The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks

Nature Microbiology, Год журнала: 2020, Номер 5(5), С. 668 - 674

Опубликована: Апрель 27, 2020

Abstract Virus taxonomy emerged as a discipline in the middle of twentieth century. Traditionally, classification by virus taxonomists has been focussed on grouping relatively closely related viruses. However, during past few years, International Committee Taxonomy Viruses (ICTV) recognized that it develops can be usefully extended to include basal evolutionary relationships among distantly Consequently, ICTV changed its Code allow 15-rank hierarchy aligns with Linnaean taxonomic system and may accommodate entire spectrum genetic divergence virosphere. The current taxonomies three human pathogens, Ebola virus, severe acute respiratory syndrome coronavirus herpes simplex 1 are used illustrate impact expanded rank structure. This new will stimulate further research origins evolution, vice versa, could promote crosstalk cellular organisms.

Язык: Английский

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Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome

Nature Microbiology, Год журнала: 2020, Номер 5(10), С. 1262 - 1270

Опубликована: Июль 20, 2020

Abstract RNA viruses in aquatic environments remain poorly studied. Here, we analysed the virome from approximately 10 l water Yangshan Deep-Water Harbour near Yangtze River estuary China and identified more than 4,500 distinct viruses, doubling previously known set of viruses. Phylogenomic analysis several major lineages, roughly, at taxonomic ranks class, order family. The 719-member-strong virus assemblage is sister clade to expansive class Alsuviricetes consists with simple genomes that typically encode only RNA-dependent polymerase (RdRP), capping enzyme capsid protein. Several clades within independently evolved domain permutation RdRP. Another unknown shares ancestry Potyviridae , largest plant ‘Aquatic picorna-like viruses/ Marnaviridae ’ was greatly expanded, 800 added RdRP-linked protein domains not detected any were identified, such as small ubiquitin-like modifier (SUMO) domain, phospholipase A2 PrsW-family protease domain. Multiple utilize alternative genetic codes implying protist (especially ciliate) hosts. results reveal a vast includes many groups. However, phylogenetic RdRPs supports established five-branch structure evolutionary tree, no additional phyla.

Язык: Английский

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Cold Plasma, a New Hope in the Field of Virus Inactivation

