, 2083 and 5486 sequence variants observed for RNA1, RNA2 and RNA3 respectively. The RNA2 had the lowest diversity of sequences compared to RNA1 and RNA3, reflecting the lack of flexibility tolerated by the replicase gene that is encoded by this RNA component. Distinct PNRSV phylo-groups, consisting of closely related clusters of sequence variants, were observed in each of PNRSV RNA1, RNA2 and RNA3. Most plant samples had a single phylo-group for each RNA component. Haplotype network analysis showed that smaller clusters of PNRSV sequence variants were genetically connected to the largest sequence variant cluster within a phylo-group of each RNA component. Some plant samples had sequence variants occurring in multiple PNRSV phylo-groups in at least one of each RNA and these phylo-groups formed distinct clades that represent PNRSV genetic strains. Variants within the same phylo-group of each Prunus plant sample had ≥97% similarity and phylo-groups within a Prunus plant sample and between samples had less ≤97% similarity. Based on the analysis of diversity, a definition of a PNRSV genetic strain was proposed. The proposed definition was applied to determine the number of PNRSV genetic strains in each of the plant samples and the complexity in defining genetic strains in multipartite genome viruses was explored.
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Affiliation(s)
- Wycliff M. Kinoti
- Agriculture Victoria, AgriBio, La Trobe University, Melbourne, VIC, Australia
- School of Applied Systems Biology, AgriBio, La Trobe University, Melbourne, VIC, Australia
| | - Fiona E. Constable
- Agriculture Victoria, AgriBio, La Trobe University, Melbourne, VIC, Australia
| | - Narelle Nancarrow
- Agriculture Victoria, AgriBio, La Trobe University, Melbourne, VIC, Australia
| | - Kim M. Plummer
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Melbourne, VIC, Australia
| | - Brendan Rodoni
- Agriculture Victoria, AgriBio, La Trobe University, Melbourne, VIC, Australia
- School of Applied Systems Biology, AgriBio, La Trobe University, Melbourne, VIC, Australia
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Bolduc B, Jang HB, Doulcier G, You ZQ, Roux S, Sullivan MB. vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria. PeerJ 2017; 5:e3243. [PMID: 28480138 PMCID: PMC5419219 DOI: 10.7717/peerj.3243] [Citation(s) in RCA: 161] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 03/28/2017] [Indexed: 12/15/2022] Open
Abstract
Taxonomic classification of archaeal and bacterial viruses is challenging, yet also fundamental for developing a predictive understanding of microbial ecosystems. Recent identification of hundreds of thousands of new viral genomes and genome fragments, whose hosts remain unknown, requires a paradigm shift away from traditional classification approaches and towards the use of genomes for taxonomy. Here we revisited the use of genomes and their protein content as a means for developing a viral taxonomy for bacterial and archaeal viruses. A network-based analytic was evaluated and benchmarked against authority-accepted taxonomic assignments and found to be largely concordant. Exceptions were manually examined and found to represent areas of viral genome 'sequence space' that are under-sampled or prone to excessive genetic exchange. While both cases are poorly resolved by genome-based taxonomic approaches, the former will improve as viral sequence space is better sampled and the latter are uncommon. Finally, given the largely robust taxonomic capabilities of this approach, we sought to enable researchers to easily and systematically classify new viruses. Thus, we established a tool, vConTACT, as an app at iVirus, where it operates as a fast, highly scalable, user-friendly app within the free and powerful CyVerse cyberinfrastructure.
