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Roach MJ, Beecroft SJ, Mihindukulasuriya KA, Wang L, Paredes A, Cárdenas LAC, Henry-Cocks K, Lima LFO, Dinsdale EA, Edwards RA, Handley SA. Hecatomb: an integrated software platform for viral metagenomics. Gigascience 2024; 13:giae020. [PMID: 38832467 PMCID: PMC11148595 DOI: 10.1093/gigascience/giae020] [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: 07/17/2023] [Revised: 01/18/2024] [Accepted: 04/08/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND Modern sequencing technologies offer extraordinary opportunities for virus discovery and virome analysis. Annotation of viral sequences from metagenomic data requires a complex series of steps to ensure accurate annotation of individual reads and assembled contigs. In addition, varying study designs will require project-specific statistical analyses. FINDINGS Here we introduce Hecatomb, a bioinformatic platform coordinating commonly used tasks required for virome analysis. Hecatomb means "a great sacrifice." In this setting, Hecatomb is "sacrificing" false-positive viral annotations using extensive quality control and tiered-database searches. Hecatomb processes metagenomic data obtained from both short- and long-read sequencing technologies, providing annotations to individual sequences and assembled contigs. Results are provided in commonly used data formats useful for downstream analysis. Here we demonstrate the functionality of Hecatomb through the reanalysis of a primate enteric and a novel coral reef virome. CONCLUSION Hecatomb provides an integrated platform to manage many commonly used steps for virome characterization, including rigorous quality control, host removal, and both read- and contig-based analysis. Each step is managed using the Snakemake workflow manager with dependency management using Conda. Hecatomb outputs several tables properly formatted for immediate use within popular data analysis and visualization tools, enabling effective data interpretation for a variety of study designs. Hecatomb is hosted on GitHub (github.com/shandley/hecatomb) and is available for installation from Bioconda and PyPI.
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Affiliation(s)
- Michael J Roach
- Flinders Accelerator for Microbiome Exploration, Flinders University, Adelaide, SA, Australia
- Adelaide Centre for Epigenetics, University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Immunogenomics Cancer Institute, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Sarah J Beecroft
- Harry Perkins Institute of Medical Research, Perth, WA, 6009, Australia
| | - Kathie A Mihindukulasuriya
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Leran Wang
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Anne Paredes
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Luis Alberto Chica Cárdenas
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Kara Henry-Cocks
- Flinders Accelerator for Microbiome Exploration, Flinders University, Adelaide, SA, Australia
| | | | - Elizabeth A Dinsdale
- Flinders Accelerator for Microbiome Exploration, Flinders University, Adelaide, SA, Australia
| | - Robert A Edwards
- Flinders Accelerator for Microbiome Exploration, Flinders University, Adelaide, SA, Australia
| | - Scott A Handley
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
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2
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Yeung J, Routh AL. ViReMaShiny: an interactive application for analysis of viral recombination data. Bioinformatics 2022; 38:4420-4422. [PMID: 35904541 PMCID: PMC9477530 DOI: 10.1093/bioinformatics/btac522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/15/2022] [Accepted: 07/21/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Recombination is an essential driver of virus evolution and adaption, giving rise to new chimeric viruses, structural variants, sub-genomic RNAs and defective RNAs. Next-generation sequencing (NGS) of virus samples, either from experimental or clinical settings, has revealed a complex distribution of recombination events that contributes to intrahost diversity. We and others have previously developed alignment tools to discover and map these diverse recombination events in NGS data. However, there is no standard for data visualization to contextualize events of interest, and downstream analysis often requires bespoke coding. RESULTS We present ViReMaShiny, a web-based application built using the R Shiny framework to allow interactive exploration and point-and-click visualization of viral recombination data provided in BED format generated by computational pipelines such as ViReMa (Viral-Recombination-Mapper). AVAILABILITY AND IMPLEMENTATION The application is hosted at https://routhlab.shinyapps.io/ViReMaShiny/ with associated documentation at https://jayeung12.github.io/. Code is available at https://github.com/routhlab/ViReMaShiny. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jason Yeung
- John Sealy School of Medicine, The University of Texas Medical Branch, Galveston, TX 77550, USA
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3
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Wang S, Sotcheff SL, Gallardo CM, Jaworski E, Torbett B, Routh A. Covariation of viral recombination with single nucleotide variants during virus evolution revealed by CoVaMa. Nucleic Acids Res 2022; 50:e41. [PMID: 35018461 PMCID: PMC9023271 DOI: 10.1093/nar/gkab1259] [Citation(s) in RCA: 3] [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: 09/14/2021] [Revised: 11/29/2021] [Accepted: 12/09/2021] [Indexed: 11/17/2022] Open
Abstract