Trends in biotechnology, Год журнала: 2020, Номер 38(11), С. 1278 - 1291

Опубликована: Апрель 17, 2020

Pathogenic viruses are becoming an increasing burden for health, agriculture, and the global economy. Classic disinfection methods have several drawbacks, innovative solutions virus inactivation urgently needed.CP can be used as environmentally friendly tool inactivation. It inactivate different human, animal, plant in various matrices.When using CP it is important to set correct parameters choose treatment durations that allow particles interact with contaminated material.Reactive oxygen and/or nitrogen species been shown responsible through effects on capsid proteins nucleic acids. The development of more accurate will provide information which plasma crucial each experiment, how exactly they affect viruses. Viruses infect all cell-based organisms, from bacteria humans, animals, plants. They numerous cases hospitalization, many deaths, widespread crop destruction, result enormous medical, economical, biological burden. Each currently decontamination has drawbacks. Cold (CP) entered this field a novel, efficient, clean solution We present recent developments promising CP-mediated inactivation, describe applications mechanisms This particularly relevant because viral pandemics, such COVID-19, highlight need alternative replace, complement, or upgrade existing procedures. most abundant diverse microbes our planet. inhabited Earth billions years [1.Nasir A. Caetano-Anollés G. A phylogenomic data-driven exploration origins evolution.Sci. Adv. 2015; 1e1500527Crossref PubMed Scopus (131) Google Scholar], adapted environments, now found across ecosystems. contributed evolution life Earth, beneficial preserving ecosystems natural cycles carbon cycle sea [2.Wilhelm S.W. Suttle C.A. nutrient aquatic food webs.Bioscience. 1999; 49: 781-788Crossref (845) Scholar]. On other hand, pathogenic cause tens hundreds millions plant, human infections annually, high losses deaths (Box 1). Therefore, inactivating harmful better quality life.Box 1Viruses Methods Their DisinfectionViruses microscopic agents forms cellular life. classification living organisms historically question philosophical debate, but unquestionably one powerful engines planet [51.Koonin E.V. Starokadomskyy P. Are alive? replicator paradigm sheds decisive light old misguided question.Stud. Hist. Phil. Biol. Biomed. Sci. 2016; 59: 125-134Crossref (76) Most not harmful, some even their hosts [52.Roossinck M.J. Baz E.R. Symbiosis: intimate partners.Annu. Rev. Virol. 2017; 4: 123-139Crossref (63) In increasingly promote wellbeing. For example, lentiviruses [53.Milone M.C. O'Doherty U. Clinical use lentiviral vectors.Leukemia. 2018; 32: 1529-1541Crossref (437) Scholar] adeno-associated [54.Wang D. et al.Adeno-associated vector platform gene therapy delivery.Nat. Drug Discov. 2019; 18: 358-378Crossref (946) being genetically engineered formulate state-of-the-art therapies. Nevertheless, bad reputation causative diseases. no surprise main players epidemics pandemics throughout history (https://www.who.int/emergencies/diseases/managing-epidemics/en/). Several well-deserved 'biohazard' fame viruses, including influenza, Ebola, HIV ,and coronavirus SARS-CoV-2. Despite 'viral celebrities', waterborne pose serious health economic burdens era threatened by climate change scarcity potable water.Different physical chemical treatments traditionally applied Chlorine, alcohols, acids, alkalis, bleach examples disinfectants, whereas UV irradiation, filtration, pressure, temperature [55.Mehle N. al.Water-mediated transmission viruses.in: Malmstrom C.M. Advances Virus Research. Academic Press, 2018: 85-128Google method choice depends matrix disinfected targeted Waterborne enteric [56.Staggemeier R. al.Animal water sediment samples dairy farms.Agric. Water Manag. 152: 135-141Crossref (27) tobamoviruses [57.Zhang T. al.RNA community feces: prevalence viruses.PLoS 2006; 0108-0118Crossref (548) among stable To delicate matrix, needs strong enough at same time nontoxic maintain properties water. known chlorination, disinfection, does efficiently long term risk release toxic byproducts [58.Lyon B.A. al.Integrated toxicological investigation UV-chlorine/ chloramine drinking treatment.Environ. Technol. 2014; 48: 6743-6753Crossref (42) novel technologies developed, membrane reverse osmosis, ozone treatments, hydrodynamic cavitation, own pros cons. frequent disadvantages these cost inefficiency, scalability problems, unsustainable power usage. Laboratory-scale studies suggest potential overcome confirmation require focused pilot industrial scale deployment plasma-based devices. Different transmitted directly infected individual another indirectly via intermediates surfaces, objects, air, food, Transmission surfaces aerosols great importance COVID-19 pandemic caused severe acute respiratory syndrome 2 (SARS-CoV-2) [3.van Doremalen al.Aerosol surface stability SARS-CoV-2 compared SARS-CoV-1.N. Engl. J. Med. 2020; 382: 1564-1567Crossref (6351) also route arisen continued increase demand, combined inefficient removal traditional reuse wastewater irrigation purposes [4.Shrestha S. al.Virological sources pepper mild mottle tobacco mosaic index contamination level.Food Environ. 10: 107-120Crossref (47) Scholar,5.Mehle Ravnikar M. Plant aqueous environment – survival, mediated detection.Water Res. 2012; 46: 4902-4917Crossref (61) contributors risks we facing today, [6.Franco E.G. al.The Global Risks Report 2020.15th edn. World Economic Forum, 2020Google Various (see Glossary) prevent spread matrices, unfortunately ideal yet discovered Thus, there urgent produces neither waste nor byproducts, chemicals, easy safe work with, efficient terms emergence aims features. Plasma fourth state matter. partially fully ionized gas where atoms molecules stripped outer-shell electrons 2) [7.Filipić al.Cold atmospheric potato Y samples.Food 11: 220-228Crossref (29) Among its complex constituents, emission radiation reactive (RONS) antimicrobial [8.Guo al.Bactericidal effect non-thermal influence experimental conditions microbial inactivation: review.Food Control. 