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Affiliation(s)
- Benjamin Bolduc
- Department of Microbiology, Ohio State University, Columbus, OH, United States
| | - Ho Bin Jang
- Department of Microbiology, Ohio State University, Columbus, OH, United States
| | - Guilhem Doulcier
- Institut de Biologie de l’ENS (IBENS), École normale supérieure, PSL Research University, Paris, France
- ESPCI, PSL Research University, Paris, France
| | - Zhi-Qiang You
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, United States
| | - Simon Roux
- Department of Microbiology, Ohio State University, Columbus, OH, United States
| | - Matthew B. Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH, United States
- Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, United States
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van Aerle R, Santos EM. Advances in the application of high-throughput sequencing in invertebrate virology. J Invertebr Pathol 2017; 147:145-156. [PMID: 28249815 DOI: 10.1016/j.jip.2017.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 02/22/2017] [Accepted: 02/24/2017] [Indexed: 10/20/2022]
Abstract
Over the last decade, advances in high-throughput sequencing technologies have revolutionised biological research, making it possible for DNA/RNA sequencing of any organism of interest to be undertaken. Sequencing approaches are now routinely used in the detection and characterisation of (novel) viruses, investigation of host-pathogen interactions, and effective development of disease treatment strategies. For the sequencing and identification of viruses of interest, metagenomics approaches using infected host tissue are frequently used, as it is not always possible to culture and isolate these pathogens. High-throughput sequencing can also be used to investigate host-pathogen interactions by investigating (temporal) transcriptomic responses of both the host and virus, potentially leading to the discovery of novel opportunities for treatment and drug targets. In addition, viruses in environmental samples (e.g. water or soil samples) can be identified using eDNA/metagenomics approaches. The promise that recent developments in sequencing brings to the field of invertebrate virology are not devoid of technical challenges, including the need for better laboratory and bioinformatics strategies to sequence and assemble virus genomes within complex tissue or environmental samples, and the difficulties associated with the annotation of the large number of novel viruses being discovered.
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Affiliation(s)
- R van Aerle
- Centre for Environment, Fisheries, and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, UK.
| | - E M Santos
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK.
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Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer. Sci Rep 2017; 7:40712. [PMID: 28102365 PMCID: PMC5244389 DOI: 10.1038/srep40712] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 12/08/2016] [Indexed: 11/25/2022] Open
Abstract
The development of rapid, economical genome sequencing has shed new light on the classification of viruses. As of October 2016, the National Center for Biotechnology Information (NCBI) database contained >2 million viral genome sequences and a reference set of ~4000 viral genome sequences that cover a wide range of known viral families. Whole-genome sequences can be used to improve viral classification and provide insight into the viral “tree of life”. However, due to the lack of evolutionary conservation amongst diverse viruses, it is not feasible to build a viral tree of life using traditional phylogenetic methods based on conserved proteins. In this study, we used an alignment-free method that uses k-mers as genomic features for a large-scale comparison of complete viral genomes available in RefSeq. To determine the optimal feature length, k (an essential step in constructing a meaningful dendrogram), we designed a comprehensive strategy that combines three approaches: (1) cumulative relative entropy, (2) average number of common features among genomes, and (3) the Shannon diversity index. This strategy was used to determine k for all 3,905 complete viral genomes in RefSeq. The resulting dendrogram shows consistency with the viral taxonomy of the ICTV and the Baltimore classification of viruses.
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Abstract
The number and diversity of viral sequences that are identified in metagenomic data far exceeds that of experimentally characterized virus isolates. In a recent workshop, a panel of experts discussed the proposal that, with appropriate quality control, viruses that are known only from metagenomic data can, and should be, incorporated into the official classification scheme of the International Committee on Taxonomy of Viruses (ICTV). Although a taxonomy that is based on metagenomic sequence data alone represents a substantial departure from the traditional reliance on phenotypic properties, the development of a robust framework for sequence-based virus taxonomy is indispensable for the comprehensive characterization of the global virome. In this Consensus Statement article, we consider the rationale for why metagenomic sequence data should, and how it can, be incorporated into the ICTV taxonomy, and present proposals that have been endorsed by the Executive Committee of the ICTV.
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Deep Sequencing Analysis Reveals the Mycoviral Diversity of the Virome of an Avirulent Isolate of Rhizoctonia solani AG-2-2 IV. PLoS One 2016; 11:e0165965. [PMID: 27814394 PMCID: PMC5096721 DOI: 10.1371/journal.pone.0165965] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/20/2016] [Indexed: 02/06/2023] Open
Abstract
Rhizoctonia solani represents an important plant pathogenic Basidiomycota species complex and the host of many different mycoviruses, as indicated by frequent detection of dsRNA elements in natural populations of the fungus. To date, eight different mycoviruses have been characterized in Rhizoctonia and some of them have been reported to modulate its virulence. DsRNA extracts of the avirulent R. solani isolate DC17 (AG2-2-IV) displayed a diverse pattern, indicating multiple infections with mycoviruses. Deep sequencing analysis of the dsRNA extract, converted to cDNA, revealed that this isolate harbors at least 17 different mycovirus species. Based on the alignment of the conserved RNA-dependent RNA-polymerase (RdRp) domain, this viral community included putative members of the families Narnaviridae, Endornaviridae, Partitiviridae and Megabirnaviridae as well as of the order Tymovirales. Furthermore, viruses, which could not be assigned to any existing family or order, but showed similarities to so far unassigned species like Sclerotinia sclerotiorum RNA virus L, Rhizoctonia solani dsRNA virus 1, Aspergillus foetidus slow virus 2 or Rhizoctonia fumigata virus 1, were identified. This is the first report of a fungal isolate infected by 17 different viral species and a valuable study case to explore the diversity of mycoviruses infecting R. solani.