Adaptation of viruses to their environments occurs through the acquisition of both novel single-nucleotide variants (SNV) and recombination events including insertions, deletions, and duplications. The co-occurrence of SNVs in individual viral genomes during their evolution has been well-described. However, unlike covariation of SNVs, studying the correlation between recombination events with each other or with SNVs has been hampered by their inherent genetic complexity and a lack of bioinformatic tools. Here, we expanded our previously reported CoVaMa pipeline (v0.1) to measure linkage disequilibrium between recombination events and SNVs within both short-read and long-read sequencing datasets. We demonstrate this approach using long-read nanopore sequencing data acquired from Flock House virus (FHV) serially passaged in vitro. We found SNVs that were either correlated or anti-correlated with large genomic deletions generated by nonhomologous recombination that give rise to Defective-RNAs. We also analyzed NGS data from longitudinal HIV samples derived from a patient undergoing antiretroviral therapy who proceeded to virological failure. We found correlations between insertions in the p6Gag and mutations in Gag cleavage sites. This report confirms previous findings and provides insights on novel associations between SNVs and specific recombination events within the viral genome and their role in viral evolution.
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Affiliation(s)
- Shiyi Wang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Stephanea L Sotcheff
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Christian M Gallardo
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Elizabeth Jaworski
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Bruce E Torbett
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Andrew L Routh
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
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4
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López CB. Defective Viral Particles. Virology 2021. [DOI: 10.1002/9781119818526.ch5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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5
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Ziegler CM, Botten JW. Defective Interfering Particles of Negative-Strand RNA Viruses. Trends Microbiol 2020; 28:554-565. [PMID: 32544442 PMCID: PMC7298151 DOI: 10.1016/j.tim.2020.02.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/27/2020] [Accepted: 02/25/2020] [Indexed: 12/14/2022]
Abstract
Viral defective interfering particles (DIPs) were intensely studied several decades ago but research waned leaving open many critical questions. New technologies and other advances led to a resurgence in DIP studies for negative-strand RNA viruses. While DIPs have long been recognized, their exact contribution to the outcome of acute or persistent viral infections has remained elusive. Recent studies have identified defective viral genomes (DVGs) in human infections, including respiratory syncytial virus and influenza, and growing evidence indicates that DVGs influence disease severity and may contribute to viral persistence. Further, several studies have advanced our understanding of key viral and host factors that regulate DIP formation and activity. Here we review these discoveries and highlight key questions moving forward.
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Affiliation(s)
- Christopher M Ziegler
- Department of Medicine, Division of Immunobiology, University of Vermont, Burlington, VT 05405, USA
| | - Jason W Botten
- Department of Medicine, Division of Immunobiology, University of Vermont, Burlington, VT 05405, USA; Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA; Vaccine Testing Center, University of Vermont, Burlington, VT 05405, USA.
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6
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ClickSeq: Replacing Fragmentation and Enzymatic Ligation with Click-Chemistry to Prevent Sequence Chimeras. Methods Mol Biol 2018; 1712:71-85. [PMID: 29224069 DOI: 10.1007/978-1-4939-7514-3_6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We recently reported a fragmentation-free method for the synthesis of Next-Generation Sequencing libraries called "ClickSeq" that uses biorthogonal click-chemistry in place of enzymes for the ligation of sequencing adaptors. We found that this approach dramatically reduces artifactual chimera formation, allowing the study of rare recombination events that include viral replication intermediates and defective-interfering viral RNAs. ClickSeq illustrates how robust, bio-orthogonal chemistry can be harnessed in vitro to capture and dissect complex biological processes. Here, we describe an updated protocol for the synthesis of "ClickSeq" libraries.
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7
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Next-generation sequencing library preparation method for identification of RNA viruses on the Ion Torrent Sequencing Platform. Virus Genes 2018; 54:536-542. [PMID: 29744712 PMCID: PMC7088580 DOI: 10.1007/s11262-018-1568-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 05/04/2018] [Indexed: 12/19/2022]
Abstract
Next generation sequencing (NGS) is a powerful tool for the characterization, discovery, and molecular identification of RNA viruses. There were multiple NGS library preparation methods published for strand-specific RNA-seq, but some methods are not suitable for identifying and characterizing RNA viruses. In this study, we report a NGS library preparation method to identify RNA viruses using the Ion Torrent PGM platform. The NGS sequencing adapters were directly inserted into the sequencing library through reverse transcription and polymerase chain reaction, without fragmentation and ligation of nucleic acids. The results show that this method is simple to perform, able to identify multiple species of RNA viruses in clinical samples.