50: 482-490Crossref (151) damage acids [9.US Environmental Protection Agency Office Ultraviolet Disinfection Guidance Manual Final Long Term Enhanced Surface Treatment Rule. US EPA, 2006Google RONS oxidize proteins, lipids, affinities depend [10.Mittler ROS good.Trends 22: 11-19Abstract Full Text PDF (1741) These inherent plasma, specifically CP, motivated extensive microorganisms. target bacteria, investigations fields production [11.Bourke cold sustainable production.Trends Biotechnol. 36: 615-626Abstract (236) medicine, dentistry [12.Sakudo al.Disinfection sterilization technology: fundamentals future perspectives applications.Int. Mol. 20: 5216Crossref (143) extended oncotherapy applications, cancer cells instead microorganisms [13.Dai X. emerging role oncotherapy.Trends 1183-1198Abstract (81) Scholar].Box 2Let's Talk about PlasmaPlasma matter comprises 99% visible universe. sun stars, nebulae, solar winds, lightning, aurora borealis state. TVs well neon fluorescent lights best-known man-made uses plasma. Generally, contains free electrons, atoms, neutral, ionized, excited states (including ROS/RNS). gases represents source vacuum [59.Machala Z. Pavlovich new phase biology.Trends 577-578Abstract (8) possibility particular combination constituents makes unique material-treatment technique.Plasma roughly divided into thermal equilibrium approximately (average kinetic energy random motion), nonthermal, nonequilibrium, much higher temperatures heavy molecules, often remain close room temperature. words, point application temperature, therefore suitable treating material solids, liquids, aerosols. further classified low pressure pressure. latter limited volume large electric fields, low-pressure spreads [60.Mozetič al.Introduction diagnostics.in: Thomas Non-Thermal Technology Polymeric Materials: Applications Composites, Nanostructured Materials Biomedical Fields. Elsevier, 2019: 23-65Crossref (12) usually sustained electrical discharge. almost unaffected, reactivity vast presence species. practical considerations ([61.Ehlbeck al.Low decontamination.J. Phys. Appl. 2011; 44013002Crossref (581) decontamination).Plasmas industries, mainly tailoring solids (e.g., oxidation, cleaning, nanostructuring, binding atom/molecule groups), destruction liquids; however, liquid media challenging than cannot only gaseous bubbles inside above surface. Depending place generation, either bubble liquid, dissolve. then diffuse within may eventually virus. Furthermore, penetrates liquids penetration depth greatly wavelength, concentration, type impurities [62.Bruggeman P.J. al.Plasma-liquid interactions: review roadmap.Plasma Sources 25053002Crossref (1024) There techniques measuring both long- short-lived [63.Labay C. al.Production alginate hydrogels therapies.Sci. Rep. 9: 1-12Crossref (34) frequently researchers working Many authors discharge (voltage, current, power) rather (concentration species) necessary compare sources. plasma–virus scientific niche infancy present. technique. decontamination). Plasmas Plasma-mediated relatively young research (reviewed [14.Puligundla Mok Non-thermal plasmas (NTPs) abiotic environment.Res. 91-96PubMed Scholar,15.Weiss al.Virucide clinical applications.J. 89: 952-959Crossref (39) Scholar]) started 20 ago [16.Kelly-Wintenberg K. al.Use atmosphere uniform glow kill broad spectrum microorganisms.J. Vac. 17: 1539-1544Crossref (179) despite decades-old knowledge ozone, synthesized O2 subjected conditions, [17.Burleson G.R. al.Inactivation without sonication.Appl. Microbiol. 1975; 29: 340-344Crossref However, over past few number publications CP–virus doubled, expanded defining virucidal describing modes offers comprehensive overview latest progress achievements field. discuss responsible. Almost every study specific [e.g., dielectric barrier (DBD), (micro)jets] (Figure 1) characteristics power, gas, time) deal volumes (from microliters milliliters), matrices water, solutions, cells), (surrogates viruses). Such wide diversity difficult define mechanistic conclusions any universal parameters. simplify complexities, consider here types treatments. complete list published date given Table S1, S2 supplemental online. norovirus, adenovirus, hepatitis leading causes gastroenteritis, second common infectious disease worldwide, levels hospitalization mortality [18.McMinn B.R. al.Bacteriophages indicators faecal pollution removal.Lett. 65: 11-26Crossref Working hazards, specialized laboratories equipment. Moreover, infectivity assessments owing lack cultivation [19.Cromeans al.Comprehensive comparison cultivable norovirus surrogates response treatments.Appl. 80: 5743-5751Crossref reasons, replaced surrogate Animal feline calicivirus (FCV), murine (MNV), Tulane (TV) similar sizes, morphologies, genetic material. culture/reproduce, Opinions best resembles final strongly environmental Scholar, 14.Puligundla 15.Weiss addition animal bacteriophages (viruses bacteria) pathogens 3).Box 3Bacteriophages Surrogates, Alternative TreatmentBacteriophages first establish proof concept advantages. inexpensive culture/produce, produced quantities, plaque-based assays time-efficient [64.McMinn (112) care must taken when interpreting results do always correlate actual method.The triggered expansion was conducted years,