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Pyke AT, Warrilow D. Archival Collections are Important in the Study of the Biology, Diversity, and Evolution of Arboviruses. Evol Bioinform Online 2016; 12:27-30. [PMID: 27688704 PMCID: PMC5024791 DOI: 10.4137/ebo.s40569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 08/16/2016] [Accepted: 08/17/2016] [Indexed: 11/05/2022] Open
Abstract
Historically, classifications of arboviruses were based on serological techniques. Hence, collections of arbovirus isolates have been central to this process by providing the antigenic reagents for these methods. However, with increasing concern about biosafety and security, the introduction of molecular biology techniques has led to greater emphasis on the storage of nucleic acid sequence data over the maintenance of archival material. In this commentary, we provide examples of where archival collections provide an important source of genetic material to assist in confirming the authenticity of reference strains and vaccine stocks, to clarify taxonomic relationships particularly when isolates of the same virus species have been collected across a wide expanse of time and space, for future phenotypic analysis, to determine the historical diversity of strains, and to understand the mechanisms leading to changes in genome structure and virus evolution.
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Affiliation(s)
- Alyssa T Pyke
- Public Health Virology Laboratory, Forensic and Scientific Services, Queensland Health, Archerfield, Queensland, Australia
| | - David Warrilow
- Public Health Virology Laboratory, Forensic and Scientific Services, Queensland Health, Archerfield, Queensland, Australia
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40
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Martin RR, Constable F, Tzanetakis IE. Quarantine Regulations and the Impact of Modern Detection Methods. ANNUAL REVIEW OF PHYTOPATHOLOGY 2016; 54:189-205. [PMID: 27491434 DOI: 10.1146/annurev-phyto-080615-100105] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Producers worldwide need access to the best plant varieties and cultivars available to be competitive in global markets. This often means moving plants across international borders as soon as they are available. At the same time, quarantine agencies are tasked with minimizing the risk of introducing exotic pests and pathogens along with imported plant material, with the goal to protect domestic agriculture and native fauna and flora. These two drivers, the movement of more plant material and reduced risk of pathogen introduction, are at odds. Improvements in large-scale or next-generation sequencing (NGS) and bioinformatics for data analysis have resulted in improved speed and accuracy of pathogen detection that could facilitate plant trade with reduced risk of pathogen movement. There are concerns to be addressed before NGS can replace existing tools used for pathogen detection in plant quarantine and certification programs. Here, we discuss the advantages and possible pitfalls of this technology for meeting the needs of plant quarantine and certification.
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Affiliation(s)
- Robert R Martin
- Horticultural Crops Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Corvallis, Oregon 97330;
| | - Fiona Constable
- Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, Victoria, Australia 3083:
| | - Ioannis E Tzanetakis
- Department of Plant Pathology, Division of Agriculture, University of Arkansas, Fayetteville, Arkansas 72701;
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41
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Rose R, Constantinides B, Tapinos A, Robertson DL, Prosperi M. Challenges in the analysis of viral metagenomes. Virus Evol 2016; 2:vew022. [PMID: 29492275 PMCID: PMC5822887 DOI: 10.1093/ve/vew022] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Genome sequencing technologies continue to develop with remarkable pace, yet
analytical approaches for reconstructing and classifying viral genomes from
mixed samples remain limited in their performance and usability. Existing
solutions generally target expert users and often have unclear scope, making it
challenging to critically evaluate their performance. There is a growing need
for intuitive analytical tooling for researchers lacking specialist computing
expertise and that is applicable in diverse experimental circumstances. Notable
technical challenges have impeded progress; for example, fragments of viral
genomes are typically orders of magnitude less abundant than those of host,
bacteria, and/or other organisms in clinical and environmental metagenomes;
observed viral genomes often deviate considerably from reference genomes
demanding use of exhaustive alignment approaches; high intrapopulation viral
diversity can lead to ambiguous sequence reconstruction; and finally, the
relatively few documented viral reference genomes compared to the estimated
number of distinct viral taxa renders classification problematic. Various
software tools have been developed to accommodate the unique challenges and use
cases associated with characterizing viral sequences; however, the quality of
these tools varies, and their use often necessitates computing expertise or
access to powerful computers, thus limiting their usefulness to many
researchers. In this review, we consider the general and application-specific
challenges posed by viral sequencing and analysis, outline the landscape of
available tools and methodologies, and propose ways of overcoming the current
barriers to effective analysis.