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8
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Sokoloski KJ, Nease LM, May NA, Gebhart NN, Jones CE, Morrison TE, Hardy RW. Identification of Interactions between Sindbis Virus Capsid Protein and Cytoplasmic vRNA as Novel Virulence Determinants. PLoS Pathog 2017; 13:e1006473. [PMID: 28662211 PMCID: PMC5507600 DOI: 10.1371/journal.ppat.1006473] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 07/12/2017] [Accepted: 06/15/2017] [Indexed: 12/17/2022] Open
Abstract
Alphaviruses are arthropod-borne viruses that represent a significant threat to public health at a global level. While the formation of alphaviral nucleocapsid cores, consisting of cargo nucleic acid and the viral capsid protein, is an essential molecular process of infection, the precise interactions between the two partners are ill-defined. A CLIP-seq approach was used to screen for candidate sites of interaction between the viral Capsid protein and genomic RNA of Sindbis virus (SINV), a model alphavirus. The data presented in this report indicates that the SINV capsid protein binds to specific viral RNA sequences in the cytoplasm of infected cells, but its interaction with genomic RNA in mature extracellular viral particles is largely non-specific in terms of nucleotide sequence. Mutational analyses of the cytoplasmic viral RNA-capsid interaction sites revealed a functional role for capsid binding early in infection. Interaction site mutants exhibited decreased viral growth kinetics; however, this defect was not a function of decreased particle production. Rather mutation of the cytoplasmic capsid-RNA interaction sites negatively affected the functional capacity of the incoming viral genomic RNAs leading to decreased infectivity. Furthermore, cytoplasmic capsid interaction site mutants are attenuated in a murine model of neurotropic alphavirus infection. Collectively, the findings of this study indicate that the identified cytoplasmic interactions of the viral capsid protein and genomic RNA, while not essential for particle formation, are necessary for genomic RNA function early during infection. This previously unappreciated role of capsid protein during the alphaviral replication cycle also constitutes a novel virulence determinant. Alphaviruses can cause significant disease in infected individuals; however, our understanding of the molecular interactions that enable infection and contribute to the development of disease is limited. The work detailed in this manuscript characterizes the interaction of a viral RNA-binding protein, Capsid, with the viral genomic RNA. Importantly, these interactions were found to be at specific sites on the genome but not essential for virus assembly. Mutation of the capsid / RNA interaction sites decreased the replication of the virus and the severity of disease in a mouse model of infection. Taken together, these findings identify a previously undiscovered determinant of disease severity, and provide a potential basis for the development of new vaccines.
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Affiliation(s)
- Kevin J. Sokoloski
- Department of Microbiology and Immunology, and the Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville School of Medicine, Louisville KY, United States of America
| | - Lauren M. Nease
- Department of Biology, College of Arts and Sciences, Indiana University, Bloomington IN, United States of America
| | - Nicholas A. May
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Natasha N. Gebhart
- Department of Biology, College of Arts and Sciences, Indiana University, Bloomington IN, United States of America
| | - Claire E. Jones
- Department of Microbiology and Immunology, and the Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville School of Medicine, Louisville KY, United States of America
| | - Thomas E. Morrison
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Richard W. Hardy
- Department of Biology, College of Arts and Sciences, Indiana University, Bloomington IN, United States of America
- * E-mail:
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9
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Jaworski E, Routh A. Parallel ClickSeq and Nanopore sequencing elucidates the rapid evolution of defective-interfering RNAs in Flock House virus. PLoS Pathog 2017; 13:e1006365. [PMID: 28475646 PMCID: PMC5435362 DOI: 10.1371/journal.ppat.1006365] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 05/17/2017] [Accepted: 04/19/2017] [Indexed: 11/18/2022] Open
Abstract