Язык: Английский

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Discovery of several thousand highly diverse circular DNA viruses

eLife, Год журнала: 2020, Номер 9

Опубликована: Фев. 4, 2020

Although millions of distinct virus species likely exist, only approximately 9000 are catalogued in GenBank's RefSeq database. We selectively enriched for the genomes circular DNA viruses over 70 animal samples, ranging from nematodes to human tissue specimens. A bioinformatics pipeline, Cenote-Taker, was developed automatically annotate 2500 complete a GenBank-compliant format. The new belong dozens established and emerging viral families. Some appear be result previously undescribed recombination events between ssDNA ssRNA viruses. In addition, hundreds elements that do not encode any discernable similarities characterized sequences were identified. To characterize these ‘dark matter’ sequences, we used an artificial neural network identify candidate capsid proteins, several which formed virus-like particles when expressed culture. These data further understanding sequence diversity allow high throughput documentation virosphere.

Язык: Английский

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Mycovirus Diversity and Evolution Revealed/Inferred from Recent Studies

Annual Review of Phytopathology, Год журнала: 2022, Номер 60(1), С. 307 - 336

Опубликована: Май 25, 2022

High-throughput virome analyses with various fungi, from cultured or uncultured sources, have led to the discovery of diverse viruses unique genome structures and even neo-lifestyles. Examples in former category include splipalmiviruses ambiviruses. Splipalmiviruses, related yeast narnaviruses, multiple positive-sense (+) single-stranded (ss) RNA genomic segments that separately encode RNA-dependent polymerase motifs, hallmark (members kingdom Orthornavirae). Ambiviruses appear an undivided ssRNA 3∼5 kb two large open reading frames (ORFs) separated by intergenic regions. Another narna-like virus group has fully overlapping ORFs on both strands a segment span more than 90% size. New lifestyles exhibited mycoviruses yado-kari/yado-nushi nature characterized partnership between (+)ssRNA yadokarivirus unrelated dsRNA (donor capsid for former) hadaka capsidless 10–11 segmented accessible RNase infected mycelial homogenates. Furthermore, polymycoviruses phylogenetic affinity animal caliciviruses been shown be infectious as dsRNA–protein complexes deproteinized naked dsRNA. Many previous gaps filled recently discovered fungal other viruses, which haveprovided interesting evolutionary insights. Phylogenetic natural experimental cross-kingdom infections suggest horizontal transfer may occurred continue occur fungi kingdoms.