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Affiliation(s)
- Rebecca Rose
- BioInfoExperts, Norfolk, VA, USA.,Computational and Evolutionary Biology Faculty of Life Sciences, University of Manchester, Manchester, UK.,Department of Epidemiology, University of Florida, Gainesville, FL, USA
| | - Bede Constantinides
- BioInfoExperts, Norfolk, VA, USA.,Computational and Evolutionary Biology Faculty of Life Sciences, University of Manchester, Manchester, UK.,Department of Epidemiology, University of Florida, Gainesville, FL, USA
| | - Avraam Tapinos
- BioInfoExperts, Norfolk, VA, USA.,Computational and Evolutionary Biology Faculty of Life Sciences, University of Manchester, Manchester, UK.,Department of Epidemiology, University of Florida, Gainesville, FL, USA
| | - David L Robertson
- BioInfoExperts, Norfolk, VA, USA.,Computational and Evolutionary Biology Faculty of Life Sciences, University of Manchester, Manchester, UK.,Department of Epidemiology, University of Florida, Gainesville, FL, USA
| | - Mattia Prosperi
- BioInfoExperts, Norfolk, VA, USA.,Computational and Evolutionary Biology Faculty of Life Sciences, University of Manchester, Manchester, UK.,Department of Epidemiology, University of Florida, Gainesville, FL, USA
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Valastro V, Holmes EC, Britton P, Fusaro A, Jackwood MW, Cattoli G, Monne I. S1 gene-based phylogeny of infectious bronchitis virus: An attempt to harmonize virus classification. INFECTION GENETICS AND EVOLUTION 2016; 39:349-364. [PMID: 26883378 PMCID: PMC7172980 DOI: 10.1016/j.meegid.2016.02.015] [Citation(s) in RCA: 281] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 01/27/2016] [Accepted: 02/10/2016] [Indexed: 01/01/2023]
Abstract
Infectious bronchitis virus (IBV) is the causative agent of a highly contagious disease that results in severe economic losses to the global poultry industry. The virus exists in a wide variety of genetically distinct viral types, and both phylogenetic analysis and measures of pairwise similarity among nucleotide or amino acid sequences have been used to classify IBV strains. However, there is currently no consensus on the method by which IBV sequences should be compared, and heterogeneous genetic group designations that are inconsistent with phylogenetic history have been adopted, leading to the confusing coexistence of multiple genotyping schemes. Herein, we propose a simple and repeatable phylogeny-based classification system combined with an unambiguous and rationale lineage nomenclature for the assignment of IBV strains. By using complete nucleotide sequences of the S1 gene we determined the phylogenetic structure of IBV, which in turn allowed us to define 6 genotypes that together comprise 32 distinct viral lineages and a number of inter-lineage recombinants. Because of extensive rate variation among IBVs, we suggest that the inference of phylogenetic relationships alone represents a more appropriate criterion for sequence classification than pairwise sequence comparisons. The adoption of an internationally accepted viral nomenclature is crucial for future studies of IBV epidemiology and evolution, and the classification scheme presented here can be updated and revised novel S1 sequences should become available.
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Affiliation(s)
- Viviana Valastro
- Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy; University of Padova, Padova, Italy.