Defective-Interfering RNAs (DI-RNAs) have long been known to play an important role in virus replication and transmission. DI-RNAs emerge during virus passaging in both cell-culture and their hosts as a result of non-homologous RNA recombination. However, the principles of DI-RNA emergence and their subsequent evolution have remained elusive. Using a combination of long- and short-read Next-Generation Sequencing, we have characterized the formation of DI-RNAs during serial passaging of Flock House virus (FHV) in cell-culture over a period of 30 days in order to elucidate the pathways and potential mechanisms of DI-RNA emergence and evolution. For short-read RNAseq, we employed 'ClickSeq' due to its ability to sensitively and confidently detect RNA recombination events with nucleotide resolution. In parallel, we used the Oxford Nanopore Technologies's (ONT) MinION to resolve full-length defective and wild-type viral genomes. Together, these accurately resolve both rare and common RNA recombination events, determine the correlation between recombination events, and quantifies the relative abundance of different DI-RNAs throughout passaging. We observe the formation of a diverse pool of defective RNAs at each stage of viral passaging. However, many of these 'intermediate' species, while present in early stages of passaging, do not accumulate. After approximately 9 days of passaging we observe the rapid accumulation of DI-RNAs with a correlated reduction in specific infectivity and with the Nanopore data find that DI-RNAs are characterized by multiple RNA recombination events. This suggests that intermediate DI-RNA species are not competitive and that multiple recombination events interact epistatically to confer 'mature' DI-RNAs with their selective advantage allowing for their rapid accumulation. Alternatively, it is possible that mature DI-RNA species are generated in a single event involving multiple RNA rearrangements. These insights have important consequences for our understanding of the mechanisms, determinants and limitations in the emergence and evolution of DI-RNAs.
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Affiliation(s)
- Elizabeth Jaworski
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, United States of America
| | - Andrew Routh
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, United States of America.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas, United States of America
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10
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Bertran A, Ciuffo M, Margaria P, Rosa C, Oliveira Resende R, Turina M. Host-specific accumulation and temperature effects on the generation of dimeric viral RNA species derived from the S-RNA of members of the Tospovirus genus. J Gen Virol 2016; 97:3051-3062. [PMID: 27600541 DOI: 10.1099/jgv.0.000598] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Polygonum ringspot virus (PolRSV) is a recently characterized Tospovirus reported in Italy. Northern blot analyses of PolRSV infections in Nicotiana benthamiana and tomato plants showed that a viral RNA species with nearly twice the length of the Small genomic RNA (S-RNA) accumulated abundantly in the former host, but was not detected in the latter. Additional assays confirmed that biogenesis of this novel RNA species was common to all PolRSV isolates tested and also to an isolate of Tomato spotted wilt virus (TSWV). Given its size, we hypothesized that the novel RNA species was a dimer molecule and we confirmed this hypothesis by RNA sequencing (RNAseq) analysis and reverse transcription (RT)-PCR of putative predicted dimer junction sites in RNA extracts of N. benthamiana challenged with PolRSV isolates Plg6 and Plg13/2. We also confirmed that these molecules are derived from head-to-tail dimers and often contain deletions at their junction sites. We named these novel molecules imperfect dimer RNAs (IMPD-RNAs). PolRSV IMPD-RNAs systemic accumulation in a range of host plants was restricted to N. benthamiana and Nicotiana occidentalis. Notably, IMPD-RNAs accumulation was modulated by temperature and their generation was restricted to late stages of systemic infection (12 days post-inoculation) in N. benthamiana. Differently from all other PolRSV isolates used in this study, Plg13/2 generated more IMPD-RNAs coupled with low amounts of genomic S-RNA and maintained them even at 18 °C, besides having lost the ability to infect tomato plants. This is the first characterization of S-RNA dimers for Tospovirus, and of occurrence of dimers of genomic segments at the whole organism level for Bunyaviridae.