Язык: Английский

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Biocontrol of soil borne diseases by plant growth promoting rhizobacteria

Tropical Plant Pathology, Год журнала: 2023, Номер 48(2), С. 105 - 127

Опубликована: Янв. 6, 2023

Язык: Английский

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In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem

Microbiome, Год журнала: 2023, Номер 11(1)

Опубликована: Март 28, 2023

Abstract Background In agroecosystems, viruses are well known to influence crop health and some cause phytosanitary economic problems, but their diversity in non-crop plants role outside the disease perspective is less known. Extensive virome explorations that include both diverse weed therefore needed better understand roles of agroecosystems. Such unbiased exploration available through viromics, which could generate biological ecological insights from immense high-throughput sequencing (HTS) data. Results Here, we implemented HTS-based viromics explore viral tomatoes weeds farming areas at a nation-wide scale. We detected 125 viruses, including 79 novel species, wherein 65 were found exclusively weeds. This spanned 21 higher-level plant virus taxa dominated by Potyviridae , Rhabdoviridae Tombusviridae four non-plant families. hosts viroid-like sequences demonstrated infectivity tobamovirus Solanaceae family. Diversities predominant tomato variable, cases, comparable global isolates same species. phylogenetically classified showed links between subgroup related rhabdoviruses taxonomically host plants. Ten also weeds, might indicate possible as reservoirs these be exchanged two compartments. Conclusions even relatively studied such farms, large part very viromes can still unknown mostly present understudied The overlapping presence implicate reservoir exchange compartments, may management decisions. observed variability widespread solanaceous plants, provided foundation for further investigation dynamics effect on health. extensive generated in-depth agroecosystem will valuable anticipating emergences diseases would serve baseline post-discovery characterization studies.

Язык: Английский

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Megataxonomy and global ecology of the virosphere

The ISME Journal, Год журнала: 2024, Номер 18(1)

Опубликована: Янв. 1, 2024

Nearly all organisms are hosts to multiple viruses that collectively appear be the most abundant biological entities in biosphere. With recent advances metagenomics and metatranscriptomics, known diversity of substantially expanded. Comparative analysis these using advanced computational methods culminated reconstruction evolution major groups enabled construction a virus megataxonomy, which has been formally adopted by International Committee on Taxonomy Viruses. This comprehensive taxonomy consists six realms, aspired monophyletic assembled based conservation hallmark proteins involved capsid structure formation or genome replication. The different taxa differ host range accordingly ecological niches. In this review article, we outline latest developments megataxonomy discoveries will likely lead reassessment some taxa, particular, split three current realms into two more independent realms. We then discuss correspondence between distribution among niches, as well abundance versus cells habitats. across environments appears primarily determined ranges, i.e. virome is shaped composition biome given habitat, itself affected abiotic factors.

Язык: Английский

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An Ecosystems Perspective on Virus Evolution and Emergence

Trends in Microbiology, Год журнала: 2019, Номер 28(3), С. 165 - 175

Опубликована: Ноя. 16, 2019

Язык: Английский

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Aphid Transmission of Potyvirus: The Largest Plant-Infecting RNA Virus Genus

Viruses, Год журнала: 2020, Номер 12(7), С. 773 - 773

Опубликована: Июль 17, 2020

Potyviruses are the largest group of plant infecting RNA viruses that cause significant losses in a wide range crops across globe. The majority genus Potyvirus transmitted by aphids non-persistent, non-circulative manner and have been extensively studied vis-à-vis their structure, taxonomy, evolution, diagnosis, transmission, molecular interactions with hosts. This comprehensive review exclusively discusses potyviruses transmission aphid vectors, specifically light several virus, factors, how interplay influences potyviral binding aphids, behavior fitness, host biochemistry, virus epidemics, bottlenecks. We present heatmap global distribution potyvirus species, variation coat protein gene, top vectors potyviruses. Lastly, we examine fundamental understanding these multi-partite through multi-omics approaches is already contributing to, can future implications for, devising effective sustainable management strategies against aphid-transmitted to agriculture.

Язык: Английский

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