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Paul Britton
- Pirbright Institute, Compton Laboratory, Compton, UK
| | - Alice Fusaro
- Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy
| | - Mark W Jackwood
- Department of Population Health, College of Veterinary Medicine, Poultry Diagnostic and Research Center, University of Georgia, Athens, GA 30602, USA
| | - Giovanni Cattoli
- Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy
| | - Isabella Monne
- Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy
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New Insights into Asian Prunus Viruses in the Light of NGS-Based Full Genome Sequencing. PLoS One 2016; 11:e0146420. [PMID: 26741704 PMCID: PMC4704818 DOI: 10.1371/journal.pone.0146420] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 12/16/2015] [Indexed: 11/20/2022] Open
Abstract
Double stranded RNAs were purified from five Prunus sources of Asian origin and submitted to 454 pyrosequencing after a random, whole genome amplification. Four complete genomes of Asian prunus virus 1 (APV1), APV2 and APV3 were reconstructed from the sequencing reads, as well as four additional, near-complete genome sequences. Phylogenetic analyses confirmed the close relationships of these three viruses and the taxonomical position previously proposed for APV1, the only APV so far completely sequenced. The genetic distances in the respective polymerase and coat protein genes as well as their gene products suggest that APV2 should be considered as a distinct viral species in the genus Foveavirus, even if the amino acid identity levels in the polymerase are very close to the species demarcation criteria for the family Betaflexiviridae. However, the situation is more complex for APV1 and APV3, for which opposite conclusions are obtained depending on the gene (polymerase or coat protein) analyzed. Phylogenetic and recombination analyses suggest that recombination events may have been involved in the evolution of APV. Moreover, genome comparisons show that the unusually long 3’ non-coding region (3' NCR) is highly variable and a hot spot for indel polymorphisms. In particular, two APV3 variants differing only in their 3’ NCR were identified in a single Prunus source, with 3' NCRs of 214–312 nt, a size similar to that observed in other foveaviruses, but 567–850 nt smaller than in other APV3 isolates. Overall, this study provides critical genome information of these viruses, frequently associated with Prunus materials, even though their precise role as pathogens remains to be elucidated.
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Khalifa ME, Varsani A, Ganley ARD, Pearson MN. Comparison of Illumina de novo assembled and Sanger sequenced viral genomes: A case study for RNA viruses recovered from the plant pathogenic fungus Sclerotinia sclerotiorum. Virus Res 2015; 219:51-57. [PMID: 26581665 DOI: 10.1016/j.virusres.2015.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 10/21/2015] [Accepted: 11/01/2015] [Indexed: 10/22/2022]
Abstract
The advent of 'next generation sequencing' (NGS) technologies has led to the discovery of many novel mycoviruses, the majority of which are sufficiently different from previously sequenced viruses that there is no appropriate reference sequence on which to base the sequence assembly. Although many new genome sequences are generated by NGS, confirmation of the sequence by Sanger sequencing is still essential for formal classification by the International Committee for the Taxonomy of Viruses (ICTV), although this is currently under review. To empirically test the validity of de novo assembled mycovirus genomes from dsRNA extracts, we compared the results from Illumina sequencing with those from random cloning plus targeted PCR coupled with Sanger sequencing for viruses from five Sclerotinia sclerotiorum isolates. Through Sanger sequencing we detected nine viral genomes while through Illumina sequencing we detected the same nine viruses plus one additional virus from the same samples. Critically, the Illumina derived sequences share >99.3 % identity to those obtained by cloning and Sanger sequencing. Although, there is scope for errors in de novo assembled viral genomes, our results demonstrate that by maximising the proportion of viral sequence in the data and using sufficiently rigorous quality controls, it is possible to generate de novo genome sequences of comparable accuracy from Illumina sequencing to those obtained by Sanger sequencing.
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Affiliation(s)
- Mahmoud E Khalifa
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand; Faculty of Sciences, Damietta University, Damietta, Egypt
| | - Arvind Varsani
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa; Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, FL 32611, USA
| | - Austen R D Ganley
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Michael N Pearson
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand.
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45
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Krupovic M, Dolja VV, Koonin EV. Plant viruses of the Amalgaviridae family evolved via recombination between viruses with double-stranded and negative-strand RNA genomes. Biol Direct 2015; 10:12. [PMID: 25886840 PMCID: PMC4377212 DOI: 10.1186/s13062-015-0047-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 03/10/2015] [Indexed: 12/13/2022] Open
Abstract
Plant viruses of the recently recognized family Amalgaviridae have monopartite double-stranded (ds) RNA genomes and encode two proteins: an RNA-dependent RNA polymerase (RdRp) and a putative capsid protein (CP). Whereas the RdRp of amalgaviruses has been found to be most closely related to the RdRps of dsRNA viruses of the family Partitiviridae, the provenance of their CP remained obscure. Here we show that the CP of amalgaviruses is homologous to the nucleocapsid proteins of negative-strand RNA viruses of the genera Phlebovirus (Bunyaviridae) and Tenuivirus. The chimeric genomes of amalgaviruses are a testament to the effectively limitless gene exchange between viruses that shaped the evolution of the virosphere.
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Affiliation(s)
- Mart Krupovic
- Department of Microbiology, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, Paris, 75015, France.
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA.
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
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