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Affiliation(s)
- André Bertran
- Institute for Sustainable Plant Protection, CNR, Turin, Piemonte, Italy
- Plant Virology Laboratory, Institute of Biological Sciences, University of Brasília, Brazil
| | - Marina Ciuffo
- Institute for Sustainable Plant Protection, CNR, Turin, Piemonte, Italy
| | - Paolo Margaria
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, USA
| | - Cristina Rosa
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, USA
| | - Renato Oliveira Resende
- Institute for Sustainable Plant Protection, CNR, Turin, Piemonte, Italy
- Plant Virology Laboratory, Institute of Biological Sciences, University of Brasília, Brazil
| | - Massimo Turina
- Institute for Sustainable Plant Protection, CNR, Turin, Piemonte, Italy
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11
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Routh A, Chang MW, Okulicz JF, Johnson JE, Torbett BE. CoVaMa: Co-Variation Mapper for disequilibrium analysis of mutant loci in viral populations using next-generation sequence data. Methods 2015; 91:40-47. [PMID: 26408523 DOI: 10.1016/j.ymeth.2015.09.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 09/18/2015] [Accepted: 09/21/2015] [Indexed: 11/29/2022] Open
Abstract
Next-Generation Sequencing (NGS) has transformed our understanding of the dynamics and diversity of virus populations for human pathogens and model systems alike. Due to the sensitivity and depth of coverage in NGS, it is possible to measure the frequency of mutations that may be present even at vanishingly low frequencies within the viral population. Here, we describe a simple bioinformatic pipeline called CoVaMa (Co-Variation Mapper) scripted in Python that detects correlated patterns of mutations in a viral sample. Our algorithm takes NGS alignment data and populates large matrices of contingency tables that correspond to every possible pairwise interaction of nucleotides in the viral genome or amino acids in the chosen open reading frame. These tables are then analysed using classical linkage disequilibrium to detect and report evidence of epistasis. We test our analysis with simulated data and then apply the approach to find epistatically linked loci in Flock House Virus genomic RNA grown under controlled cell culture conditions. We also reanalyze NGS data from a large cohort of HIV infected patients and find correlated amino acid substitution events in the protease gene that have arisen in response to anti-viral therapy. This both confirms previous findings and suggests new pairs of interactions within HIV protease. The script is publically available at http://sourceforge.net/projects/covama.
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Affiliation(s)
- Andrew Routh
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA.
| | - Max W Chang
- Integrative Genomics and Bioinformatics Core, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jason F Okulicz
- Infectious Disease Service, San Antonio Military Medical Center, Fort Sam Houston, TX 78234, USA; Infectious Disease Clinical Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - John E Johnson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bruce E Torbett
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
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12
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Tao Y, Rotem A, Zhang H, Cockrell SK, Koehler SA, Chang CB, Ung LW, Cantalupo PG, Ren Y, Lin JS, Feldman AB, Wobus CE, Pipas JM, Weitz DA. Artifact-Free Quantification and Sequencing of Rare Recombinant Viruses by Using Drop-Based Microfluidics. Chembiochem 2015; 16:2167-71. [PMID: 26247541 DOI: 10.1002/cbic.201500384] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Indexed: 01/23/2023]
Abstract
Recombination is an important driver in the evolution of viruses and thus is key to understanding viral epidemics and improving strategies to prevent future outbreaks. Characterization of rare recombinant subpopulations remains technically challenging because of artifacts such as artificial recombinants, known as chimeras, and amplification bias. To overcome this, we have developed a high-throughput microfluidic technique with a second verification step in order to amplify and sequence single recombinant viruses with high fidelity in picoliter drops. We obtained the first artifact-free estimate of in vitro recombination rate between murine norovirus strains MNV-1 and WU20 co-infecting a cell (P(rec) = 3.3 × 10(-4) ± 2 × 10(-5) ) for a 1205 nt region. Our approach represents a time- and cost-effective improvement over current methods, and can be adapted for genomic studies requiring artifact- and bias-free selective amplification, such as microbial pathogens, or rare cancer cells.
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Affiliation(s)
- Ye Tao
- School of Engineering and Applied Sciences, Harvard University, 29 Oxford Street, Pierce 231, Cambridge, MA, 02138, USA.,School of Mechatronics Engineering, Harbin Institute of Technology, 92 West Dazhi Street, Nan Gang District, Harbin, 150001, China
| | - Assaf Rotem
- School of Engineering and Applied Sciences, Harvard University, 29 Oxford Street, Pierce 231, Cambridge, MA, 02138, USA
| | - Huidan Zhang
- School of Engineering and Applied Sciences, Harvard University, 29 Oxford Street, Pierce 231, Cambridge, MA, 02138, USA.,Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, 92 Beier Road, Heping District, Shenyang, 110001, China
| | - Shelley K Cockrell
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA, 15260, USA
| | - Stephan A Koehler
- School of Engineering and Applied Sciences, Harvard University, 29 Oxford Street, Pierce 231, Cambridge, MA, 02138, USA
| | - Connie B Chang
- School of Engineering and Applied Sciences, Harvard University, 29 Oxford Street, Pierce 231, Cambridge, MA, 02138, USA.,Chemical and Biological Engineering Department, Montana State University, Bozeman, MT, 59717, USA
| | - Lloyd W Ung
- School of Engineering and Applied Sciences, Harvard University, 29 Oxford Street, Pierce 231, Cambridge, MA, 02138, USA
| | - Paul G Cantalupo
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA, 15260, USA
| | - Yukun Ren
- School of Mechatronics Engineering, Harbin Institute of Technology, 92 West Dazhi Street, Nan Gang District, Harbin, 150001, China
| | - Jeffrey S Lin
- Applied Physics Laboratory, Johns Hopkins University, 11100 Johns Hopkins Road, Laurel, MD, 20723, USA
| | - Andrew B Feldman
- Applied Physics Laboratory, Johns Hopkins University, 11100 Johns Hopkins Road, Laurel, MD, 20723, USA.,Department of Emergency Medicine, Johns Hopkins Medicine, 5801 Smith Avenue, Suite 3220, Baltimore, MD, 21209, USA
| | - Christiane E Wobus
- Department of Microbiology and Immunology, University of Michigan, 1150 West Medical Center Drive, 5622 Medical Science II, Ann Arbor, MI, 48109, USA
| | - James M Pipas
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA, 15260, USA
| | - David A Weitz
- School of Engineering and Applied Sciences, Harvard University, 29 Oxford Street, Pierce 231, Cambridge, MA, 02138, USA. .,Department of Physics, Harvard University, 29 Oxford Street, Pierce 231, Cambridge, MA, 02138, USA.
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13
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Routh A, Head SR, Ordoukhanian P, Johnson JE. ClickSeq: Fragmentation-Free Next-Generation Sequencing via Click Ligation of Adaptors to Stochastically Terminated 3'-Azido cDNAs. J Mol Biol 2015; 427:2610-6. [PMID: 26116762 DOI: 10.1016/j.jmb.2015.06.011] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 06/17/2015] [Accepted: 06/18/2015] [Indexed: 10/23/2022]
Abstract
We present a simple method called "ClickSeq" for NGS (next-generation sequencing) library synthesis that uses click chemistry rather than enzymatic reactions for the ligation of Illumina sequencing adaptors. In ClickSeq, randomly primed reverse transcription reactions are supplemented with azido-2',3'-dideoxynucleotides that randomly terminate DNA synthesis and release 3'-azido-blocked cDNA fragments in a process akin to dideoxy-Sanger sequencing. Purified fragments are "click ligated" via copper-catalyzed alkyne-azide cycloaddition to DNA oligos modified with a 5'-alkyne group. This generates ssDNA molecules containing an unnatural triazole-linked DNA backbone that is sufficiently biocompatible for PCR amplification to generate a cDNA library for RNAseq. Here, we analyze viral RNAs and mRNA to demonstrate that ClickSeq produces unbiased NGS libraries with low error rates comparable to standard methods. Importantly, ClickSeq is robust against common artifacts of NGS such as chimera formation and artifactual recombination with fewer than 3 aberrant events detected per million reads.
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Affiliation(s)
- Andrew Routh
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Steven R Head
- The Next Generation Sequencing Core, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Phillip Ordoukhanian
- The Next Generation Sequencing Core, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John E Johnson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Deep sequencing of virus-derived small interfering RNAs and RNA from viral particles shows highly similar mutational landscapes of a plant virus population. J Virol 2015; 89:4760-9. [PMID: 25673712 DOI: 10.1128/jvi.03685-14] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 02/04/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED RNA viruses exist within a host as a population of mutant sequences, often referred to as quasispecies. Within a host, sequences of RNA viruses constitute several distinct but interconnected pools, such as RNA packed in viral particles, double-stranded RNA, and virus-derived small interfering RNAs. We aimed to test if the same representation of within-host viral population structure could be obtained by sequencing different viral sequence pools. Using ultradeep Illumina sequencing, the diversity of two coexisting Potato virus Y sequence pools present within a plant was investigated: RNA isolated from viral particles and virus-derived small interfering RNAs (the derivatives of a plant RNA silencing mechanism). The mutational landscape of the within-host virus population was highly similar between both pools, with no notable hotspots across the viral genome. Notably, all of the single-nucleotide polymorphisms with a frequency of higher than 1.6% were found in both pools. Some unique single-nucleotide polymorphisms (SNPs) with very low frequencies were found in each of the pools, with more of them occurring in the small RNA (sRNA) pool, possibly arising through genetic drift in localized virus populations within a plant and the errors introduced during the amplification of silencing signal. Sequencing of the viral particle pool enhanced the efficiency of consensus viral genome sequence reconstruction. Nonhomologous recombinations were commonly detected in the viral particle pool, with a hot spot in the 3' untranslated and coat protein regions of the genome. We stress that they present an important but often overlooked aspect of virus population diversity. IMPORTANCE This study is the most comprehensive whole-genome characterization of a within-plant virus population to date and the first study comparing diversity of different pools of viral sequences within a host. We show that both virus-derived small RNAs and RNA from viral particles could be used for diversity assessment of within-plant virus population, since they show a highly congruent portrayal of the virus mutational landscape within a plant. The study is an important baseline for future studies of virus population dynamics, for example, during the adaptation to a new host. The comparison of the two virus sequence enrichment techniques, sequencing of virus-derived small interfering RNAs and RNA from purified viral particles, shows the strength of the latter for the detection of recombinant viral genomes and reconstruction of complete consensus viral genome sequence.
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Routh A, Johnson JE. Discovery of functional genomic motifs in viruses with ViReMa-a Virus Recombination Mapper-for analysis of next-generation sequencing data. Nucleic Acids Res 2013; 42:e11. [PMID: 24137010 PMCID: PMC3902915 DOI: 10.1093/nar/gkt916] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
We developed an algorithm named ViReMa (Viral-Recombination-Mapper) to provide a versatile platform for rapid, sensitive and nucleotide-resolution detection of recombination junctions in viral genomes using next-generation sequencing data. Rather than mapping read segments of pre-defined lengths and positions, ViReMa dynamically generates moving read segments. ViReMa initially attempts to align the 5' end of a read to the reference genome(s) with the Bowtie seed-based alignment. A new read segment is then made by either extracting any unaligned nucleotides at the 3' end of the read or by trimming the first nucleotide from the read. This continues iteratively until all portions of the read are either mapped or trimmed. With multiple reference genomes, it is possible to detect virus-to-host or inter-virus recombination. ViReMa is also capable of detecting insertion and substitution events and multiple recombination junctions within a single read. By mapping the distribution of recombination events in the genome of flock house virus, we demonstrate that this information can be used to discover de novo functional motifs located in conserved regions of the viral genome.
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Affiliation(s)
- Andrew Routh
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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16
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Chen GQ, Zhuang QY, Wang KC, Liu S, Shao JZ, Jiang WM, Hou GY, Li JP, Yu JM, Li YP, Chen JM. Identification and survey of a novel avian coronavirus in ducks. PLoS One 2013; 8:e72918. [PMID: 24023656 PMCID: PMC3758261 DOI: 10.1371/journal.pone.0072918] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 07/16/2013] [Indexed: 01/08/2023] Open
Abstract
The rapid discovery of novel viruses using next generation sequencing (NGS) technologies including DNA-Seq and RNA-Seq, has greatly expanded our understanding of viral diversity in recent years. The timely identification of novel viruses using NGS technologies is also important for us to control emerging infectious diseases caused by novel viruses. In this study, we identified a novel duck coronavirus (CoV), distinct with chicken infectious bronchitis virus (IBV), using RNA-Seq. The novel duck-specific CoV was a potential novel species within the genus Gammacoronavirus, as indicated by sequences of three regions in the viral 1b gene. We also performed a survey of CoVs in domestic fowls in China using reverse-transcription polymerase chain reaction (RT-PCR), targeting the viral nucleocapsid (N) gene. A total of 102 CoV positives were identified through the survey. Phylogenetic analysis of the viral N sequences suggested that CoVs in domestic fowls have diverged into several region-specific or host-specific clades or subclades in the world, and IBVs can infect ducks, geese and pigeons, although they mainly circulate in chickens. Moreover, this study provided novel data supporting the notion that some host-specific CoVs other than IBVs circulate in ducks, geese and pigeons, and indicated that the novel duck-specific CoV identified through RNA-Seq in this study is genetically closer to some CoVs circulating in wild water fowls. Taken together, this study shed new insight into the diversity, distribution, evolution and control of avian CoVs.
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Affiliation(s)
- Gui-Qian Chen
- Institute of Cell Biology and Genetics, College of Life Sciences, Zhejiang University, Hangzhou, China
- The Laboratory of Avian Disease Surveillance, China Animal Health and Epidemiology Center, Qingdao, China
| | - Qing-Ye Zhuang
- The Laboratory of Avian Disease Surveillance, China Animal Health and Epidemiology Center, Qingdao, China
| | - Kai-Cheng Wang
- The Laboratory of Avian Disease Surveillance, China Animal Health and Epidemiology Center, Qingdao, China
| | - Shuo Liu
- The Laboratory of Avian Disease Surveillance, China Animal Health and Epidemiology Center, Qingdao, China
| | - Jian-Zhong Shao
- Institute of Cell Biology and Genetics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Wen-Ming Jiang
- The Laboratory of Avian Disease Surveillance, China Animal Health and Epidemiology Center, Qingdao, China
| | - Guang-Yu Hou
- The Laboratory of Avian Disease Surveillance, China Animal Health and Epidemiology Center, Qingdao, China
| | - Jin-Ping Li
- The Laboratory of Avian Disease Surveillance, China Animal Health and Epidemiology Center, Qingdao, China
| | - Jian-Min Yu
- The Laboratory of Avian Disease Surveillance, China Animal Health and Epidemiology Center, Qingdao, China
| | - Yi-Ping Li
- Institute of Cell Biology and Genetics, College of Life Sciences, Zhejiang University, Hangzhou, China
- * E-mail: (JMC); (YPL)
| | - Ji-Ming Chen
- The Laboratory of Avian Disease Surveillance, China Animal Health and Epidemiology Center, Qingdao, China
- * E-mail: (JMC); (YPL)
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Abstract
This is a personal history of my structural studies of icosahedral viruses that evolved from crystallographic studies, to hybrid methods with electron cryo-microscopy and image reconstruction (cryoEM) and then developed further by incorporating a variety of physical methods to augment the high resolution crystallographic studies. It is not meant to be comprehensive, even for my own work, but hopefully provides some perspective on the growth of our understanding of these remarkable biologic assemblies. The goal is to provide a historical perspective for those new to the field and to emphasize the limitations of any one method, even those that provide atomic resolution information about viruses.
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Affiliation(s)
- John E Johnson
- Department of Molecular Biology, MB31, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA.
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18
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Bujarski JJ. Genetic recombination in plant-infecting messenger-sense RNA viruses: overview and research perspectives. FRONTIERS IN PLANT SCIENCE 2013; 4:68. [PMID: 23533000 PMCID: PMC3607795 DOI: 10.3389/fpls.2013.00068] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 03/11/2013] [Indexed: 05/09/2023]
Abstract
RNA recombination is one of the driving forces of genetic variability in (+)-strand RNA viruses. Various types of RNA-RNA crossovers were described including crosses between the same or different viral RNAs or between viral and cellular RNAs. Likewise, a variety of molecular mechanisms are known to support RNA recombination, such as replicative events (based on internal or end-to-end replicase switchings) along with non-replicative joining among RNA fragments of viral and/or cellular origin. Such mechanisms as RNA decay or RNA interference are responsible for RNA fragmentation and trans-esterification reactions which are likely accountable for ligation of RNA fragments. Numerous host factors were found to affect the profiles of viral RNA recombinants and significant differences in recombination frequency were observed among various RNA viruses. Comparative analyses of viral sequences allowed for the development of evolutionary models in order to explain adaptive phenotypic changes and co-evolving sites. Many questions remain to be answered by forthcoming RNA recombination research. (1) How various factors modulate the ability of viral replicase to switch templates, (2) What is the intracellular location of RNA-RNA template switchings, (3) Mechanisms and factors responsible for non-replicative RNA recombination, (4) Mechanisms of integration of RNA viral sequences with cellular genomic DNA, and (5) What is the role of RNA splicing and ribozyme activity. From an evolutionary stand point, it is not known how RNA viruses parasitize new host species via recombination, nor is it obvious what the contribution of RNA recombination is among other RNA modification pathways. We do not understand why the frequency of RNA recombination varies so much among RNA viruses and the status of RNA recombination as a form of sex is not well documented.
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Affiliation(s)
- Jozef J. Bujarski
- Plant Molecular Biology Center and the Department of Biological Sciences, Northern Illinois UniversityDeKalb, IL, USA
- Laboratory of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
- *Correspondence: Jozef J. Bujarski, Plant Molecular Biology Center and the Department of Biological Sciences, Northern Illinois University, Montgomery Hall, DeKalb, IL 60115, USA. e-mail:
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